HEADER DNA BINDING PROTEIN/DNA 09-MAR-23 8GH8 TITLE RUVA HOLLIDAY JUNCTION DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOLLIDAY JUNCTION BRANCH MIGRATION COMPLEX SUBUNIT RUVA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 3.6.4.12; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (34-MER); COMPND 8 CHAIN: E, G; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (34-MER); COMPND 12 CHAIN: F, H; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS HB8; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 GENE: RUVA, TTHA0291; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS HOLLIDAY JUNCTION, TETRAMER, RUVA, DNA BINDING PROTEIN, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR A.D.RISH,T.FU REVDAT 3 20-NOV-24 8GH8 1 JRNL REVDAT 2 19-JUN-24 8GH8 1 REMARK REVDAT 1 10-MAY-23 8GH8 0 JRNL AUTH A.D.RISH,Z.SHEN,Z.CHEN,N.ZHANG,Q.ZHENG,T.M.FU JRNL TITL MOLECULAR MECHANISMS OF HOLLIDAY JUNCTION BRANCH MIGRATION JRNL TITL 2 CATALYZED BY AN ASYMMETRIC RUVB HEXAMER. JRNL REF NAT COMMUN V. 14 3549 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37322069 JRNL DOI 10.1038/S41467-023-39250-6 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.F.PETTERSEN,T.D.GODDARD,C.C.HUANG,E.C.MENG,G.S.COUCH, REMARK 1 AUTH 2 T.I.CROLL,J.H.MORRIS,T.E.FERRIN REMARK 1 TITL UCSF CHIMERAX: STRUCTURE VISUALIZATION FOR RESEARCHERS, REMARK 1 TITL 2 EDUCATORS, AND DEVELOPERS REMARK 1 REF PROTEIN SCI. V. 30 70 2021 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 28710774 REMARK 1 DOI 10.1002/PRO.3943 REMARK 2 REMARK 2 RESOLUTION. 4.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL 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) : 4.300 REMARK 3 NUMBER OF PARTICLES : 130426 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 8GH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272870. 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 : RUVA DNA BINDING PROTEIN REMARK 245 COMPLEXED WITH HOLLIDAY REMARK 245 JUNCTION DNA; TETRAMERIC RUVA REMARK 245 BINDING PROTEIN; HOLLIDAY REMARK 245 JUNCTION DNA ADAPTED FROM PDB REMARK 245 2HOI REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 5000.00 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 LYS B 140 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 GLU A 39 -52.77 -120.23 REMARK 500 LYS A 42 -173.08 -171.97 REMARK 500 GLU A 66 61.59 60.47 REMARK 500 ALA A 85 -6.12 72.17 REMARK 500 LEU A 92 74.13 -155.52 REMARK 500 ALA A 124 7.03 -68.62 REMARK 500 TYR B 4 66.74 60.97 REMARK 500 GLU B 54 -107.49 50.76 REMARK 500 ALA B 87 48.22 -93.02 REMARK 500 LEU B 89 -6.99 103.63 REMARK 500 ALA B 91 -82.33 -124.93 REMARK 500 LEU B 92 143.21 -33.08 REMARK 500 LEU B 96 -12.87 72.90 REMARK 500 LEU B 97 -5.37 -146.11 REMARK 500 VAL B 131 71.67 57.97 REMARK 500 PHE C 17 140.10 -175.19 REMARK 500 PRO C 63 -179.66 -64.56 REMARK 500 GLU C 65 -104.41 58.73 REMARK 500 ASN C 67 29.59 -143.35 REMARK 500 LEU C 89 -65.30 -120.23 REMARK 500 SER C 90 78.17 -35.99 REMARK 500 ALA C 112 -169.86 -165.82 REMARK 500 ALA C 120 -168.81 -166.51 REMARK 500 GLU C 121 -6.14 77.37 REMARK 500 LEU C 135 24.96 -142.19 REMARK 500 TYR D 4 60.34 62.85 REMARK 500 LEU D 20 35.98 -140.07 REMARK 500 GLU D 66 -137.25 55.13 REMARK 500 ALA D 85 -114.65 56.41 REMARK 500 ALA D 87 -2.98 67.06 REMARK 500 LEU D 101 24.55 -143.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-40036 RELATED DB: EMDB REMARK 900 RUVA HOLLIDAY JUNCTION DNA COMPLEX DBREF 8GH8 A 1 140 UNP Q9F1Q3 RUVA_THET8 1 140 DBREF 8GH8 B 1 140 UNP Q9F1Q3 RUVA_THET8 1 140 DBREF 8GH8 C 1 140 UNP Q9F1Q3 RUVA_THET8 1 140 DBREF 8GH8 D 1 140 UNP Q9F1Q3 RUVA_THET8 1 140 DBREF 8GH8 E 2 35 PDB 8GH8 8GH8 2 35 DBREF 8GH8 F 2 35 PDB 8GH8 8GH8 2 35 DBREF 8GH8 G 2 35 PDB 8GH8 8GH8 2 35 DBREF 8GH8 H 2 35 PDB 8GH8 8GH8 2 35 SEQRES 1 A 140 MET ILE ARG TYR LEU ARG GLY LEU VAL LEU LYS LYS GLU SEQRES 2 A 140 ALA GLY GLY PHE VAL LEU LEU ALA GLY GLY VAL GLY PHE SEQRES 3 A 140 PHE LEU GLN ALA PRO THR PRO PHE LEU GLN ALA LEU GLU SEQRES 4 A 140 GLU GLY LYS GLU VAL GLY VAL HIS THR HIS LEU LEU LEU SEQRES 5 A 140 LYS GLU GLU GLY LEU SER LEU TYR GLY PHE PRO ASP GLU SEQRES 6 A 140 GLU ASN LEU ALA LEU PHE GLU LEU LEU LEU SER VAL SER SEQRES 7 A 140 GLY VAL GLY PRO LYS VAL ALA LEU ALA LEU LEU SER ALA SEQRES 8 A 140 LEU PRO PRO ARG LEU LEU ALA ARG ALA LEU LEU GLU GLY SEQRES 9 A 140 ASP ALA ARG LEU LEU THR SER ALA SER GLY VAL GLY ARG SEQRES 10 A 140 ARG LEU ALA GLU ARG ILE ALA LEU GLU LEU LYS GLY LYS SEQRES 11 A 140 VAL PRO PRO HIS LEU LEU ALA GLY GLU LYS SEQRES 1 B 140 MET ILE ARG TYR LEU ARG GLY LEU VAL LEU LYS LYS GLU SEQRES 2 B 140 ALA GLY GLY PHE VAL LEU LEU ALA GLY GLY VAL GLY PHE SEQRES 3 B 140 PHE LEU GLN ALA PRO THR PRO PHE LEU GLN ALA LEU GLU SEQRES 4 B 140 GLU GLY LYS GLU VAL GLY VAL HIS THR HIS LEU LEU LEU SEQRES 5 B 140 LYS GLU GLU GLY LEU SER LEU TYR GLY PHE PRO ASP GLU SEQRES 6 B 140 GLU ASN LEU ALA LEU PHE GLU LEU LEU LEU SER VAL SER SEQRES 7 B 140 GLY VAL GLY PRO LYS VAL ALA LEU ALA LEU LEU SER ALA SEQRES 8 B 140 LEU PRO PRO ARG LEU LEU ALA ARG ALA LEU LEU GLU GLY SEQRES 9 B 140 ASP ALA ARG LEU LEU THR SER ALA SER GLY VAL GLY ARG SEQRES 10 B 140 ARG LEU ALA GLU ARG ILE ALA LEU GLU LEU LYS GLY LYS SEQRES 11 B 140 VAL PRO PRO HIS LEU LEU ALA GLY GLU LYS SEQRES 1 C 140 MET ILE ARG TYR LEU ARG GLY LEU VAL LEU LYS LYS GLU SEQRES 2 C 140 ALA GLY GLY PHE VAL LEU LEU ALA GLY GLY VAL GLY PHE SEQRES 3 C 140 PHE LEU GLN ALA PRO THR PRO PHE LEU GLN ALA LEU GLU SEQRES 4 C 140 GLU GLY LYS GLU VAL GLY VAL HIS THR HIS LEU LEU LEU SEQRES 5 C 140 LYS GLU GLU GLY LEU SER LEU TYR GLY PHE PRO ASP GLU SEQRES 6 C 140 GLU ASN LEU ALA LEU PHE GLU LEU LEU LEU SER VAL SER SEQRES 7 C 140 GLY VAL GLY PRO LYS VAL ALA LEU ALA LEU LEU SER ALA SEQRES 8 C 140 LEU PRO PRO ARG LEU LEU ALA ARG ALA LEU LEU GLU GLY SEQRES 9 C 140 ASP ALA ARG LEU LEU THR SER ALA SER GLY VAL GLY ARG SEQRES 10 C 140 ARG LEU ALA GLU ARG ILE ALA LEU GLU LEU LYS GLY LYS SEQRES 11 C 140 VAL PRO PRO HIS LEU LEU ALA GLY GLU LYS SEQRES 1 D 140 MET ILE ARG TYR LEU ARG GLY LEU VAL LEU LYS LYS GLU SEQRES 2 D 140 ALA GLY GLY PHE VAL LEU LEU ALA GLY GLY VAL GLY PHE SEQRES 3 D 140 PHE LEU GLN ALA PRO THR PRO PHE LEU GLN ALA LEU GLU SEQRES 4 D 140 GLU GLY LYS GLU VAL GLY VAL HIS THR HIS LEU LEU LEU SEQRES 5 D 140 LYS GLU GLU GLY LEU SER LEU TYR GLY PHE PRO ASP GLU SEQRES 6 D 140 GLU ASN LEU ALA LEU PHE GLU LEU LEU LEU SER VAL SER SEQRES 7 D 140 GLY VAL GLY PRO LYS VAL ALA LEU ALA LEU LEU SER ALA SEQRES 8 D 140 LEU PRO PRO ARG LEU LEU ALA ARG ALA LEU LEU GLU GLY SEQRES 9 D 140 ASP ALA ARG LEU LEU THR SER ALA SER GLY VAL GLY ARG SEQRES 10 D 140 ARG LEU ALA GLU ARG ILE ALA LEU GLU LEU LYS GLY LYS SEQRES 11 D 140 VAL PRO PRO HIS LEU LEU ALA GLY GLU LYS SEQRES 1 E 34 DA DT DA DA DC DT DT DC DG DT DA DT DA SEQRES 2 E 34 DG DC DA DT DA DC DA DT DT DA DT DA DC SEQRES 3 E 34 DG DA DA DC DT DT DA DT SEQRES 1 F 34 DA DT DA DA DG DT DT DC DG DT DA DT DA SEQRES 2 F 34 DA DT DG DT DA DT DG DC DT DA DT DA DC SEQRES 3 F 34 DG DA DA DG DT DT DA DT SEQRES 1 G 34 DA DT DA DA DC DT DT DC DG DT DA DT DA SEQRES 2 G 34 DG DC DA DT DA DC DA DT DT DA DT DA DC SEQRES 3 G 34 DG DA DA DC DT DT DA DT SEQRES 1 H 34 DA DT DA DA DG DT DT DC DG DT DA DT DA SEQRES 2 H 34 DA DT DG DT DA DT DG DC DT DA DT DA DC SEQRES 3 H 34 DG DA DA DG DT DT DA DT HELIX 1 AA1 PRO A 31 GLN A 36 1 6 HELIX 2 AA2 LEU A 68 LEU A 75 1 8 HELIX 3 AA3 LEU A 96 LEU A 102 1 7 HELIX 4 AA4 GLY A 104 SER A 111 1 8 HELIX 5 AA5 ARG A 117 ARG A 122 1 6 HELIX 6 AA6 ALA A 124 GLY A 129 1 6 HELIX 7 AA7 PRO B 31 LEU B 38 1 8 HELIX 8 AA8 LEU B 70 LEU B 75 1 6 HELIX 9 AA9 ALA B 98 LEU B 102 5 5 HELIX 10 AB1 LEU B 119 ALA B 124 1 6 HELIX 11 AB2 GLU B 126 VAL B 131 5 6 HELIX 12 AB3 THR C 32 ALA C 37 5 6 HELIX 13 AB4 ASN C 67 LEU C 74 1 8 HELIX 14 AB5 GLY C 81 LEU C 86 1 6 HELIX 15 AB6 ARG C 122 LYS C 128 1 7 HELIX 16 AB7 PRO D 31 GLN D 36 1 6 HELIX 17 AB8 ASN D 67 LEU D 75 1 9 HELIX 18 AB9 LEU D 96 LEU D 101 1 6 HELIX 19 AC1 ALA D 106 THR D 110 5 5 HELIX 20 AC2 LEU D 119 ALA D 124 1 6 SHEET 1 AA1 2 PHE A 17 LEU A 20 0 SHEET 2 AA1 2 GLY A 25 LEU A 28 -1 O PHE A 26 N LEU A 19 SHEET 1 AA2 3 PHE B 17 LEU B 19 0 SHEET 2 AA2 3 PHE B 26 GLN B 29 -1 O PHE B 26 N LEU B 19 SHEET 3 AA2 3 LEU B 59 TYR B 60 1 O LEU B 59 N PHE B 27 SHEET 1 AA3 3 VAL C 18 LEU C 20 0 SHEET 2 AA3 3 GLY C 25 GLN C 29 -1 O PHE C 26 N LEU C 19 SHEET 3 AA3 3 LEU C 59 TYR C 60 1 O LEU C 59 N GLN C 29 SHEET 1 AA4 2 LEU D 5 GLY D 7 0 SHEET 2 AA4 2 VAL D 44 VAL D 46 -1 O VAL D 46 N LEU D 5 SHEET 1 AA5 3 PHE D 17 LEU D 19 0 SHEET 2 AA5 3 PHE D 26 GLN D 29 -1 O PHE D 26 N LEU D 19 SHEET 3 AA5 3 LEU D 59 TYR D 60 1 O LEU D 59 N PHE D 27 CISPEP 1 PRO D 132 PRO D 133 0 -5.63 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 TER 1054 LYS A 140 TER 2099 GLU B 139 TER 3153 LYS C 140 TER 4207 LYS D 140 TER 4901 DT E 35 TER 5603 DT F 35 TER 6297 DT G 35 TER 6999 DT H 35 MASTER 168 0 0 20 13 0 0 6 6991 8 0 56 END