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- PDB-5oy3: The structural basis of the histone demethylase KDM6B histone 3 l... -

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Basic information

Entry
Database: PDB / ID: 5oy3
TitleThe structural basis of the histone demethylase KDM6B histone 3 lysine 27 specificity
Components
  • Histone 3 peptide H3(17-33)A21M
  • Lysine-specific demethylase 6B
KeywordsOXIDOREDUCTASE / Epigenetics / Histone demethylase / substrate complex
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / histone demethylase activity / cell fate commitment / Chromatin modifying enzymes ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / histone demethylase activity / cell fate commitment / Chromatin modifying enzymes / response to fungicide / 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 / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / 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 / response to activity / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / hippocampus development / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / chromatin DNA binding / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to hydrogen peroxide / beta-catenin binding / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / positive regulation of cold-induced thermogenesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Cupin ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Ribbon / Histone-fold / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / TERTIARY-BUTYL ALCOHOL / Lysine-specific demethylase 6B / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.136 Å
AuthorsJones, S.E. / Olsen, L. / Gajhede, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research Denmark
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis of Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity.
Authors: Jones, S.E. / Olsen, L. / Gajhede, M.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 6B
B: Histone 3 peptide H3(17-33)A21M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,57714
Polymers59,7392
Non-polymers83812
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint8 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.908, 68.908, 228.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Lysine-specific demethylase 6B / JmjC domain-containing protein 3 / Jumonji domain-containing protein 3 / Lysine demethylase 6B


Mass: 57919.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM6B, JMJD3, KIAA0346 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O15054, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Protein/peptide Histone 3 peptide H3(17-33)A21M


Mass: 1820.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS

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Non-polymers , 6 types, 312 molecules

#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H6O5
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M TRIS pH 7.5, 15%(v/v) Tert-butanol,

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.136→48.726 Å / Num. all: 343768 / Num. obs: 31653 / % possible obs: 99.86 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.055 / Rrim(I) all: 0.182 / Net I/σ(I): 12.67
Reflection shellRmerge(I) obs: 1.397 / Num. measured obs: 33112 / Num. unique all: 2951 / Rpim(I) all: 0.43 / Rrim(I) all: 1.463

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AVR

3avr


Resolution: 2.136→48.726 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 2000 6.33 %
Rwork0.165 --
obs0.1686 31572 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.136→48.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 49 300 4080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123880
X-RAY DIFFRACTIONf_angle_d1.1095259
X-RAY DIFFRACTIONf_dihedral_angle_d14.8092305
X-RAY DIFFRACTIONf_chiral_restr0.064571
X-RAY DIFFRACTIONf_plane_restr0.007675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1358-2.18920.30851360.24542012X-RAY DIFFRACTION99
2.1892-2.24840.29491400.24242068X-RAY DIFFRACTION100
2.2484-2.31460.29071410.22972072X-RAY DIFFRACTION100
2.3146-2.38930.27421400.19632086X-RAY DIFFRACTION100
2.3893-2.47470.2451400.19182065X-RAY DIFFRACTION100
2.4747-2.57380.24671410.1792087X-RAY DIFFRACTION100
2.5738-2.69090.25411400.17392079X-RAY DIFFRACTION100
2.6909-2.83270.23831420.17022098X-RAY DIFFRACTION100
2.8327-3.01020.21941430.16842109X-RAY DIFFRACTION100
3.0102-3.24260.25981420.1652100X-RAY DIFFRACTION100
3.2426-3.56880.21921440.16422131X-RAY DIFFRACTION100
3.5688-4.0850.2061460.13642149X-RAY DIFFRACTION100
4.085-5.14580.16511470.12132182X-RAY DIFFRACTION100
5.1458-48.73830.18861580.16642334X-RAY DIFFRACTION100

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