HEADER GENE REGULATION 31-OCT-20 7KLR TITLE SOLUTION STRUCTURE OF THE PHD1 DOMAIN OF HISTONE DEMETHYLASE KDM5A IN TITLE 2 COMPLEX WITH A HISTONE H3(1-10) PEPTIDE 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; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HISTONE H3.1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE COMPND 13 H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE COMPND 14 H3/L; COMPND 15 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); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC SOURCE 14 HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, SOURCE 15 HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, SOURCE 16 HIST1H3I, H3C12, H3FJ, HIST1H3J; SOURCE 17 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 32630 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 7KLR 1 REMARK REVDAT 1 03-MAR-21 7KLR 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 7KLR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252685. 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; U-15N] HISTONE REMARK 210 LYSINE DEMETHYLASE 5A, KDM5A, REMARK 210 4000 UM HISTONE H3.1, 50 MM REMARK 210 HEPES, 150 MM SODIUM CHLORIDE, 5 REMARK 210 MM BETA-MERCAPTOETHANOL, 0.1 MM REMARK 210 ZNCL2, 95% H2O/5% D2O; 550 UM [U- REMARK 210 13C; U-15N] HISTONE LYSINE REMARK 210 DEMETHYLASE 5A, KDM5A, 800 UM REMARK 210 HISTONE H3.1, 50 MM HEPES, 150 REMARK 210 MM SODIUM CHLORIDE, 5 MM BETA- REMARK 210 MERCAPTOETHANOL, 0.1 MM ZNCL2, REMARK 210 95% H2O/5% D2O; 1250 UM [U-13C; REMARK 210 U-15N] HISTONE LYSINE REMARK 210 DEMETHYLASE 5A, KDM5A, 400 UM REMARK 210 HISTONE H3.1, 50 MM HEPES, 150 REMARK 210 MM SODIUM CHLORIDE, 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; 3D FILTERED INTERMOLECULAR REMARK 210 NOESY; 2D INTRA-PEPTIDE TOCSY; REMARK 210 2D INTRA-PEPTIDE NOESY 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: 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 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 CYS A 11 151.61 -43.08 REMARK 500 1 PHE A 13 -59.59 71.75 REMARK 500 1 ASN A 18 -149.08 -110.18 REMARK 500 1 ASN A 19 3.41 -44.57 REMARK 500 1 GLU A 20 -21.56 -34.35 REMARK 500 1 ASP A 27 103.10 -38.50 REMARK 500 1 ASP A 30 27.68 -45.71 REMARK 500 1 SER A 32 142.59 -173.69 REMARK 500 1 TYR A 33 112.45 -162.72 REMARK 500 1 LEU A 38 99.26 -169.27 REMARK 500 1 PRO A 40 -178.98 -54.80 REMARK 500 2 PHE A 5 37.93 -91.88 REMARK 500 2 PHE A 13 -66.38 70.88 REMARK 500 2 ASN A 18 -148.85 -110.00 REMARK 500 2 ASN A 19 2.62 -50.85 REMARK 500 2 GLU A 20 -3.36 -43.38 REMARK 500 2 CYS A 29 -60.81 -120.51 REMARK 500 2 ASP A 30 29.47 -77.11 REMARK 500 2 ASP A 31 9.49 -44.40 REMARK 500 2 SER A 32 114.59 -162.71 REMARK 500 2 THR A 35 -19.06 -48.48 REMARK 500 2 CYS A 37 -71.41 -76.95 REMARK 500 2 PRO A 40 176.56 -41.94 REMARK 500 3 PHE A 5 33.48 -98.02 REMARK 500 3 PHE A 13 -68.37 70.08 REMARK 500 3 ASN A 18 -148.65 -110.31 REMARK 500 3 ASN A 19 2.17 -48.84 REMARK 500 3 GLU A 20 -14.36 -43.08 REMARK 500 3 ASP A 30 -1.63 -44.43 REMARK 500 3 ASP A 31 34.94 -74.34 REMARK 500 3 PRO A 40 178.83 -46.15 REMARK 500 3 ARG B 2 144.25 66.11 REMARK 500 4 PHE A 13 -34.68 74.58 REMARK 500 4 ASN A 18 -148.61 -110.24 REMARK 500 4 ASN A 19 3.56 -45.51 REMARK 500 4 GLU A 20 -20.46 -34.05 REMARK 500 4 CYS A 29 -60.88 -120.57 REMARK 500 4 ASP A 30 29.72 -76.29 REMARK 500 4 ASP A 31 7.04 -44.19 REMARK 500 4 LEU A 38 99.65 -166.48 REMARK 500 4 PRO A 40 -178.89 -48.62 REMARK 500 4 PRO A 41 2.74 -67.70 REMARK 500 4 GLU A 58 75.47 -101.33 REMARK 500 5 VAL A 3 26.63 43.96 REMARK 500 5 PHE A 5 24.74 -141.39 REMARK 500 5 CYS A 11 152.99 -46.14 REMARK 500 5 PHE A 13 -33.09 73.79 REMARK 500 5 ASN A 18 -150.56 -110.41 REMARK 500 5 ASN A 19 2.96 -50.61 REMARK 500 5 GLU A 20 -0.99 -42.78 REMARK 500 REMARK 500 THIS ENTRY HAS 216 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 11 SG REMARK 620 2 CYS A 14 SG 109.2 REMARK 620 3 HIS A 34 ND1 109.2 106.4 REMARK 620 4 CYS A 37 SG 112.4 109.9 109.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 26 SG REMARK 620 2 CYS A 29 SG 108.9 REMARK 620 3 CYS A 52 SG 110.0 106.1 REMARK 620 4 CYS A 55 SG 108.1 116.8 106.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7KLO RELATED DB: PDB REMARK 900 7KLO IS THE APO STRUCTURE OF PHD1 REMARK 900 RELATED ID: 30809 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE PHD1 DOMAIN OF HISTONE DEMETHYLASE KDM5A REMARK 900 IN COMPLEX WITH A HISTONE H3(1-10) PEPTIDE DBREF 7KLR A 2 59 UNP P29375 KDM5A_HUMAN 287 344 DBREF 7KLR B 1 10 UNP P68431 H31_HUMAN 2 11 SEQADV 7KLR GLY A 1 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 SEQRES 1 B 10 ALA ARG THR LYS GLN THR ALA ARG LYS SER HET ZN A 401 1 HET ZN A 402 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 SER A 2 VAL A 6 5 5 HELIX 2 AA2 ASN A 19 ASP A 21 5 3 HELIX 3 AA3 CYS A 52 ALA A 57 1 6 HELIX 4 AA4 THR B 3 ARG B 8 1 6 SHEET 1 AA1 2 LEU A 23 LEU A 24 0 SHEET 2 AA1 2 TYR A 33 HIS A 34 -1 O TYR A 33 N LEU A 24 LINK SG CYS A 11 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 14 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 26 ZN ZN A 402 1555 1555 2.30 LINK SG CYS A 29 ZN ZN A 402 1555 1555 2.30 LINK ND1 HIS A 34 ZN ZN A 401 1555 1555 2.00 LINK SG CYS A 37 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 52 ZN ZN A 402 1555 1555 2.30 LINK SG CYS A 55 ZN ZN A 402 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