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- PDB-7klr: Solution structure of the PHD1 domain of histone demethylase KDM5... -

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Basic information

Entry
Database: PDB / ID: 7klr
TitleSolution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide
Components
  • Histone H3.1
  • Lysine-specific demethylase 5A
KeywordsGENE REGULATION / PHD / H3 / Epigenetics / KDM5A
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / facultative heterochromatin formation / : / histone demethylase activity / enzyme inhibitor activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening ...[histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / facultative heterochromatin formation / : / histone demethylase activity / enzyme inhibitor activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / circadian regulation of gene expression / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / protein-DNA complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / chromatin DNA binding / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / histone binding / gene expression / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / cadherin binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
: / : / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger ...: / : / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Lysine-specific demethylase 5A / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLongbotham, E.J. / Kelly, M.J.S. / Fujimori, D.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114044 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114044-03S1 United States
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A.
Authors: Longbotham, J.E. / Kelly, M.J.S. / Fujimori, D.G.
History
DepositionOct 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine-specific demethylase 5A
B: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8874
Polymers7,7562
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area920 Å2
ΔGint-4 kcal/mol
Surface area5170 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Lysine-specific demethylase 5A / Histone demethylase JARID1A / Jumonji/ARID domain-containing protein 1A / Retinoblastoma-binding ...Histone demethylase JARID1A / Jumonji/ARID domain-containing protein 1A / Retinoblastoma-binding protein 2 / RBBP-2 / [histone H3]-trimethyl-L-lysine(4) demethylase 5A


Mass: 6605.556 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM5A, JARID1A, RBBP2, RBP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P29375, [histone H3]-trimethyl-L-lysine4 demethylase
#2: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1150.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
Production host: synthetic construct (others) / References: UniProt: P68431
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic1CBCA(CO)NH
123isotropic1CBCANH
132isotropic13D (H)CC(CO)NH-TOCSY
142isotropic13D H(CC)(CO)NH-TOCSY
152isotropic13D (H)CCH-TOCSY
1102isotropic13D NOESY
192isotropic1N HSQC
182isotropic1C HSQC
172isotropic13D filtered intermolecular NOESY
164isotropic12D intra-peptide TOCSY
1114isotropic12D intra-peptide NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution2900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O3D_structure_sample95% H2O/5% D2O
solution3550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O3D_assignment_sample95% H2O/5% D2O
solution41250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2OH3_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
900 uMHistone lysine demethylase 5A, KDM5A[U-13C; U-15N]2
4000 uMHistone H3.1natural abundance2
50 mMHEPESnatural abundance2
150 mMsodium chloridenatural abundance2
5 mMbeta-mercaptoethanolnatural abundance2
0.1 mMZnCl2natural abundance2
550 uMHistone lysine demethylase 5A, KDM5A[U-13C; U-15N]3
800 uMHistone H3.1natural abundance3
50 mMHEPESnatural abundance3
150 mMsodium chloridenatural abundance3
5 mMbeta-mercaptoethanolnatural abundance3
0.1 mMZnCl2natural abundance3
1250 uMHistone lysine demethylase 5A, KDM5A[U-13C; U-15N]4
400 uMHistone H3.1natural abundance4
50 mMHEPESnatural abundance4
150 mMsodium chloridenatural abundance4
5 mMbeta-mercaptoethanolnatural abundance4
0.1 mMZnCl2natural abundance4
Sample conditionsIonic strength: 150 mM / Label: Standard_conditions / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3.2Linge, O'Donoghue and Nilgesrefinement
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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