PDB Short entry for 6O1D HEADER NUCLEAR PROTEIN 19-FEB-19 6O1D TITLE CRYO-EM STRUCTURE OF THE CENTROMERIC NUCLEOSOME WITH NATIVE ALPHA TITLE 2 SATELLITE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3-LIKE CENTROMERIC PROTEIN A; COMPND 3 CHAIN: A, E; COMPND 4 SYNONYM: CENTROMERE AUTOANTIGEN A,CENTROMERE PROTEIN A,CENP-A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H4; COMPND 8 CHAIN: B, F; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: HISTONE H2A TYPE 1-B/E; COMPND 12 CHAIN: C, G; COMPND 13 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: HISTONE H2B TYPE 1-J; COMPND 17 CHAIN: D, H; COMPND 18 SYNONYM: HISTONE H2B.1,HISTONE H2B.R,H2B/R; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 5; COMPND 21 MOLECULE: DNA (145-MER); COMPND 22 CHAIN: I; COMPND 23 ENGINEERED: YES; COMPND 24 MOL_ID: 6; COMPND 25 MOLECULE: DNA (145-MER); COMPND 26 CHAIN: J; COMPND 27 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CENPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, SOURCE 13 H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, SOURCE 14 H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, SOURCE 15 H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, SOURCE 16 H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 GENE: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 26 MOL_ID: 4; SOURCE 27 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 28 ORGANISM_COMMON: HUMAN; SOURCE 29 ORGANISM_TAXID: 9606; SOURCE 30 GENE: HIST1H2BJ, H2BFR; SOURCE 31 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 32 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 33 MOL_ID: 5; SOURCE 34 SYNTHETIC: YES; SOURCE 35 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 36 ORGANISM_COMMON: HUMAN; SOURCE 37 ORGANISM_TAXID: 9606; SOURCE 38 MOL_ID: 6; SOURCE 39 SYNTHETIC: YES; SOURCE 40 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 41 ORGANISM_COMMON: HUMAN; SOURCE 42 ORGANISM_TAXID: 9606 KEYWDS CENP-A, CENTROMERE, NATIVE ALPHA SATELLITE DNA, NUCLEOSOME, NUCLEAR KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR B.-R.ZHOU REVDAT 6 20-MAR-24 6O1D 1 REMARK REVDAT 5 18-DEC-19 6O1D 1 SCALE REVDAT 4 04-DEC-19 6O1D 1 REMARK REVDAT 3 19-JUN-19 6O1D 1 JRNL REVDAT 2 12-JUN-19 6O1D 1 JRNL REVDAT 1 22-MAY-19 6O1D 0 JRNL AUTH B.R.ZHOU,K.N.S.YADAV,M.BORGNIA,J.HONG,B.CAO,A.L.OLINS, JRNL AUTH 2 D.E.OLINS,Y.BAI,P.ZHANG JRNL TITL ATOMIC RESOLUTION CRYO-EM STRUCTURE OF A NATIVE-LIKE CENP-A JRNL TITL 2 NUCLEOSOME AIDED BY AN ANTIBODY FRAGMENT. JRNL REF NAT COMMUN V. 10 2301 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31127102 JRNL DOI 10.1038/S41467-019-10247-4 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : LATITUDE, UCSF CHIMERA, RELION, RELION, REMARK 3 RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6E0P REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.395 REMARK 3 NUMBER OF PARTICLES : 303863 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6O1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000239826. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : CENP-A NUCLEOSOME WITH NATIVE REMARK 245 ALPHA SATELLITE DNA SEQUENCE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FOR 2.5 SEC BEFORE REMARK 245 PLUNGING REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1256 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 SER A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 SER A -7 REMARK 465 SER A -6 REMARK 465 GLY A -5 REMARK 465 LEU A -4 REMARK 465 PRO A -3 REMARK 465 ARG A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 PRO A 3 REMARK 465 ARG A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 6 REMARK 465 SER A 7 REMARK 465 ARG A 8 REMARK 465 LYS A 9 REMARK 465 PRO A 10 REMARK 465 GLU A 11 REMARK 465 ALA A 12 REMARK 465 PRO A 13 REMARK 465 ARG A 14 REMARK 465 ARG A 15 REMARK 465 ARG A 16 REMARK 465 SER A 17 REMARK 465 PRO A 18 REMARK 465 SER A 19 REMARK 465 PRO A 20 REMARK 465 THR A 21 REMARK 465 PRO A 22 REMARK 465 THR A 23 REMARK 465 PRO A 24 REMARK 465 GLY A 25 REMARK 465 PRO A 26 REMARK 465 SER A 27 REMARK 465 ARG A 28 REMARK 465 ARG A 29 REMARK 465 GLY A 30 REMARK 465 PRO A 31 REMARK 465 SER A 32 REMARK 465 LEU A 33 REMARK 465 GLY A 34 REMARK 465 ALA A 35 REMARK 465 SER A 36 REMARK 465 SER A 37 REMARK 465 HIS A 38 REMARK 465 GLN A 39 REMARK 465 HIS A 40 REMARK 465 SER A 41 REMARK 465 MET B 0 REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 ARG B 3 REMARK 465 GLY B 4 REMARK 465 LYS B 5 REMARK 465 GLY B 6 REMARK 465 GLY B 7 REMARK 465 LYS B 8 REMARK 465 GLY B 9 REMARK 465 LEU B 10 REMARK 465 GLY B 11 REMARK 465 LYS B 12 REMARK 465 GLY B 13 REMARK 465 GLY B 14 REMARK 465 ALA B 15 REMARK 465 LYS B 16 REMARK 465 ARG B 17 REMARK 465 HIS B 18 REMARK 465 ARG B 19 REMARK 465 LYS B 20 REMARK 465 VAL B 21 REMARK 465 LEU B 22 REMARK 465 MET C 0 REMARK 465 SER C 1 REMARK 465 GLY C 2 REMARK 465 ARG C 3 REMARK 465 GLY C 4 REMARK 465 LYS C 5 REMARK 465 GLN C 6 REMARK 465 GLY C 7 REMARK 465 GLY C 8 REMARK 465 LYS C 9 REMARK 465 PRO C 117 REMARK 465 LYS C 118 REMARK 465 LYS C 119 REMARK 465 THR C 120 REMARK 465 GLU C 121 REMARK 465 SER C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 LYS C 125 REMARK 465 ALA C 126 REMARK 465 LYS C 127 REMARK 465 GLY C 128 REMARK 465 LYS C 129 REMARK 465 MET D 0 REMARK 465 PRO D 1 REMARK 465 GLU D 2 REMARK 465 PRO D 3 REMARK 465 ALA D 4 REMARK 465 LYS D 5 REMARK 465 SER D 6 REMARK 465 ALA D 7 REMARK 465 PRO D 8 REMARK 465 ALA D 9 REMARK 465 PRO D 10 REMARK 465 LYS D 11 REMARK 465 LYS D 12 REMARK 465 GLY D 13 REMARK 465 SER D 14 REMARK 465 LYS D 15 REMARK 465 LYS D 16 REMARK 465 ALA D 17 REMARK 465 VAL D 18 REMARK 465 THR D 19 REMARK 465 LYS D 20 REMARK 465 ALA D 21 REMARK 465 GLN D 22 REMARK 465 LYS D 23 REMARK 465 LYS D 24 REMARK 465 ASP D 25 REMARK 465 GLY D 26 REMARK 465 LYS D 27 REMARK 465 LYS D 28 REMARK 465 ARG D 29 REMARK 465 LYS D 30 REMARK 465 LYS D 125 REMARK 465 MET E -17 REMARK 465 GLY E -16 REMARK 465 SER E -15 REMARK 465 SER E -14 REMARK 465 HIS E -13 REMARK 465 HIS E -12 REMARK 465 HIS E -11 REMARK 465 HIS E -10 REMARK 465 HIS E -9 REMARK 465 HIS E -8 REMARK 465 SER E -7 REMARK 465 SER E -6 REMARK 465 GLY E -5 REMARK 465 LEU E -4 REMARK 465 PRO E -3 REMARK 465 ARG E -2 REMARK 465 SER E -1 REMARK 465 HIS E 0 REMARK 465 MET E 1 REMARK 465 GLY E 2 REMARK 465 PRO E 3 REMARK 465 ARG E 4 REMARK 465 ARG E 5 REMARK 465 ARG E 6 REMARK 465 SER E 7 REMARK 465 ARG E 8 REMARK 465 LYS E 9 REMARK 465 PRO E 10 REMARK 465 GLU E 11 REMARK 465 ALA E 12 REMARK 465 PRO E 13 REMARK 465 ARG E 14 REMARK 465 ARG E 15 REMARK 465 ARG E 16 REMARK 465 SER E 17 REMARK 465 PRO E 18 REMARK 465 SER E 19 REMARK 465 PRO E 20 REMARK 465 THR E 21 REMARK 465 PRO E 22 REMARK 465 THR E 23 REMARK 465 PRO E 24 REMARK 465 GLY E 25 REMARK 465 PRO E 26 REMARK 465 SER E 27 REMARK 465 ARG E 28 REMARK 465 ARG E 29 REMARK 465 GLY E 30 REMARK 465 PRO E 31 REMARK 465 SER E 32 REMARK 465 LEU E 33 REMARK 465 GLY E 34 REMARK 465 ALA E 35 REMARK 465 SER E 36 REMARK 465 SER E 37 REMARK 465 HIS E 38 REMARK 465 GLN E 39 REMARK 465 HIS E 40 REMARK 465 SER E 41 REMARK 465 MET F 0 REMARK 465 SER F 1 REMARK 465 GLY F 2 REMARK 465 ARG F 3 REMARK 465 GLY F 4 REMARK 465 LYS F 5 REMARK 465 GLY F 6 REMARK 465 GLY F 7 REMARK 465 LYS F 8 REMARK 465 GLY F 9 REMARK 465 LEU F 10 REMARK 465 GLY F 11 REMARK 465 LYS F 12 REMARK 465 GLY F 13 REMARK 465 GLY F 14 REMARK 465 ALA F 15 REMARK 465 LYS F 16 REMARK 465 ARG F 17 REMARK 465 HIS F 18 REMARK 465 ARG F 19 REMARK 465 LYS F 20 REMARK 465 VAL F 21 REMARK 465 LEU F 22 REMARK 465 MET G 0 REMARK 465 SER G 1 REMARK 465 GLY G 2 REMARK 465 ARG G 3 REMARK 465 GLY G 4 REMARK 465 LYS G 5 REMARK 465 GLN G 6 REMARK 465 GLY G 7 REMARK 465 GLY G 8 REMARK 465 PRO G 117 REMARK 465 LYS G 118 REMARK 465 LYS G 119 REMARK 465 THR G 120 REMARK 465 GLU G 121 REMARK 465 SER G 122 REMARK 465 HIS G 123 REMARK 465 HIS G 124 REMARK 465 LYS G 125 REMARK 465 ALA G 126 REMARK 465 LYS G 127 REMARK 465 GLY G 128 REMARK 465 LYS G 129 REMARK 465 MET H 0 REMARK 465 PRO H 1 REMARK 465 GLU H 2 REMARK 465 PRO H 3 REMARK 465 ALA H 4 REMARK 465 LYS H 5 REMARK 465 SER H 6 REMARK 465 ALA H 7 REMARK 465 PRO H 8 REMARK 465 ALA H 9 REMARK 465 PRO H 10 REMARK 465 LYS H 11 REMARK 465 LYS H 12 REMARK 465 GLY H 13 REMARK 465 SER H 14 REMARK 465 LYS H 15 REMARK 465 LYS H 16 REMARK 465 ALA H 17 REMARK 465 VAL H 18 REMARK 465 THR H 19 REMARK 465 LYS H 20 REMARK 465 ALA H 21 REMARK 465 GLN H 22 REMARK 465 LYS H 23 REMARK 465 LYS H 24 REMARK 465 ASP H 25 REMARK 465 GLY H 26 REMARK 465 LYS H 27 REMARK 465 LYS H 28 REMARK 465 ARG H 29 REMARK 465 LYS H 30 REMARK 465 LYS H 125 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC J 100 O3' DC J 100 C3' -0.039 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA I 28 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT I 37 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG I 39 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT I 48 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC I 140 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT J 53 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG J 93 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT J 95 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA J 98 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG J 136 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG C 99 56.98 -91.88 REMARK 500 SER D 36 -167.28 -162.47 REMARK 500 ARG G 99 50.50 -93.21 REMARK 500 SER H 32 171.81 -57.73 REMARK 500 LYS H 46 36.95 -96.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-8949 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8945 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8938 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-0586 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE CENTROMERIC NUCLEOSOME WITH NATIVE ALPHA REMARK 900 SATELLITE DNA DBREF 6O1D A 1 140 UNP P49450 CENPA_HUMAN 1 140 DBREF 6O1D B 0 102 UNP P62805 H4_HUMAN 1 103 DBREF 6O1D C 0 129 UNP P04908 H2A1B_HUMAN 1 130 DBREF 6O1D D 0 125 UNP P06899 H2B1J_HUMAN 1 126 DBREF 6O1D E 1 140 UNP P49450 CENPA_HUMAN 1 140 DBREF 6O1D F 0 102 UNP P62805 H4_HUMAN 1 103 DBREF 6O1D G 0 129 UNP P04908 H2A1B_HUMAN 1 130 DBREF 6O1D H 0 125 UNP P06899 H2B1J_HUMAN 1 126 DBREF 6O1D I 1 145 PDB 6O1D 6O1D 1 145 DBREF 6O1D J 1 145 PDB 6O1D 6O1D 1 145 SEQADV 6O1D MET A -17 UNP P49450 INITIATING METHIONINE SEQADV 6O1D GLY A -16 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER A -15 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER A -14 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS A -13 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS A -12 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS A -11 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS A -10 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS A -9 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS A -8 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER A -7 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER A -6 UNP P49450 EXPRESSION TAG SEQADV 6O1D GLY A -5 UNP P49450 EXPRESSION TAG SEQADV 6O1D LEU A -4 UNP P49450 EXPRESSION TAG SEQADV 6O1D PRO A -3 UNP P49450 EXPRESSION TAG SEQADV 6O1D ARG A -2 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER A -1 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS A 0 UNP P49450 EXPRESSION TAG SEQADV 6O1D MET E -17 UNP P49450 INITIATING METHIONINE SEQADV 6O1D GLY E -16 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER E -15 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER E -14 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS E -13 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS E -12 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS E -11 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS E -10 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS E -9 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS E -8 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER E -7 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER E -6 UNP P49450 EXPRESSION TAG SEQADV 6O1D GLY E -5 UNP P49450 EXPRESSION TAG SEQADV 6O1D LEU E -4 UNP P49450 EXPRESSION TAG SEQADV 6O1D PRO E -3 UNP P49450 EXPRESSION TAG SEQADV 6O1D ARG E -2 UNP P49450 EXPRESSION TAG SEQADV 6O1D SER E -1 UNP P49450 EXPRESSION TAG SEQADV 6O1D HIS E 0 UNP P49450 EXPRESSION TAG SEQRES 1 A 158 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 158 LEU PRO ARG SER HIS MET GLY PRO ARG ARG ARG SER ARG SEQRES 3 A 158 LYS PRO GLU ALA PRO ARG ARG ARG SER PRO SER PRO THR SEQRES 4 A 158 PRO THR PRO GLY PRO SER ARG ARG GLY PRO SER LEU GLY SEQRES 5 A 158 ALA SER SER HIS GLN HIS SER ARG ARG ARG GLN GLY TRP SEQRES 6 A 158 LEU LYS GLU ILE ARG LYS LEU GLN LYS SER THR HIS LEU SEQRES 7 A 158 LEU ILE ARG LYS LEU PRO PHE SER ARG LEU ALA ARG GLU SEQRES 8 A 158 ILE CYS VAL LYS PHE THR ARG GLY VAL ASP PHE ASN TRP SEQRES 9 A 158 GLN ALA GLN ALA LEU LEU ALA LEU GLN GLU ALA ALA GLU SEQRES 10 A 158 ALA PHE LEU VAL HIS LEU PHE GLU ASP ALA TYR LEU LEU SEQRES 11 A 158 THR LEU HIS ALA GLY ARG VAL THR LEU PHE PRO LYS ASP SEQRES 12 A 158 VAL GLN LEU ALA ARG ARG ILE ARG GLY LEU GLU GLU GLY SEQRES 13 A 158 LEU GLY SEQRES 1 B 103 MET SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS SEQRES 2 B 103 GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN SEQRES 3 B 103 ILE GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA SEQRES 4 B 103 ARG ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR SEQRES 5 B 103 GLU GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN SEQRES 6 B 103 VAL ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS SEQRES 7 B 103 ARG LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU SEQRES 8 B 103 LYS ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 C 130 MET SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA SEQRES 2 C 130 LYS ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE SEQRES 3 C 130 PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN SEQRES 4 C 130 TYR SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU SEQRES 5 C 130 ALA ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU SEQRES 6 C 130 LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG SEQRES 7 C 130 ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP SEQRES 8 C 130 GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA SEQRES 9 C 130 GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU SEQRES 10 C 130 PRO LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 D 126 MET PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS SEQRES 2 D 126 GLY SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP SEQRES 3 D 126 GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER SEQRES 4 D 126 ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP SEQRES 5 D 126 THR GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER SEQRES 6 D 126 PHE VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SEQRES 7 D 126 SER ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SEQRES 8 D 126 SER ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO SEQRES 9 D 126 GLY GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS SEQRES 10 D 126 ALA VAL THR LYS TYR THR SER ALA LYS SEQRES 1 E 158 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 E 158 LEU PRO ARG SER HIS MET GLY PRO ARG ARG ARG SER ARG SEQRES 3 E 158 LYS PRO GLU ALA PRO ARG ARG ARG SER PRO SER PRO THR SEQRES 4 E 158 PRO THR PRO GLY PRO SER ARG ARG GLY PRO SER LEU GLY SEQRES 5 E 158 ALA SER SER HIS GLN HIS SER ARG ARG ARG GLN GLY TRP SEQRES 6 E 158 LEU LYS GLU ILE ARG LYS LEU GLN LYS SER THR HIS LEU SEQRES 7 E 158 LEU ILE ARG LYS LEU PRO PHE SER ARG LEU ALA ARG GLU SEQRES 8 E 158 ILE CYS VAL LYS PHE THR ARG GLY VAL ASP PHE ASN TRP SEQRES 9 E 158 GLN ALA GLN ALA LEU LEU ALA LEU GLN GLU ALA ALA GLU SEQRES 10 E 158 ALA PHE LEU VAL HIS LEU PHE GLU ASP ALA TYR LEU LEU SEQRES 11 E 158 THR LEU HIS ALA GLY ARG VAL THR LEU PHE PRO LYS ASP SEQRES 12 E 158 VAL GLN LEU ALA ARG ARG ILE ARG GLY LEU GLU GLU GLY SEQRES 13 E 158 LEU GLY SEQRES 1 F 103 MET SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS SEQRES 2 F 103 GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN SEQRES 3 F 103 ILE GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA SEQRES 4 F 103 ARG ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR SEQRES 5 F 103 GLU GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN SEQRES 6 F 103 VAL ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS SEQRES 7 F 103 ARG LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU SEQRES 8 F 103 LYS ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 G 130 MET SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA SEQRES 2 G 130 LYS ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE SEQRES 3 G 130 PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN SEQRES 4 G 130 TYR SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU SEQRES 5 G 130 ALA ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU SEQRES 6 G 130 LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG SEQRES 7 G 130 ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP SEQRES 8 G 130 GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA SEQRES 9 G 130 GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU SEQRES 10 G 130 PRO LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 H 126 MET PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS SEQRES 2 H 126 GLY SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP SEQRES 3 H 126 GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER SEQRES 4 H 126 ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP SEQRES 5 H 126 THR GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER SEQRES 6 H 126 PHE VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SEQRES 7 H 126 SER ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SEQRES 8 H 126 SER ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO SEQRES 9 H 126 GLY GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS SEQRES 10 H 126 ALA VAL THR LYS TYR THR SER ALA LYS SEQRES 1 I 145 DA DT DC DA DA DT DA DT DC DC DA DC DC SEQRES 2 I 145 DT DG DC DA DG DA DT DT DC DT DA DC DC SEQRES 3 I 145 DA DA DA DA DG DT DG DT DA DT DT DT DG SEQRES 4 I 145 DG DA DA DA DC DT DG DC DT DC DC DA DT SEQRES 5 I 145 DC DA DA DA DA DG DG DC DA DT DG DT DT SEQRES 6 I 145 DC DA DG DC DT DC DT DG DT DG DA DG DT SEQRES 7 I 145 DG DA DA DA DC DT DC DC DA DT DC DA DT SEQRES 8 I 145 DC DA DC DA DA DA DG DA DA DT DA DT DT SEQRES 9 I 145 DC DT DG DA DG DA DA DT DG DC DT DT DC SEQRES 10 I 145 DC DG DT DT DT DG DC DC DT DT DT DT DA SEQRES 11 I 145 DT DA DT DG DA DA DC DT DT DC DC DT DG SEQRES 12 I 145 DA DT SEQRES 1 J 145 DA DT DC DA DG DG DA DA DG DT DT DC DA SEQRES 2 J 145 DT DA DT DA DA DA DA DG DG DC DA DA DA SEQRES 3 J 145 DC DG DG DA DA DG DC DA DT DT DC DT DC SEQRES 4 J 145 DA DG DA DA DT DA DT DT DC DT DT DT DG SEQRES 5 J 145 DT DG DA DT DG DA DT DG DG DA DG DT DT SEQRES 6 J 145 DT DC DA DC DT DC DA DC DA DG DA DG DC SEQRES 7 J 145 DT DG DA DA DC DA DT DG DC DC DT DT DT SEQRES 8 J 145 DT DG DA DT DG DG DA DG DC DA DG DT DT SEQRES 9 J 145 DT DC DC DA DA DA DT DA DC DA DC DT DT SEQRES 10 J 145 DT DT DG DG DT DA DG DA DA DT DC DT DG SEQRES 11 J 145 DC DA DG DG DT DG DG DA DT DA DT DT DG SEQRES 12 J 145 DA DT HELIX 1 AA1 GLY A 46 LYS A 56 1 11 HELIX 2 AA2 ARG A 63 ARG A 69 1 7 HELIX 3 AA3 ARG A 69 CYS A 75 1 7 HELIX 4 AA4 LEU A 94 PHE A 101 1 8 HELIX 5 AA5 PHE A 101 ALA A 116 1 16 HELIX 6 AA6 PHE A 122 GLY A 134 1 13 HELIX 7 AA7 ASP B 24 ILE B 29 5 6 HELIX 8 AA8 THR B 30 GLY B 42 1 13 HELIX 9 AA9 LEU B 49 ALA B 76 1 28 HELIX 10 AB1 THR B 82 GLN B 93 1 12 HELIX 11 AB2 THR C 16 GLY C 22 1 7 HELIX 12 AB3 PRO C 26 LYS C 36 1 11 HELIX 13 AB4 GLY C 46 ASP C 72 1 27 HELIX 14 AB5 ILE C 79 ASP C 90 1 12 HELIX 15 AB6 GLU C 92 LEU C 97 1 6 HELIX 16 AB7 TYR D 37 HIS D 49 1 13 HELIX 17 AB8 SER D 56 ASN D 84 1 29 HELIX 18 AB9 THR D 90 LEU D 102 1 13 HELIX 19 AC1 GLY D 104 ALA D 124 1 21 HELIX 20 AC2 GLY E 46 LYS E 56 1 11 HELIX 21 AC3 ARG E 63 ARG E 69 1 7 HELIX 22 AC4 ARG E 69 CYS E 75 1 7 HELIX 23 AC5 VAL E 76 THR E 79 5 4 HELIX 24 AC6 GLN E 89 ALA E 116 1 28 HELIX 25 AC7 PHE E 122 ARG E 133 1 12 HELIX 26 AC8 ASN F 25 ILE F 29 5 5 HELIX 27 AC9 THR F 30 GLY F 42 1 13 HELIX 28 AD1 LEU F 49 ALA F 76 1 28 HELIX 29 AD2 THR F 82 ARG F 92 1 11 HELIX 30 AD3 PRO G 26 GLY G 37 1 12 HELIX 31 AD4 GLY G 46 ASN G 73 1 28 HELIX 32 AD5 PRO G 80 ASN G 89 1 10 HELIX 33 AD6 GLU G 92 LEU G 97 1 6 HELIX 34 AD7 TYR H 37 HIS H 49 1 13 HELIX 35 AD8 SER H 55 ASN H 84 1 30 HELIX 36 AD9 THR H 90 LEU H 102 1 13 HELIX 37 AE1 LYS H 108 THR H 122 1 15 SHEET 1 AA1 2 ASN A 85 TRP A 86 0 SHEET 2 AA1 2 THR B 80 VAL B 81 1 O VAL B 81 N ASN A 85 SHEET 1 AA2 2 THR A 120 LEU A 121 0 SHEET 2 AA2 2 ARG B 45 ILE B 46 1 O ARG B 45 N LEU A 121 SHEET 1 AA3 2 THR B 96 TYR B 98 0 SHEET 2 AA3 2 VAL G 100 ILE G 102 1 O THR G 101 N THR B 96 SHEET 1 AA4 2 ARG C 42 VAL C 43 0 SHEET 2 AA4 2 THR D 88 ILE D 89 1 O ILE D 89 N ARG C 42 SHEET 1 AA5 2 ARG C 77 ILE C 78 0 SHEET 2 AA5 2 GLY D 53 ILE D 54 1 O GLY D 53 N ILE C 78 SHEET 1 AA6 2 VAL C 100 ILE C 102 0 SHEET 2 AA6 2 THR F 96 TYR F 98 1 O TYR F 98 N THR C 101 SHEET 1 AA7 2 ASN E 85 TRP E 86 0 SHEET 2 AA7 2 THR F 80 VAL F 81 1 O VAL F 81 N ASN E 85 SHEET 1 AA8 2 THR E 120 LEU E 121 0 SHEET 2 AA8 2 ARG F 45 ILE F 46 1 O ARG F 45 N LEU E 121 SHEET 1 AA9 2 ARG G 42 VAL G 43 0 SHEET 2 AA9 2 THR H 88 ILE H 89 1 O ILE H 89 N ARG G 42 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000