HEADER NUCLEAR PROTEIN 06-MAR-20 6M4D TITLE STRUCTURAL MECHANISM OF NUCLEOSOME DYNAMICS GOVERNED BY HUMAN HISTONE TITLE 2 VARIANTS H2A.B AND H2A.Z.2.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.1; COMPND 3 CHAIN: A, E; 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 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE H4; COMPND 10 CHAIN: B, F; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: HISTONE H2A.V; COMPND 14 CHAIN: C, G; COMPND 15 SYNONYM: H2A.F/Z; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: HISTONE H2B TYPE 2-E; COMPND 19 CHAIN: D, H; COMPND 20 SYNONYM: HISTONE H2B-GL105,HISTONE H2B.Q,H2B/Q; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 5; COMPND 23 MOLECULE: DNA (125-MER); COMPND 24 CHAIN: I; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 6; COMPND 27 MOLECULE: DNA (125-MER); COMPND 28 CHAIN: J; COMPND 29 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: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, SOURCE 6 H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, SOURCE 7 H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, SOURCE 15 H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, SOURCE 16 H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, SOURCE 17 H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, SOURCE 18 H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: H2AFV, H2AV; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 28 MOL_ID: 4; SOURCE 29 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 30 ORGANISM_COMMON: HUMAN; SOURCE 31 ORGANISM_TAXID: 9606; SOURCE 32 GENE: HIST2H2BE, H2BFQ; SOURCE 33 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 34 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 35 MOL_ID: 5; SOURCE 36 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 37 ORGANISM_TAXID: 9606; SOURCE 38 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 39 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 40 MOL_ID: 6; SOURCE 41 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 42 ORGANISM_TAXID: 9606; SOURCE 43 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 44 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS HISTONE; H2A.Z; H2A.Z.2.2; NUCLEOSOME, NUCLEAR PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.ZHOU,L.C.DAI,C.M.LI,L.X.SHI,Y.HUANG,Z.Q.GUO REVDAT 3 27-MAR-24 6M4D 1 REMARK REVDAT 2 07-APR-21 6M4D 1 JRNL REVDAT 1 23-SEP-20 6M4D 0 JRNL AUTH M.ZHOU,L.DAI,C.LI,L.SHI,Y.HUANG,Z.GUO,F.WU,P.ZHU,Z.ZHOU JRNL TITL STRUCTURAL BASIS OF NUCLEOSOME DYNAMICS MODULATION BY JRNL TITL 2 HISTONE VARIANTS H2A.B AND H2A.Z.2.2. JRNL REF EMBO J. V. 40 05907 2021 JRNL REFN ESSN 1460-2075 JRNL PMID 33073403 JRNL DOI 10.15252/EMBJ.2020105907 REMARK 2 REMARK 2 RESOLUTION. 4.40 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) : 4.400 REMARK 3 NUMBER OF PARTICLES : 111800 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 6M4D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016061. 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 : H2A.Z.2.2 NUCLEOSOME 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 K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 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 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 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 PRO A 43 REMARK 465 GLY A 44 REMARK 465 THR A 45 REMARK 465 VAL A 46 REMARK 465 ALA A 47 REMARK 465 LEU A 48 REMARK 465 ARG A 49 REMARK 465 GLU A 50 REMARK 465 ILE A 51 REMARK 465 ARG A 52 REMARK 465 ARG A 53 REMARK 465 TYR A 54 REMARK 465 GLN A 55 REMARK 465 LYS A 56 REMARK 465 SER A 57 REMARK 465 THR A 58 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 VAL B 21 REMARK 465 LEU B 22 REMARK 465 MET C 0 REMARK 465 ALA C 1 REMARK 465 GLY C 2 REMARK 465 GLY C 3 REMARK 465 LYS C 4 REMARK 465 ALA C 5 REMARK 465 GLY C 6 REMARK 465 LYS C 7 REMARK 465 ASP C 8 REMARK 465 SER C 9 REMARK 465 GLY C 10 REMARK 465 LYS C 11 REMARK 465 ALA C 12 REMARK 465 LYS C 13 REMARK 465 ALA C 14 REMARK 465 LYS C 15 REMARK 465 GLY C 107 REMARK 465 GLU C 108 REMARK 465 LYS C 109 REMARK 465 ARG C 110 REMARK 465 ARG C 111 REMARK 465 CYS C 112 REMARK 465 SER C 113 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 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 HIS E 39 REMARK 465 ARG E 40 REMARK 465 TYR E 41 REMARK 465 ARG E 42 REMARK 465 PRO E 43 REMARK 465 GLY E 44 REMARK 465 THR E 45 REMARK 465 VAL E 46 REMARK 465 ALA E 47 REMARK 465 LEU E 48 REMARK 465 ARG E 49 REMARK 465 GLU E 50 REMARK 465 ILE E 51 REMARK 465 ARG E 52 REMARK 465 ARG E 53 REMARK 465 TYR E 54 REMARK 465 GLN E 55 REMARK 465 LYS E 56 REMARK 465 SER E 57 REMARK 465 THR E 58 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 ALA G 1 REMARK 465 GLY G 2 REMARK 465 GLY G 3 REMARK 465 LYS G 4 REMARK 465 ALA G 5 REMARK 465 GLY G 6 REMARK 465 LYS G 7 REMARK 465 ASP G 8 REMARK 465 SER G 9 REMARK 465 GLY G 10 REMARK 465 LYS G 11 REMARK 465 ALA G 12 REMARK 465 LYS G 13 REMARK 465 ALA G 14 REMARK 465 LYS G 15 REMARK 465 GLY G 107 REMARK 465 GLU G 108 REMARK 465 LYS G 109 REMARK 465 ARG G 110 REMARK 465 ARG G 111 REMARK 465 CYS G 112 REMARK 465 SER G 113 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 DA I 1 REMARK 465 DT I 2 REMARK 465 DC I 3 REMARK 465 DG I 4 REMARK 465 DA I 5 REMARK 465 DG I 6 REMARK 465 DA I 7 REMARK 465 DA I 8 REMARK 465 DT I 9 REMARK 465 DC I 10 REMARK 465 DC I 11 REMARK 465 DA I 137 REMARK 465 DT I 138 REMARK 465 DA I 139 REMARK 465 DC I 140 REMARK 465 DA I 141 REMARK 465 DT I 142 REMARK 465 DC I 143 REMARK 465 DC I 144 REMARK 465 DG I 145 REMARK 465 DA I 146 REMARK 465 DT I 147 REMARK 465 DA J 1 REMARK 465 DT J 2 REMARK 465 DC J 3 REMARK 465 DG J 4 REMARK 465 DG J 5 REMARK 465 DA J 6 REMARK 465 DT J 7 REMARK 465 DG J 8 REMARK 465 DT J 9 REMARK 465 DA J 10 REMARK 465 DT J 11 REMARK 465 DG J 137 REMARK 465 DG J 138 REMARK 465 DA J 139 REMARK 465 DT J 140 REMARK 465 DT J 141 REMARK 465 DC J 142 REMARK 465 DT J 143 REMARK 465 DC J 144 REMARK 465 DG J 145 REMARK 465 DA J 146 REMARK 465 DT J 147 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG B 35 OP2 DC I 82 2.07 REMARK 500 OG SER C 73 O VAL C 78 2.09 REMARK 500 OG SER G 73 O VAL G 78 2.09 REMARK 500 N2 DG I 132 O2 DC J 16 2.10 REMARK 500 O HIS F 75 NH1 ARG H 92 2.15 REMARK 500 N4 DC I 17 O6 DG J 130 2.16 REMARK 500 O GLU G 95 OG SER G 98 2.16 REMARK 500 O GLU C 95 OG SER C 98 2.16 REMARK 500 NZ LYS G 37 OP1 DA J 113 2.18 REMARK 500 NH2 ARG G 22 O TYR H 121 2.19 REMARK 500 N1 DG I 132 N3 DC J 16 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 101 O3' DG I 101 C3' -0.037 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 12 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG I 19 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC I 23 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC I 24 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC I 36 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG I 37 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC I 42 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG I 44 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC I 56 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA I 60 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG I 67 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG I 67 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT I 68 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT I 68 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC I 74 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT I 88 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG I 94 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC I 96 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT I 104 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC I 110 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC I 111 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC I 111 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC I 118 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC I 118 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT I 127 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT J 13 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA J 14 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT J 15 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG J 53 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC J 65 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG J 69 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DA J 90 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA J 90 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC J 135 C3' - O3' - P ANGL. DEV. = 11.4 DEGREES REMARK 500 DG J 136 O3' - P - O5' ANGL. DEV. = 13.9 DEGREES REMARK 500 DG J 136 O4' - C1' - N9 ANGL. DEV. = 4.6 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 LYS A 115 16.86 55.82 REMARK 500 ARG A 134 48.53 36.20 REMARK 500 SER B 47 -89.21 -66.29 REMARK 500 LEU B 49 41.21 -96.01 REMARK 500 SER C 42 -9.11 72.67 REMARK 500 LYS E 115 16.87 55.84 REMARK 500 ARG E 134 48.53 36.20 REMARK 500 SER F 47 -89.24 -66.32 REMARK 500 LEU F 49 41.25 -95.98 REMARK 500 SER G 42 -9.07 72.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30076 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN H2A.Z.2.2 NUCLEOSOME DBREF 6M4D A 0 135 UNP P68431 H31_HUMAN 1 136 DBREF 6M4D B 0 102 UNP P62805 H4_HUMAN 1 103 DBREF 6M4D C 0 113 UNP Q71UI9 H2AV_HUMAN 1 114 DBREF 6M4D D 0 125 UNP Q16778 H2B2E_HUMAN 1 126 DBREF 6M4D E 0 135 UNP P68431 H31_HUMAN 1 136 DBREF 6M4D F 0 102 UNP P62805 H4_HUMAN 1 103 DBREF 6M4D G 0 113 UNP Q71UI9 H2AV_HUMAN 1 114 DBREF 6M4D H 0 125 UNP Q16778 H2B2E_HUMAN 1 126 DBREF 6M4D I 1 147 PDB 6M4D 6M4D 1 147 DBREF 6M4D J 1 147 PDB 6M4D 6M4D 1 147 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 CYS GLU ALA TYR LEU VAL GLY 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 114 MET ALA GLY GLY LYS ALA GLY LYS ASP SER GLY LYS ALA SEQRES 2 C 114 LYS ALA LYS ALA VAL SER ARG SER GLN ARG ALA GLY LEU SEQRES 3 C 114 GLN PHE PRO VAL GLY ARG ILE HIS ARG HIS LEU LYS THR SEQRES 4 C 114 ARG THR THR SER HIS GLY ARG VAL GLY ALA THR ALA ALA SEQRES 5 C 114 VAL TYR SER ALA ALA ILE LEU GLU TYR LEU THR ALA GLU SEQRES 6 C 114 VAL LEU GLU LEU ALA GLY ASN ALA SER LYS ASP LEU LYS SEQRES 7 C 114 VAL LYS ARG ILE THR PRO ARG HIS LEU GLN LEU ALA ILE SEQRES 8 C 114 ARG GLY ASP GLU GLU LEU ASP SER LEU ILE LYS ALA THR SEQRES 9 C 114 ILE ALA GLY GLY GLU LYS ARG ARG CYS SER SEQRES 1 D 126 MET PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS SEQRES 2 D 126 GLY SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP SEQRES 3 D 126 GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER SEQRES 4 D 126 ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP SEQRES 5 D 126 THR GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER SEQRES 6 D 126 PHE VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SEQRES 7 D 126 SER ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SEQRES 8 D 126 SER ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO SEQRES 9 D 126 GLY GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS SEQRES 10 D 126 ALA VAL THR LYS TYR THR SER SER 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 CYS GLU ALA TYR LEU VAL GLY 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 114 MET ALA GLY GLY LYS ALA GLY LYS ASP SER GLY LYS ALA SEQRES 2 G 114 LYS ALA LYS ALA VAL SER ARG SER GLN ARG ALA GLY LEU SEQRES 3 G 114 GLN PHE PRO VAL GLY ARG ILE HIS ARG HIS LEU LYS THR SEQRES 4 G 114 ARG THR THR SER HIS GLY ARG VAL GLY ALA THR ALA ALA SEQRES 5 G 114 VAL TYR SER ALA ALA ILE LEU GLU TYR LEU THR ALA GLU SEQRES 6 G 114 VAL LEU GLU LEU ALA GLY ASN ALA SER LYS ASP LEU LYS SEQRES 7 G 114 VAL LYS ARG ILE THR PRO ARG HIS LEU GLN LEU ALA ILE SEQRES 8 G 114 ARG GLY ASP GLU GLU LEU ASP SER LEU ILE LYS ALA THR SEQRES 9 G 114 ILE ALA GLY GLY GLU LYS ARG ARG CYS SER SEQRES 1 H 126 MET PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS SEQRES 2 H 126 GLY SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP SEQRES 3 H 126 GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER SEQRES 4 H 126 ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP SEQRES 5 H 126 THR GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER SEQRES 6 H 126 PHE VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SEQRES 7 H 126 SER ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SEQRES 8 H 126 SER ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO SEQRES 9 H 126 GLY GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS SEQRES 10 H 126 ALA VAL THR LYS TYR THR SER SER 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 HELIX 1 AA1 ARG A 63 ASP A 77 1 15 HELIX 2 AA2 GLN A 85 ALA A 114 1 30 HELIX 3 AA3 MET A 120 GLY A 132 1 13 HELIX 4 AA4 ASN B 25 ILE B 29 5 5 HELIX 5 AA5 THR B 30 GLY B 41 1 12 HELIX 6 AA6 ILE B 50 ALA B 76 1 27 HELIX 7 AA7 THR B 82 GLN B 93 1 12 HELIX 8 AA8 SER C 18 GLY C 24 1 7 HELIX 9 AA9 PRO C 28 THR C 38 1 11 HELIX 10 AB1 GLY C 47 ASP C 75 1 29 HELIX 11 AB2 THR C 82 ARG C 91 1 10 HELIX 12 AB3 ASP C 93 ILE C 100 1 8 HELIX 13 AB4 TYR D 37 HIS D 49 1 13 HELIX 14 AB5 SER D 55 ASN D 84 1 30 HELIX 15 AB6 THR D 90 LEU D 102 1 13 HELIX 16 AB7 PRO D 103 SER D 123 1 21 HELIX 17 AB8 ARG E 63 ASP E 77 1 15 HELIX 18 AB9 GLN E 85 ALA E 114 1 30 HELIX 19 AC1 MET E 120 GLY E 132 1 13 HELIX 20 AC2 ASN F 25 ILE F 29 5 5 HELIX 21 AC3 THR F 30 GLY F 41 1 12 HELIX 22 AC4 ILE F 50 ALA F 76 1 27 HELIX 23 AC5 THR F 82 GLN F 93 1 12 HELIX 24 AC6 SER G 18 GLY G 24 1 7 HELIX 25 AC7 PRO G 28 THR G 38 1 11 HELIX 26 AC8 GLY G 47 ASP G 75 1 29 HELIX 27 AC9 THR G 82 ARG G 91 1 10 HELIX 28 AD1 ASP G 93 ILE G 100 1 8 HELIX 29 AD2 TYR H 37 HIS H 49 1 13 HELIX 30 AD3 SER H 55 ASN H 84 1 30 HELIX 31 AD4 THR H 90 LEU H 102 1 13 HELIX 32 AD5 PRO H 103 SER H 123 1 21 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 ARG E 83 PHE E 84 0 SHEET 2 AA3 2 THR F 80 VAL F 81 1 O VAL F 81 N ARG E 83 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