[English] 日本語
Yorodumi
- PDB-3sqd: Crystal structure of human PTIP BRCT5/6-gamma H2AX complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sqd
TitleCrystal structure of human PTIP BRCT5/6-gamma H2AX complex
Components
  • Histone H2A.x
  • PAX-interacting protein 1
KeywordsCELL CYCLE / tandem brct domains / H2AX
Function / homology
Function and homology information


chorion development / positive regulation of isotype switching / positive regulation of isotype switching to IgG isotypes / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / XY body / chromatin-protein adaptor activity / protein localization to site of double-strand break / regulation of cell cycle G2/M phase transition / response to ionizing radiation ...chorion development / positive regulation of isotype switching / positive regulation of isotype switching to IgG isotypes / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / XY body / chromatin-protein adaptor activity / protein localization to site of double-strand break / regulation of cell cycle G2/M phase transition / response to ionizing radiation / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / site of DNA damage / adipose tissue development / positive regulation of transcription initiation by RNA polymerase II / endothelial cell migration / vasculogenesis / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of protein ubiquitination / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / negative regulation of DNA-binding transcription factor activity / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / positive regulation of DNA repair / DNA methylation / Condensation of Prophase Chromosomes / DNA damage checkpoint signaling / Chromatin modifications during the maternal to zygotic transition (MZT) / male germ cell nucleus / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / condensed nuclear chromosome / replication fork / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / meiotic cell cycle / double-strand break repair via homologous recombination / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / DNA damage response, signal transduction by p53 class mediator / 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 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / heterochromatin formation / site of double-strand break / double-strand break repair / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / Processing of DNA double-strand break ends / chromosome / Senescence-Associated Secretory Phenotype (SASP) / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / histone binding / spermatogenesis / DNA recombination / damaged DNA binding / Estrogen-dependent gene expression / nuclear speck / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / DNA repair / centrosome / DNA damage response / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
: / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...: / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H2AX / PAX-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.153 Å
AuthorsYan, W. / Shao, Z.H.
CitationJournal: To be Published
Title: Crystal structure of human PTIP BRCT5/6-gamma H2AX
Authors: Yan, W. / Shao, Z.H.
History
DepositionJul 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.2Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PAX-interacting protein 1
B: PAX-interacting protein 1
C: Histone H2A.x
D: Histone H2A.x


Theoretical massNumber of molelcules
Total (without water)52,7654
Polymers52,7654
Non-polymers00
Water4,918273
1
A: PAX-interacting protein 1
C: Histone H2A.x


Theoretical massNumber of molelcules
Total (without water)26,3822
Polymers26,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-8 kcal/mol
Surface area12760 Å2
MethodPISA
2
B: PAX-interacting protein 1
D: Histone H2A.x


Theoretical massNumber of molelcules
Total (without water)26,3822
Polymers26,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-7 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.973, 101.812, 61.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PAX-interacting protein 1 / ptip / PAX transactivation activation domain-interacting protein


Mass: 25147.156 Da / Num. of mol.: 2 / Fragment: BRCT 5-BRCT 6 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTIP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6ZW49
#2: Protein/peptide Histone H2A.x / H2AX / H2a/x


Mass: 1235.236 Da / Num. of mol.: 2 / Fragment: UNP residues 134-143 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P16104
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.53 Å3/Da / Density % sol: 51.46 % / Mosaicity: 0.744 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18% PEG4000, 100mM Nacacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 287K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 2, 2010
RadiationMonochromator: PLANE GRATING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. all: 29527 / Num. obs: 29232 / % possible obs: 99 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 5.8 % / Rmerge(I) obs: 0.105 / Χ2: 1.212 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.194.20.44713331.02193
2.19-2.234.50.39313981.051196.3
2.23-2.274.90.38714271.125198.3
2.27-2.325.30.37514451.074199.2
2.32-2.375.60.36514311.048199.4
2.37-2.4260.32114601.099199.6
2.42-2.486.20.29314461.159199.9
2.48-2.556.30.25914531.207199.7
2.55-2.626.40.22914591.283199.7
2.62-2.716.40.20214651.336199.7
2.71-2.86.40.1714701.343199.8
2.8-2.926.40.15414681.51199.8
2.92-3.056.40.12814501.488199.6
3.05-3.216.30.10614551.34199.9
3.21-3.416.20.09414971.388199.8
3.41-3.6760.08414761.07199.9
3.67-4.045.80.07715011.179199.8
4.04-4.625.70.06714861.19199.8
4.62-5.815.60.06315440.849199.8
5.81-255.10.05715681.193197.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 59.03 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å44.87 Å
Translation3 Å44.87 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L40

3l40


Resolution: 2.153→24.994 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8178 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1482 5.08 %random
Rwork0.1972 ---
all0.22 29527 --
obs0.1997 29188 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.896 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 84.86 Å2 / Biso mean: 35.8765 Å2 / Biso min: 14.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.1726 Å20 Å20 Å2
2---0.0503 Å2-0 Å2
3----0.1223 Å2
Refinement stepCycle: LAST / Resolution: 2.153→24.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 0 273 3741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073541
X-RAY DIFFRACTIONf_angle_d1.0284784
X-RAY DIFFRACTIONf_chiral_restr0.067545
X-RAY DIFFRACTIONf_plane_restr0.004597
X-RAY DIFFRACTIONf_dihedral_angle_d12.91312
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.153-2.22990.3141360.25572389252587
2.2299-2.31910.31171490.23352730287998
2.3191-2.42460.26831380.2262780291899
2.4246-2.55230.30731530.21827792932100
2.5523-2.7120.28711610.214727762937100
2.712-2.92110.26161310.211828222953100
2.9211-3.21450.27841510.200927802931100
3.2145-3.67840.21711590.182528423001100
3.6784-4.62960.20831560.160728483004100
4.6296-24.99540.21411480.18932960310898

+
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