HEADER GENE REGULATION 30-OCT-20 7KLO TITLE SOLUTION STRUCTURE OF THE PHD1 DOMAIN OF HISTONE DEMETHYLASE KDM5A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTONE DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING COMPND 5 PROTEIN 1A,RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2,[HISTONE H3]- COMPND 6 TRIMETHYL-L-LYSINE(4) DEMETHYLASE 5A; COMPND 7 EC: 1.14.11.67; 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: KDM5A, JARID1A, RBBP2, RBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PHD, H3, EPIGENETICS, KDM5A, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.J.LONGBOTHAM,M.J.S.KELLY,D.G.FUJIMORI REVDAT 2 01-MAY-24 7KLO 1 REMARK REVDAT 1 03-MAR-21 7KLO 0 JRNL AUTH J.E.LONGBOTHAM,M.J.S.KELLY,D.G.FUJIMORI JRNL TITL RECOGNITION OF HISTONE H3 METHYLATION STATES BY THE PHD1 JRNL TITL 2 DOMAIN OF HISTONE DEMETHYLASE KDM5A. JRNL REF ACS CHEM.BIOL. 2021 JRNL REFN ESSN 1554-8937 JRNL PMID 33621062 JRNL DOI 10.1021/ACSCHEMBIO.0C00976 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7KLO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252035. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 900 UM U-13C, 99%; U-15N, 99 % REMARK 210 PHD1, 50 MM HEPES, 150 MM NACL, REMARK 210 5 MM BETA-MERCAPTOETHANOL, 0.1 REMARK 210 MM ZNCL2, 95% H2O/5% D2O; 550 UM REMARK 210 U-13C, 99%; U-15N, 99 % PHD1, 50 REMARK 210 MM HEPES, 150 MM NACL, 5 MM BETA- REMARK 210 MERCAPTOETHANOL, 0.1 MM ZNCL2, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : CBCACONH; CBCANH; 3D (H)CCCONH REMARK 210 -TOCSY; 3D H(CC)(CO)NH-TOCSY; 3D REMARK 210 HCCH-TOCSY; 3D NOESY; N HSQC; C REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.3.2, CCPNMR ANALYSIS REMARK 210 2.4.2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 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 LEU A 293 5.16 -64.70 REMARK 500 1 MET A 297 167.72 -24.15 REMARK 500 1 CYS A 299 166.17 -40.78 REMARK 500 1 ASN A 304 0.17 -55.58 REMARK 500 1 GLU A 305 -13.73 -38.10 REMARK 500 1 ASP A 329 115.74 -173.19 REMARK 500 2 VAL A 291 99.27 -59.09 REMARK 500 2 ASP A 292 -70.34 -130.89 REMARK 500 2 TYR A 294 31.26 -90.19 REMARK 500 2 MET A 297 166.91 -24.30 REMARK 500 2 CYS A 299 -94.95 -25.10 REMARK 500 2 ASN A 303 119.15 -39.35 REMARK 500 2 GLU A 305 -19.04 -37.76 REMARK 500 2 ASP A 312 97.04 -57.63 REMARK 500 2 ASP A 316 38.06 -96.88 REMARK 500 2 ASP A 329 159.39 -38.20 REMARK 500 3 VAL A 288 15.19 -141.06 REMARK 500 3 TYR A 294 40.03 -100.08 REMARK 500 3 MET A 297 167.61 -24.51 REMARK 500 3 CYS A 299 160.97 -41.33 REMARK 500 3 ASN A 304 0.14 -45.63 REMARK 500 3 GLU A 305 -13.07 -41.48 REMARK 500 3 ASP A 312 94.87 -55.67 REMARK 500 3 ASP A 316 38.43 -95.23 REMARK 500 3 ASP A 329 99.30 -173.03 REMARK 500 3 VAL A 330 107.43 -48.43 REMARK 500 4 VAL A 288 18.35 -160.27 REMARK 500 4 ASP A 292 20.32 -74.07 REMARK 500 4 MET A 297 167.59 -24.28 REMARK 500 4 CYS A 299 165.32 -43.26 REMARK 500 4 ASN A 304 -0.32 -43.94 REMARK 500 4 GLU A 305 -9.75 -44.43 REMARK 500 4 ASP A 312 96.12 -54.27 REMARK 500 4 ASP A 329 155.99 -36.39 REMARK 500 5 SER A 287 81.94 56.37 REMARK 500 5 PHE A 290 24.10 -159.39 REMARK 500 5 MET A 297 168.43 -24.89 REMARK 500 5 CYS A 299 157.57 -38.64 REMARK 500 5 ASN A 304 0.03 -43.63 REMARK 500 5 GLU A 305 -6.40 -45.83 REMARK 500 5 ASP A 312 97.33 -53.49 REMARK 500 5 ASP A 316 38.16 -95.77 REMARK 500 5 ASP A 329 108.78 -173.39 REMARK 500 5 VAL A 330 108.51 -50.75 REMARK 500 6 PHE A 290 -41.13 -130.44 REMARK 500 6 MET A 297 167.50 -24.87 REMARK 500 6 CYS A 299 168.81 -42.25 REMARK 500 6 ASN A 303 -149.02 -110.19 REMARK 500 6 ASN A 304 -0.61 -37.99 REMARK 500 6 GLU A 305 -2.69 -58.68 REMARK 500 REMARK 500 THIS ENTRY HAS 202 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 296 SG REMARK 620 2 CYS A 299 SG 107.5 REMARK 620 3 HIS A 319 ND1 107.8 107.8 REMARK 620 4 CYS A 322 SG 112.1 109.4 112.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 311 SG REMARK 620 2 CYS A 314 SG 109.8 REMARK 620 3 CYS A 337 SG 111.2 111.7 REMARK 620 4 CYS A 340 SG 108.7 108.2 107.1 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30808 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE PHD1 DOMAIN OF HISTONE DEMETHYLASE KDM5A DBREF 7KLO A 287 344 UNP P29375 KDM5A_HUMAN 287 344 SEQADV 7KLO GLY A 286 UNP P29375 EXPRESSION TAG SEQRES 1 A 59 GLY SER VAL ASN PHE VAL ASP LEU TYR VAL CYS MET PHE SEQRES 2 A 59 CYS GLY ARG GLY ASN ASN GLU ASP LYS LEU LEU LEU CYS SEQRES 3 A 59 ASP GLY CYS ASP ASP SER TYR HIS THR PHE CYS LEU ILE SEQRES 4 A 59 PRO PRO LEU PRO ASP VAL PRO LYS GLY ASP TRP ARG CYS SEQRES 5 A 59 PRO LYS CYS VAL ALA GLU GLU HET ZN A 1 1 HET ZN A 2 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 ASN A 304 LEU A 308 5 5 HELIX 2 AA2 HIS A 319 LEU A 323 5 5 HELIX 3 AA3 CYS A 337 GLU A 343 1 7 LINK ZN ZN A 1 SG CYS A 296 1555 1555 2.30 LINK ZN ZN A 1 SG CYS A 299 1555 1555 2.30 LINK ZN ZN A 1 ND1 HIS A 319 1555 1555 2.00 LINK ZN ZN A 1 SG CYS A 322 1555 1555 2.30 LINK ZN ZN A 2 SG CYS A 311 1555 1555 2.30 LINK ZN ZN A 2 SG CYS A 314 1555 1555 2.30 LINK ZN ZN A 2 SG CYS A 337 1555 1555 2.30 LINK ZN ZN A 2 SG CYS A 340 1555 1555 2.30 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