HEADER NUCLEAR PROTEIN/DNA 24-NOV-23 8X7I TITLE CRYO-EM STRUCTURES OF RNF168/UBCH5C-UB IN COMPLEX WITH H2AK13UB TITLE 2 NUCLEOSOMES DETERMINED BY INTEIN-BASED E2-UB-NCP CONJUGATION STRATEGY 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-B/E; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: HISTONE H2A TYPE 1-B/E; COMPND 18 CHAIN: G; COMPND 19 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: DNA (147-MER); COMPND 23 CHAIN: I; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 6; COMPND 26 MOLECULE: DNA (147-MER); COMPND 27 CHAIN: J; COMPND 28 ENGINEERED: YES; COMPND 29 MOL_ID: 7; COMPND 30 MOLECULE: HISTONE H2B TYPE 1-K; COMPND 31 CHAIN: D, H; COMPND 32 ENGINEERED: YES; COMPND 33 MOL_ID: 8; COMPND 34 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D3; COMPND 35 CHAIN: K; COMPND 36 SYNONYM: (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D3,E2 COMPND 37 UBIQUITIN-CONJUGATING ENZYME D3,UBIQUITIN CARRIER PROTEIN D3, COMPND 38 UBIQUITIN-CONJUGATING ENZYME E2(17)KB 3,UBIQUITIN-CONJUGATING ENZYME COMPND 39 E2-17 KDA 3,UBIQUITIN-PROTEIN LIGASE D3; COMPND 40 EC: 2.3.2.23,2.3.2.24; COMPND 41 ENGINEERED: YES; COMPND 42 MOL_ID: 9; COMPND 43 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF168; COMPND 44 CHAIN: L; COMPND 45 SYNONYM: HRNF168,RING FINGER PROTEIN 168,RING-TYPE E3 UBIQUITIN COMPND 46 TRANSFERASE RNF168; COMPND 47 EC: 2.3.2.27; COMPND 48 ENGINEERED: YES; COMPND 49 MOL_ID: 10; COMPND 50 MOLECULE: UBIQUITIN; COMPND 51 CHAIN: M; COMPND 52 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, H4C16, SOURCE 18 H4-16, 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: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 28 MOL_ID: 4; SOURCE 29 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 30 ORGANISM_COMMON: HUMAN; SOURCE 31 ORGANISM_TAXID: 9606; SOURCE 32 GENE: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE; SOURCE 33 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 34 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 35 MOL_ID: 5; SOURCE 36 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 37 ORGANISM_COMMON: HUMAN; SOURCE 38 ORGANISM_TAXID: 9606; SOURCE 39 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 40 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 41 MOL_ID: 6; SOURCE 42 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 43 ORGANISM_COMMON: HUMAN; SOURCE 44 ORGANISM_TAXID: 9606; SOURCE 45 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 46 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 47 MOL_ID: 7; SOURCE 48 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 49 ORGANISM_COMMON: HUMAN; SOURCE 50 ORGANISM_TAXID: 9606; SOURCE 51 GENE: H2BC12; SOURCE 52 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 53 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 54 MOL_ID: 8; SOURCE 55 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 56 ORGANISM_COMMON: HUMAN; SOURCE 57 ORGANISM_TAXID: 9606; SOURCE 58 GENE: UBE2D3, UBC5C, UBCH5C; SOURCE 59 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 60 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 61 MOL_ID: 9; SOURCE 62 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 63 ORGANISM_COMMON: HUMAN; SOURCE 64 ORGANISM_TAXID: 9606; SOURCE 65 GENE: RNF168; SOURCE 66 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 67 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 68 MOL_ID: 10; SOURCE 69 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 70 ORGANISM_COMMON: HUMAN; SOURCE 71 ORGANISM_TAXID: 9606; SOURCE 72 GENE: RPS27A, UBA80, UBCEP1; SOURCE 73 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 74 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNF168, NUCLEOSOME, H2AK13/15 UBIQUITINATION, NUCLEAR PROTEIN, KEYWDS 2 NUCLEAR PROTEIN-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR H.S.AI,Z.B.TONG,Z.H.DENG,M.PAN,L.LIU REVDAT 1 07-AUG-24 8X7I 0 JRNL AUTH H.AI,Z.TONG,Z.DENG,Q.SHI,S.TAO,J.LIANG,M.SUN,X.WU,Q.ZHENG, JRNL AUTH 2 L.LIANG,J.B.LI,S.GAO,C.TIAN,L.LIU,M.PAN JRNL TITL CAPTURING SNAPSHOTS OF NUCLEOSOMAL H2A K13/K15 JRNL TITL 2 UBIQUITINATION MEDIATED BY THE MONOMERIC E3 LIGASE RNF168 JRNL REF BIORXIV 2024 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2024.01.02.573964 REMARK 2 REMARK 2 RESOLUTION. 3.27 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) : 3.270 REMARK 3 NUMBER OF PARTICLES : 178994 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8X7I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042790. 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 : RNF168/UBCH5C-UB/NUCLEOSOMES REMARK 245 DETERMINED BY INTEIN-BASED E2- REMARK 245 UB-NCP CONJUGATION STRATEGY 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 : 7.50 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 K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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: TRIDECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, E, F, G, I, J, D, H, REMARK 350 AND CHAINS: K, L, M 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 E 37 REMARK 465 MET L 1 REMARK 465 ALA L 2 REMARK 465 ARG L 86 REMARK 465 GLU L 87 REMARK 465 CYS L 88 REMARK 465 LYS L 89 REMARK 465 LEU L 90 REMARK 465 ARG L 91 REMARK 465 ALA L 92 REMARK 465 SER L 93 REMARK 465 GLY L 94 REMARK 465 GLN L 95 REMARK 465 GLU L 96 REMARK 465 SER L 97 REMARK 465 GLU L 98 REMARK 465 GLU L 99 REMARK 465 VAL L 100 REMARK 465 ALA L 101 REMARK 465 ASP L 102 REMARK 465 ASP L 103 REMARK 465 TYR L 104 REMARK 465 GLN L 105 REMARK 465 PRO L 106 REMARK 465 VAL L 107 REMARK 465 ARG L 108 REMARK 465 LEU L 109 REMARK 465 LEU L 110 REMARK 465 SER L 111 REMARK 465 LYS L 112 REMARK 465 PRO L 113 REMARK 465 THR M 7 REMARK 465 LEU M 8 REMARK 465 THR M 9 REMARK 465 GLY M 10 REMARK 465 LYS M 11 REMARK 465 ALA M 46 REMARK 465 GLY M 47 REMARK 465 LYS M 48 REMARK 465 GLN M 49 REMARK 465 LEU M 50 REMARK 465 GLU M 51 REMARK 465 VAL M 70 REMARK 465 LEU M 71 REMARK 465 ARG M 72 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 LYS C 118 CG CD CE NZ REMARK 470 LYS C 119 CG CD CE NZ REMARK 470 ARG F 23 CG CD NE CZ NH1 NH2 REMARK 470 LYS G 118 CG CD CE NZ REMARK 470 LYS K 8 CG CD CE NZ REMARK 470 GLU K 9 CG CD OE1 OE2 REMARK 470 ARG K 15 CG CD NE CZ NH1 NH2 REMARK 470 ASP K 28 CG OD1 OD2 REMARK 470 ASP K 42 CG OD1 OD2 REMARK 470 LYS K 66 CG CD CE NZ REMARK 470 ARG K 72 CG CD NE CZ NH1 NH2 REMARK 470 ASN K 81 CG OD1 ND2 REMARK 470 ARG K 90 CG CD NE CZ NH1 NH2 REMARK 470 LYS K 101 CG CD CE NZ REMARK 470 ASP K 116 CG OD1 OD2 REMARK 470 ASP K 117 CG OD1 OD2 REMARK 470 LYS L 5 CG CD CE NZ REMARK 470 GLU L 13 CG CD OE1 OE2 REMARK 470 LYS L 37 CG CD CE NZ REMARK 470 LYS L 46 CG CD CE NZ REMARK 470 GLU L 75 CG CD OE1 OE2 REMARK 470 LYS L 82 CG CD CE NZ REMARK 470 GLN M 2 CG CD OE1 NE2 REMARK 470 ILE M 3 CG1 CG2 CD1 REMARK 470 LYS M 6 CG CD CE NZ REMARK 470 ILE M 13 CG1 CG2 CD1 REMARK 470 LEU M 15 CG CD1 CD2 REMARK 470 SER M 20 OG REMARK 470 LYS M 27 CG CD CE NZ REMARK 470 GLN M 31 CG CD OE1 NE2 REMARK 470 LYS M 33 CG CD CE NZ REMARK 470 GLU M 34 CG CD OE1 OE2 REMARK 470 ASP M 39 CG OD1 OD2 REMARK 470 GLN M 40 CG CD OE1 NE2 REMARK 470 GLN M 41 CG CD OE1 NE2 REMARK 470 ARG M 42 CG CD NE CZ NH1 NH2 REMARK 470 LEU M 43 CG CD1 CD2 REMARK 470 ILE M 44 CG1 CG2 CD1 REMARK 470 ARG M 54 CG CD NE CZ NH1 NH2 REMARK 470 LEU M 56 CG CD1 CD2 REMARK 470 TYR M 59 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU M 69 CG CD1 CD2 REMARK 470 LEU M 73 CG CD1 CD2 REMARK 470 ARG M 74 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 N2 DG I 51 O2 DC J -51 2.09 REMARK 500 N2 DG I 46 O2 DC J -46 2.09 REMARK 500 O2 DC I 52 N2 DG J -52 2.11 REMARK 500 O2 DC I 40 N2 DG J -40 2.11 REMARK 500 O2 DC I -52 N2 DG J 52 2.12 REMARK 500 N2 DG I 0 O2 DC J 0 2.12 REMARK 500 O2 DC I 30 N2 DG J -30 2.13 REMARK 500 N2 DG I -10 O2 DC J 10 2.14 REMARK 500 OG SER K 22 OG1 THR K 36 2.14 REMARK 500 SG CYS L 31 ND1 HIS L 33 2.15 REMARK 500 N2 DG I 56 O2 DC J -56 2.16 REMARK 500 N2 DG I -56 O2 DC J 56 2.16 REMARK 500 N2 DG I -42 O2 DC J 42 2.16 REMARK 500 N2 DG I -21 O2 DC J 21 2.17 REMARK 500 O2 DC I 53 N2 DG J -53 2.17 REMARK 500 OH TYR K 45 OH TYR K 134 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 DG I -7 O4' - C1' - N9 ANGL. DEV. = 1.8 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 LYS B 20 42.60 -103.93 REMARK 500 ALA C 12 168.64 174.79 REMARK 500 LYS C 119 -109.43 -177.74 REMARK 500 GLN K 92 20.08 -79.18 REMARK 500 ARG L 55 10.52 58.89 REMARK 500 PRO M 19 54.65 -65.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS L 16 SG REMARK 620 2 CYS L 19 SG 108.3 REMARK 620 3 CYS L 36 SG 111.6 107.2 REMARK 620 4 CYS L 39 SG 110.2 113.6 106.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS L 31 SG REMARK 620 2 HIS L 33 ND1 58.3 REMARK 620 3 CYS L 51 SG 108.5 132.1 REMARK 620 4 CYS L 54 SG 115.0 119.4 108.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38099 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURES OF RNF168/UBCH5C-UB IN COMPLEX WITH H2AK13UB REMARK 900 NUCLEOSOMES DETERMINED BY INTEIN-BASED E2-UB-NCP CONJUGATION REMARK 900 STRATEGY DBREF 8X7I A 37 134 UNP Q71DI3 H32_HUMAN 38 135 DBREF 8X7I B 19 101 UNP P62805 H4_HUMAN 20 102 DBREF 8X7I C 10 120 UNP P04908 H2A1B_HUMAN 11 121 DBREF 8X7I E 37 134 UNP Q71DI3 H32_HUMAN 38 135 DBREF 8X7I F 19 101 UNP P62805 H4_HUMAN 20 102 DBREF 8X7I G 10 118 UNP P04908 H2A1B_HUMAN 11 119 DBREF 8X7I I -73 73 PDB 8X7I 8X7I -73 73 DBREF 8X7I J -73 73 PDB 8X7I 8X7I -73 73 DBREF 8X7I D 31 124 UNP O60814 H2B1K_HUMAN 32 125 DBREF 8X7I H 31 124 UNP O60814 H2B1K_HUMAN 32 125 DBREF 8X7I K 1 147 UNP P61077 UB2D3_HUMAN 1 147 DBREF 8X7I L 1 113 UNP Q8IYW5 RN168_HUMAN 1 113 DBREF 8X7I M 1 75 UNP P62979 RS27A_HUMAN 1 75 SEQADV 8X7I SER A 110 UNP Q71DI3 CYS 111 CONFLICT SEQADV 8X7I CYS C 15 UNP P04908 LYS 16 CONFLICT SEQADV 8X7I SER E 110 UNP Q71DI3 CYS 111 CONFLICT SEQADV 8X7I SER K 21 UNP P61077 CYS 21 CONFLICT SEQADV 8X7I SER K 107 UNP P61077 CYS 107 CONFLICT SEQADV 8X7I SER K 111 UNP P61077 CYS 111 CONFLICT SEQADV 8X7I CYS M 76 UNP P62979 EXPRESSION TAG SEQRES 1 A 98 LYS PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG SEQRES 2 A 98 GLU ILE ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE SEQRES 3 A 98 ARG LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA SEQRES 4 A 98 GLN ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA SEQRES 5 A 98 VAL MET ALA LEU GLN GLU ALA SER GLU ALA TYR LEU VAL SEQRES 6 A 98 GLY LEU PHE GLU ASP THR ASN LEU SER ALA ILE HIS ALA SEQRES 7 A 98 LYS ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA SEQRES 8 A 98 ARG ARG ILE ARG GLY GLU ARG SEQRES 1 B 83 ARG LYS VAL LEU ARG ASP ASN ILE GLN GLY ILE THR LYS SEQRES 2 B 83 PRO ALA ILE ARG ARG LEU ALA ARG ARG GLY GLY VAL LYS SEQRES 3 B 83 ARG ILE SER GLY LEU ILE TYR GLU GLU THR ARG GLY VAL SEQRES 4 B 83 LEU LYS VAL PHE LEU GLU ASN VAL ILE ARG ASP ALA VAL SEQRES 5 B 83 THR TYR THR GLU HIS ALA LYS ARG LYS THR VAL THR ALA SEQRES 6 B 83 MET ASP VAL VAL TYR ALA LEU LYS ARG GLN GLY ARG THR SEQRES 7 B 83 LEU TYR GLY PHE GLY SEQRES 1 C 111 ALA ARG ALA LYS ALA CYS THR ARG SER SER ARG ALA GLY SEQRES 2 C 111 LEU GLN PHE PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG SEQRES 3 C 111 LYS GLY ASN TYR SER GLU ARG VAL GLY ALA GLY ALA PRO SEQRES 4 C 111 VAL TYR LEU ALA ALA VAL LEU GLU TYR LEU THR ALA GLU SEQRES 5 C 111 ILE LEU GLU LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS SEQRES 6 C 111 LYS THR ARG ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE SEQRES 7 C 111 ARG ASN ASP GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL SEQRES 8 C 111 THR ILE ALA GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA SEQRES 9 C 111 VAL LEU LEU PRO LYS LYS THR SEQRES 1 E 98 LYS PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG SEQRES 2 E 98 GLU ILE ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE SEQRES 3 E 98 ARG LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA SEQRES 4 E 98 GLN ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA SEQRES 5 E 98 VAL MET ALA LEU GLN GLU ALA SER GLU ALA TYR LEU VAL SEQRES 6 E 98 GLY LEU PHE GLU ASP THR ASN LEU SER ALA ILE HIS ALA SEQRES 7 E 98 LYS ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA SEQRES 8 E 98 ARG ARG ILE ARG GLY GLU ARG SEQRES 1 F 83 ARG LYS VAL LEU ARG ASP ASN ILE GLN GLY ILE THR LYS SEQRES 2 F 83 PRO ALA ILE ARG ARG LEU ALA ARG ARG GLY GLY VAL LYS SEQRES 3 F 83 ARG ILE SER GLY LEU ILE TYR GLU GLU THR ARG GLY VAL SEQRES 4 F 83 LEU LYS VAL PHE LEU GLU ASN VAL ILE ARG ASP ALA VAL SEQRES 5 F 83 THR TYR THR GLU HIS ALA LYS ARG LYS THR VAL THR ALA SEQRES 6 F 83 MET ASP VAL VAL TYR ALA LEU LYS ARG GLN GLY ARG THR SEQRES 7 F 83 LEU TYR GLY PHE GLY SEQRES 1 G 109 ALA ARG ALA LYS ALA LYS THR ARG SER SER ARG ALA GLY SEQRES 2 G 109 LEU GLN PHE PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG SEQRES 3 G 109 LYS GLY ASN TYR SER GLU ARG VAL GLY ALA GLY ALA PRO SEQRES 4 G 109 VAL TYR LEU ALA ALA VAL LEU GLU TYR LEU THR ALA GLU SEQRES 5 G 109 ILE LEU GLU LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS SEQRES 6 G 109 LYS THR ARG ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE SEQRES 7 G 109 ARG ASN ASP GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL SEQRES 8 G 109 THR ILE ALA GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA SEQRES 9 G 109 VAL LEU LEU PRO LYS SEQRES 1 I 147 DA DC DA DG DG DA DT DG DT DA DT DA DT SEQRES 2 I 147 DA DT DC DT DG DA DC DA DC DG DT DG DC SEQRES 3 I 147 DC DT DG DG DA DG DA DC DT DA DG DG DG SEQRES 4 I 147 DA DG DT DA DA DT DC DC DC DC DT DT DG SEQRES 5 I 147 DG DC DG DG DT DT DA DA DA DA DC DG DC SEQRES 6 I 147 DG DG DG DG DG DA DC DA DG DC DG DC DG SEQRES 7 I 147 DT DA DC DG DT DG DC DG DT DT DT DA DA SEQRES 8 I 147 DG DC DG DG DT DG DC DT DA DG DA DG DC SEQRES 9 I 147 DT DG DT DC DT DA DC DG DA DC DC DA DA SEQRES 10 I 147 DT DT DG DA DG DC DG DG DC DC DT DC DG SEQRES 11 I 147 DG DC DA DC DC DG DG DG DA DT DT DC DT SEQRES 12 I 147 DC DC DA DG SEQRES 1 J 147 DC DT DG DG DA DG DA DA DT DC DC DC DG SEQRES 2 J 147 DG DT DG DC DC DG DA DG DG DC DC DG DC SEQRES 3 J 147 DT DC DA DA DT DT DG DG DT DC DG DT DA SEQRES 4 J 147 DG DA DC DA DG DC DT DC DT DA DG DC DA SEQRES 5 J 147 DC DC DG DC DT DT DA DA DA DC DG DC DA SEQRES 6 J 147 DC DG DT DA DC DG DC DG DC DT DG DT DC SEQRES 7 J 147 DC DC DC DC DG DC DG DT DT DT DT DA DA SEQRES 8 J 147 DC DC DG DC DC DA DA DG DG DG DG DA DT SEQRES 9 J 147 DT DA DC DT DC DC DC DT DA DG DT DC DT SEQRES 10 J 147 DC DC DA DG DG DC DA DC DG DT DG DT DC SEQRES 11 J 147 DA DG DA DT DA DT DA DT DA DC DA DT DC SEQRES 12 J 147 DC DT DG DT SEQRES 1 D 94 ARG SER ARG LYS GLU SER TYR SER VAL TYR VAL TYR LYS SEQRES 2 D 94 VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SER SER SEQRES 3 D 94 LYS ALA MET GLY ILE MET ASN SER PHE VAL ASN ASP ILE SEQRES 4 D 94 PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU ALA HIS SEQRES 5 D 94 TYR ASN LYS ARG SER THR ILE THR SER ARG GLU ILE GLN SEQRES 6 D 94 THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU ALA LYS SEQRES 7 D 94 HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR LYS TYR SEQRES 8 D 94 THR SER ALA SEQRES 1 H 94 ARG SER ARG LYS GLU SER TYR SER VAL TYR VAL TYR LYS SEQRES 2 H 94 VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SER SER SEQRES 3 H 94 LYS ALA MET GLY ILE MET ASN SER PHE VAL ASN ASP ILE SEQRES 4 H 94 PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU ALA HIS SEQRES 5 H 94 TYR ASN LYS ARG SER THR ILE THR SER ARG GLU ILE GLN SEQRES 6 H 94 THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU ALA LYS SEQRES 7 H 94 HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR LYS TYR SEQRES 8 H 94 THR SER ALA SEQRES 1 K 147 MET ALA LEU LYS ARG ILE ASN LYS GLU LEU SER ASP LEU SEQRES 2 K 147 ALA ARG ASP PRO PRO ALA GLN SER SER ALA GLY PRO VAL SEQRES 3 K 147 GLY ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY SEQRES 4 K 147 PRO ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU SEQRES 5 K 147 THR ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO SEQRES 6 K 147 LYS VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE SEQRES 7 K 147 ASN SER ASN GLY SER ILE CYS LEU ASP ILE LEU ARG SER SEQRES 8 K 147 GLN TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU LEU SEQRES 9 K 147 SER ILE SER SER LEU LEU SER ASP PRO ASN PRO ASP ASP SEQRES 10 K 147 PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP SEQRES 11 K 147 ARG ASP LYS TYR ASN ARG ILE SER ARG GLU TRP THR GLN SEQRES 12 K 147 LYS TYR ALA MET SEQRES 1 L 113 MET ALA LEU PRO LYS ASP ALA ILE PRO SER LEU SER GLU SEQRES 2 L 113 CYS GLN CYS GLY ILE CYS MET GLU ILE LEU VAL GLU PRO SEQRES 3 L 113 VAL THR LEU PRO CYS ASN HIS THR LEU CYS LYS PRO CYS SEQRES 4 L 113 PHE GLN SER THR VAL GLU LYS ALA SER LEU CYS CYS PRO SEQRES 5 L 113 PHE CYS ARG ARG ARG VAL SER SER TRP THR ARG TYR HIS SEQRES 6 L 113 THR ARG ARG ASN SER LEU VAL ASN VAL GLU LEU TRP THR SEQRES 7 L 113 ILE ILE GLN LYS HIS TYR PRO ARG GLU CYS LYS LEU ARG SEQRES 8 L 113 ALA SER GLY GLN GLU SER GLU GLU VAL ALA ASP ASP TYR SEQRES 9 L 113 GLN PRO VAL ARG LEU LEU SER LYS PRO SEQRES 1 M 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 M 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 M 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 M 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 M 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 M 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY CYS HET ZN L 201 1 HET ZN L 202 1 HETNAM ZN ZINC ION FORMUL 14 ZN 2(ZN 2+) HELIX 1 AA1 GLY A 44 GLN A 55 1 12 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 ARG B 92 1 11 HELIX 9 AA9 THR C 16 GLY C 22 1 7 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 GLY E 44 GLN E 55 1 12 HELIX 15 AB6 ARG E 63 GLN E 76 1 14 HELIX 16 AB7 GLN E 85 ALA E 114 1 30 HELIX 17 AB8 MET E 120 ARG E 131 1 12 HELIX 18 AB9 ARG F 23 ILE F 29 5 7 HELIX 19 AC1 THR F 30 GLY F 42 1 13 HELIX 20 AC2 LEU F 49 ALA F 76 1 28 HELIX 21 AC3 THR F 82 ARG F 92 1 11 HELIX 22 AC4 THR G 16 GLY G 22 1 7 HELIX 23 AC5 PRO G 26 LYS G 36 1 11 HELIX 24 AC6 ALA G 45 ASN G 73 1 29 HELIX 25 AC7 ILE G 79 ASP G 90 1 12 HELIX 26 AC8 ASP G 90 LEU G 97 1 8 HELIX 27 AC9 TYR D 37 HIS D 49 1 13 HELIX 28 AD1 SER D 55 ASN D 84 1 30 HELIX 29 AD2 THR D 90 LEU D 102 1 13 HELIX 30 AD3 GLY D 104 ALA D 124 1 21 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 GLY H 104 ALA H 124 1 21 HELIX 35 AD8 ALA K 2 ASP K 16 1 15 HELIX 36 AD9 LEU K 86 SER K 91 1 6 HELIX 37 AE1 THR K 98 ASP K 112 1 15 HELIX 38 AE2 VAL K 120 ASP K 130 1 11 HELIX 39 AE3 ASP K 130 TYR K 145 1 16 HELIX 40 AE4 SER L 10 GLN L 15 1 6 HELIX 41 AE5 CYS L 36 ALA L 47 1 12 HELIX 42 AE6 VAL L 58 ASN L 69 1 12 HELIX 43 AE7 ASN L 73 TYR L 84 1 12 HELIX 44 AE8 THR M 22 GLY M 35 1 14 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 LEU B 97 TYR B 98 0 SHEET 2 AA3 2 THR G 101 ILE G 102 1 O THR G 101 N TYR B 98 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 VAL C 100 ILE C 102 0 SHEET 2 AA6 2 THR F 96 TYR F 98 1 O TYR F 98 N THR C 101 SHEET 1 AA7 2 ARG E 83 PHE E 84 0 SHEET 2 AA7 2 THR F 80 VAL F 81 1 O VAL F 81 N ARG E 83 SHEET 1 AA8 2 THR E 118 ILE E 119 0 SHEET 2 AA8 2 ARG F 45 ILE F 46 1 O ARG F 45 N ILE E 119 SHEET 1 AA9 2 ARG G 42 VAL G 43 0 SHEET 2 AA9 2 THR H 88 ILE H 89 1 O ILE H 89 N ARG G 42 SHEET 1 AB1 2 ARG G 77 ILE G 78 0 SHEET 2 AB1 2 GLY H 53 ILE H 54 1 O GLY H 53 N ILE G 78 SHEET 1 AB2 3 HIS K 32 MET K 38 0 SHEET 2 AB2 3 VAL K 49 HIS K 55 -1 O LEU K 52 N ALA K 35 SHEET 3 AB2 3 LYS K 66 PHE K 69 -1 O LYS K 66 N HIS K 55 SHEET 1 AB3 2 VAL L 27 THR L 28 0 SHEET 2 AB3 2 THR L 34 LEU L 35 -1 O LEU L 35 N VAL L 27 SHEET 1 AB4 2 ILE M 3 LYS M 6 0 SHEET 2 AB4 2 SER M 65 HIS M 68 1 O LEU M 67 N LYS M 6 LINK SG CYS L 16 ZN ZN L 202 1555 1555 2.32 LINK SG CYS L 19 ZN ZN L 202 1555 1555 2.33 LINK SG CYS L 31 ZN ZN L 201 1555 1555 2.32 LINK ND1 HIS L 33 ZN ZN L 201 1555 1555 2.07 LINK SG CYS L 36 ZN ZN L 202 1555 1555 2.32 LINK SG CYS L 39 ZN ZN L 202 1555 1555 2.33 LINK SG CYS L 51 ZN ZN L 201 1555 1555 2.31 LINK SG CYS L 54 ZN ZN L 201 1555 1555 2.32 CISPEP 1 TYR K 60 PRO K 61 0 4.73 CISPEP 2 PRO L 4 LYS L 5 0 -8.97 CISPEP 3 LYS L 5 ASP L 6 0 7.90 CISPEP 4 THR M 14 LEU M 15 0 3.51 CISPEP 5 GLN M 40 GLN M 41 0 0.07 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