PDB Short entry for 2KKF HEADER DNA BINDING PROTEIN/DNA 18-JUN-09 2KKF TITLE SOLUTION STRUCTURE OF MLL CXXC DOMAIN IN COMPLEX WITH PALINDROMIC CPG TITLE 2 DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE HRX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CXXC DOMAIN: UNP RESIDUES 1147-1203; COMPND 5 SYNONYM: ZINC FINGER PROTEIN HRX, ALL-1, TRITHORAX-LIKE PROTEIN, COMPND 6 LYSINE N-METHYLTRANSFERASE 2A, CXXC-TYPE ZINC FINGER PROTEIN 7; COMPND 7 EC: 2.1.1.43; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*CP*CP*CP*TP*GP*CP*GP*CP*AP*GP*GP*G)-3'; COMPND 11 CHAIN: B, C; COMPND 12 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: ALL1, CXXC7, HRX, HTRX, KMT2A, MLL, TRX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4-T2; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: PALINDROMIC DNA KEYWDS PROTEIN-DNA COMPLEX, CXXC DOMAIN, MLL, CPG DNA, CHROMOSOMAL KEYWDS 2 REARRANGEMENT, DNA-BINDING, METAL-BINDING, NUCLEUS, ZINC-FINGER, DNA KEYWDS 3 BINDING PROTEIN-DNA COMPLEX, ALTERNATIVE SPLICING, APOPTOSIS, KEYWDS 4 BROMODOMAIN, CHROMATIN REGULATOR, ISOPEPTIDE BOND, KEYWDS 5 METHYLTRANSFERASE, PHOSPHOPROTEIN, POLYMORPHISM, PROTO-ONCOGENE, S- KEYWDS 6 ADENOSYL-L-METHIONINE, TRANSCRIPTION, TRANSCRIPTION REGULATION, KEYWDS 7 TRANSFERASE, UBL CONJUGATION, ZINC EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.CIERPICKI,J.E.RIESBECK,J.E.GREMBECKA,S.M.LUKASIK,R.POPOVIC, AUTHOR 2 M.OMONKOWSKA,D.S.SHULTIS,N.J.ZELEZNIK-LE,J.H.BUSHWELLER REVDAT 3 16-MAR-22 2KKF 1 REMARK DBREF SEQADV REVDAT 2 19-JAN-10 2KKF 1 JRNL REVDAT 1 08-DEC-09 2KKF 0 JRNL AUTH T.CIERPICKI,L.E.RISNER,J.GREMBECKA,S.M.LUKASIK,R.POPOVIC, JRNL AUTH 2 M.OMONKOWSKA,D.D.SHULTIS,N.J.ZELEZNIK-LE,J.H.BUSHWELLER JRNL TITL STRUCTURE OF THE MLL CXXC DOMAIN-DNA COMPLEX AND ITS JRNL TITL 2 FUNCTIONAL ROLE IN MLL-AF9 LEUKEMIA. JRNL REF NAT.STRUCT.MOL.BIOL. V. 17 62 2010 JRNL REFN ISSN 1545-9993 JRNL PMID 20010842 JRNL DOI 10.1038/NSMB.1714 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY 3.110, CNS 1.2 REMARK 3 AUTHORS : GODDARD (SPARKY), BRUNGER, ADAMS, CLORE, GROS, REMARK 3 NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HIGH TEMP ANNEALING WITHOUT RRDCS, LOW REMARK 3 TEMP ANNEALING WITH RDCS REMARK 4 REMARK 4 2KKF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000101230. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-98% 13C; U-98% 15N] CXXC REMARK 210 DOMAIN-1, 1 MM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP* REMARK 210 DGP*DGP*DG)-3')-2, 95% H2O/5% D2O; 1 MM [U-98% 13C; U-98% 15N] REMARK 210 CXXC DOMAIN-3, 1 MM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP* REMARK 210 DAP*DGP*DGP*DG)-3')-4, 100% D2O; 1 MM [U-98% 13C; U-98% 15N] REMARK 210 CXXC DOMAIN-5, 1 MM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP* REMARK 210 DAP*DGP*DGP*DG)-3')-6, 95% H2O/5% D2O; 1 MM [U-98% 15N] CXXC REMARK 210 DOMAIN-7, 1 MM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP* REMARK 210 DGP*DGP*DG)-3')-8, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; HNCO NCO; HNCO COCA; REMARK 210 HACAN; IPAP; 2D 1H-13C HSQC NO REMARK 210 DECOUPLING REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.5, CNS 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, DISTANCE REMARK 210 GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1145 REMARK 465 SER A 1146 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H22 DG B 105 O2 DC C 108 1.58 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 1 ARG A1150 -81.56 -84.79 REMARK 500 1 ARG A1151 94.65 37.25 REMARK 500 1 ASN A1183 59.96 80.22 REMARK 500 1 ASN A1196 57.40 -142.81 REMARK 500 1 MET A1200 78.83 58.12 REMARK 500 2 ARG A1151 99.94 73.31 REMARK 500 2 ASN A1196 57.76 -144.42 REMARK 500 2 MET A1200 165.31 56.51 REMARK 500 3 ASN A1183 61.07 80.62 REMARK 500 3 GLN A1198 -162.07 -106.83 REMARK 500 3 MET A1200 179.09 58.12 REMARK 500 3 SER A1202 61.95 69.72 REMARK 500 4 ARG A1150 81.18 84.53 REMARK 500 4 ARG A1151 81.27 -176.49 REMARK 500 4 ASN A1196 58.22 -146.88 REMARK 500 4 MET A1200 -179.21 57.06 REMARK 500 4 SER A1202 -54.96 -156.26 REMARK 500 5 ARG A1150 145.61 83.33 REMARK 500 5 ARG A1151 -154.82 61.63 REMARK 500 5 ASN A1183 58.47 77.60 REMARK 500 5 ASN A1196 56.77 -143.61 REMARK 500 5 MET A1200 164.62 66.97 REMARK 500 5 SER A1202 111.78 73.19 REMARK 500 6 ARG A1150 105.70 -3.82 REMARK 500 6 ASN A1183 58.93 82.09 REMARK 500 6 ASN A1196 57.83 -141.90 REMARK 500 6 MET A1200 78.12 57.39 REMARK 500 6 SER A1202 139.31 72.13 REMARK 500 7 LYS A1148 137.31 70.92 REMARK 500 7 ARG A1150 87.47 73.56 REMARK 500 7 ARG A1151 47.40 -177.11 REMARK 500 7 ASN A1183 54.75 73.33 REMARK 500 7 ASN A1196 55.33 -146.60 REMARK 500 7 GLN A1198 -153.12 -109.19 REMARK 500 7 SER A1202 84.40 -155.65 REMARK 500 8 ARG A1150 167.48 80.08 REMARK 500 8 ARG A1151 105.72 81.02 REMARK 500 8 ASN A1183 59.88 76.89 REMARK 500 8 ASN A1196 59.27 -144.54 REMARK 500 8 MET A1200 61.64 62.76 REMARK 500 8 SER A1202 -64.29 77.87 REMARK 500 9 ARG A1150 -72.44 -173.56 REMARK 500 9 SER A1152 -176.81 -65.34 REMARK 500 9 ASN A1183 58.31 79.28 REMARK 500 9 ASN A1196 58.37 -147.88 REMARK 500 10 LYS A1148 128.54 68.97 REMARK 500 10 ARG A1150 117.08 88.91 REMARK 500 10 ARG A1151 106.40 -173.57 REMARK 500 10 ASN A1196 55.54 -142.58 REMARK 500 10 MET A1200 -177.06 53.27 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1155 SG REMARK 620 2 CYS A1158 SG 99.5 REMARK 620 3 CYS A1161 SG 124.9 99.0 REMARK 620 4 CYS A1194 SG 99.9 108.9 121.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1167 SG REMARK 620 2 CYS A1170 SG 107.9 REMARK 620 3 CYS A1173 SG 125.2 98.3 REMARK 620 4 CYS A1189 SG 104.9 122.1 100.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2002 DBREF 2KKF A 1147 1203 UNP Q03164 HRX_HUMAN 1147 1203 DBREF 2KKF B 101 112 PDB 2KKF 2KKF 101 112 DBREF 2KKF C 101 112 PDB 2KKF 2KKF 101 112 SEQADV 2KKF GLY A 1145 UNP Q03164 EXPRESSION TAG SEQADV 2KKF SER A 1146 UNP Q03164 EXPRESSION TAG SEQRES 1 A 59 GLY SER LYS LYS GLY ARG ARG SER ARG ARG CYS GLY GLN SEQRES 2 A 59 CYS PRO GLY CYS GLN VAL PRO GLU ASP CYS GLY VAL CYS SEQRES 3 A 59 THR ASN CYS LEU ASP LYS PRO LYS PHE GLY GLY ARG ASN SEQRES 4 A 59 ILE LYS LYS GLN CYS CYS LYS MET ARG LYS CYS GLN ASN SEQRES 5 A 59 LEU GLN TRP MET PRO SER LYS SEQRES 1 B 12 DC DC DC DT DG DC DG DC DA DG DG DG SEQRES 1 C 12 DC DC DC DT DG DC DG DC DA DG DG DG HET ZN A2001 1 HET ZN A2002 1 HETNAM ZN ZINC ION FORMUL 4 ZN 2(ZN 2+) HELIX 1 1 CYS A 1158 VAL A 1163 1 6 HELIX 2 2 CYS A 1170 LYS A 1176 1 7 HELIX 3 3 PRO A 1177 GLY A 1180 5 4 LINK SG CYS A1155 ZN ZN A2001 1555 1555 2.25 LINK SG CYS A1158 ZN ZN A2001 1555 1555 2.30 LINK SG CYS A1161 ZN ZN A2001 1555 1555 2.29 LINK SG CYS A1167 ZN ZN A2002 1555 1555 2.24 LINK SG CYS A1170 ZN ZN A2002 1555 1555 2.30 LINK SG CYS A1173 ZN ZN A2002 1555 1555 2.28 LINK SG CYS A1189 ZN ZN A2002 1555 1555 2.28 LINK SG CYS A1194 ZN ZN A2001 1555 1555 2.29 SITE 1 AC1 5 CYS A1155 GLY A1156 CYS A1158 CYS A1161 SITE 2 AC1 5 CYS A1194 SITE 1 AC2 4 CYS A1167 CYS A1170 CYS A1173 CYS A1189 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