[English] 日本語
Yorodumi
- PDB-4a7j: Symmetric Dimethylation of H3 Arginine 2 is a Novel Histone Mark ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a7j
TitleSymmetric Dimethylation of H3 Arginine 2 is a Novel Histone Mark that Supports Euchromatin Maintenance
Components
  • HISTONE H3.1T
  • WD REPEAT-CONTAINING PROTEIN 5
KeywordsTRANSCRIPTION / HISTONE METHYLATION
Function / homology
Function and homology information


spermatogonial cell division / histone H3Q5ser reader activity / histone H3K4me1 reader activity / Loss of Function of KMT2D in MLL4 Complex Formation in Kabuki Syndrome / DNA replication-dependent chromatin assembly / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex ...spermatogonial cell division / histone H3Q5ser reader activity / histone H3K4me1 reader activity / Loss of Function of KMT2D in MLL4 Complex Formation in Kabuki Syndrome / DNA replication-dependent chromatin assembly / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell differentiation / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / regulation of cell division / heterochromatin / Chromatin modifying enzymes / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / sperm principal piece / epigenetic regulation of gene expression / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / condensed nuclear chromosome / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / gluconeogenesis / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / skeletal system development / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Negative Regulation of CDH1 Gene Transcription / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / 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 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / mitotic spindle / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / regulation of cell cycle / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region
Similarity search - Function
: / WDR5 beta-propeller domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 ...: / WDR5 beta-propeller domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5 / Histone H3.1 / Histone H3.1t
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMigliori, V. / Muller, J. / Phalke, S. / Low, D. / Bezzi, M. / ChuenMok, W. / Gunaratne, J. / Capasso, P. / Bassi, C. / Cecatiello, V. ...Migliori, V. / Muller, J. / Phalke, S. / Low, D. / Bezzi, M. / ChuenMok, W. / Gunaratne, J. / Capasso, P. / Bassi, C. / Cecatiello, V. / DeMarco, A. / Blackstock, W. / Kuznetsov, V. / Amati, B. / Mapelli, M. / Guccione, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Symmetric Dimethylation of H3R2 is a Newly Identified Histone Mark that Supports Euchromatin Maintenance
Authors: Migliori, V. / Muller, J. / Phalke, S. / Low, D. / Bezzi, M. / Chuenmok, W. / Sahu, S.K. / Gunaratne, J. / Capasso, P. / Bassi, C. / Cecatiello, V. / Demarco, A. / Blackstock, W. / ...Authors: Migliori, V. / Muller, J. / Phalke, S. / Low, D. / Bezzi, M. / Chuenmok, W. / Sahu, S.K. / Gunaratne, J. / Capasso, P. / Bassi, C. / Cecatiello, V. / Demarco, A. / Blackstock, W. / Kuznetsov, V. / Amati, B. / Mapelli, M. / Guccione, E.
History
DepositionNov 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD REPEAT-CONTAINING PROTEIN 5
B: HISTONE H3.1T


Theoretical massNumber of molelcules
Total (without water)36,5262
Polymers36,5262
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8.7 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 46.800, 65.000
Angle α, β, γ (deg.)90.00, 104.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein WD REPEAT-CONTAINING PROTEIN 5 / BMP2-INDUCED 3-KB GENE PROTEIN


Mass: 34802.449 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: P61964
#2: Protein/peptide HISTONE H3.1T / H3/T / H3T / H3/G


Mass: 1724.038 Da / Num. of mol.: 1 / Fragment: HISTONE TAIL, RESIDUES 1-16 / Source method: obtained synthetically / Details: SYMMETRICALLY DIMETHYLATED ARGININE 2 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q16695, UniProt: P68431*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5; 60 MM AMMONIUM SULPHATE; 30% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.937
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 23998 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 5.2 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 3.4 / % possible all: 90

-
Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H13

2h13


Resolution: 1.9→28.31 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1249102.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1109 4.9 %RANDOM
Rwork0.184 ---
obs0.184 22754 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.054 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å21.33 Å2
2--0.95 Å20 Å2
3----2.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 0 244 2645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 171 4.8 %
Rwork0.202 3373 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION22MR_080229.PARAM2MR_080229.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

+
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