HEADER DNA BINDING PROTEIN/DNA 16-MAY-25 9UZ7 TITLE CRYO-EM STRUCTURE OF THE NUCLEOSOME CORE PARTICLE WITH SITE-SPECIFIC TITLE 2 DNA-HISTONE CROSSLINKING COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE COMPND 5 H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE COMPND 6 H3/L; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HISTONE H3.1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE COMPND 13 H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE COMPND 14 H3/L; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: HISTONE H4; COMPND 19 CHAIN: C, D; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 4; COMPND 22 MOLECULE: HISTONE H2A TYPE 1-B/E; COMPND 23 CHAIN: E, F; COMPND 24 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 5; COMPND 27 MOLECULE: HISTONE H2B TYPE 1-J; COMPND 28 CHAIN: G, H; COMPND 29 SYNONYM: HISTONE H2B.1,HISTONE H2B.R,H2B/R; COMPND 30 ENGINEERED: YES; COMPND 31 MOL_ID: 6; COMPND 32 MOLECULE: DNA (145-MER); COMPND 33 CHAIN: I; COMPND 34 ENGINEERED: YES; COMPND 35 MOL_ID: 7; COMPND 36 MOLECULE: DNA (145-MER); COMPND 37 CHAIN: J; COMPND 38 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC SOURCE 6 HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, SOURCE 7 HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, SOURCE 8 HIST1H3I, H3C12, H3FJ, HIST1H3J; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC SOURCE 16 HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, SOURCE 17 HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, SOURCE 18 HIST1H3I, H3C12, H3FJ, HIST1H3J; 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: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, SOURCE 26 H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, SOURCE 27 HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, SOURCE 28 H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, SOURCE 29 H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, SOURCE 30 H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, SOURCE 31 H4-16, HIST4H4; SOURCE 32 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 33 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 34 MOL_ID: 4; SOURCE 35 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 36 ORGANISM_COMMON: HUMAN; SOURCE 37 ORGANISM_TAXID: 9606; SOURCE 38 GENE: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE; SOURCE 39 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 40 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 41 MOL_ID: 5; SOURCE 42 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 43 ORGANISM_COMMON: HUMAN; SOURCE 44 ORGANISM_TAXID: 9606; SOURCE 45 GENE: H2BC11, H2BFR, HIST1H2BJ; SOURCE 46 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 47 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 48 MOL_ID: 6; SOURCE 49 SYNTHETIC: YES; SOURCE 50 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 51 ORGANISM_TAXID: 32630; SOURCE 52 MOL_ID: 7; SOURCE 53 SYNTHETIC: YES; SOURCE 54 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 55 ORGANISM_TAXID: 32630 KEYWDS HISTONE, NUCLEOSOME, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.Z.ZHOU,H.T.LI,X.J.SHAN,G.Y.JI REVDAT 2 27-MAY-26 9UZ7 1 JRNL REVDAT 1 06-MAY-26 9UZ7 0 JRNL AUTH X.SHAN,G.JI,J.LI,M.REN,J.MA,Y.ZHOU,H.LI,C.ZHOU JRNL TITL DNA-HISTONE CROSS-LINK LOCKS THE NUCLEOSOME STRUCTURE AND JRNL TITL 2 DISRUPTS ITS RECOGNITION AND PROCESSING. JRNL REF PROTEIN CELL V. 17 476 2026 JRNL REFN ESSN 1674-8018 JRNL PMID 41206067 JRNL DOI 10.1093/PROCEL/PWAF094 REMARK 2 REMARK 2 RESOLUTION. 3.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8JBX REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.240 REMARK 3 NUMBER OF PARTICLES : 199160 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 9UZ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 20-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059520. 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; POINT; POINT; POINT; REMARK 245 POINT; POINT; POINT; POINT; REMARK 245 POINT; POINT; POINT; POINT; REMARK 245 POINT; POINT; POINT; POINT REMARK 245 NAME OF SAMPLE : HUMAN CANONICAL HISTONE AND 601 REMARK 245 DNA; HUMAN CANONICAL HISTONE REMARK 245 WITH MUTANTION C96S/C110S/K115C; REMARK 245 601 DNA WITH AN ALKYNYL-DU REMARK 245 MODIFICATION AT POSITION 74 AND REMARK 245 A CY5 FLUOROPHORE; HISTONE H3.1; REMARK 245 HISTONE H3.1; HISTONE H4; REMARK 245 HISTONE H2A TYPE 1-B/E; HISTONE REMARK 245 H2B TYPE 1-J REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.18 REMARK 245 SAMPLE SUPPORT DETAILS : PDC-32G PLASMA CLEANER REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.60 REMARK 245 SAMPLE DETAILS : H3 MUTANT, H3-C96S/C110S/K115C, REMARK 245 IN WHICH CYS96 AND CYS110 WERE SUBSTITUTED WITH SER, LEAVING REMARK 245 CYS115 AS THE SOLE REACTIVE THIOL; H3 MUTANT, H3-C96S/C110S/ REMARK 245 K115C, IN WHICH CYS96 AND CYS110 WERE SUBSTITUTED WITH SER, REMARK 245 LEAVING CYS115 AS THE SOLE REACTIVE THIOL THAT IS CROSSLINKED; REMARK 245 RECOMBINANTLY EXPRESSED HUMAN HISTONE H4; RECOMBINANTLY REMARK 245 EXPRESSED HUMAN HISTONE H2A.2; RECOMBINANTLY EXPRESSED HUMAN REMARK 245 HISTONE H2B.1 REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1978 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) : 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 : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : 64000 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: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J 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 PRO A 38 REMARK 465 HIS A 39 REMARK 465 ARG A 40 REMARK 465 TYR A 41 REMARK 465 ARG A 42 REMARK 465 ALA B 1 REMARK 465 ARG B 2 REMARK 465 THR B 3 REMARK 465 LYS B 4 REMARK 465 GLN B 5 REMARK 465 THR B 6 REMARK 465 ALA B 7 REMARK 465 ARG B 8 REMARK 465 LYS B 9 REMARK 465 SER B 10 REMARK 465 THR B 11 REMARK 465 GLY B 12 REMARK 465 GLY B 13 REMARK 465 LYS B 14 REMARK 465 ALA B 15 REMARK 465 PRO B 16 REMARK 465 ARG B 17 REMARK 465 LYS B 18 REMARK 465 GLN B 19 REMARK 465 LEU B 20 REMARK 465 ALA B 21 REMARK 465 THR B 22 REMARK 465 LYS B 23 REMARK 465 ALA B 24 REMARK 465 ALA B 25 REMARK 465 ARG B 26 REMARK 465 LYS B 27 REMARK 465 SER B 28 REMARK 465 ALA B 29 REMARK 465 PRO B 30 REMARK 465 ALA B 31 REMARK 465 THR B 32 REMARK 465 GLY B 33 REMARK 465 GLY B 34 REMARK 465 VAL B 35 REMARK 465 LYS B 36 REMARK 465 LYS B 37 REMARK 465 PRO B 38 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 GLY C 6 REMARK 465 GLY C 7 REMARK 465 LYS C 8 REMARK 465 GLY C 9 REMARK 465 LEU C 10 REMARK 465 GLY C 11 REMARK 465 LYS C 12 REMARK 465 GLY C 13 REMARK 465 GLY C 14 REMARK 465 ALA C 15 REMARK 465 LYS C 16 REMARK 465 ARG C 17 REMARK 465 HIS C 18 REMARK 465 ARG C 19 REMARK 465 LYS C 20 REMARK 465 SER D 1 REMARK 465 GLY D 2 REMARK 465 ARG D 3 REMARK 465 GLY D 4 REMARK 465 LYS D 5 REMARK 465 GLY D 6 REMARK 465 GLY D 7 REMARK 465 LYS D 8 REMARK 465 GLY D 9 REMARK 465 LEU D 10 REMARK 465 GLY D 11 REMARK 465 LYS D 12 REMARK 465 GLY D 13 REMARK 465 GLY D 14 REMARK 465 ALA D 15 REMARK 465 LYS D 16 REMARK 465 ARG D 17 REMARK 465 HIS D 18 REMARK 465 ARG D 19 REMARK 465 SER E 1 REMARK 465 GLY E 2 REMARK 465 ARG E 3 REMARK 465 GLY E 4 REMARK 465 LYS E 5 REMARK 465 GLN E 6 REMARK 465 GLY E 7 REMARK 465 GLY E 8 REMARK 465 LYS E 9 REMARK 465 LYS E 118 REMARK 465 LYS E 119 REMARK 465 THR E 120 REMARK 465 GLU E 121 REMARK 465 SER E 122 REMARK 465 HIS E 123 REMARK 465 HIS E 124 REMARK 465 LYS E 125 REMARK 465 ALA E 126 REMARK 465 LYS E 127 REMARK 465 GLY E 128 REMARK 465 LYS E 129 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 GLN F 6 REMARK 465 GLY F 7 REMARK 465 GLY F 8 REMARK 465 LYS F 9 REMARK 465 ALA F 10 REMARK 465 PRO F 117 REMARK 465 LYS F 118 REMARK 465 LYS F 119 REMARK 465 THR F 120 REMARK 465 GLU F 121 REMARK 465 SER F 122 REMARK 465 HIS F 123 REMARK 465 HIS F 124 REMARK 465 LYS F 125 REMARK 465 ALA F 126 REMARK 465 LYS F 127 REMARK 465 GLY F 128 REMARK 465 LYS F 129 REMARK 465 PRO G 1 REMARK 465 GLU G 2 REMARK 465 PRO G 3 REMARK 465 ALA G 4 REMARK 465 LYS G 5 REMARK 465 SER G 6 REMARK 465 ALA G 7 REMARK 465 PRO G 8 REMARK 465 ALA G 9 REMARK 465 PRO G 10 REMARK 465 LYS G 11 REMARK 465 LYS G 12 REMARK 465 GLY G 13 REMARK 465 SER G 14 REMARK 465 LYS G 15 REMARK 465 LYS G 16 REMARK 465 ALA G 17 REMARK 465 VAL G 18 REMARK 465 THR G 19 REMARK 465 LYS G 20 REMARK 465 ALA G 21 REMARK 465 GLN G 22 REMARK 465 LYS G 23 REMARK 465 LYS G 24 REMARK 465 ASP G 25 REMARK 465 GLY G 26 REMARK 465 LYS G 27 REMARK 465 PRO H 1 REMARK 465 GLU H 2 REMARK 465 PRO H 3 REMARK 465 ALA H 4 REMARK 465 LYS H 5 REMARK 465 SER H 6 REMARK 465 ALA H 7 REMARK 465 PRO H 8 REMARK 465 ALA H 9 REMARK 465 PRO H 10 REMARK 465 LYS H 11 REMARK 465 LYS H 12 REMARK 465 GLY H 13 REMARK 465 SER H 14 REMARK 465 LYS H 15 REMARK 465 LYS H 16 REMARK 465 ALA H 17 REMARK 465 VAL H 18 REMARK 465 THR H 19 REMARK 465 LYS H 20 REMARK 465 ALA H 21 REMARK 465 GLN H 22 REMARK 465 LYS H 23 REMARK 465 LYS H 24 REMARK 465 ASP H 25 REMARK 465 GLY H 26 REMARK 465 DC I 141 REMARK 465 DT I 142 REMARK 465 DG I 143 REMARK 465 DA I 144 REMARK 465 DT I 145 REMARK 465 DA J 1 REMARK 465 DT J 2 REMARK 465 DC J 3 REMARK 465 DA J 4 REMARK 465 DG J 5 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 DC I 48 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG I 100 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG J 39 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA J 48 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG J 100 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT J 111 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG J 131 O4' - C1' - N9 ANGL. DEV. = 2.2 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 ALA B 114 42.21 -89.51 REMARK 500 YCM B 115 48.87 31.71 REMARK 500 LEU D 22 108.80 -57.41 REMARK 500 ARG E 99 35.50 -99.45 REMARK 500 ARG F 99 31.54 -95.34 REMARK 500 TYR G 37 33.39 -93.09 REMARK 500 HIS G 49 86.51 -158.17 REMARK 500 TYR H 37 34.05 -95.74 REMARK 500 PRO H 103 -176.16 -69.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64640 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE NUCLEOSOME CORE PARTICLE WITH SITE- REMARK 900 SPECIFIC DNA-HISTONE CROSSLINKING DBREF 9UZ7 A 1 135 UNP P68431 H31_HUMAN 2 136 DBREF 9UZ7 B 1 135 UNP P68431 H31_HUMAN 2 136 DBREF 9UZ7 C 1 102 UNP P62805 H4_HUMAN 2 103 DBREF 9UZ7 D 1 102 UNP P62805 H4_HUMAN 2 103 DBREF 9UZ7 E 1 129 UNP P04908 H2A1B_HUMAN 2 130 DBREF 9UZ7 F 1 129 UNP P04908 H2A1B_HUMAN 2 130 DBREF 9UZ7 G 1 125 UNP P06899 H2B1J_HUMAN 2 126 DBREF 9UZ7 H 1 125 UNP P06899 H2B1J_HUMAN 2 126 DBREF 9UZ7 I 1 145 PDB 9UZ7 9UZ7 1 145 DBREF 9UZ7 J 1 145 PDB 9UZ7 9UZ7 1 145 SEQADV 9UZ7 SER A 96 UNP P68431 CYS 97 ENGINEERED MUTATION SEQADV 9UZ7 SER A 110 UNP P68431 CYS 111 ENGINEERED MUTATION SEQADV 9UZ7 CYS A 115 UNP P68431 LYS 116 ENGINEERED MUTATION SEQADV 9UZ7 SER B 96 UNP P68431 CYS 97 ENGINEERED MUTATION SEQADV 9UZ7 SER B 110 UNP P68431 CYS 111 ENGINEERED MUTATION SEQADV 9UZ7 YCM B 115 UNP P68431 LYS 116 ENGINEERED MUTATION SEQRES 1 A 135 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 A 135 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 A 135 LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO HIS SEQRES 4 A 135 ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE ARG SEQRES 5 A 135 ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS LEU SEQRES 6 A 135 PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP PHE SEQRES 7 A 135 LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET ALA SEQRES 8 A 135 LEU GLN GLU ALA SER GLU ALA TYR LEU VAL GLY LEU PHE SEQRES 9 A 135 GLU ASP THR ASN LEU SER ALA ILE HIS ALA CYS 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 135 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 B 135 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 B 135 LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO HIS SEQRES 4 B 135 ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE ARG SEQRES 5 B 135 ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS LEU SEQRES 6 B 135 PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP PHE SEQRES 7 B 135 LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET ALA SEQRES 8 B 135 LEU GLN GLU ALA SER GLU ALA TYR LEU VAL GLY LEU PHE SEQRES 9 B 135 GLU ASP THR ASN LEU SER ALA ILE HIS ALA YCM ARG VAL SEQRES 10 B 135 THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG ILE SEQRES 11 B 135 ARG GLY GLU ARG ALA SEQRES 1 C 102 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 C 102 GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN ILE SEQRES 3 C 102 GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA ARG SEQRES 4 C 102 ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR GLU SEQRES 5 C 102 GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN VAL SEQRES 6 C 102 ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS ARG SEQRES 7 C 102 LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU LYS SEQRES 8 C 102 ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 D 102 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 D 102 GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN ILE SEQRES 3 D 102 GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA ARG SEQRES 4 D 102 ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR GLU SEQRES 5 D 102 GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN VAL SEQRES 6 D 102 ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS ARG SEQRES 7 D 102 LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU LYS SEQRES 8 D 102 ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 E 129 SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA LYS SEQRES 2 E 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 E 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 E 129 SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 E 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 E 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 E 129 ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU SEQRES 8 E 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 E 129 GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO SEQRES 10 E 129 LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 F 129 SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA LYS SEQRES 2 F 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 F 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 F 129 SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 F 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 F 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 F 129 ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU SEQRES 8 F 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 F 129 GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO SEQRES 10 F 129 LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 G 125 PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SEQRES 2 G 125 SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP GLY SEQRES 3 G 125 LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER ILE SEQRES 4 G 125 TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR SEQRES 5 G 125 GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER PHE SEQRES 6 G 125 VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SER SEQRES 7 G 125 ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SER SEQRES 8 G 125 ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY SEQRES 9 G 125 GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA SEQRES 10 G 125 VAL THR LYS TYR THR SER ALA LYS SEQRES 1 H 125 PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SEQRES 2 H 125 SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP GLY SEQRES 3 H 125 LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER ILE SEQRES 4 H 125 TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR SEQRES 5 H 125 GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER PHE SEQRES 6 H 125 VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SER SEQRES 7 H 125 ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SER SEQRES 8 H 125 ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY SEQRES 9 H 125 GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA SEQRES 10 H 125 VAL THR LYS TYR THR SER ALA LYS SEQRES 1 I 145 DA DT DC DG DA DT DG DT DA DT DA DT DA SEQRES 2 I 145 DT DC DT DG DA DC DA DC DG DT DG DC DC SEQRES 3 I 145 DT DG DG DA DG DA DC DT DA DG DG DG DA SEQRES 4 I 145 DG DT DA DA DT DC DC DC DC DT DT DG DG SEQRES 5 I 145 DC DG DG DT DT DA DA DA DA DC DG DC DG SEQRES 6 I 145 DG DG DG DG DA DC DA DG DC DG DC DG DT SEQRES 7 I 145 DA DC DG DT DG DC DG DT DT DT DG DA DG SEQRES 8 I 145 DC DG DG DT DG DC DT DA DG DA DG DC DT SEQRES 9 I 145 DG DT DC DT DA DC DG DA DC DC DA DA DT SEQRES 10 I 145 DT DG DA DG DC DG DG DC DC DT DC DG DG SEQRES 11 I 145 DC DA DC DC DG DG DG DA DT DT DC DT DG SEQRES 12 I 145 DA DT SEQRES 1 J 145 DA DT DC DA DG DA DA DT DC DC DC DG DG SEQRES 2 J 145 DT DG DC DC DG DA DG DG DC DC DG DC DT SEQRES 3 J 145 DC DA DA DT DT DG DG DT DC DG DT DA DG SEQRES 4 J 145 DA DC DA DG DC DT DC DT DA DG DC DA DC SEQRES 5 J 145 DC DG DC DT DC DA DA DA DC DG DC DA DC SEQRES 6 J 145 DG DT DA DC DG DC DG DC DT DG DT DC DC SEQRES 7 J 145 DC DC DC DG DC DG DT DT DT DT DA DA DC SEQRES 8 J 145 DC DG DC DC DA DA DG DG DG DG DA DT DT SEQRES 9 J 145 DA DC DT DC DC DC DT DA DG DT DC DT DC SEQRES 10 J 145 DC DA DG DG DC DA DC DG DT DG DT DC DA SEQRES 11 J 145 DG DA DT DA DT DA DT DA DC DA DT DC DG SEQRES 12 J 145 DA DT HET YCM B 115 10 HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETSYN YCM CYSTEINE-S-ACETAMIDE FORMUL 2 YCM C5 H10 N2 O3 S 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 MET A 90 1 6 HELIX 4 AA4 LEU A 92 ALA A 114 1 23 HELIX 5 AA5 MET A 120 ARG A 131 1 12 HELIX 6 AA6 GLY B 44 SER B 57 1 14 HELIX 7 AA7 ARG B 63 LYS B 79 1 17 HELIX 8 AA8 GLN B 85 ALA B 114 1 30 HELIX 9 AA9 MET B 120 ARG B 131 1 12 HELIX 10 AB1 ASN C 25 ILE C 29 5 5 HELIX 11 AB2 THR C 30 GLY C 41 1 12 HELIX 12 AB3 ILE C 50 ALA C 76 1 27 HELIX 13 AB4 THR C 82 ARG C 92 1 11 HELIX 14 AB5 ASP D 24 ILE D 29 5 6 HELIX 15 AB6 THR D 30 GLY D 41 1 12 HELIX 16 AB7 LEU D 49 ALA D 76 1 28 HELIX 17 AB8 THR D 82 ARG D 92 1 11 HELIX 18 AB9 THR E 16 GLY E 22 1 7 HELIX 19 AC1 PRO E 26 LYS E 36 1 11 HELIX 20 AC2 ALA E 45 ASN E 73 1 29 HELIX 21 AC3 ILE E 79 ASP E 90 1 12 HELIX 22 AC4 ASP E 90 LEU E 97 1 8 HELIX 23 AC5 THR F 16 ALA F 21 1 6 HELIX 24 AC6 PRO F 26 GLY F 37 1 12 HELIX 25 AC7 ALA F 45 ASN F 73 1 29 HELIX 26 AC8 ILE F 79 ASP F 90 1 12 HELIX 27 AC9 ASP F 90 LEU F 97 1 8 HELIX 28 AD1 TYR G 37 HIS G 49 1 13 HELIX 29 AD2 SER G 55 ASN G 84 1 30 HELIX 30 AD3 THR G 90 LEU G 102 1 13 HELIX 31 AD4 PRO G 103 ALA G 124 1 22 HELIX 32 AD5 TYR H 37 HIS H 49 1 13 HELIX 33 AD6 SER H 55 ASN H 84 1 30 HELIX 34 AD7 THR H 90 LEU H 102 1 13 HELIX 35 AD8 PRO H 103 ALA H 124 1 22 SHEET 1 AA1 2 ARG A 83 PHE A 84 0 SHEET 2 AA1 2 THR C 80 VAL C 81 1 O VAL C 81 N ARG A 83 SHEET 1 AA2 2 THR A 118 ILE A 119 0 SHEET 2 AA2 2 ARG C 45 ILE C 46 1 O ARG C 45 N ILE A 119 SHEET 1 AA3 2 ARG B 83 PHE B 84 0 SHEET 2 AA3 2 THR D 80 VAL D 81 1 O VAL D 81 N ARG B 83 SHEET 1 AA4 2 THR B 118 ILE B 119 0 SHEET 2 AA4 2 ARG D 45 ILE D 46 1 O ARG D 45 N ILE B 119 SHEET 1 AA5 2 THR C 96 TYR C 98 0 SHEET 2 AA5 2 VAL E 100 ILE E 102 1 O THR E 101 N TYR C 98 SHEET 1 AA6 2 THR D 96 TYR D 98 0 SHEET 2 AA6 2 VAL F 100 ILE F 102 1 O THR F 101 N TYR D 98 SHEET 1 AA7 2 ARG F 42 VAL F 43 0 SHEET 2 AA7 2 THR H 88 ILE H 89 1 O ILE H 89 N ARG F 42 LINK C ALA B 114 N YCM B 115 1555 1555 1.33 LINK C YCM B 115 N ARG B 116 1555 1555 1.30 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 CONECT 1377 1380 CONECT 1380 1377 1381 CONECT 1381 1380 1382 1388 CONECT 1382 1381 1383 CONECT 1383 1382 1384 CONECT 1384 1383 1385 CONECT 1385 1384 1386 1387 CONECT 1386 1385 CONECT 1387 1385 CONECT 1388 1381 1389 1390 CONECT 1389 1388 CONECT 1390 1388 MASTER 399 0 1 35 14 0 0 611818 10 12 102 END