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- PDB-6f6d: The catalytic domain of KDM6B in complex with H3(17-33)K18IA21M p... -

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Basic information

Entry
Database: PDB / ID: 6f6d
TitleThe catalytic domain of KDM6B in complex with H3(17-33)K18IA21M peptide
Components
  • Histone 3 peptide H3(17-33)K18IA21M
  • Lysine-specific demethylase 6B
KeywordsOXIDOREDUCTASE / Epigenetics / Histone demethylase / substrate based inhibitor
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 / epigenetic regulation of gene expression / response to fungicide / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / response to activity / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / chromatin DNA binding / PKMTs methylate histone lysines / cellular response to hydrogen peroxide / RMTs methylate histone arginines / beta-catenin binding / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cold-induced thermogenesis / chromatin organization / gene expression / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus
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 / JmjC domain, hydroxylase ...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: 1.81810675209 Å
AuthorsJones, S.E. / Olsen, L. / Gajhede, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research4004-00075B 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
DepositionDec 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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)K18IA21M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3448
Polymers59,8542
Non-polymers4906
Water8,161453
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-4 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.480, 68.480, 230.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: 58050.285 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)K18IA21M


Mass: 1804.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS

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Non-polymers , 5 types, 459 molecules

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


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 / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#6: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M TRIS pH 8.0, 15%(v/v) Tert-butanol,

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.818→65.633 Å / Num. obs: 49999 / % possible obs: 99.2 % / Redundancy: 12.3 % / Biso Wilson estimate: 25.2613075966 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.037 / Rrim(I) all: 0.131 / Net I/σ(I): 12.3
Reflection shellResolution: 1.818→1.85 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2490 / CC1/2: 0.73 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
autoPROC1.1.7data scaling
PHENIX1.10.1_2155model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OY3

5oy3


Resolution: 1.81810675209→57.5 Å / SU ML: 0.208963891217 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.8996379797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213586891495 1946 3.9823189948 %
Rwork0.165095998862 46920 -
obs0.166994950638 48866 96.9371156517 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.2566323525 Å2
Refinement stepCycle: LAST / Resolution: 1.81810675209→57.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 27 453 4213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01023875065683880
X-RAY DIFFRACTIONf_angle_d1.032919913385285
X-RAY DIFFRACTIONf_chiral_restr0.0592793064018577
X-RAY DIFFRACTIONf_plane_restr0.00698714723375680
X-RAY DIFFRACTIONf_dihedral_angle_d15.73701578012329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8181-1.86360.3475525411071270.240179509743110X-RAY DIFFRACTION91.4923685698
1.8636-1.9140.3421020186791060.2679902034742655X-RAY DIFFRACTION78.7282577702
1.914-1.97030.3065585123781320.2197057210273220X-RAY DIFFRACTION94.8231966054
1.9703-2.03390.2793945392481360.1919944506343285X-RAY DIFFRACTION97.022121384
2.0339-2.10660.2440427514721410.1809239468473321X-RAY DIFFRACTION97.1653101319
2.1066-2.19090.2224452486591380.1750965463073365X-RAY DIFFRACTION98.7873660462
2.1909-2.29060.2054201464921410.1605559259043392X-RAY DIFFRACTION99.1858506457
2.2906-2.41140.2234036768811430.1517725863883406X-RAY DIFFRACTION99.6630160067
2.4114-2.56250.2355693670441420.1600574810453423X-RAY DIFFRACTION99.7481813095
2.5625-2.76030.1877862004591440.1607140599733454X-RAY DIFFRACTION99.8612267555
2.7603-3.03810.2052143919281460.1671579313433471X-RAY DIFFRACTION99.9723604201
3.0381-3.47770.2023957344621450.1625880579963506X-RAY DIFFRACTION99.9726177437
3.4777-4.38130.1931905389821480.14493932333544X-RAY DIFFRACTION99.9729217438
4.3813-57.52870.1938864214171570.1573125034343768X-RAY DIFFRACTION99.8727735369

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