PDB Short entry for 6E83 HEADER GENE REGULATION 27-JUL-18 6E83 TITLE SOLUTION STRUCTURE OF ZZZ3 ZZ DOMAIN IN COMPLEX WITH HISTONE H3 TAIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZZ-TYPE ZINC FINGER-CONTAINING PROTEIN 3; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HISTONE H3; COMPND 7 CHAIN: A; COMPND 8 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: ZZZ3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS ZZZ3, ZZ DOMAIN, HISTONE, CHROMATIN, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.ZHANG,T.G.KUTATELADZE REVDAT 2 03-OCT-18 6E83 1 JRNL REVDAT 1 19-SEP-18 6E83 0 JRNL AUTH W.MI,Y.ZHANG,J.LYU,X.WANG,Q.TONG,D.PENG,Y.XUE,A.H.TENCER, JRNL AUTH 2 H.WEN,W.LI,T.G.KUTATELADZE,X.SHI JRNL TITL THE ZZ-TYPE ZINC FINGER OF ZZZ3 MODULATES THE ATAC JRNL TITL 2 COMPLEX-MEDIATED HISTONE ACETYLATION AND GENE ACTIVATION. JRNL REF NAT COMMUN V. 9 3759 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30217978 JRNL DOI 10.1038/S41467-018-06247-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : D.A. CASE, I.Y. BEN-SHALOM, S.R. BROZELL, D.S. REMARK 3 CERUTTI, T.E. CHEATHAM, III, V.W.D. CRUZEIRO, T.A. REMARK 3 DARDEN, R.E. DUKE, D. GHOREISHI, M.K. GILSON, H. REMARK 3 GOHLKE, A.W. GOETZ, D. GREENE, R HARRIS, N. REMARK 3 HOMEYER, S. IZADI, A. KOVALENKO, T. KURTZMAN, T.S. REMARK 3 LEE, S. LEGRAND, P. LI, C. LIN, J. LIU, T. LUCHKO, REMARK 3 R. LUO, D.J. MERMELSTEIN, K.M. MERZ, Y. MIAO, G. REMARK 3 MONARD, C. NGUYEN, H. NGUYEN, I. OMELYAN, A. REMARK 3 ONUFRIEV, F. PAN, R. QI, D.R. ROE, A. ROITBERG, C. REMARK 3 SAGUI, S. SCHOTT-VERDUGO, J. SHEN, C.L. SIMMERLING, REMARK 3 J. SMITH, R. SALOMON-FERRER, J. SWAILS, R.C. REMARK 3 WALKER, J. WANG, H. WEI, R.M. WOLF, X. WU, L. XIAO, REMARK 3 D.M. YORK AND P.A. KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6E83 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000228930. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM [U-13C; U-15N] ZZ DOMAIN OF REMARK 210 ZZZ3, 10 MM HISTONE H3, 100 MM REMARK 210 SODIUM CHLORIDE, 20 MM TRIS, 7 % REMARK 210 [U-99% 2H] D2O, 90% H2O/10% D2O; REMARK 210 4 MM [U-13C; U-15N] ZZ DOMAIN OF REMARK 210 ZZZ3, 100 MM SODIUM CHLORIDE, 20 REMARK 210 MM TRIS, 7 % [U-99% 2H] D2O, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HNCACB; 2D 1H-1H TOCSY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-15N REMARK 210 NOESY; 3D FILTERED 1H-13C NOESY REMARK 210 ALIPHATIC; 3D FILTERED 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, NMRDRAW, ANALYSIS, X-PLOR REMARK 210 NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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: B, 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 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 A 8 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 ARG A 2 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG B 835 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 CYS B 841 CA - CB - SG ANGL. DEV. = 7.4 DEGREES REMARK 500 6 ARG B 835 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 7 ARG B 835 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 8 CYS B 841 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 10 ARG A 2 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG B 835 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 12 ARG B 835 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 12 CYS B 841 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 14 CYS B 841 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 14 ARG A 2 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG B 835 NE - CZ - NH1 ANGL. DEV. = -3.0 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 VAL B 819 98.65 -53.01 REMARK 500 1 LEU B 857 57.16 -141.13 REMARK 500 1 THR B 860 -156.78 -115.99 REMARK 500 1 ILE B 862 -44.26 -136.46 REMARK 500 2 LEU B 813 -128.23 55.40 REMARK 500 2 GLN B 817 98.96 -160.78 REMARK 500 2 VAL B 819 87.64 -52.88 REMARK 500 2 THR B 860 -167.03 -129.58 REMARK 500 2 ARG A 2 78.71 -69.65 REMARK 500 3 VAL B 819 106.09 -50.29 REMARK 500 3 MET B 845 50.51 -140.70 REMARK 500 3 LEU B 857 152.34 60.62 REMARK 500 3 THR B 860 -156.62 -128.43 REMARK 500 3 ILE B 862 -44.78 -132.77 REMARK 500 4 VAL B 819 72.71 -57.27 REMARK 500 4 LEU B 857 58.19 -141.29 REMARK 500 4 ASP B 861 -54.47 57.73 REMARK 500 4 ILE B 862 -36.99 -139.64 REMARK 500 5 VAL B 819 103.84 -49.48 REMARK 500 5 GLN B 839 0.92 -64.22 REMARK 500 5 LEU B 857 57.24 -150.61 REMARK 500 5 THR B 860 -156.58 -120.81 REMARK 500 5 ILE B 862 -42.64 -135.36 REMARK 500 5 THR A 6 -33.25 58.97 REMARK 500 6 VAL B 819 101.18 -49.86 REMARK 500 6 THR B 860 -156.10 -122.06 REMARK 500 6 ILE B 862 -43.26 -136.75 REMARK 500 7 VAL B 819 108.11 -47.86 REMARK 500 7 LEU B 857 56.12 -144.49 REMARK 500 7 THR B 860 -159.25 -125.93 REMARK 500 7 ILE B 862 -44.82 -135.61 REMARK 500 8 LEU B 813 -115.91 46.75 REMARK 500 8 VAL B 819 82.42 -56.53 REMARK 500 8 GLN B 839 1.86 -65.18 REMARK 500 8 SER B 846 79.26 -67.74 REMARK 500 8 LEU B 857 69.46 -153.09 REMARK 500 8 ILE B 862 -44.82 -134.12 REMARK 500 8 THR A 6 150.72 65.71 REMARK 500 9 VAL B 819 107.97 -48.14 REMARK 500 9 ASP B 861 -51.10 56.62 REMARK 500 9 ILE B 862 -42.37 -141.13 REMARK 500 10 VAL B 819 107.53 -49.87 REMARK 500 10 THR B 860 -157.45 -115.56 REMARK 500 10 ILE B 862 -44.63 -136.27 REMARK 500 10 THR A 6 -1.38 63.01 REMARK 500 10 LYS A 9 -26.97 64.08 REMARK 500 11 VAL B 819 102.08 -48.55 REMARK 500 11 GLN B 839 4.28 -63.09 REMARK 500 11 SER B 846 79.26 -67.73 REMARK 500 11 LEU B 857 57.41 -149.99 REMARK 500 REMARK 500 THIS ENTRY HAS 98 RAMACHANDRAN OUTLIERS. 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 9 HIS B 867 0.13 SIDE CHAIN REMARK 500 17 HIS B 867 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 B 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 823 SG REMARK 620 2 CYS B 826 SG 110.2 REMARK 620 3 CYS B 850 SG 112.2 106.6 REMARK 620 4 CYS B 853 SG 112.2 105.4 109.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 838 SG REMARK 620 2 CYS B 841 SG 123.9 REMARK 620 3 HIS B 863 ND1 109.7 105.7 REMARK 620 4 HIS B 867 NE2 100.6 113.0 101.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30501 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF ZZZ3 ZZ DOMAIN IN COMPLEX WITH HISTONE H3 TAIL DBREF 6E83 B 816 874 UNP Q8IYH5 ZZZ3_HUMAN 816 874 DBREF 6E83 A 1 12 PDB 6E83 6E83 1 12 SEQADV 6E83 GLY B 811 UNP Q8IYH5 EXPRESSION TAG SEQADV 6E83 PRO B 812 UNP Q8IYH5 EXPRESSION TAG SEQADV 6E83 LEU B 813 UNP Q8IYH5 EXPRESSION TAG SEQADV 6E83 GLY B 814 UNP Q8IYH5 EXPRESSION TAG SEQADV 6E83 SER B 815 UNP Q8IYH5 EXPRESSION TAG SEQRES 1 B 64 GLY PRO LEU GLY SER VAL GLN HIS VAL GLY PHE LYS CYS SEQRES 2 B 64 ASP ASN CYS GLY ILE GLU PRO ILE GLN GLY VAL ARG TRP SEQRES 3 B 64 HIS CYS GLN ASP CYS PRO PRO GLU MET SER LEU ASP PHE SEQRES 4 B 64 CYS ASP SER CYS SER ASP CYS LEU HIS GLU THR ASP ILE SEQRES 5 B 64 HIS LYS GLU ASP HIS GLN LEU GLU PRO ILE TYR ARG SEQRES 1 A 12 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY HET ZN B 101 1 HET ZN B 102 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 PRO B 842 SER B 846 5 5 SHEET 1 AA1 2 VAL B 816 GLN B 817 0 SHEET 2 AA1 2 GLN B 832 GLY B 833 -1 O GLY B 833 N VAL B 816 SHEET 1 AA2 3 ASP B 848 PHE B 849 0 SHEET 2 AA2 3 ARG B 835 CYS B 838 -1 N TRP B 836 O PHE B 849 SHEET 3 AA2 3 LEU B 869 ILE B 872 -1 O GLU B 870 N HIS B 837 LINK SG CYS B 823 ZN ZN B 101 1555 1555 2.13 LINK SG CYS B 826 ZN ZN B 101 1555 1555 2.13 LINK SG CYS B 838 ZN ZN B 102 1555 1555 2.11 LINK SG CYS B 841 ZN ZN B 102 1555 1555 2.13 LINK SG CYS B 850 ZN ZN B 101 1555 1555 2.13 LINK SG CYS B 853 ZN ZN B 101 1555 1555 2.13 LINK ND1 HIS B 863 ZN ZN B 102 1555 1555 2.05 LINK NE2 HIS B 867 ZN ZN B 102 1555 1555 2.03 SITE 1 AC1 4 CYS B 823 CYS B 826 CYS B 850 CYS B 853 SITE 1 AC2 4 CYS B 838 CYS B 841 HIS B 863 HIS B 867 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