HEADER NUCLEAR PROTEIN/DNA 24-NOV-23 8X7K TITLE CRYO-EM STRUCTURES OF RNF168/UBCH5C-UB IN COMPLEX WITH H2AK13UB TITLE 2 NUCLEOSOMES DETERMINED BY ACTIVITY-BASED CHEMICAL TRAPPING STRATEGY TITLE 3 (ADJACENT H2AK13/15 DUAL-MONOUBIQUITINATION) 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 H2B TYPE 1-K; COMPND 18 CHAIN: D, H; COMPND 19 SYNONYM: H2B K,HIRA-INTERACTING PROTEIN 1; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: HISTONE H2A TYPE 1-B/E; COMPND 23 CHAIN: G; COMPND 24 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 6; COMPND 27 MOLECULE: DNA (143-MER); COMPND 28 CHAIN: I; COMPND 29 ENGINEERED: YES; COMPND 30 MOL_ID: 7; COMPND 31 MOLECULE: DNA (143-MER); COMPND 32 CHAIN: J; COMPND 33 ENGINEERED: YES; COMPND 34 MOL_ID: 8; COMPND 35 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D3; COMPND 36 CHAIN: K; COMPND 37 SYNONYM: (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D3,E2 COMPND 38 UBIQUITIN-CONJUGATING ENZYME D3,UBIQUITIN CARRIER PROTEIN D3, COMPND 39 UBIQUITIN-CONJUGATING ENZYME E2(17)KB 3,UBIQUITIN-CONJUGATING ENZYME COMPND 40 E2-17 KDA 3,UBIQUITIN-PROTEIN LIGASE D3; COMPND 41 EC: 2.3.2.23,2.3.2.24; COMPND 42 ENGINEERED: YES; COMPND 43 MOL_ID: 9; COMPND 44 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF168; COMPND 45 CHAIN: L; COMPND 46 SYNONYM: HRNF168,RING FINGER PROTEIN 168,RING-TYPE E3 UBIQUITIN COMPND 47 TRANSFERASE RNF168; COMPND 48 EC: 2.3.2.27; COMPND 49 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: H2BC12, H2BFT, HIRIP1, HIST1H2BK; 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 GENE: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE; SOURCE 40 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 41 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 42 MOL_ID: 6; SOURCE 43 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 44 ORGANISM_COMMON: HUMAN; SOURCE 45 ORGANISM_TAXID: 9606; SOURCE 46 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 47 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 48 MOL_ID: 7; SOURCE 49 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 50 ORGANISM_COMMON: HUMAN; SOURCE 51 ORGANISM_TAXID: 9606; 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 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 8X7K 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 : 147576 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 8X7K 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_1300042792. 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 : CRYO-EM STRUCTURES OF REMARK 245 RNF168/UBCH5C-UB IN COMPLEX REMARK 245 WITH H2AK13UB NUCLEOSOMES REMARK 245 DETERMINED BY ACTIVITY-BASED REMARK 245 CHEMICAL TRAPPING STRATEGY REMARK 245 (ADJACENT H2AK13/15 DUAL- REMARK 245 MONOUBIQUITINATION) 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: DODECAMERIC 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 PRO A 38 REMARK 465 LYS B 20 REMARK 465 ALA D 124 REMARK 465 GLY K 27 REMARK 465 ASP K 28 REMARK 465 ASP K 29 REMARK 465 MET L 1 REMARK 465 ALA L 2 REMARK 465 LEU L 3 REMARK 465 PRO L 4 REMARK 465 LYS L 5 REMARK 465 ASP L 6 REMARK 465 ALA L 7 REMARK 465 ILE L 8 REMARK 465 PRO L 9 REMARK 465 SER L 10 REMARK 465 LEU L 11 REMARK 465 SER L 12 REMARK 465 GLU L 13 REMARK 465 CYS L 14 REMARK 465 ASN L 69 REMARK 465 SER L 70 REMARK 465 LEU L 71 REMARK 465 VAL L 72 REMARK 465 ASN L 73 REMARK 465 VAL L 74 REMARK 465 GLU L 75 REMARK 465 LEU L 76 REMARK 465 TRP L 77 REMARK 465 THR L 78 REMARK 465 ILE L 79 REMARK 465 ILE L 80 REMARK 465 GLN L 81 REMARK 465 LYS L 82 REMARK 465 HIS L 83 REMARK 465 TYR L 84 REMARK 465 PRO L 85 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 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 ARG B 23 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 118 CG CD CE NZ REMARK 470 LYS F 20 CG CD CE NZ REMARK 470 ARG F 23 CG CD NE CZ NH1 NH2 REMARK 470 MET K 30 CG SD CE REMARK 470 ARG K 90 CG CD NE CZ NH1 NH2 REMARK 470 ARG K 125 CG CD NE CZ NH1 NH2 REMARK 470 TRP L 61 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP L 61 CZ3 CH2 REMARK 470 TYR L 64 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS L 65 CG ND1 CD2 CE1 NE2 REMARK 470 ARG L 67 CG CD NE CZ NH1 NH2 REMARK 470 ARG L 68 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 -21 O2 DC J 21 2.02 REMARK 500 N2 DG I 46 O2 DC J -46 2.04 REMARK 500 N2 DG I 56 O2 DC J -56 2.04 REMARK 500 N2 DG I -56 O2 DC J 56 2.05 REMARK 500 N2 DG I 0 O2 DC J 0 2.05 REMARK 500 O2 DC I -20 N2 DG J 20 2.07 REMARK 500 N2 DG I 20 O2 DC J -20 2.07 REMARK 500 O2 DC I 40 N2 DG J -40 2.07 REMARK 500 N2 DG I 50 O2 DC J -50 2.08 REMARK 500 N2 DG I 21 O2 DC J -21 2.08 REMARK 500 O2 DC I -52 N2 DG J 52 2.09 REMARK 500 O2 DC I 19 N2 DG J -19 2.09 REMARK 500 O2 DC I 53 N2 DG J -53 2.09 REMARK 500 O2 DC I 30 N2 DG J -30 2.10 REMARK 500 O2 DC I -11 N2 DG J 11 2.10 REMARK 500 N2 DG I -10 O2 DC J 10 2.10 REMARK 500 N2 DG I -42 O2 DC J 42 2.10 REMARK 500 N2 DG I 51 O2 DC J -51 2.12 REMARK 500 O2 DC I -40 N2 DG J 40 2.14 REMARK 500 O2 DC I 52 N2 DG J -52 2.15 REMARK 500 N2 DG I -4 O2 DC J 4 2.16 REMARK 500 O2 DC I 1 N2 DG J -1 2.17 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 77 62.75 60.07 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 107.2 REMARK 620 3 CYS L 36 SG 110.6 104.7 REMARK 620 4 CYS L 39 SG 112.2 112.4 109.4 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 71.8 REMARK 620 3 CYS L 51 SG 108.5 122.3 REMARK 620 4 CYS L 54 SG 111.9 120.9 112.3 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38101 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURES OF RNF168/UBCH5C-UB IN COMPLEX WITH H2AK13UB REMARK 900 NUCLEOSOMES DETERMINED BY ACTIVITY-BASED CHEMICAL TRAPPING STRATEGY REMARK 900 (ADJACENT H2AK13/15 DUAL-MONOUBIQUITINATION) DBREF 8X7K A 38 134 UNP Q71DI3 H32_HUMAN 39 135 DBREF 8X7K B 20 101 UNP P62805 H4_HUMAN 21 102 DBREF 8X7K C 14 118 UNP P04908 H2A1B_HUMAN 15 119 DBREF 8X7K D 31 124 UNP O60814 H2B1K_HUMAN 32 125 DBREF 8X7K E 38 134 UNP Q71DI3 H32_HUMAN 39 135 DBREF 8X7K F 20 101 UNP P62805 H4_HUMAN 21 102 DBREF 8X7K G 10 117 UNP P04908 H2A1B_HUMAN 11 118 DBREF 8X7K H 31 124 UNP O60814 H2B1K_HUMAN 32 125 DBREF 8X7K I -72 70 PDB 8X7K 8X7K -72 70 DBREF 8X7K J -70 72 PDB 8X7K 8X7K -70 72 DBREF 8X7K K 1 147 UNP P61077 UB2D3_HUMAN 1 147 DBREF 8X7K L 1 113 UNP Q8IYW5 RN168_HUMAN 1 113 SEQADV 8X7K SER A 110 UNP Q71DI3 CYS 111 CONFLICT SEQADV 8X7K CYS C 15 UNP P04908 LYS 16 CONFLICT SEQADV 8X7K SER E 110 UNP Q71DI3 CYS 111 CONFLICT SEQADV 8X7K SER K 21 UNP P61077 CYS 21 CONFLICT SEQADV 8X7K SER K 107 UNP P61077 CYS 107 CONFLICT SEQADV 8X7K SER K 111 UNP P61077 CYS 111 CONFLICT SEQRES 1 A 97 PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU SEQRES 2 A 97 ILE ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG SEQRES 3 A 97 LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN SEQRES 4 A 97 ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL SEQRES 5 A 97 MET ALA LEU GLN GLU ALA SER GLU ALA TYR LEU VAL GLY SEQRES 6 A 97 LEU PHE GLU ASP THR ASN LEU SER ALA ILE HIS ALA LYS SEQRES 7 A 97 ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG SEQRES 8 A 97 ARG ILE ARG GLY GLU ARG SEQRES 1 B 82 LYS VAL LEU ARG ASP ASN ILE GLN GLY ILE THR LYS PRO SEQRES 2 B 82 ALA ILE ARG ARG LEU ALA ARG ARG GLY GLY VAL LYS ARG SEQRES 3 B 82 ILE SER GLY LEU ILE TYR GLU GLU THR ARG GLY VAL LEU SEQRES 4 B 82 LYS VAL PHE LEU GLU ASN VAL ILE ARG ASP ALA VAL THR SEQRES 5 B 82 TYR THR GLU HIS ALA LYS ARG LYS THR VAL THR ALA MET SEQRES 6 B 82 ASP VAL VAL TYR ALA LEU LYS ARG GLN GLY ARG THR LEU SEQRES 7 B 82 TYR GLY PHE GLY SEQRES 1 C 105 ALA CYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 2 C 105 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 3 C 105 SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 4 C 105 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 5 C 105 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 6 C 105 ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU SEQRES 7 C 105 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 8 C 105 GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO SEQRES 9 C 105 LYS 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 E 97 PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU SEQRES 2 E 97 ILE ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG SEQRES 3 E 97 LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN SEQRES 4 E 97 ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL SEQRES 5 E 97 MET ALA LEU GLN GLU ALA SER GLU ALA TYR LEU VAL GLY SEQRES 6 E 97 LEU PHE GLU ASP THR ASN LEU SER ALA ILE HIS ALA LYS SEQRES 7 E 97 ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG SEQRES 8 E 97 ARG ILE ARG GLY GLU ARG SEQRES 1 F 82 LYS VAL LEU ARG ASP ASN ILE GLN GLY ILE THR LYS PRO SEQRES 2 F 82 ALA ILE ARG ARG LEU ALA ARG ARG GLY GLY VAL LYS ARG SEQRES 3 F 82 ILE SER GLY LEU ILE TYR GLU GLU THR ARG GLY VAL LEU SEQRES 4 F 82 LYS VAL PHE LEU GLU ASN VAL ILE ARG ASP ALA VAL THR SEQRES 5 F 82 TYR THR GLU HIS ALA LYS ARG LYS THR VAL THR ALA MET SEQRES 6 F 82 ASP VAL VAL TYR ALA LEU LYS ARG GLN GLY ARG THR LEU SEQRES 7 F 82 TYR GLY PHE GLY SEQRES 1 G 108 ALA ARG ALA LYS ALA LYS THR ARG SER SER ARG ALA GLY SEQRES 2 G 108 LEU GLN PHE PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG SEQRES 3 G 108 LYS GLY ASN TYR SER GLU ARG VAL GLY ALA GLY ALA PRO SEQRES 4 G 108 VAL TYR LEU ALA ALA VAL LEU GLU TYR LEU THR ALA GLU SEQRES 5 G 108 ILE LEU GLU LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS SEQRES 6 G 108 LYS THR ARG ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE SEQRES 7 G 108 ARG ASN ASP GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL SEQRES 8 G 108 THR ILE ALA GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA SEQRES 9 G 108 VAL LEU LEU PRO 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 I 143 DC DA DG DG DA DT DG DT DA DT DA DT DA SEQRES 2 I 143 DT DC DT DG DA DC DA DC DG DT DG DC DC SEQRES 3 I 143 DT DG DG DA DG DA DC DT DA DG DG DG DA SEQRES 4 I 143 DG DT DA DA DT DC DC DC DC DT DT DG DG SEQRES 5 I 143 DC DG DG DT DT DA DA DA DA DC DG DC DG SEQRES 6 I 143 DG DG DG DG DA DC DA DG DC DG DC DG DT SEQRES 7 I 143 DA DC DG DT DG DC DG DT DT DT DA DA DG SEQRES 8 I 143 DC DG DG DT DG DC DT DA DG DA DG DC DT SEQRES 9 I 143 DG DT DC DT DA DC DG DA DC DC DA DA DT SEQRES 10 I 143 DT DG DA DG DC DG DG DC DC DT DC DG DG SEQRES 11 I 143 DC DA DC DC DG DG DG DA DT DT DC DT DC SEQRES 1 J 143 DG DA DG DA DA DT DC DC DC DG DG DT DG SEQRES 2 J 143 DC DC DG DA DG DG DC DC DG DC DT DC DA SEQRES 3 J 143 DA DT DT DG DG DT DC DG DT DA DG DA DC SEQRES 4 J 143 DA DG DC DT DC DT DA DG DC DA DC DC DG SEQRES 5 J 143 DC DT DT DA DA DA DC DG DC DA DC DG DT SEQRES 6 J 143 DA DC DG DC DG DC DT DG DT DC DC DC DC SEQRES 7 J 143 DC DG DC DG DT DT DT DT DA DA DC DC DG SEQRES 8 J 143 DC DC DA DA DG DG DG DG DA DT DT DA DC SEQRES 9 J 143 DT DC DC DC DT DA DG DT DC DT DC DC DA SEQRES 10 J 143 DG DG DC DA DC DG DT DG DT DC DA DG DA SEQRES 11 J 143 DT DA DT DA DT DA DC DA DT DC DC DT DG 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 HET ZN L 201 1 HET ZN L 202 1 HETNAM ZN ZINC ION FORMUL 13 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 ARG A 131 1 12 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 LYS B 77 1 29 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 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 PRO D 103 SER D 123 1 21 HELIX 18 AB9 GLY E 44 GLN E 55 1 12 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 ARG E 131 1 12 HELIX 22 AC4 LEU F 22 ILE F 29 5 8 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 ARG F 92 1 11 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 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 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 ALA K 146 1 17 HELIX 40 AE4 CYS L 36 VAL L 44 1 9 HELIX 41 AE5 VAL L 58 ARG L 67 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 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 4 SER K 22 PRO K 25 0 SHEET 2 AB2 4 HIS K 32 MET K 38 -1 O THR K 36 N SER K 22 SHEET 3 AB2 4 VAL K 49 HIS K 55 -1 O LEU K 52 N ALA K 35 SHEET 4 AB2 4 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 LINK SG CYS L 16 ZN ZN L 202 1555 1555 2.33 LINK SG CYS L 19 ZN ZN L 202 1555 1555 2.32 LINK SG CYS L 31 ZN ZN L 201 1555 1555 2.31 LINK ND1 HIS L 33 ZN ZN L 201 1555 1555 2.06 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 2.31 CISPEP 1 TYR K 60 PRO K 61 0 4.75 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