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- PDB-4u4a: Complex Structure of BRCA1 BRCT with singly phospho Abraxas -

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Basic information

Entry
Database: PDB / ID: 4u4a
TitleComplex Structure of BRCA1 BRCT with singly phospho Abraxas
Components
  • BRCA1-A complex subunit Abraxas
  • Breast cancer type 1 susceptibility protein
KeywordsANTITUMOR PROTEIN/SIGNALING PROTEIN / complex / phosphospecific / ANTITUMOR PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / 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 / negative regulation of centriole replication / sex-chromosome dosage compensation ...histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / 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 / negative regulation of centriole replication / sex-chromosome dosage compensation / attachment of spindle microtubules to kinetochore / negative regulation of intracellular estrogen receptor signaling pathway / random inactivation of X chromosome / nuclear ubiquitin ligase complex / ubiquitin-modified histone reader activity / chordate embryonic development / cellular response to indole-3-methanol / gamma-tubulin ring complex / negative regulation of fatty acid biosynthetic process / DNA strand resection involved in replication fork processing / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / homologous recombination / lateral element / protein K6-linked ubiquitination / Impaired BRCA2 binding to PALB2 / regulation of DNA damage checkpoint / XY body / mitotic G2/M transition checkpoint / centrosome cycle / RNA polymerase binding / postreplication repair / DNA repair complex / Homologous DNA Pairing and Strand Exchange / 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 / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / intracellular membraneless organelle / HDR through Single Strand Annealing (SSA) / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / negative regulation of reactive oxygen species metabolic process / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / polyubiquitin modification-dependent protein binding / mitotic spindle assembly / ubiquitin ligase complex / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein autoubiquitination / Meiotic synapsis / tubulin binding / male germ cell nucleus / positive regulation of DNA repair / cellular response to ionizing radiation / chromosome segregation / Nonhomologous End-Joining (NHEJ) / TP53 Regulates Transcription of DNA Repair Genes / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / negative regulation of cell growth / RING-type E3 ubiquitin transferase / Meiotic recombination / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / fatty acid biosynthetic process / ubiquitin-protein transferase activity / p53 binding / KEAP1-NFE2L2 pathway / cellular response to tumor necrosis factor / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / Neddylation / chromosome / Processing of DNA double-strand break ends / microtubule binding / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / protein ubiquitination / nuclear body / chromatin remodeling / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / positive regulation of gene expression / regulation of transcription by RNA polymerase II
Similarity search - Function
FAM175 family, BRCA1-A complex, Abraxas 1 subunit / FAM175 family / BRCA1-A complex subunit Abraxas 1 MPN domain / 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 / FAM175 family / BRCA1-A complex subunit Abraxas 1 MPN domain / 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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / MPN domain / MPN domain profile. / 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 / Resolution: 3.51 Å
AuthorsBadgujar, D. / Hosur, M.V. / Varma, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/PR12565/BID/07/303/2009 India
CitationJournal: To Be Published
Title: Complex Structure of BRCA1 BRCT with singly phospho Abraxas
Authors: Badgujar, D. / Hosur, M.V. / Varma, A.K.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Breast cancer type 1 susceptibility protein
C: Breast cancer type 1 susceptibility protein
D: BRCA1-A complex subunit Abraxas
E: BRCA1-A complex subunit Abraxas
F: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)77,5796
Polymers77,5796
Non-polymers00
Water00
1
A: Breast cancer type 1 susceptibility protein
D: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)25,8602
Polymers25,8602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-7 kcal/mol
Surface area11840 Å2
MethodPISA
2
B: Breast cancer type 1 susceptibility protein
E: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)25,8602
Polymers25,8602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-8 kcal/mol
Surface area11970 Å2
MethodPISA
3
C: Breast cancer type 1 susceptibility protein
F: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)25,8602
Polymers25,8602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-7 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.500, 187.500, 85.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Breast cancer type 1 susceptibility protein / RING finger protein 53


Mass: 24531.234 Da / Num. of mol.: 3 / Fragment: BRCT (UNP RESIDUES 1646-1859)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Plasmid: GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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: 1328.301 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 399-409 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6UWZ7
Has protein modificationY

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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: 4.85 Å3/Da / Density % sol: 74.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01M Cobalt Chloride, 0.1 M(MES), pH 6.5, 30% PEG Mono Methyl Ether (MME) 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.51→59.89 Å / Num. obs: 15491 / % possible obs: 100 % / Redundancy: 6.9 % / Net I/σ(I): 9.5

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementResolution: 3.51→59.89 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.808 / SU B: 105.472 / SU ML: 0.757 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.876 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3618 754 5.1 %RANDOM
Rwork0.3009 14041 --
obs0.3042 14795 75.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 245.24 Å2 / Biso mean: 57.2 Å2 / Biso min: 19.94 Å2
Baniso -1Baniso -2Baniso -3
1--7.45 Å2-0 Å2-0 Å2
2---7.45 Å20 Å2
3---14.9 Å2
Refinement stepCycle: LAST / Resolution: 3.51→59.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 0 0 5332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195475
X-RAY DIFFRACTIONr_bond_other_d0.0050.025172
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9447424
X-RAY DIFFRACTIONr_angle_other_deg1.046311883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0745661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77123.454249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79715931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1941536
X-RAY DIFFRACTIONr_chiral_restr0.0920.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216091
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021299
LS refinement shellResolution: 3.513→3.604 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 17 -
Rwork0.391 261 -
all-278 -
obs--19.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4194-0.4856-0.0039.8042-3.17134.48130.5471-0.3096-0.59830.02890.04070.440.0591-0.0898-0.58780.7349-0.0793-0.23371.10150.29670.252868.8336164.827916.7168
28.96811.88360.52827.543-0.33421.91620.024-0.21740.28590.40050.5592.3655-0.19590.0546-0.5831.27550.12380.47971.12990.53411.038747.0771191.553114.5838
32.41170.07270.38010.31090.21975.66950.26481.1629-1.1609-0.43560.1398-0.14810.3346-0.1781-0.40451.8234-0.0982-0.4731.7871-0.31660.882966.6048142.3219-10.232
416.15342.4424-3.15930.4964-0.74681.4484-0.9117-1.04171.0392-0.39550.1223-0.08590.6308-0.13640.78941.2984-0.05270.29941.2904-0.12741.392243.2151209.509716.6616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1646 - 1859
2X-RAY DIFFRACTION2B1646 - 1859
3X-RAY DIFFRACTION3C1648 - 1859
4X-RAY DIFFRACTION4E399 - 409

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