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- PDB-4w5a: Complex structure of ATRX ADD bound to H3K9me3S10ph peptide -

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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, subtelomeric region / chromosome organization involved in meiotic cell cycle / negative regulation of chromosome condensation / Sertoli cell development / 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, subtelomeric region / chromosome organization involved in meiotic cell cycle / negative regulation of chromosome condensation / Sertoli cell development / Barr body / regulation of centromere complex assembly / cellular response to hydroxyurea / meiotic spindle organization / chromo shadow domain binding / DNA translocase activity / condensed chromosome, centromeric region / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / protein localization to chromosome, telomeric region / nucleosomal DNA binding / nuclear chromosome / seminiferous tubule development / nucleus organization / spermatid development / positive regulation of telomere maintenance / replication fork processing / single fertilization / subtelomeric heterochromatin formation / heterochromatin / pericentric heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / forebrain development / : / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA damage response, signal transduction by p53 class mediator / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / PML body / multicellular organism growth / B-WICH complex positively regulates rRNA expression / Meiotic recombination / chromatin DNA binding / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / male gonad development / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / spermatogenesis / DNA helicase / Estrogen-dependent gene expression / histone binding / transcription by RNA polymerase II / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / cell population proliferation / nuclear body / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity
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 / 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 / Helicase conserved C-terminal domain / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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