[English] 日本語
Yorodumi
- PDB-7d4a: The Crystal Structure of human JMJD2A Tudor domain from Biortus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d4a
TitleThe Crystal Structure of human JMJD2A Tudor domain from Biortus
ComponentsLysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / catalytic activity / demethylase activity / histone demethylase activity
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / negative regulation of autophagy / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / zinc ion binding / nucleoplasm / nucleus / 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. / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsWang, F. / Lv, Z. / Cheng, W. / Lin, D. / Ju, C. / Bao, X. / Zhu, B.
CitationJournal: To Be Published
Title: The Crystal Structure of human JMJD2A from Biortus.
Authors: Wang, F. / Lv, Z. / Cheng, W. / Lin, D. / Ju, C. / Bao, X. / Zhu, B.
History
DepositionSep 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1412
Polymers15,0441
Non-polymers961
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.110, 135.110, 135.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132

-
Components

#1: Protein Lysine-specific demethylase 4A / JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A / ...JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A / [histone H3]-trimethyl-L-lysine(36) demethylase 4A / [histone H3]-trimethyl-L-lysine(9) demethylase 4A


Mass: 15044.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Production host: Escherichia coli (E. coli)
References: UniProt: O75164, [histone H3]-trimethyl-L-lysine9 demethylase, [histone H3]-trimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaCl, 0.1M HEPES pH7.5, 1.6M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976253 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976253 Å / Relative weight: 1
ReflectionResolution: 2.2→67.56 Å / Num. obs: 11007 / % possible obs: 99.9 % / Redundancy: 41.4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 21.4
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 2.749 / Num. unique obs: 836

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gf7

2gf7


Resolution: 2.201→55.219 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.948 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.196 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2722 558 5.077 %
Rwork0.2297 10433 -
all0.232 --
obs-10991 99.918 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.144 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.201→55.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 5 20 955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.013955
X-RAY DIFFRACTIONr_bond_other_d0.0010.017823
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.6471297
X-RAY DIFFRACTIONr_angle_other_deg1.1971.5791921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5695115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97624.38657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45715153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.616154
X-RAY DIFFRACTIONr_chiral_restr0.0460.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02199
X-RAY DIFFRACTIONr_nbd_refined0.1770.2145
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.2741
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2454
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2415
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.227
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0520.28
X-RAY DIFFRACTIONr_nbd_other0.190.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0810.26
X-RAY DIFFRACTIONr_mcbond_it2.4355.359463
X-RAY DIFFRACTIONr_mcbond_other2.3925.352462
X-RAY DIFFRACTIONr_mcangle_it3.688.026577
X-RAY DIFFRACTIONr_mcangle_other3.6988.032578
X-RAY DIFFRACTIONr_scbond_it3.2115.904492
X-RAY DIFFRACTIONr_scbond_other3.1855.877488
X-RAY DIFFRACTIONr_scangle_it5.2678.696720
X-RAY DIFFRACTIONr_scangle_other5.258.656714
X-RAY DIFFRACTIONr_lrange_it6.8960.986981
X-RAY DIFFRACTIONr_lrange_other6.87260.972980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.2580.323320.323761X-RAY DIFFRACTION100
2.258-2.320.288410.288731X-RAY DIFFRACTION99.8706
2.32-2.3870.353270.303735X-RAY DIFFRACTION100
2.387-2.4610.419360.304685X-RAY DIFFRACTION100
2.461-2.5410.383350.327671X-RAY DIFFRACTION99.7175
2.541-2.630.307400.305652X-RAY DIFFRACTION100
2.63-2.7290.26310.26632X-RAY DIFFRACTION100
2.729-2.8410.32380.301606X-RAY DIFFRACTION99.845
2.841-2.9670.29290.276581X-RAY DIFFRACTION100
2.967-3.1110.304340.298578X-RAY DIFFRACTION100
3.111-3.2790.352300.278543X-RAY DIFFRACTION99.4792
3.279-3.4770.356320.245505X-RAY DIFFRACTION100
3.477-3.7170.268250.22483X-RAY DIFFRACTION100
3.717-4.0140.252310.203444X-RAY DIFFRACTION100
4.014-4.3950.228230.177423X-RAY DIFFRACTION100
4.395-4.9110.165120.148388X-RAY DIFFRACTION100
4.911-5.6660.241200.186343X-RAY DIFFRACTION100
5.666-6.9270.201230.201291X-RAY DIFFRACTION100
6.927-9.7460.243100.195246X-RAY DIFFRACTION100
9.746-55.2190.241100.21149X-RAY DIFFRACTION99.375

+
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