HEADER REPLICATION 03-MAR-05 1Z1D TITLE STRUCTURAL MODEL FOR THE INTERACTION BETWEEN RPA32 C-TERMINAL DOMAIN TITLE 2 AND SV40 T ANTIGEN ORIGIN BINDING DOMAIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION PROTEIN A 32 KDA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RPA32 C-TERMINAL DOMAIN; COMPND 5 SYNONYM: RP-A, RF-A, REPLICATION FACTOR-A PROTEIN 2, RPA32; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: LARGE T ANTIGEN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: SV40 T ANTIGEN ORIGIN BINDING DOMAIN; COMPND 11 SYNONYM: SV40 T ANTIGEN; 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: RPA2, REPA2, RPA32; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET15B; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SIMIAN VIRUS 40; SOURCE 13 ORGANISM_TAXID: 10633; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PSV278; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PLASMID KEYWDS WINGED HELIX-TURN-HELIX MOTIF, ORIGIN BINDING DOMAIN, PROTEIN-PROTEIN KEYWDS 2 COMPLEX, REPLICATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.I.ARUNKUMAR,V.KLIMOVICH,X.JIANG,R.D.OTT,L.MIZOUE,E.FANNING, AUTHOR 2 W.J.CHAZIN REVDAT 3 02-MAR-22 1Z1D 1 REMARK SEQADV REVDAT 2 24-FEB-09 1Z1D 1 VERSN REVDAT 1 17-MAY-05 1Z1D 0 JRNL AUTH A.I.ARUNKUMAR,V.KLIMOVICH,X.JIANG,R.D.OTT,L.MIZOUE, JRNL AUTH 2 E.FANNING,W.J.CHAZIN JRNL TITL INSIGHTS INTO HRPA32 C-TERMINAL DOMAIN--MEDIATED ASSEMBLY OF JRNL TITL 2 THE SIMIAN VIRUS 40 REPLISOME. JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 332 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 15793585 JRNL DOI 10.1038/NSMB916 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.MER,A.BOCHKAREV,R.GUPTA,E.BOCHKAREVA,L.FRAPPIER, REMARK 1 AUTH 2 C.M.INGLES,A.M.EDWARDS,W.J.CHAZIN REMARK 1 TITL STRUCTURAL BASIS FOR THE RECOGNITION OF DNA REPAIR PROTEINS REMARK 1 TITL 2 UNG2, XPA, AND RAD52 BY REPLICATION FACTOR A REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 103 449 2000 REMARK 1 REFN ISSN 0092-8674 REMARK 1 REFERENCE 2 REMARK 1 AUTH X.LUO,D.G.SANFORD,P.A.BULLOCK,W.W.BACHOVCHIN REMARK 1 TITL SOLUTION STRUCTURE OF THE ORIGIN DNA BINDING DOMAIN OF SV40 REMARK 1 TITL 2 T ANTIGEN REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 3 1034 1996 REMARK 1 REFN ISSN 1545-9993 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 2.3, HADDOCK 1.3 REMARK 3 AUTHORS : BRUKER SOFTWARE (UXNMR), BONVIN, A.M. (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1500 CONFORMERS WERE OBTAINED IN THE REMARK 3 RIGID BODY DOCKING AND 200 BEST CONFORMERS WERE SELECTED FOR REMARK 3 SEMI-FLEXIBLE SIMULATED ANNEALING FOLLOWED BY REFINEMENT. REMARK 4 REMARK 4 1Z1D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032174. 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 : 0.03 M REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2MM RPA32C U-15N, 0.6MM TAG REMARK 210 -OBD, 20MM TRIS BUFFER PH 7.0, 2 REMARK 210 MM DTT, 5MM MGCL2, 90% H2O, 10% REMARK 210 D2O; 0.2MM TAG-OBD U-15N, 0.6MM REMARK 210 RPA32C, 20MM TRIS BUFFER PH 7.0, REMARK 210 2MM DTT, 5MM MGCL2, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 15N-1H HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, HADDOCK 1.3 REMARK 210 METHOD USED : RIGID BODY DOCKING, SEMI REMARK 210 -FLEXIBLE SIMULATED ANNEALING, REMARK 210 REFINEMENT USING EXPLICIT WATER REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS MODEL STRUCTURE WAS OBTAINED USING AMBIGOUS CHEMICAL REMARK 210 SHIFT PERTUBATION CONSTRAINTS AND VALIDATED USING RESIDUAL REMARK 210 DIPOLAR COUPLINGS AND POINT MUTATIONS ON THE INTERFACE 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 168 REMARK 465 SER A 169 REMARK 465 HIS A 170 REMARK 465 MET A 171 REMARK 465 ALA A 172 REMARK 465 ASN A 173 REMARK 465 SER A 174 REMARK 465 GLN A 175 REMARK 465 PRO A 176 REMARK 465 SER A 177 REMARK 465 ALA A 178 REMARK 465 GLY A 179 REMARK 465 ARG A 180 REMARK 465 ALA A 181 REMARK 465 PRO A 182 REMARK 465 ILE A 183 REMARK 465 SER A 184 REMARK 465 ASN A 185 REMARK 465 PRO A 186 REMARK 465 GLY A 187 REMARK 465 MET A 188 REMARK 465 SER A 189 REMARK 465 GLU A 190 REMARK 465 ALA A 191 REMARK 465 GLY A 192 REMARK 465 ASN A 193 REMARK 465 PHE A 194 REMARK 465 GLY A 195 REMARK 465 GLY A 196 REMARK 465 ASN A 197 REMARK 465 SER A 198 REMARK 465 PHE A 199 REMARK 465 MET A 200 REMARK 465 PRO A 201 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 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 LEU A 234 78.76 -102.59 REMARK 500 1 THR A 267 -59.10 -155.73 REMARK 500 1 ALA A 269 25.96 -154.87 REMARK 500 1 HIS B 20 -55.84 71.94 REMARK 500 1 ALA B 29 -46.04 -133.35 REMARK 500 1 SER B 61 -88.56 -103.06 REMARK 500 1 TYR B 62 -66.30 -132.03 REMARK 500 1 LEU B 87 36.35 -93.87 REMARK 500 1 PHE B 92 -178.06 -65.57 REMARK 500 1 ASP B 111 -85.33 23.31 REMARK 500 1 ILE B 116 -75.76 -89.90 REMARK 500 1 PHE B 129 -158.95 -125.25 REMARK 500 2 PRO A 220 44.82 -77.88 REMARK 500 2 LEU A 234 73.46 -103.54 REMARK 500 2 THR A 258 -100.19 -95.04 REMARK 500 2 THR A 267 -65.30 -142.38 REMARK 500 2 LYS B 3 -155.18 -113.89 REMARK 500 2 HIS B 20 -57.86 73.98 REMARK 500 2 SER B 61 -76.05 -106.15 REMARK 500 2 TYR B 62 -78.84 -135.11 REMARK 500 2 ASP B 111 -84.45 22.79 REMARK 500 2 ILE B 116 -84.65 -101.79 REMARK 500 2 ASP B 128 -61.22 -93.23 REMARK 500 3 LEU A 225 107.23 -163.51 REMARK 500 3 THR A 267 -85.90 -100.80 REMARK 500 3 HIS B 20 -66.08 70.61 REMARK 500 3 ALA B 29 -38.54 -143.03 REMARK 500 3 SER B 61 -94.34 -150.17 REMARK 500 3 TYR B 62 -62.82 -138.81 REMARK 500 3 PHE B 92 -177.20 -66.10 REMARK 500 3 ARG B 110 -156.75 -103.36 REMARK 500 3 ILE B 116 -77.11 -106.36 REMARK 500 3 PHE B 129 -130.28 -119.57 REMARK 500 4 LEU A 234 69.32 -105.13 REMARK 500 4 THR A 258 -88.21 -86.63 REMARK 500 4 THR A 267 30.27 -153.04 REMARK 500 4 HIS B 20 -57.02 71.97 REMARK 500 4 ALA B 29 -30.58 -135.99 REMARK 500 4 SER B 61 -101.10 -98.46 REMARK 500 4 PHE B 92 -174.51 -68.28 REMARK 500 4 ARG B 110 -154.44 -98.44 REMARK 500 4 ILE B 116 -72.81 -108.97 REMARK 500 4 PHE B 129 -157.82 -123.72 REMARK 500 5 LEU A 234 72.62 -101.44 REMARK 500 5 HIS A 254 -47.25 -137.79 REMARK 500 5 THR A 258 -94.53 -83.40 REMARK 500 5 HIS A 263 87.67 -159.03 REMARK 500 5 THR A 267 15.69 -153.07 REMARK 500 5 ASP A 268 -98.34 -95.18 REMARK 500 5 LYS B 3 -160.29 -121.54 REMARK 500 REMARK 500 THIS ENTRY HAS 252 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DPU RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN RPA32 REMARK 900 COMPLEXED WITH UNG2(73-88) REMARK 900 RELATED ID: 1TBD RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE ORIGIN DNA BINDING DOMAIN OF SV40 T- REMARK 900 ANTIGEN, NMR, MINIMIZED AVERAGE STRUCTURE REMARK 900 RELATED ID: 4460 RELATED DB: BMRB REMARK 900 1H, 15N AND 13C RESONANCE ASSIGNMENTS FOR THE C-TERMINAL PROTEIN REMARK 900 INTERACTION DOMAIN OF THE 32 KDA SUBUNIT OF HUMAN REPLICATION REMARK 900 PROTEIN A REMARK 900 RELATED ID: 4127 RELATED DB: BMRB REMARK 900 SEQUENCE-SPECIFIC 1H, 13C, AND 15N RESONANCE ASSIGNMENT OF THE REMARK 900 ORIGIN DNA-BINDING DOMAIN OF SV40 T ANTIGEN DBREF 1Z1D A 172 270 UNP P15927 RFA2_HUMAN 172 270 DBREF 1Z1D B 3 131 UNP P03070 TALA_SV40 131 259 SEQADV 1Z1D GLY A 168 UNP P15927 CLONING ARTIFACT SEQADV 1Z1D SER A 169 UNP P15927 CLONING ARTIFACT SEQADV 1Z1D HIS A 170 UNP P15927 CLONING ARTIFACT SEQADV 1Z1D MET A 171 UNP P15927 CLONING ARTIFACT SEQADV 1Z1D GLY B 1 UNP P03070 CLONING ARTIFACT SEQADV 1Z1D SER B 2 UNP P03070 CLONING ARTIFACT SEQRES 1 A 103 GLY SER HIS MET ALA ASN SER GLN PRO SER ALA GLY ARG SEQRES 2 A 103 ALA PRO ILE SER ASN PRO GLY MET SER GLU ALA GLY ASN SEQRES 3 A 103 PHE GLY GLY ASN SER PHE MET PRO ALA ASN GLY LEU THR SEQRES 4 A 103 VAL ALA GLN ASN GLN VAL LEU ASN LEU ILE LYS ALA CYS SEQRES 5 A 103 PRO ARG PRO GLU GLY LEU ASN PHE GLN ASP LEU LYS ASN SEQRES 6 A 103 GLN LEU LYS HIS MET SER VAL SER SER ILE LYS GLN ALA SEQRES 7 A 103 VAL ASP PHE LEU SER ASN GLU GLY HIS ILE TYR SER THR SEQRES 8 A 103 VAL ASP ASP ASP HIS PHE LYS SER THR ASP ALA GLU SEQRES 1 B 131 GLY SER LYS VAL GLU ASP PRO LYS ASP PHE PRO SER GLU SEQRES 2 B 131 LEU LEU SER PHE LEU SER HIS ALA VAL PHE SER ASN ARG SEQRES 3 B 131 THR LEU ALA CYS PHE ALA ILE TYR THR THR LYS GLU LYS SEQRES 4 B 131 ALA ALA LEU LEU TYR LYS LYS ILE MET GLU LYS TYR SER SEQRES 5 B 131 VAL THR PHE ILE SER ARG HIS ASN SER TYR ASN HIS ASN SEQRES 6 B 131 ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG VAL SER SEQRES 7 B 131 ALA ILE ASN ASN TYR ALA GLN LYS LEU CYS THR PHE SER SEQRES 8 B 131 PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR LEU MET SEQRES 9 B 131 TYR SER ALA LEU THR ARG ASP PRO PHE SER VAL ILE GLU SEQRES 10 B 131 GLU SER LEU PRO GLY GLY LEU LYS GLU HIS ASP PHE ASN SEQRES 11 B 131 PRO HELIX 1 1 THR A 206 ALA A 218 1 13 HELIX 2 2 PHE A 227 LEU A 234 1 8 HELIX 3 3 SER A 238 GLU A 252 1 15 HELIX 4 4 PRO B 11 SER B 16 1 6 HELIX 5 5 THR B 36 SER B 52 1 17 HELIX 6 6 VAL B 77 LEU B 87 1 11 HELIX 7 7 LYS B 100 LEU B 108 1 9 SHEET 1 A 3 LEU A 225 ASN A 226 0 SHEET 2 A 3 HIS A 263 SER A 266 -1 O PHE A 264 N LEU A 225 SHEET 3 A 3 ILE A 255 SER A 257 -1 N TYR A 256 O LYS A 265 SHEET 1 B 5 ILE B 94 GLY B 97 0 SHEET 2 B 5 THR B 27 THR B 35 -1 N TYR B 34 O ILE B 94 SHEET 3 B 5 ASN B 65 ARG B 76 -1 O LEU B 67 N ILE B 33 SHEET 4 B 5 PHE B 55 ASN B 60 -1 N HIS B 59 O ILE B 66 SHEET 5 B 5 SER B 114 GLU B 118 -1 O GLU B 117 N ARG B 58 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 MODEL 1