HEADER GENE REGULATION 07-MAY-20 6WW4 TITLE CRYSTAL STRUCTURE OF HERC2 ZZ DOMAIN IN COMPLEX WITH HISTONE H3 TAIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.1,E3 UBIQUITIN-PROTEIN LIGASE HERC2; COMPND 3 CHAIN: B, A; COMPND 4 FRAGMENT: FUSION PROTEIN; COMPND 5 EC: 2.3.2.26; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: RESIDUES 1-6 OF THIS CONSTRUCT BELONG TO HISTONE H3 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, HERC2; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ZINC FINGER PROTEIN, HISTONE READER, HERC2, ZZ DOMAIN, GENE KEYWDS 2 REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,K.R.VANN,T.G.KUTATELADZE REVDAT 4 18-OCT-23 6WW4 1 REMARK REVDAT 3 11-NOV-20 6WW4 1 JRNL REVDAT 2 12-AUG-20 6WW4 1 JRNL REVDAT 1 05-AUG-20 6WW4 0 JRNL AUTH J.LIU,Z.XUE,Y.ZHANG,K.R.VANN,X.SHI,T.G.KUTATELADZE JRNL TITL STRUCTURAL INSIGHT INTO BINDING OF THE ZZ DOMAIN OF HERC2 TO JRNL TITL 2 HISTONE H3 AND SUMO1. JRNL REF STRUCTURE V. 28 1225 2020 JRNL REFN ISSN 0969-2126 JRNL PMID 32726574 JRNL DOI 10.1016/J.STR.2020.07.003 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 3 NUMBER OF REFLECTIONS : 5192 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 520 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.2100 - 3.5744 0.96 1255 140 0.1988 0.2386 REMARK 3 2 3.5744 - 2.8374 0.99 1285 143 0.1898 0.2287 REMARK 3 3 2.8374 - 2.4788 0.98 1264 141 0.2062 0.2542 REMARK 3 4 2.4788 - 2.2522 0.67 868 96 0.2109 0.3044 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 934 REMARK 3 ANGLE : 0.850 1244 REMARK 3 CHIRALITY : 0.047 126 REMARK 3 PLANARITY : 0.005 164 REMARK 3 DIHEDRAL : 21.114 558 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6WW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000249065. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOXDS REMARK 200 DATA SCALING SOFTWARE : AUTOXDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5256 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.15700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6DS6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM ACETATE, 0.1 M BIS REMARK 280 -TRIS, PH 5.5, AND 17% PEG 10000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 38.21950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS B 4 CG CD CE NZ REMARK 480 GLN B 5 CG CD OE1 NE2 REMARK 480 LYS B 2737 CG CD CE NZ REMARK 480 ASN B 2751 CB CG OD1 ND2 REMARK 480 LYS A 4 CA CB CG CD CE NZ REMARK 480 ARG A 2744 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 2749 CD NE CZ NH1 NH2 REMARK 480 ASN A 2751 CB CG OD1 ND2 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 ASP B2728 60.37 -152.86 REMARK 500 HIS B2741 -131.28 -123.27 REMARK 500 HIS A2741 -62.88 -132.28 REMARK 500 ASN A2742 113.10 -169.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2924 DISTANCE = 6.38 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B2708 SG REMARK 620 2 CYS B2711 SG 106.0 REMARK 620 3 CYS B2732 SG 117.6 114.2 REMARK 620 4 CYS B2735 SG 99.1 113.0 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B2723 SG REMARK 620 2 CYS B2726 SG 118.2 REMARK 620 3 HIS B2741 NE2 122.1 99.0 REMARK 620 4 HIS B2745 ND1 100.5 103.6 112.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A2708 SG REMARK 620 2 CYS A2711 SG 108.9 REMARK 620 3 CYS A2732 SG 117.6 116.1 REMARK 620 4 CYS A2735 SG 98.3 108.9 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A2723 SG REMARK 620 2 CYS A2726 SG 124.0 REMARK 620 3 HIS A2741 NE2 111.9 107.5 REMARK 620 4 HIS A2745 ND1 100.8 111.6 97.8 REMARK 620 N 1 2 3 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 2-7 OF HISTONE H3 FUSED TO THE ZZ DOMAIN OF HERC2 DBREF 6WW4 B 1 6 UNP P68431 H31_HUMAN 2 7 DBREF 6WW4 B 2702 2751 UNP O95714 HERC2_HUMAN 2702 2751 DBREF 6WW4 A 1 6 UNP P68431 H31_HUMAN 2 7 DBREF 6WW4 A 2702 2751 UNP O95714 HERC2_HUMAN 2702 2751 SEQRES 1 B 56 ALA ARG THR LYS GLN THR ILE HIS PRO GLY VAL THR CYS SEQRES 2 B 56 ASP GLY CYS GLN MET PHE PRO ILE ASN GLY SER ARG PHE SEQRES 3 B 56 LYS CYS ARG ASN CYS ASP ASP PHE ASP PHE CYS GLU THR SEQRES 4 B 56 CYS PHE LYS THR LYS LYS HIS ASN THR ARG HIS THR PHE SEQRES 5 B 56 GLY ARG ILE ASN SEQRES 1 A 56 ALA ARG THR LYS GLN THR ILE HIS PRO GLY VAL THR CYS SEQRES 2 A 56 ASP GLY CYS GLN MET PHE PRO ILE ASN GLY SER ARG PHE SEQRES 3 A 56 LYS CYS ARG ASN CYS ASP ASP PHE ASP PHE CYS GLU THR SEQRES 4 A 56 CYS PHE LYS THR LYS LYS HIS ASN THR ARG HIS THR PHE SEQRES 5 A 56 GLY ARG ILE ASN HET ZN B2801 1 HET ZN B2802 1 HET GOL B2803 14 HET ZN A2801 1 HET ZN A2802 1 HET GOL A2803 14 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 4(ZN 2+) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 9 HOH *53(H2 O) HELIX 1 AA1 CYS B 2732 LYS B 2739 1 8 HELIX 2 AA2 CYS A 2732 LYS A 2739 1 8 SHEET 1 AA1 2 ILE B2702 HIS B2703 0 SHEET 2 AA1 2 ILE B2716 ASN B2717 -1 O ILE B2716 N HIS B2703 SHEET 1 AA2 3 ASP B2730 PHE B2731 0 SHEET 2 AA2 3 ARG B2720 CYS B2723 -1 N PHE B2721 O PHE B2731 SHEET 3 AA2 3 PHE B2747 ILE B2750 -1 O GLY B2748 N LYS B2722 SHEET 1 AA3 2 ILE A2702 HIS A2703 0 SHEET 2 AA3 2 ILE A2716 ASN A2717 -1 O ILE A2716 N HIS A2703 SHEET 1 AA4 3 ASP A2730 PHE A2731 0 SHEET 2 AA4 3 ARG A2720 CYS A2723 -1 N PHE A2721 O PHE A2731 SHEET 3 AA4 3 PHE A2747 ILE A2750 -1 O ILE A2750 N ARG A2720 LINK SG CYS B2708 ZN ZN B2801 1555 1555 2.22 LINK SG CYS B2711 ZN ZN B2801 1555 1555 2.32 LINK SG CYS B2723 ZN ZN B2802 1555 1555 2.28 LINK SG CYS B2726 ZN ZN B2802 1555 1555 2.31 LINK SG CYS B2732 ZN ZN B2801 1555 1555 2.35 LINK SG CYS B2735 ZN ZN B2801 1555 1555 2.23 LINK NE2 HIS B2741 ZN ZN B2802 1555 1555 2.05 LINK ND1 HIS B2745 ZN ZN B2802 1555 1555 2.17 LINK SG CYS A2708 ZN ZN A2801 1555 1555 2.32 LINK SG CYS A2711 ZN ZN A2801 1555 1555 2.32 LINK SG CYS A2723 ZN ZN A2802 1555 1555 2.26 LINK SG CYS A2726 ZN ZN A2802 1555 1555 2.21 LINK SG CYS A2732 ZN ZN A2801 1555 1555 2.31 LINK SG CYS A2735 ZN ZN A2801 1555 1555 2.39 LINK NE2 HIS A2741 ZN ZN A2802 1555 1555 2.15 LINK ND1 HIS A2745 ZN ZN A2802 1555 1555 2.03 CISPEP 1 PHE B 2714 PRO B 2715 0 -0.87 CISPEP 2 PHE A 2714 PRO A 2715 0 -4.57 CRYST1 24.933 76.439 33.012 90.00 102.52 90.00 P 1 21 1 4 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 0.040107 0.000000 0.008906 0.00000 SCALE2 0.000000 0.013082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031030 0.00000