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- PDB-4jlu: Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas -

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Basic information

Entry
Database: PDB / ID: 4jlu
TitleCrystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas
Components
  • BRCA1-A complex subunit Abraxas
  • Breast cancer type 1 susceptibility protein
KeywordsANTITUMOR PROTEIN/SIGNALING PROTEIN / KINASE-PROTEIN BINDING complex / ANTITUMOR PROTEIN-SIGNALING PROTEIN 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 / sex-chromosome dosage compensation / 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 / sex-chromosome dosage compensation / 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 / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / homologous recombination / lateral element / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / 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 / negative regulation of gene expression via chromosomal CpG island methylation / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA-binding transcription activator activity / response to ionizing radiation / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / 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 / polyubiquitin modification-dependent protein binding / protein autoubiquitination / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / Meiotic synapsis / positive regulation of DNA repair / 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 / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / negative regulation of cell growth / Meiotic recombination / fatty acid biosynthetic process / ubiquitin-protein transferase activity / 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 / chromatin organization / chromosome / cellular response to tumor necrosis factor / Neddylation / Processing of DNA double-strand break ends / microtubule binding / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / nuclear body / transcription cis-regulatory region binding / regulation of cell cycle / protein ubiquitination / 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 / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsBadgujar, D. / Varma, A.K.
CitationJournal: To be Published
Title: Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas
Authors: Badgujar, D. / Varma, A.K.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)25,5972
Polymers25,5972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-9 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.599, 113.599, 121.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 24188.820 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1649-1859
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / 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: 1408.280 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 399-409 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6UWZ7

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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: 4.42 Å3/Da / Density % sol: 72.2 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3.5→25 Å / Num. obs: 6221

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMAC5.5.0110refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y98

1y98


Resolution: 3.5→22.19 Å / Cor.coef. Fo:Fc: 0.825 / Cor.coef. Fo:Fc free: 0.743 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 31.728 / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.641
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3273 306 4.9 %RANDOM
Rwork0.2983 ---
obs0.2997 6221 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50 Å2 / Biso mean: 49.9077 Å2 / Biso min: 37.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.5→22.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 0 0 1792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221836
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9462492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8565220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.73423.7588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.04515.096313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0291512
X-RAY DIFFRACTIONr_chiral_restr0.140.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211388
X-RAY DIFFRACTIONr_mcbond_it0.0871.51103
X-RAY DIFFRACTIONr_mcangle_it0.16421795
X-RAY DIFFRACTIONr_scbond_it0.2163733
X-RAY DIFFRACTIONr_scangle_it0.4034.5697
LS refinement shellResolution: 3.5→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 19 -
Rwork0.351 421 -
all-440 -
obs--100 %

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