HEADER NUCLEAR PROTEIN/NUCLEAR PROTEIN 28-MAR-16 2RVQ TITLE SOLUTION STRUCTURE OF THE ISOLATED HISTONE H2A-H2B HETERODIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H2A TYPE 1-B/E; COMPND 3 CHAIN: C; COMPND 4 SYNONYM: HISTONE H2A.2, HISTONE H2A/A, HISTONE H2A/M; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H2B TYPE 1-J; COMPND 8 CHAIN: D; COMPND 9 SYNONYM: HISTONE H2B.1, HISTONE H2B.R, H2B/R; COMPND 10 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: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-23B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: HIST1H2BJ, H2BFR; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PET-23B KEYWDS NUCLEOSOME, HISTONE, H2A, H2B, DNA BINDING PROTEIN, CS-ROSETTA, KEYWDS 2 NUCLEAR PROTEIN-NUCLEAR PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.MORIWAKI,T.YAMANE,H.OHTOMO,M.IKEGUCHI,J.KURITA,M.SATO,A.NAGADOI, AUTHOR 2 H.SHIMOJO,Y.NISHIMURA REVDAT 1 25-MAY-16 2RVQ 0 JRNL AUTH Y.MORIWAKI,T.YAMANE,H.OHTOMO,M.IKEGUCHI,J.KURITA,M.SATO, JRNL AUTH 2 A.NAGADOI,H.SHIMOJO,Y.NISHIMURA JRNL TITL SOLUTION STRUCTURE OF THE ISOLATED HISTONE H2A-H2B JRNL TITL 2 HETERODIMER JRNL REF SCI REP V. 6 24999 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27181506 JRNL DOI 10.1038/SREP24999 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CS-ROSETTA REMARK 3 AUTHORS : SHEN, VERNON, BAKER AND BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE OF THE CORE REGIONS OF REMARK 3 H2A(VAL27-LEU96) AND H2B (SER38-LYS125) CONNECTED BY A RANDOM REMARK 3 COIL (GLY)16 POLY-GLYCINE LINKER WAS MODELED BY CS-ROSETTA- REMARK 3 ABINITIORELAX PROTOCOL.IN TOTAL 10,000 MODELS WERE GENERATED AND REMARK 3 SELECTED THE 10 MODELS WITH THE LOWEST CA-RMSD FROM THE 20 MODELS REMARK 3 WITH THE LOWEST CS-ROSETTA ENERGY., AFTER THE (GLY)16 POLY- REMARK 3 GLYCINE LINKER WAS REMOVED FROM EACH OF THE 10 SELECTED REMARK 3 STRUCTURES OF THE H2A-H2B CORE, THE FLEXIBLE TAILS OF H2A (GLY(- REMARK 3 3)-PRO26 AND LEU97-LYS129) AND H2B (GLY(-3)-TYR37) WERE CONNECTED REMARK 3 BY USING MODELLER PROGRAM. NEXT, FOR EACH OF THE THREE FLEXIBLE REMARK 3 TAILS,CS-ROSETTA-FLOPPYTAIL PROTOCOL WAS USED TO GENERATE 10,000 REMARK 3 MODELS FOR EACH OF THE 10 SELECTED CORE STRUCTURES, AND SELECTED REMARK 3 ONE MODEL WITH THE LOWEST KAI2 VALUES OF CHEMICAL SHIFTS. REMARK 4 REMARK 4 2RVQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAR-16. REMARK 100 THE RCSB ID CODE IS RCSB150324. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 400 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.1-0.3 MM [U-13C; U-15N; U-2H] REMARK 210 ENTITY_1-1, 0.1-0.3 MM [U-13C; U- REMARK 210 15N; U-2H] ENTITY_2-2, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TROSY-HN(CO)CACB; TROSY-HNCACB; REMARK 210 TROSY-HN(CA)CO; TROSY-HNCO; REMARK 210 HCCCONH; TROSY-1H-15N HSQC; TROSY REMARK 210 -1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CS-ROSETTA REMARK 210 METHOD USED : CS-ROSETTA-ABINITIORELAX, CS- REMARK 210 ROSETTA-FLOPPYTAIL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 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 1 ARG D 79 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG D 33 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG D 86 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 3 ARG D 72 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG D 79 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG C 71 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG C 71 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG C 32 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG D 79 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG C 99 NE - CZ - NH1 ANGL. DEV. = 3.2 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 1 LEU D 102 78.56 -115.69 REMARK 500 1 HIS D 109 -71.07 -66.04 REMARK 500 2 LEU C 96 -73.32 -76.15 REMARK 500 2 TYR D 40 34.16 -98.96 REMARK 500 2 ASP D 68 -63.82 -106.10 REMARK 500 3 LEU C 97 -161.02 -114.50 REMARK 500 4 SER D 36 -104.83 -135.19 REMARK 500 5 LYS D 20 64.35 39.83 REMARK 500 5 LYS D 34 106.50 53.10 REMARK 500 5 TYR D 37 142.78 47.72 REMARK 500 6 VAL C 114 119.63 60.83 REMARK 500 6 TYR D 37 36.77 -72.98 REMARK 500 7 LYS D 27 48.87 -80.08 REMARK 500 7 SER D 38 -48.06 -179.70 REMARK 500 8 LYS D 11 -120.48 -94.81 REMARK 500 8 LYS D 28 152.17 60.87 REMARK 500 8 TYR D 37 -154.85 -98.43 REMARK 500 8 SER D 38 -35.97 68.14 REMARK 500 9 VAL C 27 -25.44 64.09 REMARK 500 9 SER D 38 -29.49 67.75 REMARK 500 9 LEU D 102 68.19 -116.14 REMARK 500 10 LEU C 96 -97.80 -91.12 REMARK 500 10 LYS D 27 109.59 -56.63 REMARK 500 10 SER D 36 142.36 78.88 REMARK 500 10 SER D 38 -60.42 -163.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER D 36 TYR D 37 2 -122.57 REMARK 500 SER D 36 TYR D 37 5 135.41 REMARK 500 SER D 36 TYR D 37 10 -137.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR D 40 0.07 SIDE CHAIN REMARK 500 2 TYR D 37 0.16 SIDE CHAIN REMARK 500 5 ARG C 99 0.08 SIDE CHAIN REMARK 500 5 TYR D 37 0.07 SIDE CHAIN REMARK 500 10 TYR D 40 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 10 SER D 36 23.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11609 RELATED DB: BMRB DBREF 2RVQ C 0 129 UNP P04908 H2A1B_HUMAN 1 130 DBREF 2RVQ D 0 125 UNP P06899 H2B1J_HUMAN 1 126 SEQADV 2RVQ GLY C -3 UNP P04908 EXPRESSION TAG SEQADV 2RVQ PRO C -2 UNP P04908 EXPRESSION TAG SEQADV 2RVQ GLY C -1 UNP P04908 EXPRESSION TAG SEQADV 2RVQ GLY D -3 UNP P06899 EXPRESSION TAG SEQADV 2RVQ PRO D -2 UNP P06899 EXPRESSION TAG SEQADV 2RVQ GLY D -1 UNP P06899 EXPRESSION TAG SEQRES 1 C 133 GLY PRO GLY 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 PRO GLY 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 HELIX 1 1 PRO C 26 ASN C 38 1 13 HELIX 2 2 ALA C 45 ASN C 73 1 29 HELIX 3 3 ILE C 79 ASP C 90 1 12 HELIX 4 4 ASP C 90 LEU C 97 1 8 HELIX 5 5 TYR D 37 HIS D 49 1 13 HELIX 6 6 SER D 55 ASN D 84 1 30 HELIX 7 7 ARG D 92 LEU D 102 1 11 HELIX 8 8 GLY D 104 VAL D 111 1 8 HELIX 9 9 VAL D 111 ALA D 124 1 14 SHEET 1 A 2 ARG C 77 ILE C 78 0 SHEET 2 A 2 GLY D 53 ILE D 54 1 O GLY D 53 N ILE C 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 MODEL 1