PDB Short entry for 2DT7 HEADER RNA BINDING PROTEIN 11-JUL-06 2DT7 TITLE SOLUTION STRUCTURE OF THE SECOND SURP DOMAIN OF HUMAN SPLICING FACTOR TITLE 2 SF3A120 IN COMPLEX WITH A FRAGMENT OF HUMAN SPLICING FACTOR SF3A60 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPLICING FACTOR 3A SUBUNIT 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 70-107; COMPND 5 SYNONYM: SPLICEOSOME-ASSOCIATED PROTEIN 61, SAP 61, SF3A60; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SPLICING FACTOR 3 SUBUNIT 1; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: SURP DOMAIN; COMPND 11 SYNONYM: SPLICEOSOME-ASSOCIATED PROTEIN 114, SAP 114, SF3A120; 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: SF3A60, SF3A3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1-SF3A60 (71-107)-HIS(6)-SF3A120 SOURCE 10 SURP2 (134-217); SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: SF3A120/SF3A1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1-SF3A60 (71-107)-HIS(6)-SF3A120 SOURCE 20 SURP2 (134-217) KEYWDS STRUCTURE GENOMICS, SF3A120, SF3A60, SURP DOMAIN, STRUCTURAL KEYWDS 2 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.HE,K.KUWASAKO,M.INOUE,P.GUNTERT,Y.MUTO,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 09-MAR-22 2DT7 1 REMARK SEQADV REVDAT 3 24-FEB-09 2DT7 1 VERSN REVDAT 2 02-JAN-07 2DT7 1 REMARK REVDAT 1 26-DEC-06 2DT7 0 JRNL AUTH K.KUWASAKO,F.HE,M.INOUE,A.TANAKA,S.SUGANO,P.GUENTERT,Y.MUTO, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURES OF THE SURP DOMAINS AND THE JRNL TITL 2 SUBUNIT-ASSEMBLY MECHANISM WITHIN THE SPLICING FACTOR SF3A JRNL TITL 3 COMPLEX IN 17S U2 SNRNP JRNL REF STRUCTURE V. 14 1677 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 17098193 JRNL DOI 10.1016/J.STR.2006.09.009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 2.1, OPALP 1.4 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA), KORADI, R. REMARK 3 (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DT7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000025816. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 20MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0MM U-15N, 13C PROTEIN; 20MM REMARK 210 SODIUM PHOSPHATE; 1MM D-DTT; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9321, CYANA 2.1, OPALP REMARK 210 1.4 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINTED ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 10 ARG A 87 NE - CZ - NH2 ANGL. DEV. = -3.2 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 1 GLU A 71 -163.82 60.45 REMARK 500 1 PRO A 78 99.99 -65.79 REMARK 500 1 ALA B 134 1.21 -68.63 REMARK 500 1 ASP B 155 68.82 66.10 REMARK 500 1 SER B 158 158.08 67.26 REMARK 500 2 ASN A 73 174.38 65.68 REMARK 500 2 CYS A 103 -171.96 58.26 REMARK 500 2 ALA B 134 -13.37 58.73 REMARK 500 2 GLN B 135 26.92 -69.77 REMARK 500 2 ILE B 141 168.29 71.82 REMARK 500 2 LYS B 144 31.45 -143.50 REMARK 500 2 GLU B 149 29.90 -143.64 REMARK 500 2 ASP B 155 70.71 41.27 REMARK 500 2 SER B 158 176.48 63.44 REMARK 500 2 GLN B 190 -8.57 -57.55 REMARK 500 2 GLN B 201 3.11 -67.13 REMARK 500 3 LEU A 72 -52.47 -164.78 REMARK 500 3 ASN A 79 104.59 58.83 REMARK 500 3 ALA B 134 170.13 63.17 REMARK 500 3 GLN B 135 84.79 -152.80 REMARK 500 3 LYS B 144 34.40 -80.77 REMARK 500 3 ASP B 155 71.47 51.09 REMARK 500 3 GLN B 201 4.00 -67.66 REMARK 500 4 PRO A 78 99.30 -69.79 REMARK 500 4 GLN B 135 159.65 74.57 REMARK 500 4 ALA B 154 78.67 -150.82 REMARK 500 4 ASP B 155 78.80 52.59 REMARK 500 4 SER B 158 162.58 66.09 REMARK 500 4 GLN B 201 1.77 -64.24 REMARK 500 5 GLU A 71 79.60 50.56 REMARK 500 5 ASN A 73 -170.45 56.71 REMARK 500 5 SER A 76 -178.70 73.36 REMARK 500 5 GLU A 101 64.82 28.86 REMARK 500 5 CYS A 103 95.22 61.37 REMARK 500 5 PRO B 143 -179.92 -69.52 REMARK 500 5 LYS B 144 -174.56 76.89 REMARK 500 5 ASP B 155 71.09 39.64 REMARK 500 6 GLU A 71 162.86 68.63 REMARK 500 6 LEU A 72 13.82 59.70 REMARK 500 6 ASN A 100 -168.32 51.91 REMARK 500 6 GLU A 101 -173.42 55.02 REMARK 500 6 GLN B 135 93.39 -65.38 REMARK 500 6 ASP B 155 61.78 35.24 REMARK 500 6 SER B 158 -178.15 73.71 REMARK 500 7 ALA A 74 -173.32 57.22 REMARK 500 7 SER A 76 81.70 38.80 REMARK 500 7 ASN A 100 -147.96 51.19 REMARK 500 7 ILE A 102 88.00 51.93 REMARK 500 7 CYS A 103 -170.75 66.16 REMARK 500 7 VAL B 136 -18.61 -150.58 REMARK 500 REMARK 500 THIS ENTRY HAS 134 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 ARG B 176 0.10 SIDE CHAIN REMARK 500 2 ARG B 191 0.10 SIDE CHAIN REMARK 500 2 ARG B 199 0.08 SIDE CHAIN REMARK 500 3 ARG A 87 0.08 SIDE CHAIN REMARK 500 3 ARG A 96 0.09 SIDE CHAIN REMARK 500 6 ARG B 191 0.10 SIDE CHAIN REMARK 500 7 TYR B 193 0.07 SIDE CHAIN REMARK 500 11 ARG B 176 0.10 SIDE CHAIN REMARK 500 13 ARG B 199 0.09 SIDE CHAIN REMARK 500 15 ARG B 179 0.08 SIDE CHAIN REMARK 500 15 TYR B 215 0.07 SIDE CHAIN REMARK 500 16 ARG A 96 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DT6 RELATED DB: PDB REMARK 900 RELATED ID: HSS001001930.1 RELATED DB: TARGETDB DBREF 2DT7 A 71 107 UNP Q12874 SF3A3_HUMAN 71 107 DBREF 2DT7 B 134 217 UNP Q15459 SF3A1_HUMAN 134 217 SEQADV 2DT7 GLY A 70 UNP Q12874 CLONING ARTIFACT SEQADV 2DT7 GLY B 133 UNP Q15459 CLONING ARTIFACT SEQRES 1 A 38 GLY GLU LEU ASN ALA ILE SER GLY PRO ASN GLU PHE ALA SEQRES 2 A 38 GLU PHE TYR ASN ARG LEU LYS GLN ILE LYS GLU PHE HIS SEQRES 3 A 38 ARG LYS HIS PRO ASN GLU ILE CYS VAL PRO MET SER SEQRES 1 B 85 GLY ALA GLN VAL ILE GLN GLU THR ILE VAL PRO LYS GLU SEQRES 2 B 85 PRO PRO PRO GLU PHE GLU PHE ILE ALA ASP PRO PRO SER SEQRES 3 B 85 ILE SER ALA PHE ASP LEU ASP VAL VAL LYS LEU THR ALA SEQRES 4 B 85 GLN PHE VAL ALA ARG ASN GLY ARG GLN PHE LEU THR GLN SEQRES 5 B 85 LEU MET GLN LYS GLU GLN ARG ASN TYR GLN PHE ASP PHE SEQRES 6 B 85 LEU ARG PRO GLN HIS SER LEU PHE ASN TYR PHE THR LYS SEQRES 7 B 85 LEU VAL GLU GLN TYR THR LYS HELIX 1 1 ASN A 79 LYS A 97 1 19 HELIX 2 2 SER B 160 GLY B 178 1 19 HELIX 3 3 GLY B 178 GLU B 189 1 12 HELIX 4 4 ASN B 192 ARG B 199 5 8 HELIX 5 5 SER B 203 THR B 216 1 14 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