[English] 日本語
Yorodumi
- PDB-4hon: Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hon
TitleCrystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate
Components
  • Histone H3 Peptide
  • Lysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / Jumonji C demethylase / JMJD2/KDM4 family / beta barrel fold
Function / homology
Function and homology information


histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / negative regulation of histone H3-K9 trimethylation / positive regulation of chromatin binding / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone H3-K9 demethylation / epigenetic regulation of gene expression / Chromatin modifying enzymes / histone demethylase activity ...histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / negative regulation of histone H3-K9 trimethylation / positive regulation of chromatin binding / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone H3-K9 demethylation / epigenetic regulation of gene expression / Chromatin modifying enzymes / histone demethylase activity / pericentric heterochromatin / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / DNA methylation / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nuclear chromosome / regulation of protein phosphorylation / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / cellular response to ionizing radiation / B-WICH complex positively regulates rRNA expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RMTs methylate histone arginines / HDMs demethylate histones / nucleosome assembly / Meiotic recombination / Pre-NOTCH Transcription and Translation / PKMTs methylate histone lysines / HCMV Early Events / chromatin DNA binding / structural constituent of chromatin / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosome / site of double-strand break / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / extracellular exosome / extracellular region / membrane / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Small domain found in the jumonji family of transcription factors / JmjN domain profile. / jmjN domain / JmjN domain / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain profile. / JmjC domain / Histone H3 signature 1. ...Small domain found in the jumonji family of transcription factors / JmjN domain profile. / jmjN domain / JmjN domain / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain profile. / JmjC domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / 2-OXOGLUTARIC ACID / NICKEL (II) ION / THIOCYANATE ION / 1,3-PROPANDIOL / NITRATE ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsKrishnan, S. / Trievel, R.C.
CitationJournal: Structure / Year: 2013
Title: Structural and Functional Analysis of JMJD2D Reveals Molecular Basis for Site-Specific Demethylation among JMJD2 Demethylases.
Authors: Krishnan, S. / Trievel, R.C.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific demethylase 4D
B: Lysine-specific demethylase 4D
F: Histone H3 Peptide
G: Histone H3 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,33033
Polymers78,3174
Non-polymers2,01329
Water7,350408
1
A: Lysine-specific demethylase 4D
F: Histone H3 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,40320
Polymers39,1582
Non-polymers1,24518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-7 kcal/mol
Surface area14990 Å2
MethodPISA
2
B: Lysine-specific demethylase 4D
G: Histone H3 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,92713
Polymers39,1582
Non-polymers76911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-17 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.202, 79.675, 175.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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

#1: Protein Lysine-specific demethylase 4D / JmjC domain-containing histone demethylation protein 3D / Jumonji domain-containing protein 2D


Mass: 38137.164 Da / Num. of mol.: 2 / Fragment: UNP Residues 12-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JHDM3D, JMJD2D, KDM4D / Plasmid: pHT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Rosetta 2)
References: UniProt: Q6B0I6, 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 H3 Peptide


Mass: 1021.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS

-
Non-polymers , 7 types, 437 molecules

#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#7: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: NO3
#8: Chemical
ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol


Mass: 76.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 7% PEG 3350, 0.1M sodium thiocyanate, 0.35M potassium nitrate, vapor diffusion, hanging drop, temperature 277.15K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.799→25 Å / Num. obs: 89438 / % possible obs: 94.5 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.082 / Χ2: 1.061 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.799-1.8410.60.45562060.9281100
1.84-1.8913.20.41662291.0331100
1.89-1.94110.3454981.138188.2
1.94-214.90.28862671.0821100
2-2.06150.22362321.0871100
2.06-2.13150.18162471.0721100
2.13-2.2214.70.1662321.0831100
2.22-2.3210.20.13941831.131166.4
2.32-2.44150.11562551.0461100
2.44-2.6150.10563021.0971100
2.6-2.8150.08363171.0741100
2.8-3.08150.06863491.0591100
3.08-3.5214.30.06463440.973199.9
3.52-4.4310.30.04440871.11163.4
4.43-25140.0466901.0431100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q8C

2q8c


Resolution: 1.799→24.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.006 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 4486 5 %RANDOM
Rwork0.1892 ---
obs0.1905 89102 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.19 Å2 / Biso mean: 20.5226 Å2 / Biso min: 8.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.73 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.799→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 115 408 5921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225715
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9417736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31723.357277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55515873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.461535
X-RAY DIFFRACTIONr_chiral_restr0.110.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214498
X-RAY DIFFRACTIONr_mcbond_it0.8651.53444
X-RAY DIFFRACTIONr_mcangle_it1.55425460
X-RAY DIFFRACTIONr_scbond_it2.44232271
X-RAY DIFFRACTIONr_scangle_it3.8574.52265
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 341 -
Rwork0.249 6258 -
all-6599 -
obs--95.55 %

+
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