PDB Short entry for 2L75 HEADER TRANSCRIPTION/NUCLEAR PROTEIN 02-DEC-10 2L75 TITLE SOLUTION STRUCTURE OF CHD4-PHD2 IN COMPLEX WITH H3K9ME3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD2 DOMAIN, UNP RESIDUES 446-501; COMPND 5 SYNONYM: CHD-4, ATP-DEPENDENT HELICASE CHD4, MI-2 AUTOANTIGEN 218 KDA COMPND 6 PROTEIN, MI2-BETA; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 14-MERIC PEPTIDE FROM 1HISTONE H3.1; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 2-14; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: H3K9ME3 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CHD4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-2TE; SOURCE 10 OTHER_DETAILS: A MODIFIED VERSION OF PGEX-2T CONTAINING A HRV SOURCE 11 PROTEASE CLEAVAGE SITE.; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 OTHER_DETAILS: CHEMICAL SYNTHESIZED KEYWDS CHD4, MI2B, PHD2, H3K9ME3, TRANSCRIPTION-NUCLEAR PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.E.MANSFIELD,A.H.KWAN,J.P.MACKAY REVDAT 5 14-JUN-23 2L75 1 REMARK LINK REVDAT 4 26-FEB-20 2L75 1 REMARK SEQADV LINK REVDAT 3 13-APR-11 2L75 1 JRNL REVDAT 2 23-FEB-11 2L75 1 JRNL REVDAT 1 19-JAN-11 2L75 0 JRNL AUTH R.E.MANSFIELD,C.A.MUSSELMAN,A.H.KWAN,S.S.OLIVER,A.L.GARSKE, JRNL AUTH 2 F.DAVRAZOU,J.M.DENU,T.G.KUTATELADZE,J.P.MACKAY JRNL TITL PLANT HOMEODOMAIN (PHD) FINGERS OF CHD4 ARE HISTONE JRNL TITL 2 H3-BINDING MODULES WITH PREFERENCE FOR UNMODIFIED H3K4 AND JRNL TITL 3 METHYLATED H3K9 JRNL REF J.BIOL.CHEM. V. 286 11779 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21278251 JRNL DOI 10.1074/JBC.M110.208207 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, ARIA REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), LINGE, O'DONOGHUE AND REMARK 3 NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L75 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000102041. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM CHD4-PHD2-1; 1 MM H3K9ME3 REMARK 210 -2, 20 UM DSS-3; 1 MM DTT-4; 5 REMARK 210 MM SODIUM CHLORIDE-5; 10 MM REMARK 210 SODIUM PHOSPHATE-6; 93% H2O/7% REMARK 210 D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] CHD4-PHD2-7; 1.1 MM H3K9ME3- REMARK 210 8; 20 UM DSS-9; 1 MM DTT-10; 5 REMARK 210 MM SODIUM CHLORIDE-11; 10 MM REMARK 210 SODIUM PHOSPHATE-12; 93% H2O/7% REMARK 210 D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] CHD4-PHD2-13; 1.1 MM REMARK 210 H3K9ME3-14; 20 UM DSS-15; 1 MM REMARK 210 DTT-16; 5 MM SODIUM CHLORIDE-17; REMARK 210 10 MM SODIUM PHOSPHATE-18; 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H COSY; REMARK 210 3D HNCA; 3D CBCA(CO)NH; 3D HNHA; REMARK 210 3D HBHA(CO)NH; 3D HNCO; 3D HN(CA) REMARK 210 CO; 3D HCCH-TOCSY; 3D CC(CO)NH REMARK 210 TOCSY; 2D-HIS HSQC; (HB)CB(CGCD) REMARK 210 HD; (HB)CB(CGCDCE)HE; 3D 1H-15N REMARK 210 NOESY; 3D 1H-15N TOCSY; 2D 1H-1H REMARK 210 NOESY; 3D 1H-13C NOESY; 15N-13C REMARK 210 DHF NOESY; 13C-13C DHF NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, TALOS, CYANA, REMARK 210 ARIA, PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 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: A, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 82 REMARK 465 PRO A 83 REMARK 465 LEU A 84 REMARK 465 GLY A 85 REMARK 465 SER A 86 REMARK 465 GLY B 155 REMARK 465 GLY B 156 REMARK 465 TYR B 157 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HB3 CYS A 104 HB3 ARG B 145 1.32 REMARK 500 HA2 GLY A 100 HD2 ARG B 151 1.33 REMARK 500 H GLY A 99 HA ARG B 151 1.34 REMARK 500 O LYS A 97 HM11 M3L B 152 1.55 REMARK 500 OD2 ASP A 87 HZ1 LYS B 147 1.57 REMARK 500 HZ3 LYS A 140 OXT LYS A 142 1.59 REMARK 500 O LYS A 97 HM13 M3L B 152 1.59 REMARK 500 O LYS A 97 CM1 M3L B 152 1.63 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 PRO A 109 40.11 -77.91 REMARK 500 1 LEU A 117 -166.10 -100.23 REMARK 500 1 THR B 149 -96.48 -129.28 REMARK 500 2 HIS A 88 -36.29 167.11 REMARK 500 2 PRO A 109 36.79 -80.03 REMARK 500 2 LEU A 117 -169.59 -100.40 REMARK 500 2 ARG B 145 139.37 69.23 REMARK 500 2 GLN B 148 81.55 -152.42 REMARK 500 2 THR B 149 -107.58 -102.55 REMARK 500 3 PRO A 109 44.58 -72.84 REMARK 500 3 LEU A 117 -165.40 -102.54 REMARK 500 3 PRO A 132 -5.31 -59.87 REMARK 500 3 PRO A 137 -148.99 -84.32 REMARK 500 3 THR B 149 -143.75 -131.40 REMARK 500 4 PRO A 109 29.20 -75.66 REMARK 500 4 LEU A 117 -167.90 -100.65 REMARK 500 4 ARG B 145 140.27 71.55 REMARK 500 4 THR B 149 -139.87 -103.58 REMARK 500 4 M3L B 152 34.98 -88.84 REMARK 500 5 HIS A 88 -44.07 174.72 REMARK 500 5 MET A 90 151.12 -46.36 REMARK 500 5 PHE A 92 146.84 -173.55 REMARK 500 5 PRO A 109 40.76 -79.67 REMARK 500 5 LYS A 140 95.70 -69.98 REMARK 500 5 LYS B 147 -165.87 -109.83 REMARK 500 5 GLN B 148 66.08 -171.66 REMARK 500 5 THR B 149 -112.47 -85.09 REMARK 500 6 GLU A 91 28.61 -79.73 REMARK 500 6 PHE A 92 147.46 -171.62 REMARK 500 6 PRO A 109 37.71 -73.59 REMARK 500 6 ARG B 145 147.01 67.85 REMARK 500 6 GLN B 148 116.16 -165.16 REMARK 500 6 THR B 149 -142.72 -141.14 REMARK 500 7 PRO A 109 23.73 -73.30 REMARK 500 7 LEU A 117 -162.10 -101.18 REMARK 500 7 PRO A 119 89.94 -10.05 REMARK 500 7 ARG B 145 141.83 66.35 REMARK 500 7 THR B 149 -94.19 -117.73 REMARK 500 8 HIS A 88 108.69 -57.00 REMARK 500 8 GLU A 91 30.64 -92.02 REMARK 500 8 PHE A 92 145.48 -175.79 REMARK 500 8 PRO A 109 37.77 -74.84 REMARK 500 8 THR B 149 -137.06 -115.55 REMARK 500 8 M3L B 152 45.75 -82.16 REMARK 500 9 GLU A 91 30.29 -89.27 REMARK 500 9 PHE A 92 149.35 -173.55 REMARK 500 9 PRO A 137 40.82 -84.22 REMARK 500 9 LYS B 147 -165.20 -123.94 REMARK 500 9 GLN B 148 55.49 179.78 REMARK 500 9 THR B 149 -60.49 -90.37 REMARK 500 REMARK 500 THIS ENTRY HAS 115 RAMACHANDRAN OUTLIERS. 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 A 155 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 93 SG REMARK 620 2 CYS A 96 SG 110.2 REMARK 620 3 HIS A 113 ND1 107.4 112.1 REMARK 620 4 CYS A 116 SG 112.4 107.5 107.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 156 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 105 SG REMARK 620 2 CYS A 108 SG 109.3 REMARK 620 3 CYS A 131 SG 109.0 109.2 REMARK 620 4 CYS A 134 SG 108.4 111.4 109.7 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 A 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 156 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17344 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE C-TERMINAL TYR OF H3K9ME3 IS NON-NATIVE, AND WAS ADDED TO REMARK 999 ASSIST IN PEPTIDE CONCENTRATION DETERMINATION BY A280. DBREF 2L75 A 87 142 UNP Q14839 CHD4_HUMAN 446 501 DBREF 2L75 B 144 156 UNP P68431 H31_HUMAN 2 14 SEQADV 2L75 GLY A 82 UNP Q14839 EXPRESSION TAG SEQADV 2L75 PRO A 83 UNP Q14839 EXPRESSION TAG SEQADV 2L75 LEU A 84 UNP Q14839 EXPRESSION TAG SEQADV 2L75 GLY A 85 UNP Q14839 EXPRESSION TAG SEQADV 2L75 SER A 86 UNP Q14839 EXPRESSION TAG SEQADV 2L75 TYR B 157 UNP P68431 SEE REMARK 999 SEQRES 1 A 61 GLY PRO LEU GLY SER ASP HIS HIS MET GLU PHE CYS ARG SEQRES 2 A 61 VAL CYS LYS ASP GLY GLY GLU LEU LEU CYS CYS ASP THR SEQRES 3 A 61 CYS PRO SER SER TYR HIS ILE HIS CYS LEU ASN PRO PRO SEQRES 4 A 61 LEU PRO GLU ILE PRO ASN GLY GLU TRP LEU CYS PRO ARG SEQRES 5 A 61 CYS THR CYS PRO ALA LEU LYS GLY LYS SEQRES 1 B 14 ALA ARG THR LYS GLN THR ALA ARG M3L SER THR GLY GLY SEQRES 2 B 14 TYR MODRES 2L75 M3L B 152 LYS N-TRIMETHYLLYSINE HET M3L B 152 31 HET ZN A 155 1 HET ZN A 156 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 ZN 2(ZN 2+) SHEET 1 A 3 SER A 111 TYR A 112 0 SHEET 2 A 3 GLU A 101 CYS A 104 -1 N LEU A 103 O TYR A 112 SHEET 3 A 3 ARG B 145 GLN B 148 -1 O ARG B 145 N CYS A 104 LINK C ARG B 151 N M3L B 152 1555 1555 1.32 LINK C M3L B 152 N SER B 153 1555 1555 1.32 LINK SG CYS A 93 ZN ZN A 155 1555 1555 2.30 LINK SG CYS A 96 ZN ZN A 155 1555 1555 2.29 LINK SG CYS A 105 ZN ZN A 156 1555 1555 2.30 LINK SG CYS A 108 ZN ZN A 156 1555 1555 2.30 LINK ND1 HIS A 113 ZN ZN A 155 1555 1555 1.99 LINK SG CYS A 116 ZN ZN A 155 1555 1555 2.28 LINK SG CYS A 131 ZN ZN A 156 1555 1555 2.30 LINK SG CYS A 134 ZN ZN A 156 1555 1555 2.30 SITE 1 AC1 4 CYS A 93 CYS A 96 HIS A 113 CYS A 116 SITE 1 AC2 4 CYS A 105 CYS A 108 CYS A 131 CYS A 134 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