[English] 日本語
Yorodumi
- PDB-4tn7: Crystal structure of mouse KDM2A-H3K36ME-NO complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tn7
TitleCrystal structure of mouse KDM2A-H3K36ME-NO complex
Components
  • (Lysine-specific demethylase ...) x 2
  • Peptide
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / HDMs demethylate histones / neuroepithelial cell differentiation / unmethylated CpG binding / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / heart looping / histone demethylase activity / Chromatin modifying enzymes ...histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / HDMs demethylate histones / neuroepithelial cell differentiation / unmethylated CpG binding / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / heart looping / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / 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 / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / neural tube closure / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / transcription coregulator activity / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / circadian regulation of gene expression / multicellular organism growth / 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 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / regulation of circadian rhythm / neuron differentiation / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / double-strand break repair via nonhomologous end joining / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / in utero embryonic development / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / 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
: / NITRIC OXIDE / SUCCINIC ACID / Lysine-specific demethylase 2A / Histone H3.1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCheng, Z.
Funding support United States, 4items
OrganizationGrant numberCountry
Lymphoma Society and the STARR foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM079641 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM066569 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM097779 United States
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
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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: Peptide
F: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,81611
Polymers96,4386
Non-polymers3785
Water7,278404
1
A: Lysine-specific demethylase 2A
B: Lysine-specific demethylase 2A
E: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4236
Polymers48,2193
Non-polymers2043
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lysine-specific demethylase 2A
D: Lysine-specific demethylase 2A
F: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3935
Polymers48,2193
Non-polymers1742
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.063, 157.928, 48.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

-
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): BL(DE3)
References: UniProt: P59997, [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): BL(DE3)
References: UniProt: P59997, [histone H3]-dimethyl-L-lysine36 demethylase

-
Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Peptide /


Mass: 1652.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS

-
Non-polymers , 4 types, 409 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#6: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 % / Description: PLATE-LIKE CRYSTALS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Li-citrate 18-30% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40902 / % possible obs: 97.9 % / Redundancy: 2.9 % / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.8 / % possible all: 97.5

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1760) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YU1

2yu1


Resolution: 2.2→45.166 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.43 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 2067 5.06 %RANDOM SELECTION
Rwork0.2294 ---
obs0.232 40864 97.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6673 0 20 404 7097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026873
X-RAY DIFFRACTIONf_angle_d0.5329314
X-RAY DIFFRACTIONf_dihedral_angle_d13.1112558
X-RAY DIFFRACTIONf_chiral_restr0.0221000
X-RAY DIFFRACTIONf_plane_restr0.0021194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25440.33131380.27792367X-RAY DIFFRACTION93
2.2544-2.31080.31771240.27192634X-RAY DIFFRACTION98
2.3108-2.37330.32961360.26942596X-RAY DIFFRACTION98
2.3733-2.44310.34241550.27292608X-RAY DIFFRACTION98
2.4431-2.5220.30751330.25262571X-RAY DIFFRACTION98
2.522-2.61210.33661260.252637X-RAY DIFFRACTION98
2.6121-2.71670.30291460.24982584X-RAY DIFFRACTION98
2.7167-2.84030.28221300.24212581X-RAY DIFFRACTION98
2.8403-2.990.31281360.2442564X-RAY DIFFRACTION98
2.99-3.17730.31631400.23652608X-RAY DIFFRACTION98
3.1773-3.42250.28461490.2262586X-RAY DIFFRACTION97
3.4225-3.76680.23851290.20232604X-RAY DIFFRACTION98
3.7668-4.31150.23541380.19862625X-RAY DIFFRACTION98
4.3115-5.43060.23721390.20382612X-RAY DIFFRACTION98
5.4306-45.17570.261480.22442620X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 13.8096 Å / Origin y: -1.0164 Å / Origin z: 10.9226 Å
111213212223313233
T0.2097 Å20.0113 Å2-0.0055 Å2-0.2252 Å20.0119 Å2--0.191 Å2
L0.0586 °2-0.1748 °2-0.1084 °2-0.466 °20.1921 °2---0.033 °2
S-0.0151 Å °0.0075 Å °0.0036 Å °0.0141 Å °0.0055 Å °0.0292 Å °-0.005 Å °-0.0072 Å °0.0017 Å °
Refinement TLS groupSelection details: all

+
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