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- PDB-3sqd: Crystal structure of human PTIP BRCT5/6-gamma H2AX complex -

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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 / XY body / MLL3/4 complex ...: / chorion development / : / : / : / : / positive regulation of isotype switching / positive regulation of isotype switching to IgG isotypes / XY body / MLL3/4 complex / regulation of cell cycle G2/M phase transition / histone methyltransferase complex / response to ionizing radiation / site of DNA damage / DNA damage response, signal transduction by p53 class mediator / endothelial cell migration / positive regulation of transcription initiation by RNA polymerase II / vasculogenesis / adipose tissue development / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin organization / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / positive regulation of DNA repair / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / 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) / meiotic cell cycle / PRC2 methylates histones and DNA / condensed nuclear chromosome / replication fork / DNA damage checkpoint signaling / positive regulation of protein ubiquitination / male germ cell nucleus / Defective pyroptosis / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / 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 / G2/M DNA damage checkpoint / negative regulation of DNA-binding transcription factor activity / DNA Damage/Telomere Stress Induced Senescence / cellular response to gamma radiation / cerebral cortex development / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / double-strand break repair via nonhomologous end joining / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / cellular senescence / nucleosome / double-strand break repair / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / site of double-strand break / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / DNA recombination / Estrogen-dependent gene expression / damaged DNA binding / nuclear speck / protein heterodimerization activity / Amyloid fiber formation / 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 / 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. ...Regulator of Ty1 transposition protein 107 BRCT domain / twin 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 H2A / Histone 2A / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.53 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

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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

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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

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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

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