[English] 日本語
Yorodumi
- PDB-4w5a: Complex structure of ATRX ADD bound to H3K9me3S10ph peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w5a
TitleComplex structure of ATRX ADD bound to H3K9me3S10ph peptide
Components
  • Peptide from Histone H3.3
  • Transcriptional regulator ATRX
KeywordsHYDROLASE/STRUCTURAL PROTEIN / Epigenetic regulation / Complex / Transcription / Mitosis / HYDROLASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


post-embryonic forelimb morphogenesis / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / positive regulation of nuclear cell cycle DNA replication / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / chromosome organization involved in meiotic cell cycle / chromosome, subtelomeric region / Sertoli cell development / negative regulation of chromosome condensation / Barr body ...post-embryonic forelimb morphogenesis / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / positive regulation of nuclear cell cycle DNA replication / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / chromosome organization involved in meiotic cell cycle / chromosome, subtelomeric region / Sertoli cell development / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / meiotic spindle organization / cellular response to hydroxyurea / DNA translocase activity / muscle cell differentiation / chromo shadow domain binding / pericentric heterochromatin formation / positive regulation of telomere maintenance / inner kinetochore / condensed chromosome, centromeric region / ATP-dependent chromatin remodeler activity / oocyte maturation / protein localization to chromosome, telomeric region / nuclear chromosome / nucleus organization / seminiferous tubule development / replication fork processing / DNA damage response, signal transduction by p53 class mediator / spermatid development / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / nucleosomal DNA binding / forebrain development / Inhibition of DNA recombination at telomere / methylated histone binding / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / helicase activity / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / chromatin DNA binding / PML body / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA helicase / cell population proliferation / transcription by RNA polymerase II / chromosome, telomeric region / nuclear body / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / chromatin binding / regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / metal ion binding
Similarity search - Function
ATRX, ADD domain / Cysteine Rich ADD domain / ADD domain / ADD domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H3 signature 1. / Helicase conserved C-terminal domain ...ATRX, ADD domain / Cysteine Rich ADD domain / ADD domain / ADD domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcriptional regulator ATRX / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhao, D. / Xiang, B. / Li, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natral Science Foundation of China31270763 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: ATRX tolerates activity-dependent histone H3 methyl/phos switching to maintain repetitive element silencing in neurons
Authors: Noh, K.M. / Maze, I. / Zhao, D. / Xiang, B. / Wenderski, W. / Lewis, P.W. / Shen, L. / Li, H. / Allis, C.D.
History
DepositionAug 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_conn / struct_conn_type / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _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_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator ATRX
C: Peptide from Histone H3.3
B: Transcriptional regulator ATRX
D: Peptide from Histone H3.3
E: Transcriptional regulator ATRX
F: Peptide from Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,03415
Polymers49,4456
Non-polymers5899
Water34219
1
A: Transcriptional regulator ATRX
C: Peptide from Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6785
Polymers16,4822
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-5 kcal/mol
Surface area8310 Å2
MethodPISA
2
B: Transcriptional regulator ATRX
D: Peptide from Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6785
Polymers16,4822
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-5 kcal/mol
Surface area8310 Å2
MethodPISA
3
E: Transcriptional regulator ATRX
F: Peptide from Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6785
Polymers16,4822
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-3 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.522, 75.522, 137.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Transcriptional regulator ATRX / ATP-dependent helicase ATRX / X-linked helicase II / X-linked nuclear protein / XNP / Znf-HX


Mass: 14793.869 Da / Num. of mol.: 3 / Fragment: UNP residues 167-289 / Mutation: K251R, F284Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATRX, RAD54L, XH2 / Plasmid: pGood6p
Details (production host): Modified pGEX6p vector with N-GST and C-His tags
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46100, DNA helicase
#2: Protein/peptide Peptide from Histone H3.3


Mass: 1687.856 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.29 Å3/Da / Density % sol: 46.31 % / Description: Hexagonal rod-like
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2 / PH range: 6

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 14562 / Num. obs: 14504 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 62.8 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 26.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 3.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QL9

3ql9


Resolution: 2.6→37.5 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 1111 7.68 %Random selection
Rwork0.2211 ---
obs0.224 14463 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.4 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 9 19 3229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033257
X-RAY DIFFRACTIONf_angle_d0.84396
X-RAY DIFFRACTIONf_dihedral_angle_d15.451210
X-RAY DIFFRACTIONf_chiral_restr0.029468
X-RAY DIFFRACTIONf_plane_restr0.003567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5986-2.71690.35281570.29061599X-RAY DIFFRACTION98
2.7169-2.86010.36311500.26921613X-RAY DIFFRACTION100
2.8601-3.03920.33331330.27661658X-RAY DIFFRACTION100
3.0392-3.27370.32471180.25981712X-RAY DIFFRACTION100
3.2737-3.60290.26331490.22891618X-RAY DIFFRACTION100
3.6029-4.12370.23471350.19711685X-RAY DIFFRACTION100
4.1237-5.19320.22091300.19171681X-RAY DIFFRACTION99
5.19-37.60.241390.21581786X-RAY DIFFRACTION99

+
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://pdbjlvh1.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