[English] 日本語
Yorodumi
- PDB-4qxh: Crystal structure of histone demethylase KDM2A-H3K36ME1 with NOG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qxh
TitleCrystal structure of histone demethylase KDM2A-H3K36ME1 with NOG
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 / Zinc finger, FYVE/PHD-type / Leucine-rich repeat domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / [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: 2.2 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 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)96,85010
Polymers96,4386
Non-polymers4124
Water7,152397
1
A: Lysine-specific demethylase 2A
B: Lysine-specific demethylase 2A
E: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4255
Polymers48,2193
Non-polymers2062
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-62 kcal/mol
Surface area17660 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)48,4255
Polymers48,2193
Non-polymers2062
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-60 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.594, 86.761, 171.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
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

-
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

-
Non-polymers , 3 types, 401 molecules

#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5
#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.: 397 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.15 M CITRATE NA, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
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: Jul 1, 2009
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: 2.2→85.43 Å / Num. all: 40070 / Num. obs: 38547 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.54 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.064
Reflection shellResolution: 2.2→2.38 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.58 / Rsym value: 0.435 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0093refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→85.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.356 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24324 2047 5 %RANDOM
Rwork0.18727 ---
obs0.1901 38547 96.14 %-
all-34863 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.522 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-0 Å2
2--4.17 Å2-0 Å2
3----3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→85.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 22 397 7130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196935
X-RAY DIFFRACTIONr_bond_other_d0.0010.026480
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9549399
X-RAY DIFFRACTIONr_angle_other_deg0.838314948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77624.064342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.472151202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1691540
X-RAY DIFFRACTIONr_chiral_restr0.0870.21005
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021642
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2223.4513272
X-RAY DIFFRACTIONr_mcbond_other2.2183.453271
X-RAY DIFFRACTIONr_mcangle_it3.285.1644081
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.743.753663
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 144 -
Rwork0.325 2875 -
obs--98.08 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more