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- PDB-4qwn: Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure -

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Basic information

Entry
Database: PDB / ID: 4qwn
TitleHistone demethylase KDM2A-H3K36ME1-alpha-KG complex structure
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 H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / Interleukin-7 signaling / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / HDACs deacetylate histones / PRC2 methylates histones and DNA / HATs acetylate histones ...Chromatin modifying enzymes / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / Interleukin-7 signaling / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / HDACs deacetylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / neuroepithelial cell differentiation / Factors involved in megakaryocyte development and platelet production / unmethylated CpG binding / Estrogen-dependent gene expression / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / heart looping / transcription initiation-coupled chromatin remodeling / epigenetic regulation of gene expression / neural tube closure / circadian regulation of gene expression / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / multicellular organism growth / neuron differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / gene expression / in utero embryonic development / protein heterodimerization activity / negative regulation of gene expression / chromatin binding / positive regulation of gene expression / negative regulation of apoptotic process / chromatin / negative regulation of transcription by RNA polymerase II / 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 ...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 / F-box domain / 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. / Helix non-globular / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Special / Leucine-rich repeat domain superfamily / 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 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NICKEL (II) ION / [histone H3]-dimethyl-L-lysine(36) demethylase / Lysine-specific demethylase 2A / Histone H3.2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)96,84810
Polymers96,4386
Non-polymers4104
Water3,513195
1
A: Lysine-specific demethylase 2A
B: Lysine-specific demethylase 2A
E: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4245
Polymers48,2193
Non-polymers2052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-58 kcal/mol
Surface area17780 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)48,4245
Polymers48,2193
Non-polymers2052
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-56 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.343, 87.568, 171.681
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: 1652.940 Da / Num. of mol.: 2 / Fragment: UNP residues 30-44 / Source method: obtained synthetically / Details: mono-methylated H3 peptide was synthesized / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P84228

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Non-polymers , 3 types, 199 molecules

#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


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


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


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M Sodium citrate, 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 25, 2010
RadiationMonochromator: 0.97918 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→85.94 Å / Num. all: 48785 / Num. obs: 47906 / % possible obs: 98.2 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.108 / Rsym value: 0.105 / Net I/σ(I): 16.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3122 / Rsym value: 0.372 / % possible all: 97.5

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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: 2.1→85.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.258 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26401 2425 5.1 %RANDOM
Rwork0.21489 ---
all0.22 47873 --
obs0.21747 45448 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.463 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.1→85.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 22 195 6869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226885
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9549337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30524.172338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.404151188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8441538
X-RAY DIFFRACTIONr_chiral_restr0.1130.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215260
X-RAY DIFFRACTIONr_mcbond_it0.8381.54071
X-RAY DIFFRACTIONr_mcangle_it1.59126636
X-RAY DIFFRACTIONr_scbond_it2.57832814
X-RAY DIFFRACTIONr_scangle_it4.1284.52697
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1572tight positional0.070.05
A1654medium positional0.080.5
B1572tight thermal0.220.5
B1654medium thermal0.242
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 146 -
Rwork0.325 3234 -
obs--95.48 %

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