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- PDB-7k3s: Solution NMR Structure of the Coiled-coil BRCA1-PALB2 Heterodimer -

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Basic information

Entry
Database: PDB / ID: 7k3s
TitleSolution NMR Structure of the Coiled-coil BRCA1-PALB2 Heterodimer
Components
  • Breast cancer type 1 susceptibility protein homolog
  • Partner and localizer of BRCA2
KeywordsONCOPROTEIN / Homologous Recombination / DNA
Function / homology
Function and homology information


localization / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / SUMOylation of DNA damage response and repair proteins / G2/M DNA damage checkpoint / HDR through Single Strand Annealing (SSA) / Nonhomologous End-Joining (NHEJ) / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs ...localization / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / SUMOylation of DNA damage response and repair proteins / G2/M DNA damage checkpoint / HDR through Single Strand Annealing (SSA) / Nonhomologous End-Joining (NHEJ) / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / BRCA1-BARD1 complex / BRCA1-B complex / Processing of DNA double-strand break ends / BRCA1-A complex / BRCA1-C complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / sex-chromosome dosage compensation / random inactivation of X chromosome / chordate embryonic development / nuclear ubiquitin ligase complex / cellular response to indole-3-methanol / negative regulation of intracellular estrogen receptor signaling pathway / DNA strand resection involved in replication fork processing / Regulation of TP53 Activity through Phosphorylation / negative regulation of fatty acid biosynthetic process / homologous recombination / protein K6-linked ubiquitination / post-anal tail morphogenesis / lateral element / regulation of DNA damage checkpoint / XY body / mitotic G2/M transition checkpoint / RNA polymerase binding / DNA damage tolerance / DNA repair complex / centrosome cycle / inner cell mass cell proliferation / DNA-binding transcription activator activity / negative regulation of gene expression via chromosomal CpG island methylation / mitotic G2 DNA damage checkpoint signaling / mesoderm development / centrosome duplication / negative regulation of reactive oxygen species metabolic process / positive regulation of vascular endothelial growth factor production / embryonic organ development / somitogenesis / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of DNA repair / protein autoubiquitination / positive regulation of cell cycle / condensed chromosome / positive regulation of DNA repair / animal organ morphogenesis / condensed nuclear chromosome / cellular response to ionizing radiation / male germ cell nucleus / chromosome segregation / negative regulation of cell growth / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / positive regulation of protein import into nucleus / multicellular organism growth / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / ubiquitin-protein transferase activity / fatty acid biosynthetic process / cellular response to tumor necrosis factor / p53 binding / double-strand break repair / chromosome / in utero embryonic development / damaged DNA binding / transcription coactivator activity / transcription cis-regulatory region binding / nuclear speck / nuclear body / mitochondrial matrix / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / ubiquitin protein ligase binding / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Partner and localiser of BRCA2, WD40 domain / Partner and localizer of BRCA2 / Partner and localizer of BRCA2 WD40 domain / 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 ...Partner and localiser of BRCA2, WD40 domain / Partner and localizer of BRCA2 / Partner and localizer of BRCA2 WD40 domain / 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 / 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 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Breast cancer type 1 susceptibility protein homolog / Partner and localizer of BRCA2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsDaigham, N.S. / Liu, G. / Bunting, S.F. / Montelione, G.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA190858 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD018207 United States
Citation
Journal: To Be Published
Title: The Structural Basis for Interactions Between PALB2 and BRCA1 that Mediate the Homologous Recombination DNA Damage Repair Process
Authors: Daigham, N.S. / Liu, G. / Bunting, S.F. / Montelione, G.T.
#1: Journal: Biochemistry / Year: 2018
Title: Antiparallel Coiled-Coil Interactions Mediate the Homodimerization of the DNA Damage-Repair Protein PALB2.
Authors: Song, F. / Li, M. / Liu, G. / Swapna, G.V.T. / Daigham, N.S. / Xia, B. / Montelione, G.T. / Bunting, S.F.
History
DepositionSep 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Breast cancer type 1 susceptibility protein homolog
B: Partner and localizer of BRCA2


Theoretical massNumber of molelcules
Total (without water)14,8842
Polymers14,8842
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2810 Å2
ΔGint-23 kcal/mol
Surface area10740 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Breast cancer type 1 susceptibility protein homolog / RING-type E3 ubiquitin transferase BRCA1


Mass: 6935.690 Da / Num. of mol.: 1 / Fragment: residues 1337-1387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Gene: Brca1 / Plasmid: MmR494A-1337-1387 / Production host: Escherichia coli (E. coli)
References: UniProt: P48754, RING-type E3 ubiquitin transferase
#2: Protein Partner and localizer of BRCA2


Mass: 7948.166 Da / Num. of mol.: 1 / Fragment: residues 1-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Palb2 / Plasmid: MmR495A-1-60 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3U0P1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC NH2 only
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D HNCA
141isotropic13D HN(CO)CA
151isotropic13D (H)CCH-TOCSY
161isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
191isotropic13D 1H-15N TOCSY
181isotropic13D HNCO
1121isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY
1132isotropic12D 1H-15N HSQC NH2 only
1152isotropic12D 1H-13C HSQC aliphatic
1142isotropic13D HNCA
1162isotropic13D HN(CO)CA
1172isotropic13D (H)CCH-TOCSY
1182isotropic13D HN(CA)CB
1192isotropic13D CBCA(CO)NH
1202isotropic13D HNCO
1212isotropic13D HBHA(CO)NH
1222isotropic13D 1H-15N NOESY
1232isotropic13D 1H-13C NOESY
1251isotropic13D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.5 mM [U-100% 13C; U-100% 15N] PALB2cc, 3 mM BRCA1cc, 20 mM MES, 200 mM sodium chloride, 10 mM DTT, 5 mM CaCl2, 90% H2O/10% D2OIsotopically labeled PALB2cc mixed with unlabeled (natural abundance) BRCA1cc in the following ratio 2:1 (BRCA1:PALB2) and concentrated by centrifugation.NC_PALB2_BRCA1(NA)90% H2O/10% D2O
solution21.5 mM [U-100% 13C; U-100% 15N] BRCA1cc, 3 mM PALB2cc, 20 mM MES, 200 mM sodium chloride, 10 mM DTT, 5 mM CaCl2, 90% H2O/10% D2OIsotopically labeled BRCA1cc mixed with unlabeled (natural abundance) PALB2cc in the following ratio 2:1 (BRCA1:PALB2) and concentrated by centrifugation.NC_BRCA1_PALB2(NA)90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMPALB2cc[U-100% 13C; U-100% 15N]1
3 mMBRCA1ccnatural abundance1
20 mMMESnatural abundance1
200 mMsodium chloridenatural abundance1
10 mMDTTnatural abundance1
5 mMCaCl2natural abundance1
1.5 mMBRCA1cc[U-100% 13C; U-100% 15N]2
3 mMPALB2ccnatural abundance2
20 mMMESnatural abundance2
200 mMsodium chloridenatural abundance2
10 mMDTTnatural abundance2
5 mMCaCl2natural abundance2
Sample conditionsDetails: Buffer Conditions: 20 mM MES, 200 mM NaCl, 10 mM DTT, 5 mM CaCl2 at pH 6.5
Ionic strength: 200 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AVSMoseley and Montelionechemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 7 / Details: molecular dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 15

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