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- PDB-4qx7: Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg -

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Basic information

Entry
Database: PDB / ID: 4qx7
TitleCrystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg
Components
  • (Lysine-specific demethylase ...) x 2
  • Histone H3.2
KeywordsOxidoreductase/Structural Protein / cupin subfamily Fe(II)/2-OG dioxygenase / JmjC domain / Histone demethylase / Oxidoreductase-Structural Protein complex
Function / homology
Function and homology information


Chromatin modifying enzymes / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines ...Chromatin modifying enzymes / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / neuroepithelial cell differentiation / unmethylated CpG binding / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / heart looping / histone demethylase activity / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / neural tube closure / transcription coregulator activity / circadian regulation of gene expression / multicellular organism growth / regulation of circadian rhythm / neuron differentiation / nucleosome assembly / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / gene expression / chromatin organization / in utero embryonic development / protein heterodimerization activity / negative regulation of gene expression / chromatin binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #250 / PHD-finger / Jumonji, helical domain / Jumonji helical domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #250 / PHD-finger / Jumonji, helical domain / Jumonji helical domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / F-box domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helix non-globular / Histone H3 signature 1. / Leucine-rich repeat domain superfamily / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Special / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NICKEL (II) ION / Lysine (K)-specific demethylase 2A / Lysine-specific demethylase 2A / Histone H3.2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsCheng, Z.J. / Patel, D.J.
CitationJournal: Genes Dev. / Year: 2014
Title: A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36.
Authors: Cheng, Z. / Cheung, P. / Kuo, A.J. / Yukl, E.T. / Wilmot, C.M. / Gozani, O. / Patel, D.J.
History
DepositionJul 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 2A
B: Lysine-specific demethylase 2A
C: Lysine-specific demethylase 2A
D: Lysine-specific demethylase 2A
E: Histone H3.2
F: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,87610
Polymers96,4666
Non-polymers4104
Water4,774265
1
A: Lysine-specific demethylase 2A
B: Lysine-specific demethylase 2A
E: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4385
Polymers48,2333
Non-polymers2052
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-64 kcal/mol
Surface area17640 Å2
MethodPISA
2
C: Lysine-specific demethylase 2A
D: Lysine-specific demethylase 2A
F: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4385
Polymers48,2333
Non-polymers2052
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-59 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.343, 86.487, 170.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A36 - 364
2112B36 - 364
1212A451 - 516
2212B451 - 516

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Components

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Lysine-specific demethylase ... , 2 types, 4 molecules ACBD

#1: Protein Lysine-specific demethylase 2A / F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing ...F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing histone demethylation protein 1A / [Histone-H3]-lysine-36 demethylase 1A


Mass: 39031.324 Da / Num. of mol.: 2 / Fragment: UNP residues 36-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm2a, Fbxl11, Jhdm1a, Kiaa1004 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F6YRW4, UniProt: P59997*PLUS, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Protein Lysine-specific demethylase 2A / F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing ...F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing histone demethylation protein 1A / [Histone-H3]-lysine-36 demethylase 1A


Mass: 7534.759 Da / Num. of mol.: 2 / Fragment: UNP residues 450-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm2a, Fbxl11, Jhdm1a, Kiaa1004 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F6YRW4, UniProt: P59997*PLUS, [histone H3]-dimethyl-L-lysine36 demethylase

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Histone H3.2


Mass: 1666.967 Da / Num. of mol.: 2 / Fragment: UNP residues 30-44 / Source method: obtained synthetically / Details: methylated H3 peptide was synthesized / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P84228

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Non-polymers , 3 types, 269 molecules

#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.15 M Na citrate, 18-22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.34→85.47 Å / Num. all: 34703 / Num. obs: 34287 / % possible obs: 98.8 % / Observed criterion σ(F): 3.24 / Observed criterion σ(I): 3.24 / Redundancy: 6.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.416 / Num. unique all: 2204 / Rsym value: 0.313 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→85.47 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.256 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.627 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25846 1728 5 %RANDOM
Rwork0.1999 ---
all0.21 34259 --
obs0.20283 32531 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.764 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--3.11 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 2.34→85.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 22 265 6993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226966
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9529455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99324.128344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.826151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7841538
X-RAY DIFFRACTIONr_chiral_restr0.1060.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215340
X-RAY DIFFRACTIONr_mcbond_it0.7421.54101
X-RAY DIFFRACTIONr_mcangle_it1.46826688
X-RAY DIFFRACTIONr_scbond_it2.30632865
X-RAY DIFFRACTIONr_scangle_it3.8784.52761
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1621tight positional0.070.05
A1646medium positional0.070.5
B1621tight thermal0.190.5
B1646medium thermal0.182
LS refinement shellResolution: 2.344→2.405 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 127 -
Rwork0.25 2271 -
obs-2204 96.11 %

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