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- PDB-7klo: Solution structure of the PHD1 domain of histone demethylase KDM5A -

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Basic information

Entry
Database: PDB / ID: 7klo
TitleSolution structure of the PHD1 domain of histone demethylase KDM5A
ComponentsLysine-specific demethylase 5A
KeywordsGENE REGULATION / PHD / H3 / Epigenetics / KDM5A
Function / homology
Function and homology information


facultative heterochromatin formation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / regulation of DNA-binding transcription factor activity / enzyme inhibitor activity / histone demethylase activity / methylated histone binding / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones ...facultative heterochromatin formation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / regulation of DNA-binding transcription factor activity / enzyme inhibitor activity / histone demethylase activity / methylated histone binding / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / chromatin DNA binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / regulation of DNA-templated transcription / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger ...: / : / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / 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 / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Lysine-specific demethylase 5A
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 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7363
Polymers6,6061
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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: 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
112isotropic1CBCA(CO)NH
122isotropic1CBCANH
131isotropic13D (H)CC(CO)NH-TOCSY
141isotropic13D H(CC)(CO)NH-TOCSY
151isotropic13D (H)CCH-TOCSY
161isotropic13D NOESY
171isotropic1N HSQC
181isotropic1C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1900 uM U-13C, 99%; U-15N, 99 % PHD1, 50 mM HEPES, 150 mM NaCl, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O3D_structure_sample95% H2O/5% D2O
solution2550 uM U-13C, 99%; U-15N, 99 % PHD1, 50 mM HEPES, 150 mM NaCl, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O3D_assignment_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
900 uMPHD1U-13C, 99%; U-15N, 99 %1
50 mMHEPESnatural abundance1
150 mMNaClnatural abundance1
5 mMbeta-mercaptoethanolnatural abundance1
0.1 mMZnCl2natural abundance1
550 uMPHD1U-13C, 99%; U-15N, 99 %2
50 mMHEPESnatural abundance2
150 mMNaClnatural abundance2
5 mMbeta-mercaptoethanolnatural abundance2
0.1 mMZnCl2natural abundance2
Sample conditionsIonic strength: 150 mM / Label: 3D_structure_sample / 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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