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- PDB-1oqa: Solution structure of the BRCT-c domain from human BRCA1 -

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Basic information

Entry
Database: PDB / ID: 1oqa
TitleSolution structure of the BRCT-c domain from human BRCA1
ComponentsBreast cancer type 1 susceptibility protein
KeywordsGENE REGULATION / BRCT / breast cancer
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 / negative regulation of centriole replication / BRCA1-A complex / chordate embryonic development / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex ...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 / negative regulation of centriole replication / BRCA1-A complex / chordate embryonic development / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / ubiquitin-modified histone reader activity / cellular response to indole-3-methanol / DNA strand resection involved in replication fork processing / negative regulation of fatty acid biosynthetic process / homologous recombination / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / lateral element / XY body / mitotic G2/M transition checkpoint / Impaired BRCA2 binding to PALB2 / RNA polymerase binding / DNA damage tolerance / negative regulation of reactive oxygen species metabolic process / protein K6-linked ubiquitination / negative regulation of cell cycle / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / HDR through Single Strand Annealing (SSA) / regulation of DNA damage checkpoint / 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) / mitotic G2 DNA damage checkpoint signaling / Resolution of D-loop Structures through Holliday Junction Intermediates / Transcriptional Regulation by E2F6 / Impaired BRCA2 binding to RAD51 / positive regulation of vascular endothelial growth factor production / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Presynaptic phase of homologous DNA pairing and strand exchange / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / protein autoubiquitination / regulation of DNA repair / positive regulation of DNA repair / Meiotic synapsis / cellular response to ionizing radiation / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to tumor necrosis factor / TP53 Regulates Transcription of DNA Repair Genes / chromosome segregation / Nonhomologous End-Joining (NHEJ) / negative regulation of cell growth / tubulin binding / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / Meiotic recombination / HDR through Homologous Recombination (HRR) / fatty acid biosynthetic process / positive regulation of angiogenesis / Metalloprotease DUBs / p53 binding / ubiquitin-protein transferase activity / double-strand break repair / KEAP1-NFE2L2 pathway / chromosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Neddylation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / nuclear body / regulation of cell cycle / transcription coactivator activity / transcription cis-regulatory region binding / protein ubiquitination / chromatin remodeling / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA repair / positive regulation of gene expression / regulation of transcription by RNA polymerase II / DNA damage response / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / DNA-templated transcription / RNA binding / nucleoplasm / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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. ...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. / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, distance geometry
AuthorsGaiser, O.J. / Ball, L.J. / Schmieder, P. / Leitner, D. / Strauss, H. / Wahl, M. / Kuhne, R. / Oschkinat, H. / Heinemann, U.
CitationJournal: Biochemistry / Year: 2004
Title: Solution structure, backbone dynamics, and association behavior of the C-terminal BRCT domain from the breast cancer-associated protein BRCA1.
Authors: Gaiser, O.J. / Ball, L.J. / Schmieder, P. / Leitner, D. / Strauss, H. / Wahl, M. / Kuhne, R. / Oschkinat, H. / Heinemann, U.
History
DepositionMar 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Breast cancer type 1 susceptibility protein


Theoretical massNumber of molelcules
Total (without water)12,3671
Polymers12,3671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Breast cancer type 1 susceptibility protein / BRCA1


Mass: 12367.027 Da / Num. of mol.: 1 / Fragment: BRCT-c
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1 / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38398

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1322D NOESY
1432D NOESY
1532D TOCSY
163DQF-COSY
172HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM BRCT-c; U-15N,13C, 20mM Potassium phosphate buffer pH 6.8, 5 mM KCl, 10 mM d10-DTT, 99.98% D2O99.98% D2O
21.3 mM BRCT-c; U-15N, 20 mM Potassium phosphate buffer pH 6.8, 5 mM KCl, 10 mM d10-DTT, 93% H2O, 7% D2O93% H2O/7% D2O
31.3 mM BRCT-c; U-15N, 20 mM Potassium phosphate buffer pH 6.8, 5 mM KCl, 10 mM d10-DTT, 99.98% D2O99.98% D2O
Sample conditionspH: 6.8 / Pressure: 1 atm / Temperature: 295.9 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Bruker Analytik GmbHdata analysis
Azara2.1Boucher, W.processing
ANSIG3.3Kraulisprocessing
X-PLOR3.8Brunger, A.refinement
CNS1Brunger, A.refinement
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 15

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