HEADER DNA BINDING PROTEIN/DNA 22-NOV-23 8V28 TITLE H2BK120UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.2; COMPND 3 CHAIN: A, E; COMPND 4 SYNONYM: HISTONE H3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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; COMPND 13 CHAIN: C, G; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: HISTONE H2B 1.1; COMPND 17 CHAIN: D, H; COMPND 18 SYNONYM: H2B1.1; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: 601 DNA (147-MER); COMPND 23 CHAIN: I; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 6; COMPND 26 MOLECULE: 601 DNA (147-MER); COMPND 27 CHAIN: J; COMPND 28 ENGINEERED: YES; COMPND 29 MOL_ID: 7; COMPND 30 MOLECULE: UBIQUITIN; COMPND 31 CHAIN: K; COMPND 32 ENGINEERED: YES; COMPND 33 MUTATION: 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 9 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 10 ORGANISM_TAXID: 8355; SOURCE 11 GENE: LOC121398084; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 16 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 17 ORGANISM_TAXID: 8355; SOURCE 18 GENE: HIST1H2AJ, LOC494591, XELAEV_18003602MG; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 21 MOL_ID: 4; SOURCE 22 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 23 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 24 ORGANISM_TAXID: 8355; SOURCE 25 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 27 MOL_ID: 5; SOURCE 28 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 29 ORGANISM_TAXID: 32630; SOURCE 30 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 31 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 32 MOL_ID: 6; SOURCE 33 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 34 ORGANISM_TAXID: 32630; SOURCE 35 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 36 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 37 MOL_ID: 7; SOURCE 38 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 39 ORGANISM_COMMON: HUMAN; SOURCE 40 ORGANISM_TAXID: 9606; SOURCE 41 GENE: UBB; SOURCE 42 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 43 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOSOME, UBIQUITIN, HISTONE, CHROMATIN, DNA BINDING PROTEIN, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.W.HICKS,C.WOLBERGER REVDAT 2 11-SEP-24 8V28 1 JRNL REVDAT 1 28-AUG-24 8V28 0 JRNL AUTH C.W.HICKS,S.RAHMAN,S.L.GLOOR,J.K.FIELDS,N.L.HUSBY,A.VAIDYA, JRNL AUTH 2 K.E.MAIER,M.MORGAN,M.C.KEOGH,C.WOLBERGER JRNL TITL UBIQUITINATED HISTONE H2B AS GATEKEEPER OF THE NUCLEOSOME JRNL TITL 2 ACIDIC PATCH JRNL REF NUCLEIC ACIDS RES. 2024 JRNL REFN ESSN 1362-4962 JRNL DOI 10.1093/NAR/GKAE698 REMARK 2 REMARK 2 RESOLUTION. 3.36 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) : 3.360 REMARK 3 NUMBER OF PARTICLES : 65167 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 8V28 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1000273831. 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 : H2BK120UB-MODIFIED NUCLEOSOME; REMARK 245 HISTONES; DNA; UBIQUITIN 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 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 MET A 0 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 ALA A 135 REMARK 465 MET B 0 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 MET C 0 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 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 MET D 0 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 MET E 0 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 MET F 0 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 MET G 0 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 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 MET H 0 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 LYS H 122 REMARK 465 DA I -73 REMARK 465 DT I 73 REMARK 465 DA J -73 REMARK 465 DT J 73 REMARK 465 GLY K -3 REMARK 465 SER K -2 REMARK 465 HIS K -1 REMARK 465 MET K 0 REMARK 465 LEU K 73 REMARK 465 ARG K 74 REMARK 465 GLY K 75 REMARK 465 CYS K 76 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 I -72 P OP1 OP2 REMARK 470 DT J -72 P OP1 OP2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG I -70 C1' DG I -70 N9 -0.084 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 DT J 69 C3' - O3' - P ANGL. DEV. = -9.1 DEGREES REMARK 500 DC J 70 C3' - O3' - P ANGL. DEV. = -9.9 DEGREES REMARK 500 DG J 71 C3' - O3' - P ANGL. DEV. = -10.2 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 B 24 70.70 57.34 REMARK 500 LEU C 97 58.88 -97.45 REMARK 500 THR E 58 33.48 -140.41 REMARK 500 ASP F 24 46.68 -88.37 REMARK 500 LYS F 77 60.48 60.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8V25 RELATED DB: PDB REMARK 900 H2BK120UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 1 REMARK 900 RELATED ID: EMD-42898 RELATED DB: EMDB REMARK 900 H2BK120UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 1 REMARK 900 RELATED ID: 8V26 RELATED DB: PDB REMARK 900 H2BK120UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 2 REMARK 900 RELATED ID: EMD-42899 RELATED DB: EMDB REMARK 900 H2BK120UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 2 REMARK 900 RELATED ID: 8V27 RELATED DB: PDB REMARK 900 H2BK120UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 3 REMARK 900 RELATED ID: EMD-42900 RELATED DB: EMDB REMARK 900 H2BK120UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 3 REMARK 900 RELATED ID: EMD-42901 RELATED DB: EMDB REMARK 900 H2BK120UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 4 REMARK 900 RELATED ID: 8G6G RELATED DB: PDB REMARK 900 H2BK120UB+H3K79ME2-MODIFIED NUCLEOSOME UBIQUITIN POSITION 5 REMARK 900 RELATED ID: EMD-29767 RELATED DB: EMDB REMARK 900 H2BK120UB+H3K79ME2-MODIFIED NUCLEOSOME UBIQUITIN POSITION 5 REMARK 900 RELATED ID: 8G6H RELATED DB: PDB REMARK 900 H2BK120UB+H3K79ME2-MODIFIED NUCLEOSOME UBIQUITIN POSITION 6 REMARK 900 RELATED ID: EMD-29769 RELATED DB: EMDB REMARK 900 H2BK120UB+H3K79ME2-MODIFIED NUCLEOSOME UBIQUITIN POSITION 6 REMARK 900 RELATED ID: 8G6Q RELATED DB: PDB REMARK 900 H2AK119UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 1 REMARK 900 RELATED ID: EMD-29778 RELATED DB: EMDB REMARK 900 H2AK119UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 1 REMARK 900 RELATED ID: 8G6S RELATED DB: PDB REMARK 900 H2AK119UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 2 REMARK 900 RELATED ID: EMD-29781 RELATED DB: EMDB REMARK 900 H2AK119UB-MODIFIED NUCLEOSOME UBIQUITIN POSITION 2 DBREF 8V28 A 0 135 UNP P84233 H32_XENLA 1 136 DBREF1 8V28 B 0 102 UNP A0A8J1LTD2_XENLA DBREF2 8V28 B A0A8J1LTD2 14 116 DBREF 8V28 C 0 129 UNP Q6AZJ8 Q6AZJ8_XENLA 1 130 DBREF 8V28 D 1 122 UNP P02281 H2B11_XENLA 5 126 DBREF 8V28 E 0 135 UNP P84233 H32_XENLA 1 136 DBREF1 8V28 F 0 102 UNP A0A8J1LTD2_XENLA DBREF2 8V28 F A0A8J1LTD2 14 116 DBREF 8V28 G 0 129 UNP Q6AZJ8 Q6AZJ8_XENLA 1 130 DBREF 8V28 H 1 122 UNP P02281 H2B11_XENLA 5 126 DBREF 8V28 I -73 73 PDB 8V28 8V28 -73 73 DBREF 8V28 J -73 73 PDB 8V28 8V28 -73 73 DBREF 8V28 K 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 8V28 ALA A 102 UNP P84233 GLY 103 ENGINEERED MUTATION SEQADV 8V28 MET D 0 UNP P02281 EXPRESSION TAG SEQADV 8V28 THR D 29 UNP P02281 SER 33 ENGINEERED MUTATION SEQADV 8V28 CYS D 117 UNP P02281 LYS 121 ENGINEERED MUTATION SEQADV 8V28 ALA E 102 UNP P84233 GLY 103 ENGINEERED MUTATION SEQADV 8V28 MET H 0 UNP P02281 EXPRESSION TAG SEQADV 8V28 THR H 29 UNP P02281 SER 33 ENGINEERED MUTATION SEQADV 8V28 CYS H 117 UNP P02281 LYS 121 ENGINEERED MUTATION SEQADV 8V28 GLY K -3 UNP P0CG47 EXPRESSION TAG SEQADV 8V28 SER K -2 UNP P0CG47 EXPRESSION TAG SEQADV 8V28 HIS K -1 UNP P0CG47 EXPRESSION TAG SEQADV 8V28 MET K 0 UNP P0CG47 EXPRESSION TAG SEQADV 8V28 CYS K 76 UNP P0CG47 GLY 76 ENGINEERED MUTATION SEQRES 1 A 136 MET ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY SEQRES 2 A 136 GLY LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA SEQRES 3 A 136 ARG LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO SEQRES 4 A 136 HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE SEQRES 5 A 136 ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS SEQRES 6 A 136 LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP SEQRES 7 A 136 PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET SEQRES 8 A 136 ALA LEU GLN GLU ALA SER GLU ALA TYR LEU VAL ALA LEU SEQRES 9 A 136 PHE GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS ARG SEQRES 10 A 136 VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG SEQRES 11 A 136 ILE ARG GLY GLU ARG ALA SEQRES 1 B 103 MET SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS SEQRES 2 B 103 GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN SEQRES 3 B 103 ILE GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA SEQRES 4 B 103 ARG ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR SEQRES 5 B 103 GLU GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN SEQRES 6 B 103 VAL ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS SEQRES 7 B 103 ARG LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU SEQRES 8 B 103 LYS ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 C 130 MET SER GLY ARG GLY LYS GLN GLY GLY LYS THR ARG ALA SEQRES 2 C 130 LYS ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE SEQRES 3 C 130 PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN SEQRES 4 C 130 TYR ALA GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU SEQRES 5 C 130 ALA ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU SEQRES 6 C 130 LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG SEQRES 7 C 130 ILE ILE PRO ARG HIS LEU GLN LEU ALA VAL ARG ASN ASP SEQRES 8 C 130 GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA SEQRES 9 C 130 GLN GLY GLY VAL LEU PRO ASN ILE GLN SER VAL LEU LEU SEQRES 10 C 130 PRO LYS LYS THR GLU SER SER LYS SER ALA LYS SER LYS SEQRES 1 D 123 MET ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SER LYS SEQRES 2 D 123 LYS ALA VAL THR LYS THR GLN LYS LYS ASP GLY LYS LYS SEQRES 3 D 123 ARG ARG LYS THR ARG LYS GLU SER TYR ALA ILE TYR VAL SEQRES 4 D 123 TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SEQRES 5 D 123 SER SER LYS ALA MET SER ILE MET ASN SER PHE VAL ASN SEQRES 6 D 123 ASP VAL PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU SEQRES 7 D 123 ALA HIS TYR ASN LYS ARG SER THR ILE THR SER ARG GLU SEQRES 8 D 123 ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU SEQRES 9 D 123 ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR SEQRES 10 D 123 CYS TYR THR SER ALA LYS SEQRES 1 E 136 MET ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY SEQRES 2 E 136 GLY LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA SEQRES 3 E 136 ARG LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO SEQRES 4 E 136 HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE SEQRES 5 E 136 ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS SEQRES 6 E 136 LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP SEQRES 7 E 136 PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET SEQRES 8 E 136 ALA LEU GLN GLU ALA SER GLU ALA TYR LEU VAL ALA LEU SEQRES 9 E 136 PHE GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS ARG SEQRES 10 E 136 VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG SEQRES 11 E 136 ILE ARG GLY GLU ARG ALA SEQRES 1 F 103 MET SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS SEQRES 2 F 103 GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN SEQRES 3 F 103 ILE GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA SEQRES 4 F 103 ARG ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR SEQRES 5 F 103 GLU GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN SEQRES 6 F 103 VAL ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS SEQRES 7 F 103 ARG LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU SEQRES 8 F 103 LYS ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 G 130 MET SER GLY ARG GLY LYS GLN GLY GLY LYS THR ARG ALA SEQRES 2 G 130 LYS ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE SEQRES 3 G 130 PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN SEQRES 4 G 130 TYR ALA GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU SEQRES 5 G 130 ALA ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU SEQRES 6 G 130 LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG SEQRES 7 G 130 ILE ILE PRO ARG HIS LEU GLN LEU ALA VAL ARG ASN ASP SEQRES 8 G 130 GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA SEQRES 9 G 130 GLN GLY GLY VAL LEU PRO ASN ILE GLN SER VAL LEU LEU SEQRES 10 G 130 PRO LYS LYS THR GLU SER SER LYS SER ALA LYS SER LYS SEQRES 1 H 123 MET ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SER LYS SEQRES 2 H 123 LYS ALA VAL THR LYS THR GLN LYS LYS ASP GLY LYS LYS SEQRES 3 H 123 ARG ARG LYS THR ARG LYS GLU SER TYR ALA ILE TYR VAL SEQRES 4 H 123 TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SEQRES 5 H 123 SER SER LYS ALA MET SER ILE MET ASN SER PHE VAL ASN SEQRES 6 H 123 ASP VAL PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU SEQRES 7 H 123 ALA HIS TYR ASN LYS ARG SER THR ILE THR SER ARG GLU SEQRES 8 H 123 ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU SEQRES 9 H 123 ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR SEQRES 10 H 123 CYS 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 80 GLY SER HIS MET MET GLN ILE PHE VAL LYS THR LEU THR SEQRES 2 K 80 GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP THR SEQRES 3 K 80 ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY SEQRES 4 K 80 ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS SEQRES 5 K 80 GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE SEQRES 6 K 80 GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG SEQRES 7 K 80 GLY CYS HELIX 1 AA1 GLY A 44 SER A 57 1 14 HELIX 2 AA2 ARG A 63 ASP A 77 1 15 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 GLY C 22 1 7 HELIX 10 AB1 PRO C 26 GLY C 37 1 12 HELIX 11 AB2 GLY C 46 ASN C 73 1 28 HELIX 12 AB3 ILE C 79 ASN C 89 1 11 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 ASP E 77 1 15 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 ASP F 24 ILE F 29 5 6 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 ALA F 83 GLN F 93 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 GLY G 46 ASN G 73 1 28 HELIX 29 AD2 ILE G 79 ASN G 89 1 11 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 THR K 22 GLY K 35 1 14 HELIX 36 AD9 PRO K 37 GLN K 41 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 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 85 ILE D 86 1 O ILE D 86 N ARG C 42 SHEET 1 AA5 2 ARG C 77 ILE C 78 0 SHEET 2 AA5 2 GLY D 50 ILE D 51 1 O GLY D 50 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 THR F 96 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 85 ILE H 86 1 O ILE H 86 N ARG G 42 SHEET 1 AB1 5 THR K 12 GLU K 16 0 SHEET 2 AB1 5 GLN K 2 LYS K 6 -1 N VAL K 5 O ILE K 13 SHEET 3 AB1 5 THR K 66 VAL K 70 1 O LEU K 67 N LYS K 6 SHEET 4 AB1 5 ARG K 42 PHE K 45 -1 N ILE K 44 O HIS K 68 SHEET 5 AB1 5 LYS K 48 GLN K 49 -1 O LYS K 48 N PHE K 45 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