HEADER DNA BINDING PROTEIN 12-NOV-18 6I52 TITLE YEAST RPA BOUND TO SSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION FACTOR A PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RF-A,REPLICATION PROTEIN A 13 KDA SUBUNIT; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: REPLICATION FACTOR A PROTEIN 2; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: RF-A PROTEIN 2,DNA-BINDING PROTEIN BUF1,REPLICATION PROTEIN COMPND 10 A 36 KDA SUBUNIT; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: REPLICATION FACTOR A PROTEIN 1; COMPND 14 CHAIN: C; COMPND 15 SYNONYM: RF-A PROTEIN 1,DNA-BINDING PROTEIN BUF2,REPLICATION PROTEIN COMPND 16 A 69 KDA DNA-BINDING SUBUNIT,SINGLE-STRANDED DNA-BINDING PROTEIN; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: DNA (5'- COMPND 20 D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'); COMPND 21 CHAIN: D; COMPND 22 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 ATCC: 204508; SOURCE 6 GENE: RFA3, YJL173C, J0506; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSF-DUET-1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 13 S288C); SOURCE 14 ORGANISM_TAXID: 559292; SOURCE 15 GENE: RFA2, BUF1, YNL312W, N0368; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PRSF-DUET-1; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 21 S288C); SOURCE 22 ORGANISM_TAXID: 559292; SOURCE 23 GENE: RFA1, BUF2, RPA1, YAR007C, FUN3; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 25 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 26 EXPRESSION_SYSTEM_PLASMID: PRSF-DUET-1; SOURCE 27 MOL_ID: 4; SOURCE 28 SYNTHETIC: YES; SOURCE 29 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 30 ORGANISM_TAXID: 32630 KEYWDS COMPLEX, HETEROTRIMER, DNA BINDING, OB-FOLD, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.A.YATES,R.J.ARAMAYO,X.ZHANG REVDAT 2 02-JAN-19 6I52 1 JRNL REVDAT 1 19-DEC-18 6I52 0 JRNL AUTH L.A.YATES,R.J.ARAMAYO,N.POKHREL,C.C.CALDWELL,J.A.KAPLAN, JRNL AUTH 2 R.L.PERERA,M.SPIES,E.ANTONY,X.ZHANG JRNL TITL A STRUCTURAL AND DYNAMIC MODEL FOR THE ASSEMBLY OF JRNL TITL 2 REPLICATION PROTEIN A ON SINGLE-STRANDED DNA. JRNL REF NAT COMMUN V. 9 5447 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30575763 JRNL DOI 10.1038/S41467-018-07883-7 REMARK 2 REMARK 2 RESOLUTION. 4.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GCTF, MDFF, RELION, 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 : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE 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) : 4.700 REMARK 3 NUMBER OF PARTICLES : 340864 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6I52 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200012838. 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 : REPLICATION PROTEIN A REMARK 245 HETEROTRIMERIC COMPLEX WITH REMARK 245 SSDNA; REPLICATION PROTEIN A REMARK 245 HETEROTRIMERIC COMPLEX WITH REMARK 245 SSDNA; REPLICATION PROTEIN A REMARK 245 HETEROTRIMERIC COMPLEX WITH REMARK 245 SSDNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : GLOW-DISCHARGED GRID, WAIT TIME REMARK 245 30 SECONDS, BLOTTING TIME 1 REMARK 245 SECOND 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 : NULL 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2.10 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A 122 O REMARK 470 LEU C 619 O 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 ILE A 43 -131.29 41.79 REMARK 500 ILE A 59 -138.84 52.40 REMARK 500 ASP A 70 -11.72 69.22 REMARK 500 ASP A 82 -74.70 -82.60 REMARK 500 PHE A 97 -76.63 -102.38 REMARK 500 THR B 34 -66.01 -124.45 REMARK 500 ARG B 35 -65.31 -120.81 REMARK 500 VAL B 36 -61.57 -124.43 REMARK 500 ASN B 37 72.12 58.91 REMARK 500 ILE B 54 -67.36 -131.93 REMARK 500 ASP B 56 68.50 61.31 REMARK 500 HIS B 62 -138.30 56.04 REMARK 500 ARG B 76 -65.49 -102.78 REMARK 500 HIS B 81 -83.66 -125.97 REMARK 500 ALA B 83 -70.76 -134.45 REMARK 500 TYR B 151 -141.36 57.79 REMARK 500 ALA B 152 175.69 177.80 REMARK 500 ASP B 158 -62.90 -127.72 REMARK 500 ALA B 177 -67.51 -92.98 REMARK 500 MET B 180 -70.77 -130.85 REMARK 500 ALA C 445 -65.21 -128.12 REMARK 500 SER C 461 -78.44 -61.52 REMARK 500 PHE C 466 -148.03 42.69 REMARK 500 PHE C 467 173.86 171.32 REMARK 500 SER C 474 -65.97 -103.12 REMARK 500 PHE C 481 -65.48 -94.42 REMARK 500 PRO C 499 63.45 -65.75 REMARK 500 ASP C 500 -58.92 -128.94 REMARK 500 THR C 529 -75.10 -123.93 REMARK 500 MET C 572 68.66 61.08 REMARK 500 TYR C 586 -75.23 -90.93 REMARK 500 ASN C 587 -77.77 -126.29 REMARK 500 LEU C 602 -3.02 68.71 REMARK 500 TYR C 604 -62.41 -128.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4410 RELATED DB: EMDB REMARK 900 YEAST RPA BOUND TO SSDNA DBREF 6I52 A 1 122 UNP P26755 RFA3_YEAST 1 122 DBREF 6I52 B 32 182 UNP P26754 RFA2_YEAST 32 182 DBREF 6I52 C 442 619 UNP P22336 RFA1_YEAST 442 619 DBREF 6I52 D 8 27 PDB 6I52 6I52 8 27 SEQADV 6I52 B UNP P26754 ASN 106 DELETION SEQADV 6I52 B UNP P26754 ASP 107 DELETION SEQADV 6I52 B UNP P26754 LEU 108 DELETION SEQADV 6I52 B UNP P26754 ALA 109 DELETION SEQADV 6I52 B UNP P26754 ALA 110 DELETION SEQADV 6I52 B UNP P26754 GLY 111 DELETION SEQADV 6I52 B UNP P26754 ASN 112 DELETION SEQADV 6I52 B UNP P26754 ASP 113 DELETION SEQADV 6I52 B UNP P26754 ASP 114 DELETION SEQADV 6I52 B UNP P26754 SER 115 DELETION SEQADV 6I52 B UNP P26754 SER 116 DELETION SEQADV 6I52 B UNP P26754 GLY 117 DELETION SEQADV 6I52 B UNP P26754 LYS 118 DELETION SEQADV 6I52 B UNP P26754 GLY 119 DELETION SEQADV 6I52 B UNP P26754 TYR 120 DELETION SEQADV 6I52 B UNP P26754 GLY 121 DELETION SEQADV 6I52 B UNP P26754 SER 122 DELETION SEQADV 6I52 B UNP P26754 GLN 123 DELETION SEQADV 6I52 B UNP P26754 VAL 124 DELETION SEQRES 1 A 122 MET ALA SER GLU THR PRO ARG VAL ASP PRO THR GLU ILE SEQRES 2 A 122 SER ASN VAL ASN ALA PRO VAL PHE ARG ILE ILE ALA GLN SEQRES 3 A 122 ILE LYS SER GLN PRO THR GLU SER GLN LEU ILE LEU GLN SEQRES 4 A 122 SER PRO THR ILE SER SER LYS ASN GLY SER GLU VAL GLU SEQRES 5 A 122 MET ILE THR LEU ASN ASN ILE ARG VAL SER MET ASN LYS SEQRES 6 A 122 THR PHE GLU ILE ASP SER TRP TYR GLU PHE VAL CYS ARG SEQRES 7 A 122 ASN ASN ASP ASP GLY GLU LEU GLY PHE LEU ILE LEU ASP SEQRES 8 A 122 ALA VAL LEU CYS LYS PHE LYS GLU ASN GLU ASP LEU SER SEQRES 9 A 122 LEU ASN GLY VAL VAL ALA LEU GLN ARG LEU CYS LYS LYS SEQRES 10 A 122 TYR PRO GLU ILE TYR SEQRES 1 B 132 THR ASN THR ARG VAL ASN THR LEU THR PRO VAL THR ILE SEQRES 2 B 132 LYS GLN ILE LEU GLU SER LYS GLN ASP ILE GLN ASP GLY SEQRES 3 B 132 PRO PHE VAL SER HIS ASN GLN GLU LEU HIS HIS VAL CYS SEQRES 4 B 132 PHE VAL GLY VAL VAL ARG ASN ILE THR ASP HIS THR ALA SEQRES 5 B 132 ASN ILE PHE LEU THR ILE GLU ASP GLY THR GLY GLN ILE SEQRES 6 B 132 GLU VAL ARG LYS TRP SER GLU ASP ALA ALA GLN GLN PHE SEQRES 7 B 132 GLU ILE GLY GLY TYR VAL LYS VAL PHE GLY ALA LEU LYS SEQRES 8 B 132 GLU PHE GLY GLY LYS LYS ASN ILE GLN TYR ALA VAL ILE SEQRES 9 B 132 LYS PRO ILE ASP SER PHE ASN GLU VAL LEU THR HIS HIS SEQRES 10 B 132 LEU GLU VAL ILE LYS CYS HIS SER ILE ALA SER GLY MET SEQRES 11 B 132 MET LYS SEQRES 1 C 178 LYS PHE ILE ALA GLN ARG ILE THR ILE ALA ARG ALA GLN SEQRES 2 C 178 ALA GLU ASN LEU GLY ARG SER GLU LYS GLY ASP PHE PHE SEQRES 3 C 178 SER VAL LYS ALA ALA ILE SER PHE LEU LYS VAL ASP ASN SEQRES 4 C 178 PHE ALA TYR PRO ALA CYS SER ASN GLU ASN CYS ASN LYS SEQRES 5 C 178 LYS VAL LEU GLU GLN PRO ASP GLY THR TRP ARG CYS GLU SEQRES 6 C 178 LYS CYS ASP THR ASN ASN ALA ARG PRO ASN TRP ARG TYR SEQRES 7 C 178 ILE LEU THR ILE SER ILE ILE ASP GLU THR ASN GLN LEU SEQRES 8 C 178 TRP LEU THR LEU PHE ASP ASP GLN ALA LYS GLN LEU LEU SEQRES 9 C 178 GLY VAL ASP ALA ASN THR LEU MET SER LEU LYS GLU GLU SEQRES 10 C 178 ASP PRO ASN GLU PHE THR LYS ILE THR GLN SER ILE GLN SEQRES 11 C 178 MET ASN GLU TYR ASP PHE ARG ILE ARG ALA ARG GLU ASP SEQRES 12 C 178 THR TYR ASN ASP GLN SER ARG ILE ARG TYR THR VAL ALA SEQRES 13 C 178 ASN LEU HIS SER LEU ASN TYR ARG ALA GLU ALA ASP TYR SEQRES 14 C 178 LEU ALA ASP GLU LEU SER LYS ALA LEU SEQRES 1 D 20 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 2 D 20 DT DT DT DT DT DT DT HELIX 1 AA1 ASP A 9 ASN A 15 5 7 HELIX 2 AA2 LEU A 105 TYR A 118 1 14 HELIX 3 AA3 THR B 43 SER B 50 1 8 HELIX 4 AA4 PHE B 160 SER B 178 1 19 HELIX 5 AA5 ILE C 450 ALA C 455 1 6 HELIX 6 AA6 PHE C 537 GLY C 546 1 10 HELIX 7 AA7 ASP C 548 GLU C 557 1 10 HELIX 8 AA8 ASN C 561 GLN C 571 1 11 HELIX 9 AA9 TYR C 604 LYS C 617 1 14 SHEET 1 AA1 3 VAL A 20 ILE A 23 0 SHEET 2 AA1 3 TRP A 72 ASN A 79 -1 O CYS A 77 N PHE A 21 SHEET 3 AA1 3 PHE A 87 CYS A 95 -1 O ASP A 91 N VAL A 76 SHEET 1 AA2 3 GLN A 26 LYS A 28 0 SHEET 2 AA2 3 GLN A 35 SER A 40 -1 O GLN A 39 N GLN A 26 SHEET 3 AA2 3 GLU A 52 ASN A 57 -1 O LEU A 56 N LEU A 36 SHEET 1 AA3 2 VAL B 60 SER B 61 0 SHEET 2 AA3 2 GLN B 64 GLU B 65 -1 O GLN B 64 N SER B 61 SHEET 1 AA4 2 VAL B 69 GLY B 73 0 SHEET 2 AA4 2 VAL B 134 GLY B 138 -1 O VAL B 136 N PHE B 71 SHEET 1 AA5 3 VAL B 75 ASP B 80 0 SHEET 2 AA5 3 ILE B 85 ILE B 89 -1 O THR B 88 N ASN B 77 SHEET 3 AA5 3 ILE B 96 LYS B 100 -1 O LYS B 100 N ILE B 85 SHEET 1 AA6 6 SER C 468 LEU C 476 0 SHEET 2 AA6 6 THR C 522 ILE C 526 -1 O SER C 524 N PHE C 475 SHEET 3 AA6 6 GLN C 531 THR C 535 -1 O LEU C 534 N ILE C 523 SHEET 4 AA6 6 SER C 590 HIS C 600 1 O VAL C 596 N THR C 535 SHEET 5 AA6 6 GLU C 574 THR C 585 -1 N ARG C 578 O ALA C 597 SHEET 6 AA6 6 SER C 468 LEU C 476 -1 N ALA C 471 O TYR C 575 SHEET 1 AA7 2 ALA C 482 PRO C 484 0 SHEET 2 AA7 2 TRP C 517 TYR C 519 -1 O ARG C 518 N TYR C 483 SHEET 1 AA8 2 LEU C 496 GLU C 497 0 SHEET 2 AA8 2 TRP C 503 ARG C 504 -1 O ARG C 504 N LEU C 496 CISPEP 1 LEU C 458 GLY C 459 0 -14.82 CISPEP 2 GLY C 459 ARG C 460 0 0.15 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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