HEADER METAL BINDING PROTEIN/STRUCTURAL PROTEIN08-APR-11 2LBM TITLE SOLUTION STRUCTURE OF THE ADD DOMAIN OF ATRX COMPLEXED WITH HISTONE TITLE 2 TAIL H3 1-15 K9ME3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR ATRX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 159-296; COMPND 5 SYNONYM: ATP-DEPENDENT HELICASE ATRX, X-LINKED HELICASE II, X-LINKED COMPND 6 NUCLEAR PROTEIN, XNP, ZNF-HX; COMPND 7 EC: 3.6.4.12; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HISTONE TAIL H3 K9ME3; COMPND 11 CHAIN: C; COMPND 12 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: ATRX, RAD54L, XH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET30A; 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: SYNTHETIC PEPTIDE KEYWDS HISTONE TAIL, METAL BINDING PROTEIN-STRUCTURAL PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR S.EUSTERMANN,J.YANG,D.NEUHAUS REVDAT 1 29-JUN-11 2LBM 0 JRNL AUTH S.EUSTERMANN,J.YANG,M.J.LAW,R.AMOS,L.M.CHAPMAN,C.JELINSKA, JRNL AUTH 2 D.GARRICK,D.CLYNES,R.J.GIBBONS,D.RHODES,D.R.HIGGS,D.NEUHAUS JRNL TITL COMBINATORIAL READOUT OF HISTONE H3 MODIFICATIONS SPECIFIES JRNL TITL 2 LOCALIZATION OF ATRX TO HETEROCHROMATIN JRNL REF NAT.STRUCT.MOL.BIOL. 2011 JRNL REFN ESSN 1545-9985 JRNL PMID 21666677 JRNL DOI 10.1038/NSMB.2070 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : C.D.SCHWIETERS,J.J.KUSZEWSKI,N.TJANDRA,G.M.CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LBM COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-APR-11. REMARK 100 THE RCSB ID CODE IS RCSB102197. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 250 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 200 UM [U-98% 13C; U-98% 15N] REMARK 210 ATRX ADD DOMAIN-1, 200 UM H3 TAIL REMARK 210 1-15 K9ME3-2, 50 MM [U-99% 2H] REMARK 210 TRIS-3, 200 MM SODIUM CHLORIDE-4, REMARK 210 150 UM ZINC SULFATE-5, 1 MM [U- REMARK 210 99% 2H] DTT-6, 95% H2O/5% D2O; REMARK 210 200 UM [U-98% 13C; U-98% 15N] REMARK 210 ATRX ADD DOMAIN-7, 200 UM H3 TAIL REMARK 210 1-15 K9ME3-8, 50 MM [U-99% 2H] REMARK 210 TRIS-9, 200 MM SODIUM CHLORIDE- REMARK 210 10, 150 UM ZINC SULFATE-11, 1 MM REMARK 210 [U-99% 2H] DTT-12, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC ALIPHATIC REMARK 210 (CONSTANT-TIME); 2D 1H-13C HSQC REMARK 210 AROMATIC (CONSTANT-TIME); 2D 1H- REMARK 210 1H NOESY (13C-H REJECTED IN F1 REMARK 210 AND F2); 3D HNCA; 3D HN(CO)CA; 3D REMARK 210 HBHA(CO)NH; 3D H[C]CH-TOCSY; 3D REMARK 210 [H]CCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 2D 1H-1H TOCSY REMARK 210 (13C-H REJECTED IN F1 AND F2); 2D REMARK 210 1H-1H NOESY (15N-H REJECTED IN REMARK 210 F2); 3D 1H-13C NOESY ALIPHATIC REMARK 210 (REJECTED 13C-H IN F1, 12C-H IN REMARK 210 F3); 2D 1H-1H NOESY (13C-H REMARK 210 REJECTED F1, 12C-H REJECTED F2); REMARK 210 2D 1H-1H NOESY (13C-H AND 15N-H REMARK 210 REJECTED IN F1 AND F2) REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR-NIH 2.19, SPARKY, TOPSPIN REMARK 210 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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: A, C 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: 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 ALA A 156 -64.91 -121.99 REMARK 500 1 HIS A 180 -164.45 53.82 REMARK 500 1 PHE A 181 85.63 -64.05 REMARK 500 1 LYS A 183 40.04 -103.78 REMARK 500 1 ASP A 184 39.10 -157.39 REMARK 500 1 SER A 185 41.02 -166.27 REMARK 500 1 GLN A 193 79.09 59.48 REMARK 500 1 ASP A 212 172.84 -56.37 REMARK 500 1 ALA A 224 81.87 54.05 REMARK 500 1 GLU A 225 122.68 -172.76 REMARK 500 1 ASN A 228 94.67 52.95 REMARK 500 1 PHE A 234 -57.32 -147.49 REMARK 500 1 HIS A 236 79.59 51.95 REMARK 500 1 CYS A 240 153.24 -47.78 REMARK 500 1 ASP A 258 66.74 -114.23 REMARK 500 1 GLU A 259 44.66 -105.72 REMARK 500 1 GLN A 262 47.70 -157.00 REMARK 500 1 CYS A 265 -157.76 -143.56 REMARK 500 1 TYR A 266 40.16 -105.02 REMARK 500 1 ILE A 267 -59.04 -134.01 REMARK 500 1 HIS A 269 132.48 -179.15 REMARK 500 1 ARG C 2 96.90 53.97 REMARK 500 1 ALA C 7 -175.47 -58.03 REMARK 500 2 CYS A 171 155.99 -49.31 REMARK 500 2 HIS A 180 84.11 52.70 REMARK 500 2 PHE A 181 83.58 52.36 REMARK 500 2 SER A 185 36.32 -146.67 REMARK 500 2 GLN A 193 76.69 55.78 REMARK 500 2 SER A 210 -165.41 -119.37 REMARK 500 2 SER A 213 -73.06 63.54 REMARK 500 2 MET A 216 -67.93 -130.55 REMARK 500 2 GLN A 219 -167.68 -164.15 REMARK 500 2 ALA A 224 80.79 53.68 REMARK 500 2 GLU A 225 120.26 -171.99 REMARK 500 2 ASN A 228 90.90 51.55 REMARK 500 2 PHE A 234 -58.00 -145.70 REMARK 500 2 HIS A 236 83.38 52.27 REMARK 500 2 CYS A 240 152.71 -46.52 REMARK 500 2 ASP A 258 68.36 -116.30 REMARK 500 2 GLU A 259 42.93 -108.66 REMARK 500 2 GLN A 262 47.50 -152.05 REMARK 500 2 CYS A 265 -157.68 -142.66 REMARK 500 2 ILE A 267 -58.78 -133.63 REMARK 500 2 HIS A 269 131.66 179.97 REMARK 500 2 PRO A 270 92.81 -65.72 REMARK 500 2 ASN A 294 -59.84 -142.02 REMARK 500 2 ARG C 2 153.65 60.95 REMARK 500 2 THR C 6 -165.44 -126.60 REMARK 500 2 ALA C 7 -166.76 -74.97 REMARK 500 2 THR C 11 -65.31 -124.68 REMARK 500 REMARK 500 THIS ENTRY HAS 622 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 1 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 220 SG REMARK 620 2 CYS A 243 SG 110.3 REMARK 620 3 CYS A 240 SG 110.7 106.4 REMARK 620 4 CYS A 223 SG 111.1 111.9 106.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 171 SG REMARK 620 2 CYS A 200 SG 108.4 REMARK 620 3 CYS A 174 SG 110.8 103.8 REMARK 620 4 CYS A 197 SG 111.6 112.9 109.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 235 SG REMARK 620 2 CYS A 265 SG 104.2 REMARK 620 3 CYS A 232 SG 110.8 107.6 REMARK 620 4 CYS A 268 SG 101.6 116.9 115.0 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17569 RELATED DB: BMRB DBREF 2LBM A 160 296 UNP P46100 ATRX_HUMAN 159 296 DBREF 2LBM C 1 15 PDB 2LBM 2LBM 1 15 SEQADV 2LBM GLY A 155 UNP P46100 EXPRESSION TAG SEQADV 2LBM ALA A 156 UNP P46100 EXPRESSION TAG SEQADV 2LBM MET A 157 UNP P46100 EXPRESSION TAG SEQADV 2LBM ALA A 158 UNP P46100 EXPRESSION TAG SEQADV 2LBM ASP A 159 UNP P46100 EXPRESSION TAG SEQADV 2LBM A UNP P46100 GLU 162 DELETION SEQRES 1 A 142 GLY ALA MET ALA ASP LYS ARG GLY ASP GLY LEU HIS GLY SEQRES 2 A 142 ILE VAL SER CYS THR ALA CYS GLY GLN GLN VAL ASN HIS SEQRES 3 A 142 PHE GLN LYS ASP SER ILE TYR ARG HIS PRO SER LEU GLN SEQRES 4 A 142 VAL LEU ILE CYS LYS ASN CYS PHE LYS TYR TYR MET SER SEQRES 5 A 142 ASP ASP ILE SER ARG ASP SER ASP GLY MET ASP GLU GLN SEQRES 6 A 142 CYS ARG TRP CYS ALA GLU GLY GLY ASN LEU ILE CYS CYS SEQRES 7 A 142 ASP PHE CYS HIS ASN ALA PHE CYS LYS LYS CYS ILE LEU SEQRES 8 A 142 ARG ASN LEU GLY ARG LYS GLU LEU SER THR ILE MET ASP SEQRES 9 A 142 GLU ASN ASN GLN TRP TYR CYS TYR ILE CYS HIS PRO GLU SEQRES 10 A 142 PRO LEU LEU ASP LEU VAL THR ALA CYS ASN SER VAL PHE SEQRES 11 A 142 GLU ASN LEU GLU GLN LEU LEU GLN GLN ASN LYS LYS SEQRES 1 C 15 ALA ARG THR LYS GLN THR ALA ARG M3L SER THR GLY GLY SEQRES 2 C 15 LYS ALA MODRES 2LBM M3L C 9 LYS N-TRIMETHYLLYSINE HET M3L C 9 31 HET ZN A 1 1 HET ZN A 2 1 HET ZN A 3 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 ZN 3(ZN 2+) HELIX 1 1 LYS A 198 ASP A 207 1 10 HELIX 2 2 LYS A 241 LEU A 248 1 8 HELIX 3 3 GLY A 249 ASP A 258 1 10 HELIX 4 4 LEU A 273 GLN A 292 1 20 SHEET 1 A 2 ILE A 186 HIS A 189 0 SHEET 2 A 2 VAL A 194 CYS A 197 -1 O VAL A 194 N HIS A 189 SHEET 1 B 2 LEU A 229 CYS A 231 0 SHEET 2 B 2 ALA A 238 CYS A 240 -1 O PHE A 239 N ILE A 230 LINK C ARG C 8 N M3L C 9 1555 1555 1.32 LINK C M3L C 9 N SER C 10 1555 1555 1.32 LINK SG CYS A 220 ZN ZN A 2 1555 1555 2.30 LINK SG CYS A 243 ZN ZN A 2 1555 1555 2.30 LINK SG CYS A 240 ZN ZN A 2 1555 1555 2.30 LINK SG CYS A 223 ZN ZN A 2 1555 1555 2.30 LINK SG CYS A 171 ZN ZN A 1 1555 1555 2.30 LINK SG CYS A 235 ZN ZN A 3 1555 1555 2.30 LINK SG CYS A 265 ZN ZN A 3 1555 1555 2.30 LINK SG CYS A 200 ZN ZN A 1 1555 1555 2.31 LINK SG CYS A 174 ZN ZN A 1 1555 1555 2.31 LINK SG CYS A 232 ZN ZN A 3 1555 1555 2.31 LINK SG CYS A 197 ZN ZN A 1 1555 1555 2.31 LINK SG CYS A 268 ZN ZN A 3 1555 1555 2.32 SITE 1 AC1 4 CYS A 171 CYS A 174 CYS A 197 CYS A 200 SITE 1 AC2 4 CYS A 220 CYS A 223 CYS A 240 CYS A 243 SITE 1 AC3 4 CYS A 232 CYS A 235 CYS A 265 CYS A 268 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