[English] 日本語
Yorodumi
- PDB-2ot7: Crystal structure of JMJD2A complexed with histone H3 peptide mon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ot7
TitleCrystal structure of JMJD2A complexed with histone H3 peptide monomethylated at Lys9
Components
  • JmjC domain-containing histone demethylation protein 3A
  • histone 3 K9 monomethyl
KeywordsOXIDOREDUCTASE / Fe / double-stranded beta helix / demethylase / oxygenase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / Chromatin modifying enzymes / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / negative regulation of autophagy / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / fibrillar center / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain ...: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / 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 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4A / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.135 Å
AuthorsKavanagh, K.L. / Ng, S.S. / Pilka, E. / McDonough, M.A. / Savitsky, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. ...Kavanagh, K.L. / Ng, S.S. / Pilka, E. / McDonough, M.A. / Savitsky, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Schofield, C.J. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Nature / Year: 2007
Title: Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.
Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / ...Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / Borowski, T. / Sundstrom, M. / Schofield, C.J. / Oppermann, U.
History
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jun 29, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_radiation_wavelength ...database_2 / diffrn_radiation_wavelength / diffrn_source / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: JmjC domain-containing histone demethylation protein 3A
B: JmjC domain-containing histone demethylation protein 3A
C: histone 3 K9 monomethyl
D: histone 3 K9 monomethyl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,91710
Polymers90,3754
Non-polymers5426
Water4,738263
1
A: JmjC domain-containing histone demethylation protein 3A
C: histone 3 K9 monomethyl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4585
Polymers45,1872
Non-polymers2713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: JmjC domain-containing histone demethylation protein 3A
D: histone 3 K9 monomethyl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4585
Polymers45,1872
Non-polymers2713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.209, 149.842, 57.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A


Mass: 44326.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD2A, JHDM3A, JMJD2, KIAA0677 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O75164, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Protein/peptide histone 3 K9 monomethyl


Mass: 860.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic H3 peptide monomethylated at K9. Its sequence is based on human histone H3 fragment (residues 7-14), gene HIST1H3A
References: UniProt: P68431*PLUS

-
Non-polymers , 4 types, 269 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 3350, 100 mM Citrate, 2 mM NiCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.135→83.92 Å / Num. all: 48784 / Num. obs: 48784 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.9
Reflection shellResolution: 2.135→2.25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2 / Num. unique all: 7095 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2OQ7

2oq7


Resolution: 2.135→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.989 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.215 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24072 2031 4.2 %RANDOM
Rwork0.18676 ---
all0.18909 45914 --
obs0.18909 45914 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.135→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 24 263 6017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225929
X-RAY DIFFRACTIONr_bond_other_d0.0010.024080
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9468036
X-RAY DIFFRACTIONr_angle_other_deg0.8973.0019871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97123.309272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42215959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.221532
X-RAY DIFFRACTIONr_chiral_restr0.0770.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021296
X-RAY DIFFRACTIONr_nbd_refined0.1960.21117
X-RAY DIFFRACTIONr_nbd_other0.1830.24003
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22838
X-RAY DIFFRACTIONr_nbtor_other0.0850.22901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.38433719
X-RAY DIFFRACTIONr_mcbond_other0.63231427
X-RAY DIFFRACTIONr_mcangle_it3.33155740
X-RAY DIFFRACTIONr_scbond_it5.16572667
X-RAY DIFFRACTIONr_scangle_it6.362112295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.135→2.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 166 -
Rwork0.295 3383 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4716-0.79080.48831.9986-0.38450.93430.13410.2923-0.0292-0.2758-0.1770.15190.03590.10940.0428-0.12630.02250.0106-0.0863-0.0124-0.1478-30.3943-22.1087-22.9005
22.1617-0.4169-0.07512.1003-0.37581.7530.08780.01760.0506-0.29710.0223-0.20670.2343-0.12-0.1101-0.0888-0.0379-0.0379-0.18530.0146-0.1148-37.9127-54.81152.3462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 355
2X-RAY DIFFRACTION2B7 - 354

+
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