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- PDB-1jm7: Solution structure of the BRCA1/BARD1 RING-domain heterodimer -

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Basic information

Entry
Database: PDB / ID: 1jm7
TitleSolution structure of the BRCA1/BARD1 RING-domain heterodimer
Components
  • BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1
  • BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN
KeywordsANTITUMOR / BRCA1 / BARD1 / RING finger / zinc-binding protein / heterodimer / ubiquitin ligase
Function / homology
Function and homology information


negative regulation of mRNA 3'-end processing / 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 ...negative regulation of mRNA 3'-end processing / 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 / 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 / tissue homeostasis / XY body / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / regulation of phosphorylation / 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 / negative regulation of protein export from nucleus / 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 / negative regulation of cell cycle / 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 / cytoplasmic ribonucleoprotein granule / negative regulation of cell growth / Metalloprotease DUBs / Meiotic recombination / kinase binding / ubiquitin-protein transferase activity / fatty acid biosynthetic process / positive regulation of protein catabolic process / UCH proteinases / 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 / Processing of DNA double-strand break ends / 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 / nuclear speck / ribonucleoprotein complex / positive regulation of apoptotic process / protein heterodimerization activity / DNA repair
Similarity search - Function
BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / Zinc/RING finger domain, C3HC4 (zinc finger) ...BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ring finger / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Breast cancer type 1 susceptibility protein / BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
Model detailsBREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN/BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1 COMPLEX
AuthorsBrzovic, P.S. / Rajagopal, P. / Hoyt, D.W. / King, M.-C. / Klevit, R.E.
CitationJournal: Nat Struct Biol / Year: 2001
Title: Structure of a BRCA1-BARD1 heterodimeric RING-RING complex.
Authors: P S Brzovic / P Rajagopal / D W Hoyt / M C King / R E Klevit /
Abstract: The RING domain of the breast and ovarian cancer tumor suppressor BRCA1 interacts with multiple cognate proteins, including the RING protein BARD1. Proper function of the BRCA1 RING domain is ...The RING domain of the breast and ovarian cancer tumor suppressor BRCA1 interacts with multiple cognate proteins, including the RING protein BARD1. Proper function of the BRCA1 RING domain is critical, as evidenced by the many cancer-predisposing mutations found within this domain. We present the solution structure of the heterodimer formed between the RING domains of BRCA1 and BARD1. Comparison with the RING homodimer of the V(D)J recombination-activating protein RAG1 reveals the structural diversity of complexes formed by interactions between different RING domains. The BRCA1-BARD1 structure provides a model for its ubiquitin ligase activity, illustrates how the BRCA1 RING domain can be involved in associations with multiple protein partners and provides a framework for understanding cancer-causing mutations at the molecular level.
History
DepositionJul 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-ASSOCIATED RING DOMAIN PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2506
Polymers25,9882
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 25structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #2closest to the average

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Components

#1: Protein BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN / BRCA1


Mass: 12819.168 Da / Num. of mol.: 1 / Fragment: RING-Domain
Source method: isolated from a genetically manipulated source
Details: residues 104-112 of chain A and 123-142 of chain B are missing in each model due to disorder.
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1 / Plasmid: PET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P38398
#2: Protein BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1 / BARD1


Mass: 13169.250 Da / Num. of mol.: 1 / Fragment: RING-Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARD1 / Plasmid: PET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q99728
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1214D 13C-separated NOESY
2324D 13C-separated NOESY
2423D 15N/13C-separated NOESY
1513D 15N/13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
1sample 1: 0.8-1.1mM U-15N,13C BRCA1; unlabeled BARD1, 25mM sodium phosphate, 0.2M NaCl, 2mM DTT. Sample 2: 0.8-1.1mM U-15N,13C BARD1; unlabeled BRCA1, 25mM sodium phosphate, 0.2M NaCl, 2mM DTT. Sample 3: 0.8-1.1mM U-15N,13C,85%-2H BRCA1; unlabeled BARD1, 25mM sodium phosphate, 0.2M NaCl, 2mM DTT. SAMPLE 4: 0.8-1.1mM U-15N,13C,85%-2H BARD1; unlabeled BRCA,1 25mM sodium phosphate, 0.2M NaCl, 2mM DTT.90% H2O/10% D2O
20.8-1.1mM U-15N,13C BARD1; unlabeled BRCA1 25mM sodium phosphate 0.2M NaCl 2mM DTT90% H2O/10% D2O
30.8-1.1mM U-15N,13C,85%-2H BRCA1; unlabeled BARD1 25mM sodium phosphate 0.2M NaCl 2mM DTT90% H2O/10% D2O
40.8-1.1mM U-15N,13C,85%-2H BARD1; unlabeled BRCA1 25mM sodium phosphate 0.2M NaCl 2mM DTT90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.2M NaCl 6.8 ambient 315 K
20.2M NaCl 6.8 ambient 315 K
30.2M NaCl 6.8 ambient 315 K
40.2M NaCl 6.8 ambient 315 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 DMXBrukerDMX5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6collection
VNMRcollection
NMRPipeDelaglio, F.processing
NMRView5Johnson, B.data analysis
CNS1Brungerstructure solution
CNSBRUNGERrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: Structures are based on a total of 1664 restraints, 480 Intraresidue restraints, 475 Sequential restraints, 215 Medium-Range restraints, 256 Long-Range restraints, 82 Intermolecular ...Details: Structures are based on a total of 1664 restraints, 480 Intraresidue restraints, 475 Sequential restraints, 215 Medium-Range restraints, 256 Long-Range restraints, 82 Intermolecular restraints, 70 Hydrogen bond restraints, 16 Zinc restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 14

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