HEADER DNA BINDING PROTEIN/DNA 09-OCT-24 9DWH TITLE DNA POLYMERASE BETA BOUND TO A NUCLEOSOME CONTAINING A 1-NT GAP AT TITLE 2 SHL-4.5 (STATE 2, COMPOSITE) CAVEAT 9DWH COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.2; COMPND 3 CHAIN: A, E; COMPND 4 SYNONYM: H3-CLUSTERED HISTONE 13,H3-CLUSTERED HISTONE 14,H3-CLUSTERED COMPND 5 HISTONE 15,HISTONE H3/M,HISTONE H3/O; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HISTONE H4; COMPND 9 CHAIN: B, F; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HISTONE H2A TYPE 1; COMPND 13 CHAIN: C, G; COMPND 14 SYNONYM: H2A.1,HISTONE H2A/PTL; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: HISTONE H2B TYPE 1-C/E/F/G/I; COMPND 18 CHAIN: D, H; COMPND 19 SYNONYM: HISTONE H2B.1 A,HISTONE H2B.A,H2B/A,HISTONE H2B.G,H2B/G, COMPND 20 HISTONE H2B.H,H2B/H,HISTONE H2B.K,H2B/K,HISTONE H2B.L,H2B/L; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 5; COMPND 23 MOLECULE: 601 I STRAND (DAMAGED STRAND 1); COMPND 24 CHAIN: I; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 6; COMPND 27 MOLECULE: 601 J STRAND (NON-DAMAGED STRAND); COMPND 28 CHAIN: J; COMPND 29 ENGINEERED: YES; COMPND 30 MOL_ID: 7; COMPND 31 MOLECULE: 601 K STRAND (DAMAGED STRAND 2); COMPND 32 CHAIN: K; COMPND 33 ENGINEERED: YES; COMPND 34 MOL_ID: 8; COMPND 35 MOLECULE: DNA POLYMERASE BETA; COMPND 36 CHAIN: L; COMPND 37 EC: 2.7.7.7,4.2.99.-; COMPND 38 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: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, SOURCE 13 H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, SOURCE 14 HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, SOURCE 15 H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, SOURCE 16 H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, SOURCE 17 H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, SOURCE 18 HIST4H4; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: H2AC11, H2AFP, HIST1H2AG, H2AC13, H2AFC, HIST1H2AI, H2AC15, SOURCE 26 H2AFD, HIST1H2AK, H2AC16, H2AFI, HIST1H2AL, H2AC17, H2AFN, SOURCE 27 HIST1H2AM; SOURCE 28 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 29 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 30 MOL_ID: 4; SOURCE 31 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 32 ORGANISM_COMMON: HUMAN; SOURCE 33 ORGANISM_TAXID: 9606; SOURCE 34 GENE: H2BC4, H2BFL, HIST1H2BC, H2BC6, H2BFH, HIST1H2BE, H2BC7, SOURCE 35 H2BFG, HIST1H2BF, H2BC8, H2BFA, HIST1H2BG, H2BC10, H2BFK, HIST1H2BI; SOURCE 36 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 37 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 38 MOL_ID: 5; SOURCE 39 SYNTHETIC: YES; SOURCE 40 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 41 ORGANISM_TAXID: 32630; SOURCE 42 MOL_ID: 6; SOURCE 43 SYNTHETIC: YES; SOURCE 44 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 45 ORGANISM_TAXID: 32630; SOURCE 46 MOL_ID: 7; SOURCE 47 SYNTHETIC: YES; SOURCE 48 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 49 ORGANISM_TAXID: 32630; SOURCE 50 MOL_ID: 8; SOURCE 51 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 52 ORGANISM_COMMON: HUMAN; SOURCE 53 ORGANISM_TAXID: 9606; SOURCE 54 GENE: POLB; SOURCE 55 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 56 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOSOME, DNA POLYMERASE BETA, DNA REPAIR, DNA BINDING PROTEIN, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR T.M.WEAVER,B.J.RYAN,B.D.FREUDENTHAL REVDAT 1 15-JAN-25 9DWH 0 JRNL AUTH B.J.RYAN,T.M.WEAVER,B.D.FREUDENTHAL JRNL TITL DNA POLYMERASE BETA BOUND TO A NUCLEOSOME CONTAINING A 1-NT JRNL TITL 2 GAP AT SHL-4.5 (STATE 2, COMPOSITE) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 27265 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 9DWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1000282687. 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 : DNA POLYMERASE BETA BOUND TO A REMARK 245 NUCLEOSOME CONTAINING A 1-NT REMARK 245 GAP AT SHL-4.5 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 : 7.10 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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: 12-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 12-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L 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 ALA A 1 REMARK 465 ARG A 2 REMARK 465 THR A 3 REMARK 465 LYS A 4 REMARK 465 GLN A 5 REMARK 465 THR A 6 REMARK 465 ALA A 7 REMARK 465 ARG A 8 REMARK 465 LYS A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 GLY A 12 REMARK 465 GLY A 13 REMARK 465 LYS A 14 REMARK 465 ALA A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 LYS A 18 REMARK 465 GLN A 19 REMARK 465 LEU A 20 REMARK 465 ALA A 21 REMARK 465 THR A 22 REMARK 465 LYS A 23 REMARK 465 ALA A 24 REMARK 465 ALA A 25 REMARK 465 ARG A 26 REMARK 465 LYS A 27 REMARK 465 SER A 28 REMARK 465 ALA A 29 REMARK 465 PRO A 30 REMARK 465 ALA A 31 REMARK 465 THR A 32 REMARK 465 GLY A 33 REMARK 465 GLY A 34 REMARK 465 VAL A 35 REMARK 465 LYS A 36 REMARK 465 LYS A 37 REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 ARG B 3 REMARK 465 GLY B 4 REMARK 465 LYS B 5 REMARK 465 GLY B 6 REMARK 465 GLY B 7 REMARK 465 LYS B 8 REMARK 465 GLY B 9 REMARK 465 LEU B 10 REMARK 465 GLY B 11 REMARK 465 LYS B 12 REMARK 465 GLY B 13 REMARK 465 GLY B 14 REMARK 465 ALA B 15 REMARK 465 LYS B 16 REMARK 465 ARG B 17 REMARK 465 HIS B 18 REMARK 465 ARG B 19 REMARK 465 GLY B 102 REMARK 465 SER C 1 REMARK 465 GLY C 2 REMARK 465 ARG C 3 REMARK 465 GLY C 4 REMARK 465 LYS C 5 REMARK 465 GLN C 6 REMARK 465 GLY C 7 REMARK 465 GLY C 8 REMARK 465 LYS C 9 REMARK 465 THR C 120 REMARK 465 GLU C 121 REMARK 465 SER C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 LYS C 125 REMARK 465 ALA C 126 REMARK 465 LYS C 127 REMARK 465 GLY C 128 REMARK 465 LYS C 129 REMARK 465 PRO D 1 REMARK 465 GLU D 2 REMARK 465 PRO D 3 REMARK 465 ALA D 4 REMARK 465 LYS D 5 REMARK 465 SER D 6 REMARK 465 ALA D 7 REMARK 465 PRO D 8 REMARK 465 ALA D 9 REMARK 465 PRO D 10 REMARK 465 LYS D 11 REMARK 465 LYS D 12 REMARK 465 GLY D 13 REMARK 465 SER D 14 REMARK 465 LYS D 15 REMARK 465 LYS D 16 REMARK 465 ALA D 17 REMARK 465 VAL D 18 REMARK 465 THR D 19 REMARK 465 LYS D 20 REMARK 465 ALA D 21 REMARK 465 GLN D 22 REMARK 465 LYS D 23 REMARK 465 LYS D 24 REMARK 465 ASP D 25 REMARK 465 GLY D 26 REMARK 465 LYS D 27 REMARK 465 LYS D 28 REMARK 465 ARG D 29 REMARK 465 LYS D 30 REMARK 465 ARG D 31 REMARK 465 LYS D 125 REMARK 465 ALA E 1 REMARK 465 ARG E 2 REMARK 465 THR E 3 REMARK 465 LYS E 4 REMARK 465 GLN E 5 REMARK 465 THR E 6 REMARK 465 ALA E 7 REMARK 465 ARG E 8 REMARK 465 LYS E 9 REMARK 465 SER E 10 REMARK 465 THR E 11 REMARK 465 GLY E 12 REMARK 465 GLY E 13 REMARK 465 LYS E 14 REMARK 465 ALA E 15 REMARK 465 PRO E 16 REMARK 465 ARG E 17 REMARK 465 LYS E 18 REMARK 465 GLN E 19 REMARK 465 LEU E 20 REMARK 465 ALA E 21 REMARK 465 THR E 22 REMARK 465 LYS E 23 REMARK 465 ALA E 24 REMARK 465 ALA E 25 REMARK 465 ARG E 26 REMARK 465 LYS E 27 REMARK 465 SER E 28 REMARK 465 ALA E 29 REMARK 465 PRO E 30 REMARK 465 ALA E 31 REMARK 465 THR E 32 REMARK 465 GLY E 33 REMARK 465 GLY E 34 REMARK 465 VAL E 35 REMARK 465 LYS E 36 REMARK 465 LYS E 37 REMARK 465 ALA E 135 REMARK 465 SER F 1 REMARK 465 GLY F 2 REMARK 465 ARG F 3 REMARK 465 GLY F 4 REMARK 465 LYS F 5 REMARK 465 GLY F 6 REMARK 465 GLY F 7 REMARK 465 LYS F 8 REMARK 465 GLY F 9 REMARK 465 LEU F 10 REMARK 465 GLY F 11 REMARK 465 LYS F 12 REMARK 465 GLY F 13 REMARK 465 GLY F 14 REMARK 465 ALA F 15 REMARK 465 LYS F 16 REMARK 465 ARG F 17 REMARK 465 HIS F 18 REMARK 465 ARG F 19 REMARK 465 GLY F 102 REMARK 465 SER G 1 REMARK 465 GLY G 2 REMARK 465 ARG G 3 REMARK 465 GLY G 4 REMARK 465 LYS G 5 REMARK 465 GLN G 6 REMARK 465 GLY G 7 REMARK 465 GLY G 8 REMARK 465 LYS G 9 REMARK 465 ALA G 10 REMARK 465 ARG G 11 REMARK 465 ALA G 12 REMARK 465 LYS G 13 REMARK 465 GLU G 121 REMARK 465 SER G 122 REMARK 465 HIS G 123 REMARK 465 HIS G 124 REMARK 465 LYS G 125 REMARK 465 ALA G 126 REMARK 465 LYS G 127 REMARK 465 GLY G 128 REMARK 465 LYS G 129 REMARK 465 PRO H 1 REMARK 465 GLU H 2 REMARK 465 PRO H 3 REMARK 465 ALA H 4 REMARK 465 LYS H 5 REMARK 465 SER H 6 REMARK 465 ALA H 7 REMARK 465 PRO H 8 REMARK 465 ALA H 9 REMARK 465 PRO H 10 REMARK 465 LYS H 11 REMARK 465 LYS H 12 REMARK 465 GLY H 13 REMARK 465 SER H 14 REMARK 465 LYS H 15 REMARK 465 LYS H 16 REMARK 465 ALA H 17 REMARK 465 VAL H 18 REMARK 465 THR H 19 REMARK 465 LYS H 20 REMARK 465 ALA H 21 REMARK 465 GLN H 22 REMARK 465 LYS H 23 REMARK 465 LYS H 24 REMARK 465 ASP H 25 REMARK 465 GLY H 26 REMARK 465 LYS H 27 REMARK 465 LYS H 28 REMARK 465 ARG H 29 REMARK 465 LYS H 30 REMARK 465 ARG H 31 REMARK 465 LYS H 125 REMARK 465 MET L 1 REMARK 465 SER L 2 REMARK 465 LYS L 3 REMARK 465 ARG L 4 REMARK 465 LYS L 5 REMARK 465 ALA L 6 REMARK 465 PRO L 7 REMARK 465 GLN L 8 REMARK 465 GLU L 9 REMARK 465 THR L 10 REMARK 465 THR L 205 REMARK 465 LYS L 206 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 ARG C 11 72.68 50.72 REMARK 500 LYS D 85 11.44 59.58 REMARK 500 GLU E 50 -14.00 77.24 REMARK 500 LEU E 61 -1.06 78.66 REMARK 500 PRO L 50 45.79 -85.30 REMARK 500 ASN L 128 51.81 -115.67 REMARK 500 LYS L 244 47.82 -83.44 REMARK 500 ASN L 245 -7.23 64.85 REMARK 500 ARG L 333 34.37 -98.80 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 ARG G 71 0.28 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-47247 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-47248 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-47246 RELATED DB: EMDB REMARK 900 DNA POLYMERASE BETA BOUND TO A NUCLEOSOME CONTAINING A 1-NT GAP AT REMARK 900 SHL-4.5 (STATE 2, COMPOSITE) DBREF 9DWH A 1 135 UNP Q71DI3 H32_HUMAN 2 136 DBREF 9DWH B 1 102 UNP P62805 H4_HUMAN 2 103 DBREF 9DWH C 1 129 UNP P0C0S8 H2A1_HUMAN 2 130 DBREF 9DWH D 1 125 UNP P62807 H2B1C_HUMAN 2 126 DBREF 9DWH E 1 135 UNP Q71DI3 H32_HUMAN 2 136 DBREF 9DWH F 1 102 UNP P62805 H4_HUMAN 2 103 DBREF 9DWH G 1 129 UNP P0C0S8 H2A1_HUMAN 2 130 DBREF 9DWH H 1 125 UNP P62807 H2B1C_HUMAN 2 126 DBREF 9DWH I 1 117 PDB 9DWH 9DWH 1 117 DBREF 9DWH J 1 147 PDB 9DWH 9DWH 1 147 DBREF 9DWH K 119 147 PDB 9DWH 9DWH 119 147 DBREF 9DWH L 1 335 UNP P06746 DPOLB_HUMAN 1 335 SEQADV 9DWH ALA A 110 UNP Q71DI3 CYS 111 ENGINEERED MUTATION SEQADV 9DWH ALA E 110 UNP Q71DI3 CYS 111 ENGINEERED MUTATION SEQRES 1 A 135 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 A 135 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 A 135 LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO HIS SEQRES 4 A 135 ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE ARG SEQRES 5 A 135 ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS LEU SEQRES 6 A 135 PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP PHE SEQRES 7 A 135 LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET ALA SEQRES 8 A 135 LEU GLN GLU ALA SER GLU ALA TYR LEU VAL GLY LEU PHE SEQRES 9 A 135 GLU ASP THR ASN LEU ALA ALA ILE HIS ALA LYS ARG VAL SEQRES 10 A 135 THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG ILE SEQRES 11 A 135 ARG GLY GLU ARG ALA SEQRES 1 B 102 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 B 102 GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN ILE SEQRES 3 B 102 GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA ARG SEQRES 4 B 102 ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR GLU SEQRES 5 B 102 GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN VAL SEQRES 6 B 102 ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS ARG SEQRES 7 B 102 LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU LYS SEQRES 8 B 102 ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 C 129 SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA LYS SEQRES 2 C 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 C 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 C 129 ALA GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 C 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 C 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 C 129 ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU SEQRES 8 C 129 GLU LEU ASN LYS LEU LEU GLY LYS VAL THR ILE ALA GLN SEQRES 9 C 129 GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO SEQRES 10 C 129 LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 D 125 PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SEQRES 2 D 125 SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP GLY SEQRES 3 D 125 LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER VAL SEQRES 4 D 125 TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR SEQRES 5 D 125 GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER PHE SEQRES 6 D 125 VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SER SEQRES 7 D 125 ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SER SEQRES 8 D 125 ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY SEQRES 9 D 125 GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA SEQRES 10 D 125 VAL THR LYS TYR THR SER SER LYS SEQRES 1 E 135 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 E 135 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 E 135 LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO HIS SEQRES 4 E 135 ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE ARG SEQRES 5 E 135 ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS LEU SEQRES 6 E 135 PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP PHE SEQRES 7 E 135 LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET ALA SEQRES 8 E 135 LEU GLN GLU ALA SER GLU ALA TYR LEU VAL GLY LEU PHE SEQRES 9 E 135 GLU ASP THR ASN LEU ALA ALA ILE HIS ALA LYS ARG VAL SEQRES 10 E 135 THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG ILE SEQRES 11 E 135 ARG GLY GLU ARG ALA SEQRES 1 F 102 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 F 102 GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN ILE SEQRES 3 F 102 GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA ARG SEQRES 4 F 102 ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR GLU SEQRES 5 F 102 GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN VAL SEQRES 6 F 102 ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS ARG SEQRES 7 F 102 LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU LYS SEQRES 8 F 102 ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 G 129 SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA LYS SEQRES 2 G 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 G 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 G 129 ALA GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 G 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 G 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 G 129 ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU SEQRES 8 G 129 GLU LEU ASN LYS LEU LEU GLY LYS VAL THR ILE ALA GLN SEQRES 9 G 129 GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO SEQRES 10 G 129 LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 H 125 PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SEQRES 2 H 125 SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP GLY SEQRES 3 H 125 LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER VAL SEQRES 4 H 125 TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR SEQRES 5 H 125 GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER PHE SEQRES 6 H 125 VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SER SEQRES 7 H 125 ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SER SEQRES 8 H 125 ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY SEQRES 9 H 125 GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA SEQRES 10 H 125 VAL THR LYS TYR THR SER SER LYS SEQRES 1 I 117 DA DT DC DG DA DG DA DA DT DC DC DC DG SEQRES 2 I 117 DG DT DG DC DC DG DA DG DG DC DC DG DC SEQRES 3 I 117 DT DC DA DA DT DT DG DG DT DC DG DT DA SEQRES 4 I 117 DG DA DC DA DG DC DT DC DT DA DG DC DA SEQRES 5 I 117 DC DC DG DC DT DT DA DA DA DC DG DC DA SEQRES 6 I 117 DC DG DT DA DC DG DC DG DC DT DG DT DC SEQRES 7 I 117 DC DC DC DC DG DC DG DT DT DT DT DA DA SEQRES 8 I 117 DC DC DG DC DC DA DA DG DG DG DG DA DT SEQRES 9 I 117 DT DA DC DT DC DC DC DT DA DG DT DC DT SEQRES 1 J 147 DA DT DC DG DG DA DT DG DT DA DT DA DT SEQRES 2 J 147 DA DT DC DT DG DA DC DA DC DG DT DG DC SEQRES 3 J 147 DC DT DG DG DA DG DA DC DT DA DG DG DG SEQRES 4 J 147 DA DG DT DA DA DT DC DC DC DC DT DT DG SEQRES 5 J 147 DG DC DG DG DT DT DA DA DA DA DC DG DC SEQRES 6 J 147 DG DG DG DG DG DA DC DA DG DC DG DC DG SEQRES 7 J 147 DT DA DC DG DT DG DC DG DT DT DT DA DA SEQRES 8 J 147 DG DC DG DG DT DG DC DT DA DG DA DG DC SEQRES 9 J 147 DT DG DT DC DT DA DC DG DA DC DC DA DA SEQRES 10 J 147 DT DT DG DA DG DC DG DG DC DC DT DC DG SEQRES 11 J 147 DG DC DA DC DC DG DG DG DA DT DT DC DT SEQRES 12 J 147 DC DG DA DT SEQRES 1 K 29 DC DA DG DG DC DA DC DG DT DG DT DC DA SEQRES 2 K 29 DG DA DT DA DT DA DT DA DC DA DT DC DC SEQRES 3 K 29 DG DA DT SEQRES 1 L 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 L 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 L 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 L 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 L 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 L 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 L 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 L 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 L 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 L 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 L 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 L 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 L 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 L 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 L 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 L 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 L 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 L 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 L 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 L 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 L 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 L 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 L 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 L 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 L 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 L 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU HELIX 1 AA1 GLY A 44 SER A 57 1 14 HELIX 2 AA2 ARG A 63 GLN A 76 1 14 HELIX 3 AA3 GLN A 85 ALA A 114 1 30 HELIX 4 AA4 MET A 120 GLY A 132 1 13 HELIX 5 AA5 ASN B 25 ILE B 29 5 5 HELIX 6 AA6 THR B 30 GLY B 42 1 13 HELIX 7 AA7 LEU B 49 ALA B 76 1 28 HELIX 8 AA8 THR B 82 GLN B 93 1 12 HELIX 9 AA9 THR C 16 ALA C 21 1 6 HELIX 10 AB1 PRO C 26 GLY C 37 1 12 HELIX 11 AB2 ALA C 45 ASN C 73 1 29 HELIX 12 AB3 ILE C 79 ASP C 90 1 12 HELIX 13 AB4 ASP C 90 LEU C 97 1 8 HELIX 14 AB5 TYR D 37 HIS D 49 1 13 HELIX 15 AB6 SER D 55 ASN D 84 1 30 HELIX 16 AB7 THR D 90 LEU D 102 1 13 HELIX 17 AB8 GLY D 104 SER D 123 1 20 HELIX 18 AB9 GLY E 44 SER E 57 1 14 HELIX 19 AC1 ARG E 63 ASP E 77 1 15 HELIX 20 AC2 GLN E 85 ALA E 114 1 30 HELIX 21 AC3 MET E 120 GLY E 132 1 13 HELIX 22 AC4 ASN F 25 ILE F 29 5 5 HELIX 23 AC5 THR F 30 GLY F 42 1 13 HELIX 24 AC6 LEU F 49 ALA F 76 1 28 HELIX 25 AC7 THR F 82 GLN F 93 1 12 HELIX 26 AC8 THR G 16 GLY G 22 1 7 HELIX 27 AC9 PRO G 26 GLY G 37 1 12 HELIX 28 AD1 ALA G 45 ASP G 72 1 28 HELIX 29 AD2 ILE G 79 ASP G 90 1 12 HELIX 30 AD3 GLU G 91 LEU G 97 1 7 HELIX 31 AD4 TYR H 37 HIS H 49 1 13 HELIX 32 AD5 SER H 55 ASN H 84 1 30 HELIX 33 AD6 THR H 90 LEU H 102 1 13 HELIX 34 AD7 PRO H 103 SER H 124 1 22 HELIX 35 AD8 ASN L 12 VAL L 29 1 18 HELIX 36 AD9 ALA L 32 LYS L 48 1 17 HELIX 37 AE1 SER L 55 LYS L 60 1 6 HELIX 38 AE2 GLY L 66 GLY L 80 1 15 HELIX 39 AE3 LEU L 82 GLN L 90 1 9 HELIX 40 AE4 ASP L 91 ARG L 102 1 12 HELIX 41 AE5 GLY L 107 GLU L 117 1 11 HELIX 42 AE6 THR L 121 ASN L 128 1 8 HELIX 43 AE7 GLU L 129 LEU L 132 5 4 HELIX 44 AE8 ASN L 133 TYR L 142 1 10 HELIX 45 AE9 TYR L 142 GLU L 147 1 6 HELIX 46 AF1 ARG L 152 ASP L 170 1 19 HELIX 47 AF2 LYS L 209 VAL L 221 1 13 HELIX 48 AF3 PRO L 261 GLY L 274 1 14 HELIX 49 AF4 SER L 275 LYS L 289 1 15 HELIX 50 AF5 SER L 315 ILE L 323 1 9 HELIX 51 AF6 GLU L 329 ARG L 333 5 5 SHEET 1 AA1 2 ARG A 83 PHE A 84 0 SHEET 2 AA1 2 THR B 80 VAL B 81 1 O VAL B 81 N ARG A 83 SHEET 1 AA2 2 THR A 118 ILE A 119 0 SHEET 2 AA2 2 ARG B 45 ILE B 46 1 O ARG B 45 N ILE A 119 SHEET 1 AA3 2 THR B 96 TYR B 98 0 SHEET 2 AA3 2 VAL G 100 ILE G 102 1 O THR G 101 N THR B 96 SHEET 1 AA4 2 ARG C 42 VAL C 43 0 SHEET 2 AA4 2 THR D 88 ILE D 89 1 O ILE D 89 N ARG C 42 SHEET 1 AA5 2 ARG C 77 ILE C 78 0 SHEET 2 AA5 2 GLY D 53 ILE D 54 1 O GLY D 53 N ILE C 78 SHEET 1 AA6 2 ARG E 83 PHE E 84 0 SHEET 2 AA6 2 THR F 80 VAL F 81 1 O VAL F 81 N ARG E 83 SHEET 1 AA7 2 THR E 118 ILE E 119 0 SHEET 2 AA7 2 ARG F 45 ILE F 46 1 O ARG F 45 N ILE E 119 SHEET 1 AA8 2 ARG G 77 ILE G 78 0 SHEET 2 AA8 2 GLY H 53 ILE H 54 1 O GLY H 53 N ILE G 78 SHEET 1 AA9 2 ILE L 150 PRO L 151 0 SHEET 2 AA9 2 SER L 187 SER L 188 -1 O SER L 188 N ILE L 150 SHEET 1 AB1 5 ILE L 174 CYS L 178 0 SHEET 2 AB1 5 MET L 191 THR L 196 -1 O LEU L 194 N THR L 176 SHEET 3 AB1 5 ARG L 253 LEU L 259 1 O ARG L 258 N LEU L 195 SHEET 4 AB1 5 LYS L 234 CYS L 239 -1 N PHE L 235 O ILE L 257 SHEET 5 AB1 5 ILE L 224 LYS L 230 -1 N SER L 229 O MET L 236 SHEET 1 AB2 2 PHE L 291 ILE L 293 0 SHEET 2 AB2 2 ILE L 298 PRO L 300 -1 O ARG L 299 N THR L 292 CISPEP 1 GLY L 274 SER L 275 0 -0.43 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