HEADER NUCLEAR PROTEIN 02-MAY-23 8J92 TITLE CRYO-EM STRUCTURE OF NUCLEOSOME CONTAINING ARABIDOPSIS THALIANA H2A.W COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.1; 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: HTA6; COMPND 11 CHAIN: C, G; COMPND 12 SYNONYM: HTA6; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: HTB9; COMPND 16 CHAIN: D, H; COMPND 17 SYNONYM: H2BAT,HTB9; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: DNA (169-MER); COMPND 21 CHAIN: I; COMPND 22 ENGINEERED: YES; COMPND 23 MOL_ID: 6; COMPND 24 MOLECULE: DNA (169-MER); COMPND 25 CHAIN: J; COMPND 26 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 9 ORGANISM_COMMON: THALE CRESS; SOURCE 10 ORGANISM_TAXID: 3702; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 15 ORGANISM_COMMON: THALE CRESS; SOURCE 16 ORGANISM_TAXID: 3702; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 MOL_ID: 4; SOURCE 20 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 21 ORGANISM_COMMON: THALE CRESS; SOURCE 22 ORGANISM_TAXID: 3702; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 25 MOL_ID: 5; SOURCE 26 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 27 ORGANISM_TAXID: 32630; SOURCE 28 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 29 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 30 MOL_ID: 6; SOURCE 31 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 32 ORGANISM_TAXID: 32630; SOURCE 33 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 34 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHROMATIN, EPIGENETICS, HISTON VARIANT, CHROMATIN REMODELER, NUCLEAR KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.OSAKABE,Y.TAKIZAWA,N.HORIKOSHI,S.HATAZAWA,F.BERGER,H.KURUMIZAKA, AUTHOR 2 T.KAKUTANI REVDAT 2 24-JUL-24 8J92 1 JRNL REVDAT 1 03-JUL-24 8J92 0 JRNL AUTH A.OSAKABE,Y.TAKIZAWA,N.HORIKOSHI,S.HATAZAWA,L.NEGISHI, JRNL AUTH 2 S.SATO,F.BERGER,T.KAKUTANI,H.KURUMIZAKA JRNL TITL MOLECULAR AND STRUCTURAL BASIS OF THE CHROMATIN REMODELING JRNL TITL 2 ACTIVITY BY ARABIDOPSIS DDM1. JRNL REF NAT COMMUN V. 15 5187 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38992002 JRNL DOI 10.1038/S41467-024-49465-W REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFFIND, 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 196430 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 8J92 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300037423. 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 : NUCLEOSOME CONTAINING REMARK 245 ARABIDOPSIS THALIANA H2A.W; REMARK 245 NUCLEOSOME; DNA 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 10000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 25000.00 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) : 5910.00 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 LYS A 4 REMARK 465 GLN A 5 REMARK 465 THR A 6 REMARK 465 ALA A 7 REMARK 465 ARG A 8 REMARK 465 LYS A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 GLY A 12 REMARK 465 GLY A 13 REMARK 465 LYS A 14 REMARK 465 ALA A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 LYS A 18 REMARK 465 GLN A 19 REMARK 465 LEU A 20 REMARK 465 ALA A 21 REMARK 465 THR A 22 REMARK 465 LYS A 23 REMARK 465 ALA A 24 REMARK 465 ALA A 25 REMARK 465 ARG A 26 REMARK 465 LYS A 27 REMARK 465 SER A 28 REMARK 465 ALA A 29 REMARK 465 PRO A 30 REMARK 465 ALA A 31 REMARK 465 THR A 32 REMARK 465 GLY A 33 REMARK 465 GLY A 34 REMARK 465 VAL A 35 REMARK 465 LYS A 36 REMARK 465 LYS A 37 REMARK 465 ALA A 135 REMARK 465 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 GLY C -3 REMARK 465 SER C -2 REMARK 465 HIS C -1 REMARK 465 MET C 0 REMARK 465 GLU C 1 REMARK 465 SER C 2 REMARK 465 THR C 3 REMARK 465 GLY C 4 REMARK 465 LYS C 5 REMARK 465 VAL C 6 REMARK 465 LYS C 7 REMARK 465 LYS C 8 REMARK 465 ALA C 9 REMARK 465 PHE C 10 REMARK 465 GLY C 11 REMARK 465 GLY C 12 REMARK 465 ARG C 13 REMARK 465 LYS C 14 REMARK 465 PRO C 15 REMARK 465 PRO C 16 REMARK 465 GLY C 17 REMARK 465 ALA C 18 REMARK 465 PRO C 19 REMARK 465 LYS C 20 REMARK 465 THR C 21 REMARK 465 LYS C 127 REMARK 465 LYS C 128 REMARK 465 SER C 129 REMARK 465 ALA C 130 REMARK 465 THR C 131 REMARK 465 LYS C 132 REMARK 465 PRO C 133 REMARK 465 ALA C 134 REMARK 465 GLU C 135 REMARK 465 GLU C 136 REMARK 465 LYS C 137 REMARK 465 ALA C 138 REMARK 465 THR C 139 REMARK 465 LYS C 140 REMARK 465 SER C 141 REMARK 465 PRO C 142 REMARK 465 VAL C 143 REMARK 465 LYS C 144 REMARK 465 SER C 145 REMARK 465 PRO C 146 REMARK 465 LYS C 147 REMARK 465 LYS C 148 REMARK 465 ALA C 149 REMARK 465 GLY D -3 REMARK 465 SER D -2 REMARK 465 HIS D -1 REMARK 465 MET D 0 REMARK 465 ALA D 1 REMARK 465 PRO D 2 REMARK 465 ARG D 3 REMARK 465 ALA D 4 REMARK 465 GLU D 5 REMARK 465 LYS D 6 REMARK 465 LYS D 7 REMARK 465 PRO D 8 REMARK 465 ALA D 9 REMARK 465 GLU D 10 REMARK 465 LYS D 11 REMARK 465 LYS D 12 REMARK 465 PRO D 13 REMARK 465 ALA D 14 REMARK 465 ALA D 15 REMARK 465 GLU D 16 REMARK 465 LYS D 17 REMARK 465 PRO D 18 REMARK 465 VAL D 19 REMARK 465 GLU D 20 REMARK 465 GLU D 21 REMARK 465 LYS D 22 REMARK 465 SER D 23 REMARK 465 LYS D 24 REMARK 465 ALA D 25 REMARK 465 GLU D 26 REMARK 465 LYS D 27 REMARK 465 ALA D 28 REMARK 465 PRO D 29 REMARK 465 ALA D 30 REMARK 465 GLU D 31 REMARK 465 LYS D 32 REMARK 465 LYS D 33 REMARK 465 PRO D 34 REMARK 465 LYS D 35 REMARK 465 ALA D 36 REMARK 465 GLY D 37 REMARK 465 LYS D 38 REMARK 465 LYS D 39 REMARK 465 LEU D 40 REMARK 465 PRO D 41 REMARK 465 LYS D 42 REMARK 465 GLU D 43 REMARK 465 ALA D 44 REMARK 465 GLY D 45 REMARK 465 ALA D 46 REMARK 465 GLY D 47 REMARK 465 GLY D 48 REMARK 465 ASP D 49 REMARK 465 LYS D 50 REMARK 465 LYS D 51 REMARK 465 LYS D 52 REMARK 465 LYS D 53 REMARK 465 MET D 54 REMARK 465 LYS D 55 REMARK 465 LYS D 56 REMARK 465 LYS D 57 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 LYS E 4 REMARK 465 GLN E 5 REMARK 465 THR E 6 REMARK 465 ALA E 7 REMARK 465 ARG E 8 REMARK 465 LYS E 9 REMARK 465 SER E 10 REMARK 465 THR E 11 REMARK 465 GLY E 12 REMARK 465 GLY E 13 REMARK 465 LYS E 14 REMARK 465 ALA E 15 REMARK 465 PRO E 16 REMARK 465 ARG E 17 REMARK 465 LYS E 18 REMARK 465 GLN E 19 REMARK 465 LEU E 20 REMARK 465 ALA E 21 REMARK 465 THR E 22 REMARK 465 LYS E 23 REMARK 465 ALA E 24 REMARK 465 ALA E 25 REMARK 465 ARG E 26 REMARK 465 LYS E 27 REMARK 465 SER E 28 REMARK 465 ALA E 29 REMARK 465 PRO E 30 REMARK 465 ALA E 31 REMARK 465 THR E 32 REMARK 465 GLY E 33 REMARK 465 GLY E 34 REMARK 465 VAL E 35 REMARK 465 LYS E 36 REMARK 465 LYS E 37 REMARK 465 PRO E 38 REMARK 465 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 VAL F 21 REMARK 465 LEU F 22 REMARK 465 ARG F 23 REMARK 465 ASP F 24 REMARK 465 GLY G -3 REMARK 465 SER G -2 REMARK 465 HIS G -1 REMARK 465 MET G 0 REMARK 465 GLU G 1 REMARK 465 SER G 2 REMARK 465 THR G 3 REMARK 465 GLY G 4 REMARK 465 LYS G 5 REMARK 465 VAL G 6 REMARK 465 LYS G 7 REMARK 465 LYS G 8 REMARK 465 ALA G 9 REMARK 465 PHE G 10 REMARK 465 GLY G 11 REMARK 465 GLY G 12 REMARK 465 ARG G 13 REMARK 465 LYS G 14 REMARK 465 PRO G 15 REMARK 465 PRO G 16 REMARK 465 GLY G 17 REMARK 465 ALA G 18 REMARK 465 PRO G 19 REMARK 465 LYS G 20 REMARK 465 THR G 21 REMARK 465 LYS G 127 REMARK 465 LYS G 128 REMARK 465 SER G 129 REMARK 465 ALA G 130 REMARK 465 THR G 131 REMARK 465 LYS G 132 REMARK 465 PRO G 133 REMARK 465 ALA G 134 REMARK 465 GLU G 135 REMARK 465 GLU G 136 REMARK 465 LYS G 137 REMARK 465 ALA G 138 REMARK 465 THR G 139 REMARK 465 LYS G 140 REMARK 465 SER G 141 REMARK 465 PRO G 142 REMARK 465 VAL G 143 REMARK 465 LYS G 144 REMARK 465 SER G 145 REMARK 465 PRO G 146 REMARK 465 LYS G 147 REMARK 465 LYS G 148 REMARK 465 ALA G 149 REMARK 465 GLY H -3 REMARK 465 SER H -2 REMARK 465 HIS H -1 REMARK 465 MET H 0 REMARK 465 ALA H 1 REMARK 465 PRO H 2 REMARK 465 ARG H 3 REMARK 465 ALA H 4 REMARK 465 GLU H 5 REMARK 465 LYS H 6 REMARK 465 LYS H 7 REMARK 465 PRO H 8 REMARK 465 ALA H 9 REMARK 465 GLU H 10 REMARK 465 LYS H 11 REMARK 465 LYS H 12 REMARK 465 PRO H 13 REMARK 465 ALA H 14 REMARK 465 ALA H 15 REMARK 465 GLU H 16 REMARK 465 LYS H 17 REMARK 465 PRO H 18 REMARK 465 VAL H 19 REMARK 465 GLU H 20 REMARK 465 GLU H 21 REMARK 465 LYS H 22 REMARK 465 SER H 23 REMARK 465 LYS H 24 REMARK 465 ALA H 25 REMARK 465 GLU H 26 REMARK 465 LYS H 27 REMARK 465 ALA H 28 REMARK 465 PRO H 29 REMARK 465 ALA H 30 REMARK 465 GLU H 31 REMARK 465 LYS H 32 REMARK 465 LYS H 33 REMARK 465 PRO H 34 REMARK 465 LYS H 35 REMARK 465 ALA H 36 REMARK 465 GLY H 37 REMARK 465 LYS H 38 REMARK 465 LYS H 39 REMARK 465 LEU H 40 REMARK 465 PRO H 41 REMARK 465 LYS H 42 REMARK 465 GLU H 43 REMARK 465 ALA H 44 REMARK 465 GLY H 45 REMARK 465 ALA H 46 REMARK 465 GLY H 47 REMARK 465 GLY H 48 REMARK 465 ASP H 49 REMARK 465 LYS H 50 REMARK 465 LYS H 51 REMARK 465 LYS H 52 REMARK 465 LYS H 53 REMARK 465 MET H 54 REMARK 465 LYS H 55 REMARK 465 LYS H 56 REMARK 465 LYS H 57 REMARK 465 DA I -95 REMARK 465 DT I -94 REMARK 465 DC I -93 REMARK 465 DG I -92 REMARK 465 DG I -91 REMARK 465 DA I -90 REMARK 465 DC I -89 REMARK 465 DC I -88 REMARK 465 DC I -87 REMARK 465 DT I -86 REMARK 465 DA I -85 REMARK 465 DT I -84 REMARK 465 DC I -83 REMARK 465 DG I -82 REMARK 465 DC I -81 REMARK 465 DG I -80 REMARK 465 DA I -79 REMARK 465 DG I -78 REMARK 465 DA I 72 REMARK 465 DT I 73 REMARK 465 DA J -73 REMARK 465 DT J -72 REMARK 465 DC J 78 REMARK 465 DT J 79 REMARK 465 DC J 80 REMARK 465 DG J 81 REMARK 465 DC J 82 REMARK 465 DG J 83 REMARK 465 DA J 84 REMARK 465 DT J 85 REMARK 465 DA J 86 REMARK 465 DG J 87 REMARK 465 DG J 88 REMARK 465 DG J 89 REMARK 465 DT J 90 REMARK 465 DC J 91 REMARK 465 DC J 92 REMARK 465 DG J 93 REMARK 465 DA J 94 REMARK 465 DT J 95 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG I -58 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT J 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG J 20 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO D 128 -178.12 -66.21 REMARK 500 PRO H 128 -179.72 -64.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36083 RELATED DB: EMDB REMARK 900 DDM1-NUCLEOSOME COMPLEX REMARK 900 RELATED ID: EMD-36084 RELATED DB: EMDB REMARK 900 NUCLEOSOME CONTAINING ARABIDOPSIS THALIANA HISTONES REMARK 900 RELATED ID: EMD-36085 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF NUCLEOSOME CONTAINING ARABIDOPSIS THALIANA REMARK 900 H2A.W DBREF 8J92 A 0 135 UNP P59226 H31_ARATH 1 136 DBREF 8J92 B 0 102 UNP P59259 H4_ARATH 1 103 DBREF 8J92 C 0 149 UNP Q9FJE8 H2A7_ARATH 1 150 DBREF 8J92 D 0 149 UNP O23629 H2B6_ARATH 1 150 DBREF 8J92 E 0 135 UNP P59226 H31_ARATH 1 136 DBREF 8J92 F 0 102 UNP P59259 H4_ARATH 1 103 DBREF 8J92 G 0 149 UNP Q9FJE8 H2A7_ARATH 1 150 DBREF 8J92 H 0 149 UNP O23629 H2B6_ARATH 1 150 DBREF 8J92 I -95 73 PDB 8J92 8J92 -95 73 DBREF 8J92 J -73 95 PDB 8J92 8J92 -73 95 SEQADV 8J92 GLY A -3 UNP P59226 EXPRESSION TAG SEQADV 8J92 SER A -2 UNP P59226 EXPRESSION TAG SEQADV 8J92 HIS A -1 UNP P59226 EXPRESSION TAG SEQADV 8J92 GLY B -3 UNP P59259 EXPRESSION TAG SEQADV 8J92 SER B -2 UNP P59259 EXPRESSION TAG SEQADV 8J92 HIS B -1 UNP P59259 EXPRESSION TAG SEQADV 8J92 GLY C -3 UNP Q9FJE8 EXPRESSION TAG SEQADV 8J92 SER C -2 UNP Q9FJE8 EXPRESSION TAG SEQADV 8J92 HIS C -1 UNP Q9FJE8 EXPRESSION TAG SEQADV 8J92 GLY D -3 UNP O23629 EXPRESSION TAG SEQADV 8J92 SER D -2 UNP O23629 EXPRESSION TAG SEQADV 8J92 HIS D -1 UNP O23629 EXPRESSION TAG SEQADV 8J92 GLY E -3 UNP P59226 EXPRESSION TAG SEQADV 8J92 SER E -2 UNP P59226 EXPRESSION TAG SEQADV 8J92 HIS E -1 UNP P59226 EXPRESSION TAG SEQADV 8J92 GLY F -3 UNP P59259 EXPRESSION TAG SEQADV 8J92 SER F -2 UNP P59259 EXPRESSION TAG SEQADV 8J92 HIS F -1 UNP P59259 EXPRESSION TAG SEQADV 8J92 GLY G -3 UNP Q9FJE8 EXPRESSION TAG SEQADV 8J92 SER G -2 UNP Q9FJE8 EXPRESSION TAG SEQADV 8J92 HIS G -1 UNP Q9FJE8 EXPRESSION TAG SEQADV 8J92 GLY H -3 UNP O23629 EXPRESSION TAG SEQADV 8J92 SER H -2 UNP O23629 EXPRESSION TAG SEQADV 8J92 HIS H -1 UNP O23629 EXPRESSION TAG SEQRES 1 A 139 GLY SER HIS MET ALA ARG THR LYS GLN THR ALA ARG LYS SEQRES 2 A 139 SER THR GLY GLY LYS ALA PRO ARG LYS GLN LEU ALA THR SEQRES 3 A 139 LYS ALA ALA ARG LYS SER ALA PRO ALA THR GLY GLY VAL SEQRES 4 A 139 LYS LYS PRO HIS ARG PHE ARG PRO GLY THR VAL ALA LEU SEQRES 5 A 139 ARG GLU ILE ARG LYS TYR GLN LYS SER THR GLU LEU LEU SEQRES 6 A 139 ILE ARG LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE SEQRES 7 A 139 ALA GLN ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER SEQRES 8 A 139 ALA VAL ALA ALA LEU GLN GLU ALA ALA GLU ALA TYR LEU SEQRES 9 A 139 VAL GLY LEU PHE GLU ASP THR ASN LEU CYS ALA ILE HIS SEQRES 10 A 139 ALA LYS ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU SEQRES 11 A 139 ALA ARG ARG ILE ARG GLY GLU ARG ALA 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 ILE PHE SEQRES 6 B 106 LEU GLU ASN VAL ILE ARG ASP ALA VAL THR TYR THR GLU SEQRES 7 B 106 HIS ALA ARG 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 153 GLY SER HIS MET GLU SER THR GLY LYS VAL LYS LYS ALA SEQRES 2 C 153 PHE GLY GLY ARG LYS PRO PRO GLY ALA PRO LYS THR LYS SEQRES 3 C 153 SER VAL SER LYS SER MET LYS ALA GLY LEU GLN PHE PRO SEQRES 4 C 153 VAL GLY ARG ILE THR ARG PHE LEU LYS LYS GLY ARG TYR SEQRES 5 C 153 ALA GLN ARG LEU GLY GLY GLY ALA PRO VAL TYR MET ALA SEQRES 6 C 153 ALA VAL LEU GLU TYR LEU ALA ALA GLU VAL LEU GLU LEU SEQRES 7 C 153 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS SER ARG ILE SEQRES 8 C 153 ILE PRO ARG HIS LEU LEU LEU ALA ILE ARG ASN ASP GLU SEQRES 9 C 153 GLU LEU GLY LYS LEU LEU SER GLY VAL THR ILE ALA HIS SEQRES 10 C 153 GLY GLY VAL LEU PRO ASN ILE ASN SER VAL LEU LEU PRO SEQRES 11 C 153 LYS LYS SER ALA THR LYS PRO ALA GLU GLU LYS ALA THR SEQRES 12 C 153 LYS SER PRO VAL LYS SER PRO LYS LYS ALA SEQRES 1 D 153 GLY SER HIS MET ALA PRO ARG ALA GLU LYS LYS PRO ALA SEQRES 2 D 153 GLU LYS LYS PRO ALA ALA GLU LYS PRO VAL GLU GLU LYS SEQRES 3 D 153 SER LYS ALA GLU LYS ALA PRO ALA GLU LYS LYS PRO LYS SEQRES 4 D 153 ALA GLY LYS LYS LEU PRO LYS GLU ALA GLY ALA GLY GLY SEQRES 5 D 153 ASP LYS LYS LYS LYS MET LYS LYS LYS SER VAL GLU THR SEQRES 6 D 153 TYR LYS ILE TYR ILE PHE LYS VAL LEU LYS GLN VAL HIS SEQRES 7 D 153 PRO ASP ILE GLY ILE SER SER LYS ALA MET GLY ILE MET SEQRES 8 D 153 ASN SER PHE ILE ASN ASP ILE PHE GLU LYS LEU ALA SER SEQRES 9 D 153 GLU SER SER LYS LEU ALA ARG TYR ASN LYS LYS PRO THR SEQRES 10 D 153 ILE THR SER ARG GLU ILE GLN THR ALA VAL ARG LEU VAL SEQRES 11 D 153 LEU PRO GLY GLU LEU ALA LYS HIS ALA VAL SER GLU GLY SEQRES 12 D 153 THR LYS ALA VAL THR LYS PHE THR SER SER SEQRES 1 E 139 GLY SER HIS MET ALA ARG THR LYS GLN THR ALA ARG LYS SEQRES 2 E 139 SER THR GLY GLY LYS ALA PRO ARG LYS GLN LEU ALA THR SEQRES 3 E 139 LYS ALA ALA ARG LYS SER ALA PRO ALA THR GLY GLY VAL SEQRES 4 E 139 LYS LYS PRO HIS ARG PHE ARG PRO GLY THR VAL ALA LEU SEQRES 5 E 139 ARG GLU ILE ARG LYS TYR GLN LYS SER THR GLU LEU LEU SEQRES 6 E 139 ILE ARG LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE SEQRES 7 E 139 ALA GLN ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER SEQRES 8 E 139 ALA VAL ALA ALA LEU GLN GLU ALA ALA GLU ALA TYR LEU SEQRES 9 E 139 VAL GLY LEU PHE GLU ASP THR ASN LEU CYS ALA ILE HIS SEQRES 10 E 139 ALA LYS ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU SEQRES 11 E 139 ALA ARG ARG ILE ARG GLY GLU ARG ALA 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 ILE PHE SEQRES 6 F 106 LEU GLU ASN VAL ILE ARG ASP ALA VAL THR TYR THR GLU SEQRES 7 F 106 HIS ALA ARG 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 153 GLY SER HIS MET GLU SER THR GLY LYS VAL LYS LYS ALA SEQRES 2 G 153 PHE GLY GLY ARG LYS PRO PRO GLY ALA PRO LYS THR LYS SEQRES 3 G 153 SER VAL SER LYS SER MET LYS ALA GLY LEU GLN PHE PRO SEQRES 4 G 153 VAL GLY ARG ILE THR ARG PHE LEU LYS LYS GLY ARG TYR SEQRES 5 G 153 ALA GLN ARG LEU GLY GLY GLY ALA PRO VAL TYR MET ALA SEQRES 6 G 153 ALA VAL LEU GLU TYR LEU ALA ALA GLU VAL LEU GLU LEU SEQRES 7 G 153 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS SER ARG ILE SEQRES 8 G 153 ILE PRO ARG HIS LEU LEU LEU ALA ILE ARG ASN ASP GLU SEQRES 9 G 153 GLU LEU GLY LYS LEU LEU SER GLY VAL THR ILE ALA HIS SEQRES 10 G 153 GLY GLY VAL LEU PRO ASN ILE ASN SER VAL LEU LEU PRO SEQRES 11 G 153 LYS LYS SER ALA THR LYS PRO ALA GLU GLU LYS ALA THR SEQRES 12 G 153 LYS SER PRO VAL LYS SER PRO LYS LYS ALA SEQRES 1 H 153 GLY SER HIS MET ALA PRO ARG ALA GLU LYS LYS PRO ALA SEQRES 2 H 153 GLU LYS LYS PRO ALA ALA GLU LYS PRO VAL GLU GLU LYS SEQRES 3 H 153 SER LYS ALA GLU LYS ALA PRO ALA GLU LYS LYS PRO LYS SEQRES 4 H 153 ALA GLY LYS LYS LEU PRO LYS GLU ALA GLY ALA GLY GLY SEQRES 5 H 153 ASP LYS LYS LYS LYS MET LYS LYS LYS SER VAL GLU THR SEQRES 6 H 153 TYR LYS ILE TYR ILE PHE LYS VAL LEU LYS GLN VAL HIS SEQRES 7 H 153 PRO ASP ILE GLY ILE SER SER LYS ALA MET GLY ILE MET SEQRES 8 H 153 ASN SER PHE ILE ASN ASP ILE PHE GLU LYS LEU ALA SER SEQRES 9 H 153 GLU SER SER LYS LEU ALA ARG TYR ASN LYS LYS PRO THR SEQRES 10 H 153 ILE THR SER ARG GLU ILE GLN THR ALA VAL ARG LEU VAL SEQRES 11 H 153 LEU PRO GLY GLU LEU ALA LYS HIS ALA VAL SER GLU GLY SEQRES 12 H 153 THR LYS ALA VAL THR LYS PHE THR SER SER SEQRES 1 I 169 DA DT DC DG DG DA DC DC DC DT DA DT DC SEQRES 2 I 169 DG DC DG DA DG DC DC DA DG DG DC DC DT SEQRES 3 I 169 DG DA DG DA DA DT DC DC DG DG DT DG DC SEQRES 4 I 169 DC DG DA DG DG DC DC DG DC DT DC DA DA SEQRES 5 I 169 DT DT DG DG DT DC DG DT DA DG DA DC DA SEQRES 6 I 169 DG DC DT DC DT DA DG DC DA DC DC DG DC SEQRES 7 I 169 DT DT DA DA DA DC DG DC DA DC DG DT DA SEQRES 8 I 169 DC DG DC DG DC DT DG DT DC DC DC DC DC SEQRES 9 I 169 DG DC DG DT DT DT DT DA DA DC DC DG DC SEQRES 10 I 169 DC DA DA DG DG DG DG DA DT DT DA DC DT SEQRES 11 I 169 DC DC DC DT DA DG DT DC DT DC DC DA DG SEQRES 12 I 169 DG DC DA DC DG DT DG DT DC DA DG DA DT SEQRES 13 I 169 DA DT DA DT DA DC DA DT DC DC DG DA DT SEQRES 1 J 169 DA DT DC DG DG DA DT DG DT DA DT DA DT SEQRES 2 J 169 DA DT DC DT DG DA DC DA DC DG DT DG DC SEQRES 3 J 169 DC DT DG DG DA DG DA DC DT DA DG DG DG SEQRES 4 J 169 DA DG DT DA DA DT DC DC DC DC DT DT DG SEQRES 5 J 169 DG DC DG DG DT DT DA DA DA DA DC DG DC SEQRES 6 J 169 DG DG DG DG DG DA DC DA DG DC DG DC DG SEQRES 7 J 169 DT DA DC DG DT DG DC DG DT DT DT DA DA SEQRES 8 J 169 DG DC DG DG DT DG DC DT DA DG DA DG DC SEQRES 9 J 169 DT DG DT DC DT DA DC DG DA DC DC DA DA SEQRES 10 J 169 DT DT DG DA DG DC DG DG DC DC DT DC DG SEQRES 11 J 169 DG DC DA DC DC DG DG DA DT DT DC DT DC SEQRES 12 J 169 DA DG DG DC DC DT DG DG DC DT DC DG DC SEQRES 13 J 169 DG DA DT DA DG DG DG DT DC DC DG 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 SER C 25 GLY C 31 1 7 HELIX 10 AB1 PRO C 35 GLY C 46 1 12 HELIX 11 AB2 GLY C 55 ASN C 82 1 28 HELIX 12 AB3 ILE C 88 ASP C 99 1 12 HELIX 13 AB4 ASP C 99 LEU C 106 1 8 HELIX 14 AB5 TYR D 62 HIS D 74 1 13 HELIX 15 AB6 SER D 80 ARG D 107 1 28 HELIX 16 AB7 TYR D 108 LYS D 110 5 3 HELIX 17 AB8 THR D 115 LEU D 127 1 13 HELIX 18 AB9 PRO D 128 SER D 149 1 22 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 GLY E 132 1 13 HELIX 23 AC5 ASN F 25 ILE F 29 5 5 HELIX 24 AC6 THR F 30 GLY F 42 1 13 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 SER G 25 GLY G 31 1 7 HELIX 28 AD1 PRO G 35 GLY G 46 1 12 HELIX 29 AD2 GLY G 55 ASN G 82 1 28 HELIX 30 AD3 ILE G 88 ASP G 99 1 12 HELIX 31 AD4 ASP G 99 LEU G 106 1 8 HELIX 32 AD5 TYR H 62 HIS H 74 1 13 HELIX 33 AD6 SER H 80 ASN H 109 1 30 HELIX 34 AD7 THR H 115 LEU H 127 1 13 HELIX 35 AD8 PRO H 128 SER H 149 1 22 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 THR B 96 TYR B 98 0 SHEET 2 AA3 2 VAL G 109 ILE G 111 1 O THR G 110 N THR B 96 SHEET 1 AA4 2 ARG C 51 LEU C 52 0 SHEET 2 AA4 2 THR D 113 ILE D 114 1 O ILE D 114 N ARG C 51 SHEET 1 AA5 2 ARG C 86 ILE C 87 0 SHEET 2 AA5 2 GLY D 78 ILE D 79 1 O GLY D 78 N ILE C 87 SHEET 1 AA6 2 THR C 110 ILE C 111 0 SHEET 2 AA6 2 LEU F 97 TYR F 98 1 O TYR F 98 N THR C 110 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 51 LEU G 52 0 SHEET 2 AA9 2 THR H 113 ILE H 114 1 O ILE H 114 N ARG G 51 SHEET 1 AB1 2 ARG G 86 ILE G 87 0 SHEET 2 AB1 2 GLY H 78 ILE H 79 1 O GLY H 78 N ILE G 87 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