HEADER METAL-BINDING PROTEIN/NUCLEAR PROTEIN 24-MAR-10 2RR4 TITLE COMPLEX STRUCTURE OF THE ZF-CW DOMAIN AND THE H3K4ME3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER CW-TYPE PWWP DOMAIN PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZF-CW DOMAIN, RESIDUES 246-307; COMPND 5 SYNONYM: ZF-CW; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HISTONE H3; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: HISTONE H3 TAIL, UNP RESIDUES 2-11; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: H3K4ME3 PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ZCWPW1; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHSIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P060116-12; SOURCE 9 OTHER_DETAILS: E. COLI - CELL FREE; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 OTHER_DETAILS: CHEMICAL SYNTHESIZED, PURCHASED KEYWDS ZF-CW DOMAIN, ZCWPW1, ZINC-FINGER, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 2 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, METAL-BINDING KEYWDS 4 PROTEIN-NUCLEAR PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.HE,Y.MUTO,M.INOUE,T.KIGAWA,M.SHIROUZU,T.TERADA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 2 29-SEP-10 2RR4 1 JRNL REVDAT 1 15-SEP-10 2RR4 0 JRNL AUTH F.HE,T.UMEHARA,K.SAITO,T.HARADA,S.WATANABE,T.YABUKI, JRNL AUTH 2 T.KIGAWA,M.TAKAHASHI,K.KUWASAKO,K.TSUDA,T.MATSUDA,M.AOKI, JRNL AUTH 3 E.SEKI,N.KOBAYASHI,P.GUNTERT,S.YOKOYAMA,Y.MUTO JRNL TITL STRUCTURAL INSIGHT INTO THE ZINC FINGER CW DOMAIN AS A JRNL TITL 2 HISTONE MODIFICATION READER JRNL REF STRUCTURE V. 18 1127 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20826339 JRNL DOI 10.1016/J.STR.2010.06.012 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, AMBER 9.0 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RR4 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB150185. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20MM D-TRIS-HCL(PH 7.0); 100MM REMARK 210 NACL; 0.02% D-DTT; 50MICRO-M REMARK 210 ZNCL2+1MM IDA; 10% D2O, 90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 5.0, CYANA 2.1, NMRVIEW REMARK 210 5.0, XWINNMR 3.0, KUJIRA 0.9839 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1306 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 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 11 ARG A 269 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 14 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 19 ARG A 269 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 19 ARG A 269 NE - CZ - NH2 ANGL. DEV. = -3.7 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 PHE A 250 -14.47 70.20 REMARK 500 1 CYS A 264 -79.68 -102.66 REMARK 500 1 TYR A 293 25.03 -143.04 REMARK 500 2 GLN A 252 34.76 -160.40 REMARK 500 2 CYS A 264 -80.12 -104.86 REMARK 500 2 THR A 304 30.57 -77.78 REMARK 500 3 CYS A 264 -80.33 -102.28 REMARK 500 3 TYR A 293 28.34 -140.02 REMARK 500 3 TRP A 303 14.89 -142.79 REMARK 500 4 SER A 240 -165.93 -166.83 REMARK 500 4 CYS A 264 -80.73 -100.53 REMARK 500 4 TYR A 293 27.51 -141.36 REMARK 500 5 SER A 240 -2.55 69.56 REMARK 500 5 CYS A 264 -82.06 -102.28 REMARK 500 5 TYR A 293 29.78 -140.98 REMARK 500 6 CYS A 264 -81.57 -100.62 REMARK 500 6 TYR A 293 26.74 -142.98 REMARK 500 7 CYS A 264 -79.72 -103.82 REMARK 500 7 TYR A 293 26.56 -143.07 REMARK 500 8 SER A 243 17.01 58.09 REMARK 500 8 CYS A 264 -80.23 -101.33 REMARK 500 8 TYR A 293 26.71 -143.48 REMARK 500 8 LYS B 9 47.36 -145.38 REMARK 500 9 SER A 243 50.16 -144.91 REMARK 500 9 CYS A 264 -81.69 -102.16 REMARK 500 9 TYR A 293 27.29 -142.73 REMARK 500 10 CYS A 264 -80.48 -101.50 REMARK 500 10 TYR A 293 28.61 -142.84 REMARK 500 11 CYS A 264 -81.38 -101.46 REMARK 500 11 TYR A 293 26.70 -141.95 REMARK 500 11 TRP A 303 12.79 -141.33 REMARK 500 12 CYS A 264 -81.14 -100.83 REMARK 500 12 TYR A 293 27.96 -142.78 REMARK 500 12 TRP A 303 16.12 -147.35 REMARK 500 13 SER A 248 22.59 -65.30 REMARK 500 13 CYS A 264 -79.57 -99.65 REMARK 500 13 TYR A 293 26.70 -142.92 REMARK 500 14 CYS A 264 -81.81 -102.16 REMARK 500 14 TRP A 303 20.16 -142.85 REMARK 500 15 LEU A 254 118.45 -161.11 REMARK 500 15 CYS A 264 -80.64 -100.07 REMARK 500 15 TYR A 293 25.66 -144.03 REMARK 500 15 THR A 302 98.61 -69.31 REMARK 500 16 CYS A 264 -79.12 -100.14 REMARK 500 16 TYR A 293 26.79 -140.57 REMARK 500 16 THR A 304 49.73 -148.18 REMARK 500 17 CYS A 264 -80.76 -101.41 REMARK 500 18 CYS A 264 -79.46 -101.54 REMARK 500 18 TYR A 293 27.63 -143.54 REMARK 500 19 SER A 240 48.28 -77.46 REMARK 500 REMARK 500 THIS ENTRY HAS 55 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 4 ARG A 269 0.08 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 1 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 264 SG REMARK 620 2 CYS A 296 SG 109.7 REMARK 620 3 CYS A 259 SG 109.7 109.4 REMARK 620 4 CYS A 285 SG 109.4 109.5 109.1 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED 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 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2E61 RELATED DB: PDB REMARK 900 FREE STATE STRUCTURE OF ZF-CW DBREF 2RR4 A 246 307 UNP Q9H0M4 ZCPW1_HUMAN 246 307 DBREF 2RR4 B 1 10 UNP A8K4Y7 A8K4Y7_HUMAN 2 11 SEQADV 2RR4 GLY A 239 UNP Q9H0M4 EXPRESSION TAG SEQADV 2RR4 SER A 240 UNP Q9H0M4 EXPRESSION TAG SEQADV 2RR4 SER A 241 UNP Q9H0M4 EXPRESSION TAG SEQADV 2RR4 GLY A 242 UNP Q9H0M4 EXPRESSION TAG SEQADV 2RR4 SER A 243 UNP Q9H0M4 EXPRESSION TAG SEQADV 2RR4 SER A 244 UNP Q9H0M4 EXPRESSION TAG SEQADV 2RR4 GLY A 245 UNP Q9H0M4 EXPRESSION TAG SEQRES 1 A 69 GLY SER SER GLY SER SER GLY GLU ILE SER GLY PHE GLY SEQRES 2 A 69 GLN CYS LEU VAL TRP VAL GLN CYS SER PHE PRO ASN CYS SEQRES 3 A 69 GLY LYS TRP ARG ARG LEU CYS GLY ASN ILE ASP PRO SER SEQRES 4 A 69 VAL LEU PRO ASP ASN TRP SER CYS ASP GLN ASN THR ASP SEQRES 5 A 69 VAL GLN TYR ASN ARG CYS ASP ILE PRO GLU GLU THR TRP SEQRES 6 A 69 THR GLY LEU GLU SEQRES 1 B 10 ALA ARG THR M3L GLN THR ALA ARG LYS SER MODRES 2RR4 M3L B 4 LYS N-TRIMETHYLLYSINE HET M3L B 4 31 HET ZN A 501 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 ZN ZN 2+ HELIX 1 1 PRO A 276 VAL A 278 5 3 HELIX 2 2 CYS A 285 GLN A 287 5 3 HELIX 3 3 VAL A 291 TYR A 293 5 3 SHEET 1 A 3 TRP A 267 ARG A 269 0 SHEET 2 A 3 TRP A 256 GLN A 258 -1 LINK C THR B 3 N M3L B 4 1555 1555 1.33 LINK C M3L B 4 N GLN B 5 1555 1555 1.33 LINK SG CYS A 264 ZN ZN A 501 1555 1555 2.23 LINK SG CYS A 296 ZN ZN A 501 1555 1555 2.23 LINK SG CYS A 259 ZN ZN A 501 1555 1555 2.23 LINK SG CYS A 285 ZN ZN A 501 1555 1555 2.23 SITE 1 AC1 4 CYS A 259 CYS A 264 CYS A 285 CYS A 296 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