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- PDB-4y2g: Structure of BRCA1 BRCT domains in complex with Abraxas single ph... -

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Basic information

Entry
Database: PDB / ID: 4y2g
TitleStructure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide
Components
  • BRCA1-A complex subunit Abraxas
  • Breast cancer type 1 susceptibility protein
KeywordsANTITUMOR PROTEIN / DNA damage response / BRCT / phosphopeptide / ligase-peptide complex
Function / homology
Function and homology information


Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / : / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / attachment of spindle microtubules to kinetochore ...Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / : / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / attachment of spindle microtubules to kinetochore / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / homologous recombination / lateral element / XY body / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / dosage compensation by inactivation of X chromosome / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to PALB2 / : / mitotic G2/M transition checkpoint / postreplication repair / DNA repair complex / RNA polymerase binding / centrosome cycle / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / DNA-binding transcription activator activity / intracellular non-membrane-bounded organelle / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / polyubiquitin modification-dependent protein binding / negative regulation of cell cycle / mitotic spindle assembly / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / localization / regulation of DNA repair / protein autoubiquitination / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of DNA repair / Meiotic synapsis / tubulin binding / male germ cell nucleus / chromosome segregation / cellular response to ionizing radiation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / negative regulation of cell growth / Metalloprotease DUBs / Meiotic recombination / ubiquitin-protein transferase activity / fatty acid biosynthetic process / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / double-strand break repair / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / Neddylation / cellular response to tumor necrosis factor / chromatin organization / Processing of DNA double-strand break ends / microtubule binding / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / protein ubiquitination / nuclear body / transcription cis-regulatory region binding / regulation of cell cycle / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription
Similarity search - Function
FAM175 family, BRCA1-A complex, Abraxas 1 subunit / BRCA1-A complex subunit Abraxas 1 MPN domain / FAM175 family / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) ...FAM175 family, BRCA1-A complex, Abraxas 1 subunit / BRCA1-A complex subunit Abraxas 1 MPN domain / FAM175 family / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / MPN domain / MPN domain profile. / BRCT domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Breast cancer type 1 susceptibility protein / BRCA1-A complex subunit Abraxas 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWu, Q. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust093167/Z/10/Z United Kingdom
CitationJournal: Mol.Cell / Year: 2016
Title: Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites.
Authors: Wu, Q. / Paul, A. / Su, D. / Mehmood, S. / Foo, T.K. / Ochi, T. / Bunting, E.L. / Xia, B. / Robinson, C.V. / Wang, B. / Blundell, T.L.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Breast cancer type 1 susceptibility protein
B: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)26,7352
Polymers26,7352
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-8 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.847, 63.847, 93.367
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 Breast cancer type 1 susceptibility protein / RING finger protein 53


Mass: 25796.668 Da / Num. of mol.: 1 / Fragment: UNP residues 1646-1859
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Production host: Escherichia coli (E. coli)
References: UniProt: P38398, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide BRCA1-A complex subunit Abraxas / Coiled-coil domain-containing protein 98 / Protein FAM175A


Mass: 937.910 Da / Num. of mol.: 1 / Fragment: UNP residues 403-409 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6UWZ7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Lithium chloride, Tris, PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→47.6 Å / Num. obs: 8000 / % possible obs: 99.9 % / Redundancy: 9.3 % / Rsym value: 0.051 / Net I/σ(I): 24
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 5.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IT15

Resolution: 2.5→47.576 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 796 9.95 %
Rwork0.2149 --
obs0.2185 7998 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→47.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 0 3 1724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071763
X-RAY DIFFRACTIONf_angle_d0.8232401
X-RAY DIFFRACTIONf_dihedral_angle_d13.038622
X-RAY DIFFRACTIONf_chiral_restr0.044273
X-RAY DIFFRACTIONf_plane_restr0.004304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.65670.3741290.35621162X-RAY DIFFRACTION100
2.6567-2.86180.33691280.29131179X-RAY DIFFRACTION100
2.8618-3.14980.32671290.31561191X-RAY DIFFRACTION100
3.1498-3.60540.271330.24521185X-RAY DIFFRACTION100
3.6054-4.54190.21941350.20461212X-RAY DIFFRACTION100
4.5419-47.58470.2221420.16411273X-RAY DIFFRACTION100

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