HEADER DNA BINDING PROTEIN/DNA 28-AUG-24 9JC6 TITLE HUMAN H2BW2 NUCLEOSOME 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 TYPE 1-B/E; COMPND 14 CHAIN: C, G; COMPND 15 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: ISOFORM 2 OF HISTONE H2B TYPE F-M; COMPND 19 CHAIN: D, H; COMPND 20 SYNONYM: HISTONE H2B.S,H2B/S; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 5; COMPND 23 MOLECULE: 147-MER DNA; COMPND 24 CHAIN: I; COMPND 25 ENGINEERED: YES; COMPND 26 OTHER_DETAILS: 601 DNA; COMPND 27 MOL_ID: 6; COMPND 28 MOLECULE: 147-MER DNA; COMPND 29 CHAIN: J; COMPND 30 ENGINEERED: YES; COMPND 31 OTHER_DETAILS: 601 REVERSE COMPLEMENTARY 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 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, SOURCE 16 H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, SOURCE 17 HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, SOURCE 18 H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, SOURCE 19 H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, SOURCE 20 H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, SOURCE 21 H4-16, HIST4H4; SOURCE 22 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 24 MOL_ID: 3; SOURCE 25 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 26 ORGANISM_COMMON: HUMAN; SOURCE 27 ORGANISM_TAXID: 9606; SOURCE 28 GENE: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE; SOURCE 29 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 30 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 31 MOL_ID: 4; SOURCE 32 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 33 ORGANISM_COMMON: HUMAN; SOURCE 34 ORGANISM_TAXID: 9606; SOURCE 35 GENE: H2BW2, H2BFM; SOURCE 36 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 37 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 38 MOL_ID: 5; SOURCE 39 SYNTHETIC: YES; SOURCE 40 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 41 ORGANISM_TAXID: 32630; SOURCE 42 MOL_ID: 6; SOURCE 43 SYNTHETIC: YES; SOURCE 44 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 45 ORGANISM_TAXID: 32630 KEYWDS NUCLEOSOME, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR D.B.DING,T.ISHIBASHI,T.T.NGUYEN REVDAT 2 24-SEP-25 9JC6 1 JRNL REVDAT 1 03-SEP-25 9JC6 0 JRNL AUTH A.T.T.NGUYEN,D.DING,X.BAI,M.Y.H.PANG,M.DENG,Y.LIU,T.JIN, JRNL AUTH 2 Z.XU,Y.ZHANG,Y.ZHAI,Y.YAN,T.ISHIBASHI JRNL TITL H2B.W2, A SPERMATOCYTE-SPECIFIC HISTONE VARIANT, DISRUPTS JRNL TITL 2 NUCLEOSOME STABILITY, AND REDUCES CHROMATIN COMPACTION. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40874595 JRNL DOI 10.1093/NAR/GKAF825 REMARK 2 REMARK 2 RESOLUTION. 3.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, PHENIX, COOT REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.340 REMARK 3 NUMBER OF PARTICLES : 127551 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 9JC6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1300050874. 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 : HUMAN H2BW2 NUCLEOSOME WITH 601 REMARK 245 DNA SEQUENCE 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 : TFS TITAN THEMIS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 250.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1100.00 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 : 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 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 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 GLY B 102 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 ARG C 11 REMARK 465 ALA C 12 REMARK 465 LYS C 13 REMARK 465 ALA C 14 REMARK 465 LYS C 118 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 ALA D 7 REMARK 465 GLU D 8 REMARK 465 ALA D 9 REMARK 465 SER D 10 REMARK 465 SER D 11 REMARK 465 GLU D 12 REMARK 465 THR D 13 REMARK 465 THR D 14 REMARK 465 SER D 15 REMARK 465 GLU D 16 REMARK 465 GLU D 17 REMARK 465 GLY D 18 REMARK 465 GLN D 19 REMARK 465 SER D 20 REMARK 465 ILE D 21 REMARK 465 GLN D 22 REMARK 465 GLU D 23 REMARK 465 PRO D 24 REMARK 465 LYS D 25 REMARK 465 GLU D 26 REMARK 465 ALA D 27 REMARK 465 ASN D 28 REMARK 465 SER D 29 REMARK 465 THR D 30 REMARK 465 LYS D 31 REMARK 465 ALA D 32 REMARK 465 GLN D 33 REMARK 465 LYS D 34 REMARK 465 GLN D 35 REMARK 465 LYS D 36 REMARK 465 ARG D 37 REMARK 465 ARG D 38 REMARK 465 GLY D 39 REMARK 465 CYS D 40 REMARK 465 ARG D 41 REMARK 465 GLY D 42 REMARK 465 SER D 43 REMARK 465 ARG D 44 REMARK 465 ARG D 45 REMARK 465 ARG D 46 REMARK 465 HIS D 47 REMARK 465 ALA D 48 REMARK 465 ASN D 49 REMARK 465 ARG D 50 REMARK 465 ARG D 51 REMARK 465 GLY D 52 REMARK 465 ASP D 53 REMARK 465 SER D 54 REMARK 465 GLN D 151 REMARK 465 ARG D 152 REMARK 465 LYS D 153 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 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 GLY F 102 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 ARG G 11 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 ALA H 7 REMARK 465 GLU H 8 REMARK 465 ALA H 9 REMARK 465 SER H 10 REMARK 465 SER H 11 REMARK 465 GLU H 12 REMARK 465 THR H 13 REMARK 465 THR H 14 REMARK 465 SER H 15 REMARK 465 GLU H 16 REMARK 465 GLU H 17 REMARK 465 GLY H 18 REMARK 465 GLN H 19 REMARK 465 SER H 20 REMARK 465 ILE H 21 REMARK 465 GLN H 22 REMARK 465 GLU H 23 REMARK 465 PRO H 24 REMARK 465 LYS H 25 REMARK 465 GLU H 26 REMARK 465 ALA H 27 REMARK 465 ASN H 28 REMARK 465 SER H 29 REMARK 465 THR H 30 REMARK 465 LYS H 31 REMARK 465 ALA H 32 REMARK 465 GLN H 33 REMARK 465 LYS H 34 REMARK 465 GLN H 35 REMARK 465 LYS H 36 REMARK 465 ARG H 37 REMARK 465 ARG H 38 REMARK 465 GLY H 39 REMARK 465 CYS H 40 REMARK 465 ARG H 41 REMARK 465 GLY H 42 REMARK 465 SER H 43 REMARK 465 ARG H 44 REMARK 465 ARG H 45 REMARK 465 ARG H 46 REMARK 465 HIS H 47 REMARK 465 ALA H 48 REMARK 465 ASN H 49 REMARK 465 ARG H 50 REMARK 465 ARG H 51 REMARK 465 GLY H 52 REMARK 465 ASP H 53 REMARK 465 SER H 54 REMARK 465 PHE H 55 REMARK 465 ALA H 147 REMARK 465 ILE H 148 REMARK 465 TRP H 149 REMARK 465 GLN H 150 REMARK 465 GLN H 151 REMARK 465 ARG H 152 REMARK 465 LYS H 153 REMARK 465 DA I -73 REMARK 465 DT I -72 REMARK 465 DC I -71 REMARK 465 DG I -70 REMARK 465 DA I -69 REMARK 465 DG I -68 REMARK 465 DA I -67 REMARK 465 DA I -66 REMARK 465 DT I -65 REMARK 465 DC I -64 REMARK 465 DC I -63 REMARK 465 DC I -62 REMARK 465 DG I -61 REMARK 465 DG I -60 REMARK 465 DT I 73 REMARK 465 DA J -73 REMARK 465 DC J 60 REMARK 465 DC J 61 REMARK 465 DG J 62 REMARK 465 DG J 63 REMARK 465 DG J 64 REMARK 465 DA J 65 REMARK 465 DT J 66 REMARK 465 DT J 67 REMARK 465 DC J 68 REMARK 465 DT J 69 REMARK 465 DC J 70 REMARK 465 DG J 71 REMARK 465 DA J 72 REMARK 465 DT J 73 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DT J -72 P OP1 OP2 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 NE2 GLN D 101 OH TYR D 105 1.58 REMARK 500 N2 DG I 71 O2 DC J -71 2.10 REMARK 500 OG SER A 57 OE1 GLU A 59 2.13 REMARK 500 OG1 THR G 76 OP1 DG I 58 2.19 REMARK 500 OG SER C 40 O VAL D 109 2.19 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 -50 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC I -21 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG J 48 O4' - C1' - N9 ANGL. DEV. = 1.9 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 -2.75 67.64 REMARK 500 PRO D 61 2.25 -68.23 REMARK 500 LYS D 107 -8.08 73.00 REMARK 500 PRO D 125 -175.24 -69.49 REMARK 500 ASP E 81 57.53 34.87 REMARK 500 ASP F 24 66.61 60.03 REMARK 500 LYS G 13 -8.37 72.48 REMARK 500 ARG G 99 31.00 -97.83 REMARK 500 GLN G 104 19.46 59.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61358 RELATED DB: EMDB REMARK 900 HUMAN H2BW2 NUCLEOSOME DBREF 9JC6 A 1 135 UNP P68431 H31_HUMAN 2 136 DBREF 9JC6 B 1 102 UNP P62805 H4_HUMAN 2 103 DBREF 9JC6 C 1 129 UNP P04908 H2A1B_HUMAN 2 130 DBREF 9JC6 D 7 153 UNP P0C1H6 H2BFM_HUMAN 2 148 DBREF 9JC6 E 1 135 UNP P68431 H31_HUMAN 2 136 DBREF 9JC6 F 1 102 UNP P62805 H4_HUMAN 2 103 DBREF 9JC6 G 1 129 UNP P04908 H2A1B_HUMAN 2 130 DBREF 9JC6 H 7 153 UNP P0C1H6 H2BFM_HUMAN 2 148 DBREF 9JC6 I -73 73 PDB 9JC6 9JC6 -73 73 DBREF 9JC6 J -73 73 PDB 9JC6 9JC6 -73 73 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 CYS GLU ALA TYR LEU VAL GLY LEU PHE SEQRES 9 A 135 GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS 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 102 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 B 102 GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN ILE SEQRES 3 B 102 GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA ARG SEQRES 4 B 102 ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR GLU SEQRES 5 B 102 GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN VAL SEQRES 6 B 102 ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS ARG SEQRES 7 B 102 LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU LYS SEQRES 8 B 102 ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 C 129 SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA LYS SEQRES 2 C 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 C 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 C 129 SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 C 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 C 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 C 129 ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU SEQRES 8 C 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 C 129 GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO SEQRES 10 C 129 LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 D 147 ALA GLU ALA SER SER GLU THR THR SER GLU GLU GLY GLN SEQRES 2 D 147 SER ILE GLN GLU PRO LYS GLU ALA ASN SER THR LYS ALA SEQRES 3 D 147 GLN LYS GLN LYS ARG ARG GLY CYS ARG GLY SER ARG ARG SEQRES 4 D 147 ARG HIS ALA ASN ARG ARG GLY ASP SER PHE GLY ASP SER SEQRES 5 D 147 PHE THR PRO TYR PHE PRO ARG VAL LEU LYS GLN VAL HIS SEQRES 6 D 147 GLN GLY LEU SER LEU SER GLN GLU ALA VAL SER VAL MET SEQRES 7 D 147 ASP SER MET ILE HIS ASP ILE LEU ASP ARG ILE ALA THR SEQRES 8 D 147 GLU ALA GLY GLN LEU ALA HIS TYR THR LYS ARG VAL THR SEQRES 9 D 147 ILE THR SER ARG ASP ILE GLN MET ALA VAL ARG LEU LEU SEQRES 10 D 147 LEU PRO GLY LYS MET GLY LYS LEU ALA GLU ALA GLN GLY SEQRES 11 D 147 THR ASN ALA ALA LEU ARG THR SER LEU CYS ALA ILE TRP SEQRES 12 D 147 GLN GLN ARG LYS SEQRES 1 E 135 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 E 135 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 E 135 LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO HIS SEQRES 4 E 135 ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE ARG SEQRES 5 E 135 ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS LEU SEQRES 6 E 135 PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP PHE SEQRES 7 E 135 LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET ALA SEQRES 8 E 135 LEU GLN GLU ALA CYS GLU ALA TYR LEU VAL GLY LEU PHE SEQRES 9 E 135 GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS ARG VAL SEQRES 10 E 135 THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG ILE SEQRES 11 E 135 ARG GLY GLU ARG ALA SEQRES 1 F 102 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 F 102 GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN ILE SEQRES 3 F 102 GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA ARG SEQRES 4 F 102 ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR GLU SEQRES 5 F 102 GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN VAL SEQRES 6 F 102 ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS ARG SEQRES 7 F 102 LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU LYS SEQRES 8 F 102 ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 G 129 SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA LYS SEQRES 2 G 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 G 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 G 129 SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 G 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 G 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 G 129 ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU SEQRES 8 G 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 G 129 GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO SEQRES 10 G 129 LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 H 147 ALA GLU ALA SER SER GLU THR THR SER GLU GLU GLY GLN SEQRES 2 H 147 SER ILE GLN GLU PRO LYS GLU ALA ASN SER THR LYS ALA SEQRES 3 H 147 GLN LYS GLN LYS ARG ARG GLY CYS ARG GLY SER ARG ARG SEQRES 4 H 147 ARG HIS ALA ASN ARG ARG GLY ASP SER PHE GLY ASP SER SEQRES 5 H 147 PHE THR PRO TYR PHE PRO ARG VAL LEU LYS GLN VAL HIS SEQRES 6 H 147 GLN GLY LEU SER LEU SER GLN GLU ALA VAL SER VAL MET SEQRES 7 H 147 ASP SER MET ILE HIS ASP ILE LEU ASP ARG ILE ALA THR SEQRES 8 H 147 GLU ALA GLY GLN LEU ALA HIS TYR THR LYS ARG VAL THR SEQRES 9 H 147 ILE THR SER ARG ASP ILE GLN MET ALA VAL ARG LEU LEU SEQRES 10 H 147 LEU PRO GLY LYS MET GLY LYS LEU ALA GLU ALA GLN GLY SEQRES 11 H 147 THR ASN ALA ALA LEU ARG THR SER LEU CYS ALA ILE TRP SEQRES 12 H 147 GLN GLN ARG 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 GLY A 44 SER A 57 1 14 HELIX 2 AA2 ARG A 63 GLN A 76 1 14 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 ARG B 23 ILE B 29 5 7 HELIX 6 AA6 THR B 30 GLY B 42 1 13 HELIX 7 AA7 LEU B 49 LYS B 77 1 29 HELIX 8 AA8 THR B 82 GLY B 94 1 13 HELIX 9 AA9 THR C 16 ALA C 21 1 6 HELIX 10 AB1 PRO C 26 ASN C 38 1 13 HELIX 11 AB2 GLY C 46 ASP C 72 1 27 HELIX 12 AB3 ILE C 79 ASN C 89 1 11 HELIX 13 AB4 ASP C 90 LEU C 97 1 8 HELIX 14 AB5 GLN C 112 LEU C 116 5 5 HELIX 15 AB6 PHE D 63 LYS D 68 1 6 HELIX 16 AB7 SER D 77 THR D 106 1 30 HELIX 17 AB8 THR D 112 LEU D 124 1 13 HELIX 18 AB9 PRO D 125 CYS D 146 1 22 HELIX 19 AC1 GLY E 44 ARG E 53 1 10 HELIX 20 AC2 ARG E 63 ASP E 77 1 15 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 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 ASP G 72 1 28 HELIX 30 AD3 ILE G 79 ASN G 89 1 11 HELIX 31 AD4 ASP G 90 GLY G 98 1 9 HELIX 32 AD5 GLN G 112 LEU G 116 5 5 HELIX 33 AD6 TYR H 62 GLN H 69 1 8 HELIX 34 AD7 GLU H 79 HIS H 104 1 26 HELIX 35 AD8 THR H 112 LEU H 124 1 13 HELIX 36 AD9 PRO H 125 CYS H 146 1 22 SHEET 1 AA1 2 THR A 118 ILE A 119 0 SHEET 2 AA1 2 ARG B 45 ILE B 46 1 O ARG B 45 N ILE A 119 SHEET 1 AA2 2 THR B 96 LEU B 97 0 SHEET 2 AA2 2 VAL G 100 THR G 101 1 O THR G 101 N THR B 96 SHEET 1 AA3 2 ARG C 42 VAL C 43 0 SHEET 2 AA3 2 THR D 110 ILE D 111 1 O ILE D 111 N ARG C 42 SHEET 1 AA4 2 ARG C 77 ILE C 78 0 SHEET 2 AA4 2 SER D 75 LEU D 76 1 O SER D 75 N ILE C 78 SHEET 1 AA5 2 VAL C 100 THR C 101 0 SHEET 2 AA5 2 THR F 96 LEU F 97 1 O THR F 96 N THR C 101 SHEET 1 AA6 2 ARG E 83 PHE E 84 0 SHEET 2 AA6 2 THR F 80 VAL F 81 1 O VAL F 81 N ARG E 83 SHEET 1 AA7 2 THR E 118 ILE E 119 0 SHEET 2 AA7 2 ARG F 45 ILE F 46 1 O ARG F 45 N ILE E 119 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 TER 802 ARG A 134 TER 1436 GLY B 101 TER 2233 PRO C 117 TER 2977 GLN D 150 TER 3777 ALA E 135 TER 4446 GLY F 101 TER 5271 LYS G 118 TER 5968 CYS H 146 TER 8657 DA I 72 TER 11379 DA J 59 MASTER 476 0 0 36 14 0 0 611369 10 0 106 END