PDB Short entry for 2KGI HEADER METAL BINDING PROTEIN 12-MAR-09 2KGI TITLE SOLUTION STRUCTURE OF JARID1A C-TERMINAL PHD FINGER IN COMPLEX WITH TITLE 2 H3(1-9)K4ME3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEMETHYLASE JARID1A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD-TYPE C-TERMINAL ZINC FINGER; COMPND 5 SYNONYM: JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1A, RETINOBLASTOMA- COMPND 6 BINDING PROTEIN 2, RBBP-2; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: H3(1-9)K4ME3; COMPND 11 CHAIN: B; 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: JARID1A, RBBP2, RBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSFDUET-1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS PHD FINGER, JARID1A, HISTONE MODIFICATION, LEUKEMIA, ALTERNATIVE KEYWDS 2 SPLICING, CHROMATIN REGULATOR, DEVELOPMENTAL PROTEIN, DIOXYGENASE, KEYWDS 3 IRON, METAL-BINDING, NUCLEUS, OXIDOREDUCTASE, PHOSPHOPROTEIN, KEYWDS 4 POLYMORPHISM, TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC, ZINC- KEYWDS 5 FINGER, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.SONG,Z.WANG,D.J.PATEL REVDAT 3 26-FEB-20 2KGI 1 REMARK SEQADV LINK REVDAT 2 16-JUN-09 2KGI 1 JRNL REVDAT 1 05-MAY-09 2KGI 0 JRNL AUTH G.G.WANG,J.SONG,Z.WANG,H.L.DORMANN,F.CASADIO,H.LI,J.L.LUO, JRNL AUTH 2 D.J.PATEL,C.D.ALLIS JRNL TITL HAEMATOPOIETIC MALIGNANCIES CAUSED BY DYSREGULATION OF A JRNL TITL 2 CHROMATIN-BINDING PHD FINGER. JRNL REF NATURE V. 459 847 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 19430464 JRNL DOI 10.1038/NATURE08036 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.18 REMARK 3 AUTHORS : SCHWIETERS, C. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS FIRST CALCULATED REMARK 3 USING CYANA AND THEN REFINED USING XPLOR-NIH REMARK 4 REMARK 4 2KGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000101091. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.2; 298.2 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOSPHATE; 200 MM REMARK 210 NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2-0.5 MM [U-100% 13C; U-100% REMARK 210 15N] JARID1A PHD FINGER 3, 0.2- REMARK 210 0.5 MM H3(1-9)K4ME3, 5 MM DTT, 1 REMARK 210 MM ZINC CHLORIDE, 20 MM SODIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 0.2- REMARK 210 0.5 MM [U-100% 15N] JARID1A PHD REMARK 210 FINGER 3, 0.2-0.5 MM H3(1-9) REMARK 210 K4ME3, 5 MM DTT, 1 MM ZINC REMARK 210 CHLORIDE, 10 MM MOPS, 12 MG/ML REMARK 210 BACTERIOPHAGE PF1, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H,15N-HSQC; 1H,13C-HSQC; REMARK 210 HNCACB; HBHACONH; CBCACONH; 2D REMARK 210 1H-1H NOESY; HCCHTOCSY; 15N- REMARK 210 EDITED 1H,1H-NOESY; 13C-EDITED REMARK 210 1H,1H-NOESY; 15N IPAP HSQC; 13C, REMARK 210 15N-FILTERED, 13C-EDITED 1H,1H- REMARK 210 NOESY; 13C,15N-FILTERED, 2D 1H, REMARK 210 1H-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1 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: 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 ALA A 52 O REMARK 470 LYS B 309 O 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 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 ALA A 4 69.63 -104.51 REMARK 500 1 CYS A 12 19.16 55.97 REMARK 500 1 ASP A 26 24.03 42.88 REMARK 500 2 ASN A 7 72.11 -112.33 REMARK 500 2 LYS A 15 124.42 -176.76 REMARK 500 2 ASP A 26 36.69 86.92 REMARK 500 3 ALA A 4 68.22 -101.16 REMARK 500 3 ASP A 14 -72.27 -58.40 REMARK 500 3 ASP A 26 27.81 38.25 REMARK 500 4 ALA A 5 107.58 -166.55 REMARK 500 4 ASP A 14 -71.75 -56.56 REMARK 500 4 ASP A 26 34.62 78.60 REMARK 500 5 ALA A 4 69.22 -100.45 REMARK 500 5 ASN A 7 70.05 -114.38 REMARK 500 5 PRO A 11 60.43 -105.20 REMARK 500 5 ASP A 26 27.67 44.97 REMARK 500 6 ALA A 4 69.64 -104.49 REMARK 500 6 CYS A 12 108.34 58.92 REMARK 500 7 ALA A 4 68.10 -103.42 REMARK 500 7 ASN A 7 73.08 -110.86 REMARK 500 7 ASP A 26 40.93 38.92 REMARK 500 8 ALA A 4 68.78 -104.26 REMARK 500 8 ASP A 14 -72.54 -62.61 REMARK 500 8 ASP A 26 17.21 50.94 REMARK 500 9 ALA A 4 69.45 -102.41 REMARK 500 9 ASP A 14 -72.16 -70.39 REMARK 500 9 ASP A 26 29.12 43.99 REMARK 500 9 ALA B 307 173.14 65.14 REMARK 500 9 ARG B 308 -77.94 -135.65 REMARK 500 10 ALA A 4 68.88 -104.00 REMARK 500 10 ASN A 7 66.63 -106.49 REMARK 500 10 CYS A 12 18.66 57.51 REMARK 500 10 ASP A 26 49.70 36.43 REMARK 500 11 ALA A 4 69.14 -102.28 REMARK 500 11 CYS A 25 -73.27 -71.50 REMARK 500 11 ASP A 26 58.51 87.76 REMARK 500 12 ALA A 4 69.04 -106.57 REMARK 500 12 CYS A 12 15.82 59.07 REMARK 500 12 ASP A 14 -73.21 -62.08 REMARK 500 12 ASP A 26 38.25 38.08 REMARK 500 12 ALA B 307 93.01 60.38 REMARK 500 13 ALA A 4 68.07 -102.94 REMARK 500 13 ASN A 7 71.68 -110.33 REMARK 500 14 ALA A 4 69.13 -103.94 REMARK 500 14 ASN A 7 59.62 -111.23 REMARK 500 14 ASP A 26 21.24 43.78 REMARK 500 14 ARG B 302 105.73 70.40 REMARK 500 15 ALA A 4 69.85 -104.14 REMARK 500 15 ASN A 7 65.41 -118.46 REMARK 500 16 LYS A 13 171.48 -52.31 REMARK 500 REMARK 500 THIS ENTRY HAS 64 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 54 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 3 SG REMARK 620 2 CYS A 8 SG 108.6 REMARK 620 3 HIS A 30 ND1 110.4 109.1 REMARK 620 4 CYS A 33 SG 105.1 112.5 111.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 53 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 21 SG REMARK 620 2 CYS A 25 SG 107.5 REMARK 620 3 CYS A 48 SG 110.8 110.7 REMARK 620 4 CYS A 51 SG 109.8 108.6 109.3 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 53 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 54 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16210 RELATED DB: BMRB DBREF 2KGI A 2 52 UNP P29375 JAD1A_HUMAN 1609 1659 DBREF 2KGI B 301 309 PDB 2KGI 2KGI 301 309 SEQADV 2KGI SER A 1 UNP P29375 EXPRESSION TAG SEQRES 1 A 52 SER VAL CYS ALA ALA GLN ASN CYS GLN ARG PRO CYS LYS SEQRES 2 A 52 ASP LYS VAL ASP TRP VAL GLN CYS ASP GLY GLY CYS ASP SEQRES 3 A 52 GLU TRP PHE HIS GLN VAL CYS VAL GLY VAL SER PRO GLU SEQRES 4 A 52 MET ALA GLU ASN GLU ASP TYR ILE CYS ILE ASN CYS ALA SEQRES 1 B 9 ALA ARG THR M3L GLN THR ALA ARG LYS MODRES 2KGI M3L B 304 LYS N-TRIMETHYLLYSINE HET M3L B 304 31 HET ZN A 53 1 HET ZN A 54 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 ZN 2(ZN 2+) HELIX 1 1 SER A 37 GLU A 44 1 8 SHEET 1 A 3 TRP A 28 HIS A 30 0 SHEET 2 A 3 LYS A 15 GLN A 20 -1 N VAL A 19 O PHE A 29 SHEET 3 A 3 ARG B 302 ALA B 307 -1 O M3L B 304 N TRP A 18 LINK C THR B 303 N M3L B 304 1555 1555 1.33 LINK C M3L B 304 N GLN B 305 1555 1555 1.30 LINK SG CYS A 3 ZN ZN A 54 1555 1555 2.28 LINK SG CYS A 8 ZN ZN A 54 1555 1555 2.30 LINK SG CYS A 21 ZN ZN A 53 1555 1555 2.29 LINK SG CYS A 25 ZN ZN A 53 1555 1555 2.29 LINK ND1 HIS A 30 ZN ZN A 54 1555 1555 2.00 LINK SG CYS A 33 ZN ZN A 54 1555 1555 2.30 LINK SG CYS A 48 ZN ZN A 53 1555 1555 2.30 LINK SG CYS A 51 ZN ZN A 53 1555 1555 2.29 SITE 1 AC1 4 CYS A 21 CYS A 25 CYS A 48 CYS A 51 SITE 1 AC2 4 CYS A 3 CYS A 8 HIS A 30 CYS A 33 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