HEADER DNA BINDING PROTEIN 03-AUG-23 8KB5 TITLE CRYO-EM STRUCTURE OF THE HUMAN NUCLEOSOME CONTAINING H3.8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.8; 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 TYPE 1-B/E; COMPND 11 CHAIN: C, G; COMPND 12 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: HISTONE H2B TYPE 1-J; COMPND 16 CHAIN: D, H; COMPND 17 SYNONYM: HISTONE H2B.1,HISTONE H2B.R,H2B/R; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: DNA (145-MER); COMPND 21 CHAIN: I; COMPND 22 ENGINEERED: YES; COMPND 23 MOL_ID: 6; COMPND 24 MOLECULE: DNA (145-MER); COMPND 25 CHAIN: J; COMPND 26 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: H3F3AP5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: H4C1; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 GENE: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 21 MOL_ID: 4; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: H2BC11, H2BFR, HIST1H2BJ; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 28 MOL_ID: 5; SOURCE 29 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 30 ORGANISM_TAXID: 32630; SOURCE 31 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 32 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 33 MOL_ID: 6; SOURCE 34 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 35 ORGANISM_TAXID: 32630; SOURCE 36 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 37 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, CHROMATIN, NUCLEOSOME, GENE REGULATION, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.HIRAI,T.KUJIRAI,Y.TAKIZAWA,H.KURUMIZAKA REVDAT 2 27-DEC-23 8KB5 1 JRNL REVDAT 1 18-OCT-23 8KB5 0 JRNL AUTH S.HIRAI,T.KUJIRAI,M.AKATSU,M.OGASAWARA,H.EHARA,S.I.SEKINE, JRNL AUTH 2 Y.OHKAWA,Y.TAKIZAWA,H.KURUMIZAKA JRNL TITL CRYO-EM AND BIOCHEMICAL ANALYSES OF THE NUCLEOSOME JRNL TITL 2 CONTAINING THE HUMAN HISTONE H3 VARIANT H3.8. JRNL REF J.BIOCHEM. V. 174 549 2023 JRNL REFN ISSN 0021-924X JRNL PMID 37757444 JRNL DOI 10.1093/JB/MVAD069 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, RELION 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) : 2.261 REMARK 3 NUMBER OF PARTICLES : 390033 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 8KB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300039898. 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 : THE HUMAN NUCLEOSOME CONTAINING REMARK 245 H3.8 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 : HUMAN NUCLEOSOME WITH 145 BP REMARK 245 WIDOM 601L DNA AND H3.8 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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) : 6120.00 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: DECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DECAMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 ALA A 1 REMARK 465 ARG A 2 REMARK 465 THR A 3 REMARK 465 ARG A 4 REMARK 465 TRP 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 ILE 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 THR A 25 REMARK 465 CYS A 26 REMARK 465 LYS A 27 REMARK 465 SER A 28 REMARK 465 ALA A 29 REMARK 465 PRO A 30 REMARK 465 SER 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 SER A 136 REMARK 465 GLU A 137 REMARK 465 TYR A 138 REMARK 465 THR A 139 REMARK 465 MET A 140 REMARK 465 MET A 141 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 HIS B -1 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 LYS B 20 REMARK 465 GLY C -3 REMARK 465 SER C -2 REMARK 465 HIS C -1 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 LYS C 9 REMARK 465 ALA C 10 REMARK 465 LYS C 119 REMARK 465 THR C 120 REMARK 465 GLU C 121 REMARK 465 SER C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 LYS C 125 REMARK 465 ALA C 126 REMARK 465 LYS C 127 REMARK 465 GLY C 128 REMARK 465 LYS C 129 REMARK 465 GLY D -3 REMARK 465 SER D -2 REMARK 465 HIS D -1 REMARK 465 MET D 0 REMARK 465 PRO D 1 REMARK 465 GLU D 2 REMARK 465 PRO D 3 REMARK 465 ALA D 4 REMARK 465 LYS D 5 REMARK 465 SER D 6 REMARK 465 ALA D 7 REMARK 465 PRO D 8 REMARK 465 ALA D 9 REMARK 465 PRO D 10 REMARK 465 LYS D 11 REMARK 465 LYS D 12 REMARK 465 GLY D 13 REMARK 465 SER D 14 REMARK 465 LYS D 15 REMARK 465 LYS D 16 REMARK 465 ALA D 17 REMARK 465 VAL D 18 REMARK 465 THR D 19 REMARK 465 LYS D 20 REMARK 465 ALA D 21 REMARK 465 GLN D 22 REMARK 465 LYS D 23 REMARK 465 LYS D 24 REMARK 465 ASP D 25 REMARK 465 GLY D 26 REMARK 465 LYS D 27 REMARK 465 LYS D 28 REMARK 465 ARG D 29 REMARK 465 LYS D 30 REMARK 465 ARG D 31 REMARK 465 SER D 32 REMARK 465 LYS D 125 REMARK 465 GLY E -3 REMARK 465 SER E -2 REMARK 465 HIS E -1 REMARK 465 MET E 0 REMARK 465 ALA E 1 REMARK 465 ARG E 2 REMARK 465 THR E 3 REMARK 465 ARG E 4 REMARK 465 TRP 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 ILE 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 THR E 25 REMARK 465 CYS E 26 REMARK 465 LYS E 27 REMARK 465 SER E 28 REMARK 465 ALA E 29 REMARK 465 PRO E 30 REMARK 465 SER 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 E 136 REMARK 465 GLU E 137 REMARK 465 TYR E 138 REMARK 465 THR E 139 REMARK 465 MET E 140 REMARK 465 MET E 141 REMARK 465 GLY F -3 REMARK 465 SER F -2 REMARK 465 HIS F -1 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 GLY G -3 REMARK 465 SER G -2 REMARK 465 HIS G -1 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 ALA G 10 REMARK 465 LYS G 119 REMARK 465 THR G 120 REMARK 465 GLU G 121 REMARK 465 SER G 122 REMARK 465 HIS G 123 REMARK 465 HIS G 124 REMARK 465 LYS G 125 REMARK 465 ALA G 126 REMARK 465 LYS G 127 REMARK 465 GLY G 128 REMARK 465 LYS G 129 REMARK 465 GLY H -3 REMARK 465 SER H -2 REMARK 465 HIS H -1 REMARK 465 MET H 0 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 LYS H 27 REMARK 465 LYS H 28 REMARK 465 ARG H 29 REMARK 465 LYS H 30 REMARK 465 ARG H 31 REMARK 465 SER H 32 REMARK 465 LYS H 125 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 DC I 55 C5' DC I 55 C4' 0.043 REMARK 500 DC J -27 C5' DC J -27 C4' 0.045 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 DC I -57 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG I -53 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT I -47 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC I -46 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA I -25 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA I -15 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC I -4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG I -3 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT I 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC I 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT I 15 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA I 16 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG I 27 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG I 38 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG I 62 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT I 67 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA J -72 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC J -68 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC J -56 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC J -46 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG J -34 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC J -27 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC J -27 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA J -25 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT J -16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA J -15 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG J -11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG J 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA J 16 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT J 25 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG J 50 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC J 55 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG J 56 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC J 58 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA J 59 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT J 67 O4' - C1' - N1 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 LEU G 97 35.74 -98.56 REMARK 500 ASN G 110 112.33 -160.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37070 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE HUMAN NUCLEOSOME CONTAINING H3.8 DBREF 8KB5 A -3 141 PDB 8KB5 8KB5 -3 141 DBREF 8KB5 B 0 102 UNP P62805 H4_HUMAN 1 103 DBREF 8KB5 C 0 129 UNP P04908 H2A1B_HUMAN 1 130 DBREF 8KB5 D 0 125 UNP P06899 H2B1J_HUMAN 1 126 DBREF 8KB5 E -3 141 PDB 8KB5 8KB5 -3 141 DBREF 8KB5 F 0 102 UNP P62805 H4_HUMAN 1 103 DBREF 8KB5 G 0 129 UNP P04908 H2A1B_HUMAN 1 130 DBREF 8KB5 H 0 125 UNP P06899 H2B1J_HUMAN 1 126 DBREF1 8KB5 I -72 72 GB OU026066.1 DBREF2 8KB5 I 2041866466 1608127 1608271 DBREF1 8KB5 J -72 72 GB OU026066.1 DBREF2 8KB5 J 2041866466 1608271 1608127 SEQADV 8KB5 GLY B -3 UNP P62805 EXPRESSION TAG SEQADV 8KB5 SER B -2 UNP P62805 EXPRESSION TAG SEQADV 8KB5 HIS B -1 UNP P62805 EXPRESSION TAG SEQADV 8KB5 GLY C -3 UNP P04908 EXPRESSION TAG SEQADV 8KB5 SER C -2 UNP P04908 EXPRESSION TAG SEQADV 8KB5 HIS C -1 UNP P04908 EXPRESSION TAG SEQADV 8KB5 GLY D -3 UNP P06899 EXPRESSION TAG SEQADV 8KB5 SER D -2 UNP P06899 EXPRESSION TAG SEQADV 8KB5 HIS D -1 UNP P06899 EXPRESSION TAG SEQADV 8KB5 GLY F -3 UNP P62805 EXPRESSION TAG SEQADV 8KB5 SER F -2 UNP P62805 EXPRESSION TAG SEQADV 8KB5 HIS F -1 UNP P62805 EXPRESSION TAG SEQADV 8KB5 GLY G -3 UNP P04908 EXPRESSION TAG SEQADV 8KB5 SER G -2 UNP P04908 EXPRESSION TAG SEQADV 8KB5 HIS G -1 UNP P04908 EXPRESSION TAG SEQADV 8KB5 GLY H -3 UNP P06899 EXPRESSION TAG SEQADV 8KB5 SER H -2 UNP P06899 EXPRESSION TAG SEQADV 8KB5 HIS H -1 UNP P06899 EXPRESSION TAG SEQRES 1 A 145 GLY SER HIS MET ALA ARG THR ARG TRP THR ALA ARG LYS SEQRES 2 A 145 SER THR GLY GLY ILE ALA PRO ARG LYS GLN LEU ALA THR SEQRES 3 A 145 LYS ALA THR CYS LYS SER ALA PRO SER THR GLY GLY VAL SEQRES 4 A 145 LYS LYS PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU SEQRES 5 A 145 ARG GLU ILE ARG HIS TYR GLN LYS SER THR GLU LEU LEU SEQRES 6 A 145 ILE ARG LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE SEQRES 7 A 145 ALA GLN ASP PHE LYS THR ASP LEU ARG PHE GLN ARG ALA SEQRES 8 A 145 ALA ILE GLY THR LEU GLN GLU ALA SER GLU ALA TYR LEU SEQRES 9 A 145 VAL GLY LEU PHE GLU ASP THR ASN LEU CYS ALA ILE HIS SEQRES 10 A 145 ALA THR ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU SEQRES 11 A 145 ALA ARG HIS ILE ARG GLY GLU ARG VAL SER GLU TYR THR SEQRES 12 A 145 MET MET SEQRES 1 B 106 GLY SER HIS MET SER GLY ARG GLY LYS GLY GLY LYS GLY SEQRES 2 B 106 LEU GLY LYS GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU SEQRES 3 B 106 ARG ASP ASN ILE GLN GLY ILE THR LYS PRO ALA ILE ARG SEQRES 4 B 106 ARG LEU ALA ARG ARG GLY GLY VAL LYS ARG ILE SER GLY SEQRES 5 B 106 LEU ILE TYR GLU GLU THR ARG GLY VAL LEU LYS VAL PHE SEQRES 6 B 106 LEU GLU ASN VAL ILE ARG ASP ALA VAL THR TYR THR GLU SEQRES 7 B 106 HIS ALA LYS ARG LYS THR VAL THR ALA MET ASP VAL VAL SEQRES 8 B 106 TYR ALA LEU LYS ARG GLN GLY ARG THR LEU TYR GLY PHE SEQRES 9 B 106 GLY GLY SEQRES 1 C 133 GLY SER HIS MET SER GLY ARG GLY LYS GLN GLY GLY LYS SEQRES 2 C 133 ALA ARG ALA LYS ALA LYS THR ARG SER SER ARG ALA GLY SEQRES 3 C 133 LEU GLN PHE PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG SEQRES 4 C 133 LYS GLY ASN TYR SER GLU ARG VAL GLY ALA GLY ALA PRO SEQRES 5 C 133 VAL TYR LEU ALA ALA VAL LEU GLU TYR LEU THR ALA GLU SEQRES 6 C 133 ILE LEU GLU LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS SEQRES 7 C 133 LYS THR ARG ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE SEQRES 8 C 133 ARG ASN ASP GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL SEQRES 9 C 133 THR ILE ALA GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA SEQRES 10 C 133 VAL LEU LEU PRO LYS LYS THR GLU SER HIS HIS LYS ALA SEQRES 11 C 133 LYS GLY LYS SEQRES 1 D 129 GLY SER HIS MET PRO GLU PRO ALA LYS SER ALA PRO ALA SEQRES 2 D 129 PRO LYS LYS GLY SER LYS LYS ALA VAL THR LYS ALA GLN SEQRES 3 D 129 LYS LYS ASP GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SEQRES 4 D 129 SER TYR SER ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL SEQRES 5 D 129 HIS PRO ASP THR GLY ILE SER SER LYS ALA MET GLY ILE SEQRES 6 D 129 MET ASN SER PHE VAL ASN ASP ILE PHE GLU ARG ILE ALA SEQRES 7 D 129 GLY GLU ALA SER ARG LEU ALA HIS TYR ASN LYS ARG SER SEQRES 8 D 129 THR ILE THR SER ARG GLU ILE GLN THR ALA VAL ARG LEU SEQRES 9 D 129 LEU LEU PRO GLY GLU LEU ALA LYS HIS ALA VAL SER GLU SEQRES 10 D 129 GLY THR LYS ALA VAL THR LYS TYR THR SER ALA LYS SEQRES 1 E 145 GLY SER HIS MET ALA ARG THR ARG TRP THR ALA ARG LYS SEQRES 2 E 145 SER THR GLY GLY ILE ALA PRO ARG LYS GLN LEU ALA THR SEQRES 3 E 145 LYS ALA THR CYS LYS SER ALA PRO SER THR GLY GLY VAL SEQRES 4 E 145 LYS LYS PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU SEQRES 5 E 145 ARG GLU ILE ARG HIS TYR GLN LYS SER THR GLU LEU LEU SEQRES 6 E 145 ILE ARG LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE SEQRES 7 E 145 ALA GLN ASP PHE LYS THR ASP LEU ARG PHE GLN ARG ALA SEQRES 8 E 145 ALA ILE GLY THR LEU GLN GLU ALA SER GLU ALA TYR LEU SEQRES 9 E 145 VAL GLY LEU PHE GLU ASP THR ASN LEU CYS ALA ILE HIS SEQRES 10 E 145 ALA THR ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU SEQRES 11 E 145 ALA ARG HIS ILE ARG GLY GLU ARG VAL SER GLU TYR THR SEQRES 12 E 145 MET MET SEQRES 1 F 106 GLY SER HIS MET SER GLY ARG GLY LYS GLY GLY LYS GLY SEQRES 2 F 106 LEU GLY LYS GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU SEQRES 3 F 106 ARG ASP ASN ILE GLN GLY ILE THR LYS PRO ALA ILE ARG SEQRES 4 F 106 ARG LEU ALA ARG ARG GLY GLY VAL LYS ARG ILE SER GLY SEQRES 5 F 106 LEU ILE TYR GLU GLU THR ARG GLY VAL LEU LYS VAL PHE SEQRES 6 F 106 LEU GLU ASN VAL ILE ARG ASP ALA VAL THR TYR THR GLU SEQRES 7 F 106 HIS ALA LYS ARG LYS THR VAL THR ALA MET ASP VAL VAL SEQRES 8 F 106 TYR ALA LEU LYS ARG GLN GLY ARG THR LEU TYR GLY PHE SEQRES 9 F 106 GLY GLY SEQRES 1 G 133 GLY SER HIS MET SER GLY ARG GLY LYS GLN GLY GLY LYS SEQRES 2 G 133 ALA ARG ALA LYS ALA LYS THR ARG SER SER ARG ALA GLY SEQRES 3 G 133 LEU GLN PHE PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG SEQRES 4 G 133 LYS GLY ASN TYR SER GLU ARG VAL GLY ALA GLY ALA PRO SEQRES 5 G 133 VAL TYR LEU ALA ALA VAL LEU GLU TYR LEU THR ALA GLU SEQRES 6 G 133 ILE LEU GLU LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS SEQRES 7 G 133 LYS THR ARG ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE SEQRES 8 G 133 ARG ASN ASP GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL SEQRES 9 G 133 THR ILE ALA GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA SEQRES 10 G 133 VAL LEU LEU PRO LYS LYS THR GLU SER HIS HIS LYS ALA SEQRES 11 G 133 LYS GLY LYS SEQRES 1 H 129 GLY SER HIS MET PRO GLU PRO ALA LYS SER ALA PRO ALA SEQRES 2 H 129 PRO LYS LYS GLY SER LYS LYS ALA VAL THR LYS ALA GLN SEQRES 3 H 129 LYS LYS ASP GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SEQRES 4 H 129 SER TYR SER ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL SEQRES 5 H 129 HIS PRO ASP THR GLY ILE SER SER LYS ALA MET GLY ILE SEQRES 6 H 129 MET ASN SER PHE VAL ASN ASP ILE PHE GLU ARG ILE ALA SEQRES 7 H 129 GLY GLU ALA SER ARG LEU ALA HIS TYR ASN LYS ARG SER SEQRES 8 H 129 THR ILE THR SER ARG GLU ILE GLN THR ALA VAL ARG LEU SEQRES 9 H 129 LEU LEU PRO GLY GLU LEU ALA LYS HIS ALA VAL SER GLU SEQRES 10 H 129 GLY THR LYS ALA VAL THR LYS TYR THR SER ALA LYS SEQRES 1 I 145 DA DT DC DA DC DA DA DT DC DC DC DG DG SEQRES 2 I 145 DT DG DC DC DG DA DG DG DC DC DG DC DT SEQRES 3 I 145 DC DA DA DT DT DG DG DT DC DG DT DA DG SEQRES 4 I 145 DA DC DA DG DC DT DC DT DA DG DC DA DC SEQRES 5 I 145 DC DG DC DT DT DA DA DA DC DG DC DA DC SEQRES 6 I 145 DG DT DA DC DG DG DA DA DT DC DC DG DT SEQRES 7 I 145 DA DC DG DT DG DC DG DT DT DT DA 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 DG DT DG SEQRES 12 I 145 DA DT SEQRES 1 J 145 DA DT DC DA DC 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 DT DA DA DA DC DG DC DA DC SEQRES 6 J 145 DG DT DA DC DG DG DA DT DT DC DC DG DT SEQRES 7 J 145 DA DC DG DT DG DC DG DT DT DT DA DA DG SEQRES 8 J 145 DC DG DG DT DG DC DT DA DG DA DG DC DT SEQRES 9 J 145 DG DT DC DT DA DC DG DA DC DC DA DA DT SEQRES 10 J 145 DT DG DA DG DC DG DG DC DC DT DC DG DG SEQRES 11 J 145 DC DA DC DC DG DG DG DA DT DT DG DT DG SEQRES 12 J 145 DA DT 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 41 1 12 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 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 GLN C 112 LEU C 116 5 5 HELIX 15 AB6 TYR D 37 HIS D 49 1 13 HELIX 16 AB7 SER D 55 ASN D 84 1 30 HELIX 17 AB8 THR D 90 LEU D 102 1 13 HELIX 18 AB9 PRO D 103 SER D 123 1 21 HELIX 19 AC1 GLY E 44 SER E 57 1 14 HELIX 20 AC2 ARG E 63 GLN E 76 1 14 HELIX 21 AC3 GLN E 85 ALA E 114 1 30 HELIX 22 AC4 MET E 120 ARG E 131 1 12 HELIX 23 AC5 ASN F 25 ILE F 29 5 5 HELIX 24 AC6 THR F 30 GLY F 41 1 12 HELIX 25 AC7 LEU F 49 ALA F 76 1 28 HELIX 26 AC8 THR F 82 GLN F 93 1 12 HELIX 27 AC9 THR G 16 ALA G 21 1 6 HELIX 28 AD1 PRO G 26 GLY G 37 1 12 HELIX 29 AD2 ALA G 45 ASN G 73 1 29 HELIX 30 AD3 ILE G 79 ASP G 90 1 12 HELIX 31 AD4 ASP G 90 LEU G 97 1 8 HELIX 32 AD5 GLN G 112 LEU G 116 5 5 HELIX 33 AD6 TYR H 37 HIS H 49 1 13 HELIX 34 AD7 SER H 55 ASN H 84 1 30 HELIX 35 AD8 THR H 90 LEU H 102 1 13 HELIX 36 AD9 GLY H 104 SER H 123 1 20 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 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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