HEADER DNA BINDING PROTEIN/DNA 25-NOV-24 9KQ2 TITLE CRYO-EM STRUCTURE OF RNF168'-RNF168-UBCH5C COMPLEX BOUND TO NUCLEOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3; COMPND 3 CHAIN: A, E; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HISTONE H4; COMPND 7 CHAIN: B, F; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HISTONE H2A; COMPND 11 CHAIN: C, G; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: HISTONE H2B; COMPND 15 CHAIN: D, H; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: DNA (147-MER); COMPND 19 CHAIN: I; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: DNA (147-MER); COMPND 23 CHAIN: J; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 7; COMPND 26 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF168; COMPND 27 CHAIN: K; COMPND 28 SYNONYM: HRNF168,RING FINGER PROTEIN 168,RING-TYPE E3 UBIQUITIN COMPND 29 TRANSFERASE RNF168; COMPND 30 EC: 2.3.2.27; COMPND 31 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: LOC121398065, LOC108703785, LOC121398067; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 10 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 11 ORGANISM_TAXID: 8355; SOURCE 12 GENE: LOC121398084; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 17 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 18 ORGANISM_TAXID: 8355; SOURCE 19 GENE: LOC494591, H2AC14.L, HIST1H2AJ, HIST1H2AJ.L; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 21 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 24 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 25 ORGANISM_TAXID: 8355; SOURCE 26 GENE: LOC108704303; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 28 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 29 MOL_ID: 5; SOURCE 30 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 31 ORGANISM_TAXID: 9606; SOURCE 32 EXPRESSION_SYSTEM: ESCHERICHIA COLI STR. K-12 SUBSTR. DH10B; SOURCE 33 EXPRESSION_SYSTEM_TAXID: 316385; SOURCE 34 MOL_ID: 6; SOURCE 35 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 36 ORGANISM_TAXID: 9606; SOURCE 37 EXPRESSION_SYSTEM: ESCHERICHIA COLI STR. K-12 SUBSTR. DH10B; SOURCE 38 EXPRESSION_SYSTEM_TAXID: 316385; SOURCE 39 MOL_ID: 7; SOURCE 40 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 41 ORGANISM_COMMON: HUMAN; SOURCE 42 ORGANISM_TAXID: 9606; SOURCE 43 GENE: RNF168; SOURCE 44 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 45 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DNA REPAIR, HISTONE UBIQUITINATION, NUCLEOSOME, E3 UBIQUITIN-PROTEIN KEYWDS 2 LIGASE, RNF168, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA KEYWDS 3 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR H.Q.ZHU REVDAT 1 12-NOV-25 9KQ2 0 JRNL AUTH X.YANG,H.ZHU,L.SHI,T.SONG,W.GONG,S.HE,S.SHAN,C.XU,Z.ZHOU JRNL TITL ALPHAFOLD-GUIDED STRUCTURAL ANALYSES OF NUCLEOSOME BINDING JRNL TITL 2 PROTEINS. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40794873 JRNL DOI 10.1093/NAR/GKAF735 REMARK 2 REMARK 2 RESOLUTION. 3.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 58069 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 9KQ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053525. 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'-RNF168-UBCH5C REMARK 245 -NUCLEOSOME COMPLEX 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2300.00 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: UNDECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K 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 ALA A 135 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 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 10 REMARK 465 ARG C 11 REMARK 465 ALA C 12 REMARK 465 LYS C 13 REMARK 465 ALA C 14 REMARK 465 LYS C 15 REMARK 465 LYS C 118 REMARK 465 LYS C 119 REMARK 465 THR C 120 REMARK 465 GLU C 121 REMARK 465 SER C 122 REMARK 465 SER C 123 REMARK 465 LYS C 124 REMARK 465 SER C 125 REMARK 465 ALA C 126 REMARK 465 LYS C 127 REMARK 465 SER C 128 REMARK 465 LYS C 129 REMARK 465 ALA D 1 REMARK 465 LYS D 2 REMARK 465 SER D 3 REMARK 465 ALA D 4 REMARK 465 PRO D 5 REMARK 465 ALA D 6 REMARK 465 PRO D 7 REMARK 465 LYS D 8 REMARK 465 LYS D 9 REMARK 465 GLY D 10 REMARK 465 SER D 11 REMARK 465 LYS D 12 REMARK 465 LYS D 13 REMARK 465 ALA D 14 REMARK 465 VAL D 15 REMARK 465 THR D 16 REMARK 465 LYS D 17 REMARK 465 THR D 18 REMARK 465 GLN D 19 REMARK 465 LYS D 20 REMARK 465 LYS D 21 REMARK 465 ASP D 22 REMARK 465 GLY D 23 REMARK 465 LYS D 24 REMARK 465 LYS D 25 REMARK 465 ARG D 26 REMARK 465 ARG D 27 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 PRO E 38 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 LYS F 20 REMARK 465 VAL F 21 REMARK 465 LEU F 22 REMARK 465 ARG F 23 REMARK 465 ASP F 24 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 THR G 10 REMARK 465 ARG G 11 REMARK 465 ALA G 12 REMARK 465 LYS G 13 REMARK 465 LEU G 115 REMARK 465 LEU G 116 REMARK 465 PRO G 117 REMARK 465 LYS G 118 REMARK 465 LYS G 119 REMARK 465 THR G 120 REMARK 465 GLU G 121 REMARK 465 SER G 122 REMARK 465 SER G 123 REMARK 465 LYS G 124 REMARK 465 SER G 125 REMARK 465 ALA G 126 REMARK 465 LYS G 127 REMARK 465 SER G 128 REMARK 465 LYS G 129 REMARK 465 ALA H 1 REMARK 465 LYS H 2 REMARK 465 SER H 3 REMARK 465 ALA H 4 REMARK 465 PRO H 5 REMARK 465 ALA H 6 REMARK 465 PRO H 7 REMARK 465 LYS H 8 REMARK 465 LYS H 9 REMARK 465 GLY H 10 REMARK 465 SER H 11 REMARK 465 LYS H 12 REMARK 465 LYS H 13 REMARK 465 ALA H 14 REMARK 465 VAL H 15 REMARK 465 THR H 16 REMARK 465 LYS H 17 REMARK 465 THR H 18 REMARK 465 GLN H 19 REMARK 465 LYS H 20 REMARK 465 LYS H 21 REMARK 465 ASP H 22 REMARK 465 GLY H 23 REMARK 465 LYS H 24 REMARK 465 LYS H 25 REMARK 465 ARG H 26 REMARK 465 ARG H 27 REMARK 465 LYS H 28 REMARK 465 LYS H 122 REMARK 465 DA I -73 REMARK 465 DT I -72 REMARK 465 DT I 73 REMARK 465 DA J -73 REMARK 465 DT J 73 REMARK 465 MET K 1 REMARK 465 ALA K 2 REMARK 465 LEU K 3 REMARK 465 PRO K 4 REMARK 465 LYS K 5 REMARK 465 ASP K 6 REMARK 465 ALA K 7 REMARK 465 ILE K 8 REMARK 465 PRO K 9 REMARK 465 SER K 10 REMARK 465 GLY K 94 REMARK 465 GLN K 95 REMARK 465 GLU K 96 REMARK 465 SER K 97 REMARK 465 GLU K 98 REMARK 465 GLU K 99 REMARK 465 VAL K 100 REMARK 465 ALA K 101 REMARK 465 ASP K 102 REMARK 465 ASP K 103 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 DT J -72 P OP1 OP2 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 SG CYS K 36 ZN ZN K 202 1.60 REMARK 500 CB GLU K 21 NH1 ARG K 91 2.04 REMARK 500 OE1 GLU E 73 ND2 ASN F 25 2.11 REMARK 500 OG1 THR G 16 OG SER G 19 2.14 REMARK 500 OE1 GLU C 64 OG SER K 60 2.16 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 25 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT J -67 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT J 67 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 CYS K 16 CA - CB - SG ANGL. DEV. = 8.7 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 ASP A 81 64.56 60.46 REMARK 500 LYS C 74 62.72 64.83 REMARK 500 LEU C 97 55.50 -95.15 REMARK 500 ASP D 48 55.91 -97.33 REMARK 500 ASP E 81 62.71 61.09 REMARK 500 LYS E 115 -4.37 69.92 REMARK 500 LYS G 36 53.69 -93.29 REMARK 500 LEU G 97 44.53 -108.04 REMARK 500 MET K 20 -10.25 70.02 REMARK 500 VAL K 44 -57.39 -127.55 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 K 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS K 16 SG REMARK 620 2 CYS K 19 SG 94.5 REMARK 620 3 CYS K 39 SG 119.8 140.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN K 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS K 31 SG REMARK 620 2 CYS K 51 SG 111.1 REMARK 620 3 CYS K 54 SG 110.5 109.3 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62494 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RNF168'-RNF168-UBCH5C COMPLEX BOUND TO REMARK 900 NUCLEOSOME DBREF1 9KQ2 A 1 135 UNP A0A310TTQ1_XENLA DBREF2 9KQ2 A A0A310TTQ1 2 136 DBREF1 9KQ2 B 1 102 UNP A0A8J1LTD2_XENLA DBREF2 9KQ2 B A0A8J1LTD2 15 116 DBREF 9KQ2 C 1 129 UNP Q6AZJ8 Q6AZJ8_XENLA 2 130 DBREF1 9KQ2 D 1 122 UNP A0A8J0U496_XENLA DBREF2 9KQ2 D A0A8J0U496 5 126 DBREF1 9KQ2 E 1 135 UNP A0A310TTQ1_XENLA DBREF2 9KQ2 E A0A310TTQ1 2 136 DBREF1 9KQ2 F 1 102 UNP A0A8J1LTD2_XENLA DBREF2 9KQ2 F A0A8J1LTD2 15 116 DBREF 9KQ2 G 1 129 UNP Q6AZJ8 Q6AZJ8_XENLA 2 130 DBREF1 9KQ2 H 1 122 UNP A0A8J0U496_XENLA DBREF2 9KQ2 H A0A8J0U496 5 126 DBREF 9KQ2 I -73 73 PDB 9KQ2 9KQ2 -73 73 DBREF 9KQ2 J -73 73 PDB 9KQ2 9KQ2 -73 73 DBREF 9KQ2 K 1 103 UNP Q8IYW5 RN168_HUMAN 1 103 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 ALA LEU PHE SEQRES 9 A 135 GLU ASP THR ASN LEU CYS 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 THR 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 VAL ARG ASN ASP GLU SEQRES 8 C 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 C 129 GLY GLY VAL LEU PRO ASN ILE GLN SER VAL LEU LEU PRO SEQRES 10 C 129 LYS LYS THR GLU SER SER LYS SER ALA LYS SER LYS SEQRES 1 D 122 ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SER LYS LYS SEQRES 2 D 122 ALA VAL THR LYS THR GLN LYS LYS ASP GLY LYS LYS ARG SEQRES 3 D 122 ARG LYS THR ARG LYS GLU SER TYR ALA ILE TYR VAL TYR SEQRES 4 D 122 LYS VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SER SEQRES 5 D 122 SER LYS ALA MET SER ILE MET ASN SER PHE VAL ASN ASP SEQRES 6 D 122 VAL PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU ALA SEQRES 7 D 122 HIS TYR ASN LYS ARG SER THR ILE THR SER ARG GLU ILE SEQRES 8 D 122 GLN THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU ALA SEQRES 9 D 122 LYS HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR LYS SEQRES 10 D 122 TYR THR SER ALA 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 ALA LEU PHE SEQRES 9 E 135 GLU ASP THR ASN LEU CYS 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 THR 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 VAL ARG ASN ASP GLU SEQRES 8 G 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 G 129 GLY GLY VAL LEU PRO ASN ILE GLN SER VAL LEU LEU PRO SEQRES 10 G 129 LYS LYS THR GLU SER SER LYS SER ALA LYS SER LYS SEQRES 1 H 122 ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SER LYS LYS SEQRES 2 H 122 ALA VAL THR LYS THR GLN LYS LYS ASP GLY LYS LYS ARG SEQRES 3 H 122 ARG LYS THR ARG LYS GLU SER TYR ALA ILE TYR VAL TYR SEQRES 4 H 122 LYS VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SER SEQRES 5 H 122 SER LYS ALA MET SER ILE MET ASN SER PHE VAL ASN ASP SEQRES 6 H 122 VAL PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU ALA SEQRES 7 H 122 HIS TYR ASN LYS ARG SER THR ILE THR SER ARG GLU ILE SEQRES 8 H 122 GLN THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU ALA SEQRES 9 H 122 LYS HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR LYS SEQRES 10 H 122 TYR THR SER ALA LYS SEQRES 1 I 147 DA DT DC DG DA DG DA DA DT DC DC DC DG SEQRES 2 I 147 DG DT DG DC DC DG DA DG DG DC DC DG DC SEQRES 3 I 147 DT DC DA DA DT DT DG DG DT DC DG DT DA SEQRES 4 I 147 DG DA DC DA DG DC DT DC DT DA DG DC DA SEQRES 5 I 147 DC DC DG DC DT DT DA DA DA DC DG DC DA SEQRES 6 I 147 DC DG DT DA DC DG DC DG DC DT DG DT DC SEQRES 7 I 147 DC DC DC DC DG DC DG DT DT DT DT DA DA SEQRES 8 I 147 DC DC DG DC DC DA DA DG DG DG DG DA DT SEQRES 9 I 147 DT DA DC DT DC DC DC DT DA DG DT DC DT SEQRES 10 I 147 DC DC DA DG DG DC DA DC DG DT DG DT DC SEQRES 11 I 147 DA DG DA DT DA DT DA DT DA DC DA DT DC SEQRES 12 I 147 DC DG DA 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 103 MET ALA LEU PRO LYS ASP ALA ILE PRO SER LEU SER GLU SEQRES 2 K 103 CYS GLN CYS GLY ILE CYS MET GLU ILE LEU VAL GLU PRO SEQRES 3 K 103 VAL THR LEU PRO CYS ASN HIS THR LEU CYS LYS PRO CYS SEQRES 4 K 103 PHE GLN SER THR VAL GLU LYS ALA SER LEU CYS CYS PRO SEQRES 5 K 103 PHE CYS ARG ARG ARG VAL SER SER TRP THR ARG TYR HIS SEQRES 6 K 103 THR ARG ARG ASN SER LEU VAL ASN VAL GLU LEU TRP THR SEQRES 7 K 103 ILE ILE GLN LYS HIS TYR PRO ARG GLU CYS LYS LEU ARG SEQRES 8 K 103 ALA SER GLY GLN GLU SER GLU GLU VAL ALA ASP ASP HET ZN K 201 1 HET ZN K 202 1 HETNAM ZN ZINC ION FORMUL 12 ZN 2(ZN 2+) HELIX 1 AA1 GLY A 44 SER A 57 1 14 HELIX 2 AA2 ARG A 63 LYS A 79 1 17 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 ASP B 24 ILE B 29 5 6 HELIX 6 AA6 THR B 30 GLY B 42 1 13 HELIX 7 AA7 LEU B 49 LYS B 77 1 29 HELIX 8 AA8 THR B 82 GLN B 93 1 12 HELIX 9 AA9 ARG C 17 ALA C 21 1 5 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 34 HIS D 46 1 13 HELIX 15 AB6 SER D 52 ASN D 81 1 30 HELIX 16 AB7 THR D 87 LEU D 99 1 13 HELIX 17 AB8 PRO D 100 ALA D 121 1 22 HELIX 18 AB9 GLY E 44 SER E 57 1 14 HELIX 19 AC1 ARG E 63 LYS E 79 1 17 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 LYS F 77 1 29 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 LYS G 36 1 11 HELIX 28 AD1 ALA G 45 ASN G 73 1 29 HELIX 29 AD2 ILE G 79 ASP G 90 1 12 HELIX 30 AD3 ASP G 90 LEU G 97 1 8 HELIX 31 AD4 TYR H 34 HIS H 46 1 13 HELIX 32 AD5 SER H 52 ASN H 81 1 30 HELIX 33 AD6 THR H 87 LEU H 99 1 13 HELIX 34 AD7 PRO H 100 ALA H 121 1 22 HELIX 35 AD8 CYS K 36 VAL K 44 1 9 HELIX 36 AD9 VAL K 58 ASN K 69 1 12 HELIX 37 AE1 ASN K 73 TYR K 84 1 12 HELIX 38 AE2 TYR K 84 SER K 93 1 10 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 LEU B 97 TYR B 98 0 SHEET 2 AA2 2 THR G 101 ILE G 102 1 O THR G 101 N TYR B 98 SHEET 1 AA3 2 ARG C 42 VAL C 43 0 SHEET 2 AA3 2 THR D 85 ILE D 86 1 O ILE D 86 N ARG C 42 SHEET 1 AA4 2 ARG C 77 ILE C 78 0 SHEET 2 AA4 2 GLY D 50 ILE D 51 1 O GLY D 50 N ILE C 78 SHEET 1 AA5 2 VAL C 100 ILE C 102 0 SHEET 2 AA5 2 THR F 96 TYR F 98 1 O THR F 96 N THR C 101 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 ARG G 42 VAL G 43 0 SHEET 2 AA7 2 THR H 85 ILE H 86 1 O ILE H 86 N ARG G 42 SHEET 1 AA8 2 ARG G 77 ILE G 78 0 SHEET 2 AA8 2 GLY H 50 ILE H 51 1 O GLY H 50 N ILE G 78 SHEET 1 AA9 2 VAL K 27 THR K 28 0 SHEET 2 AA9 2 THR K 34 LEU K 35 -1 O LEU K 35 N VAL K 27 SSBOND 1 CYS K 36 CYS K 39 1555 1555 2.69 LINK SG CYS K 16 ZN ZN K 202 1555 1555 2.34 LINK SG CYS K 19 ZN ZN K 202 1555 1555 2.16 LINK SG CYS K 31 ZN ZN K 201 1555 1555 2.32 LINK SG CYS K 39 ZN ZN K 202 1555 1555 2.27 LINK SG CYS K 51 ZN ZN K 201 1555 1555 2.31 LINK SG CYS K 54 ZN ZN K 201 1555 1555 2.31 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 TER 803 ARG A 134 TER 1466 GLY B 102 TER 2253 PRO C 117 TER 2999 LYS D 122 TER 3801 ALA E 135 TER 4421 GLY F 102 TER 5199 VAL G 114 TER 5926 ALA H 121 TER 8862 DA I 72 TER 11850 DA J 72 TER 12523 SER K 93 HETATM12524 ZN ZN K 201 170.953 130.155 157.852 1.00196.29 ZN HETATM12525 ZN ZN K 202 182.184 130.825 148.492 1.00266.30 ZN CONECT1189412525 CONECT1191212525 CONECT1200312524 CONECT1204212064 CONECT120641204212525 CONECT1215312524 CONECT1217712524 CONECT12524120031215312177 CONECT12525118941191212064 MASTER 451 0 2 38 18 0 0 612514 11 9 110 END