[English] 日本語
Yorodumi
- PDB-4qwn: Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure -

+
Open data


ID or keywords:

Loading...

-
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 H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / Interleukin-7 signaling / HDMs demethylate histones / Condensation of Prophase Chromosomes / HDACs deacetylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines ...Chromatin modifying enzymes / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / Interleukin-7 signaling / HDMs demethylate histones / Condensation of Prophase Chromosomes / HDACs deacetylate 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 / 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 / histone demethylase activity / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / neural tube closure / transcription coregulator activity / circadian regulation of gene expression / neuron differentiation / multicellular organism growth / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / chromatin organization / gene expression / 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 / 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. / Helix non-globular / Zinc finger, PHD-finger / 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 / Special / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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: 2.1 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

-
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)96,84810
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

-
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, 199 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.: 195 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
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