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- PDB-8yap: Structure of human PALB2 coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 8yap
TitleStructure of human PALB2 coiled-coil domain
ComponentsPartner and localizer of BRCA2
KeywordsDNA BINDING PROTEIN / Tumor Suppressor / DNA repair / Homologous recombination / BRCA1 / BRCA2 / cancer
Function / homology
Function and homology information


post-anal tail morphogenesis / Impaired BRCA2 binding to PALB2 / 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 / inner cell mass cell proliferation ...post-anal tail morphogenesis / Impaired BRCA2 binding to PALB2 / 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 / inner cell mass cell proliferation / mesoderm development / embryonic organ development / somitogenesis / animal organ morphogenesis / double-strand break repair via homologous recombination / multicellular organism growth / HDR through Homologous Recombination (HRR) / KEAP1-NFE2L2 pathway / Neddylation / nuclear speck / apoptotic process / negative regulation of apoptotic process / protein-containing complex / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Partner and localiser of BRCA2, WD40 domain / Partner and localizer of BRCA2 / Partner and localizer of BRCA2 WD40 domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Partner and localizer of BRCA2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsReddy, P.P. / Das, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)RTI4006 India
CitationJournal: Biosci.Rep. / Year: 2025
Title: Structural analysis of genetic variants of the human tumor suppressor PALB2 coiled-coil domain.
Authors: Reddy, P.P. / Phale, A. / Das, R.
History
DepositionFeb 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Partner and localizer of BRCA2
B: Partner and localizer of BRCA2


Theoretical massNumber of molelcules
Total (without water)8,8912
Polymers8,8912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Partner and localizer of BRCA2


Mass: 4445.259 Da / Num. of mol.: 2 / Fragment: coiled-coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB2, FANCN / Production host: Escherichia coli (E. coli) / References: UniProt: Q86YC2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D 1H-13C NOESY
131isotropic13D 1H-15N NOESY
141isotropic13D C(CO)NH
151isotropic23D HN(CA)CB
171isotropic23D CBCA(CO)NH
161isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] Palb2, 90% H2O/10% D2O
Label: 13C,15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: Palb2 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 300 mM / Label: conditions_1 / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD6001
Bruker AVANCE III HDBrukerAVANCE III HD8002

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Processing

NMR software
NameDeveloperClassification
PINE-SPARKYMarkleychemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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