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- PDB-6e4h: Solution NMR Structure of the Colied-coil PALB2 Homodimer -

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Basic information

Entry
Database: PDB / ID: 6e4h
TitleSolution NMR Structure of the Colied-coil PALB2 Homodimer
ComponentsPartner and localizer of BRCA2
KeywordsONCOPROTEIN / Antiparallel Coiled coil / Homologous recombination / DNA Damage Repair
Function / homology
Function and homology information


Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Homologous Recombination (HRR) / post-anal tail morphogenesis / DNA repair complex / inner cell mass cell proliferation / mesoderm development / embryonic organ development / somitogenesis / animal organ morphogenesis ...Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Homologous Recombination (HRR) / post-anal tail morphogenesis / DNA repair complex / inner cell mass cell proliferation / mesoderm development / embryonic organ development / somitogenesis / animal organ morphogenesis / double-strand break repair via homologous recombination / multicellular organism growth / in utero embryonic development / apoptotic process / negative regulation of apoptotic process / protein-containing complex / DNA binding / nucleoplasm
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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsSong, F. / Li, M. / Liu, G. / Swapna, G.V.T. / Xia, B. / Bunting, S.F. / Montelione, G.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)NCI RO1-CA190858 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM120574 United States
CitationJournal: 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
DepositionJul 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 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

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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)15,8962
Polymers15,8962
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, X-filtered Noisy experiment shows the two chains of the homodimer to be oriented anti-parallel to each other. N15 T1/T2 measurements demonstrate it's a dimer.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2000 Å2
ΔGint-12 kcal/mol
Surface area11730 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Partner and localizer of BRCA2


Mass: 7948.166 Da / Num. of mol.: 2 / Fragment: residues 1-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Palb2 / Production host: Escherichia coli (E. coli) / 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 TROSY-HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D TROSY-HN(CO)CA
141isotropic13D TROSY-HNCA
151isotropic13D TROSY-HN(CO)CACB
171isotropic13D TROSY-HN(CA)CB
1151isotropic13D TROSY-HNCO
161isotropic13D TROSY-HBHA(CO)NH
181isotropic13D (H)CCH-TOCSY
1101isotropic13D CCH-TOCSY
191isotropic1AROMATIC CCH-TOCSY
1111isotropic13D 1H-13C NOESY
1131isotropic13D 1H-13C NOESY aromatic
1121isotropic13D simultaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1142isotropic1X-filtered NOESY (pulse sequence: noesyhsqcgpwgx13d)

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution11.2 mM [U-100% 13C; U-100% 15N] PALB2cc, 20 mM MES, 200 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT, 10 % DSS, 0.02 % sodium azide, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution21 v/v [U-100% 13C; U-100% 15N] PALB2cc, 2 v/v unlabeled PALB2cc, 20 mM MES, 200 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT, 0.02 % sodium azide, 10 % DSS, 90% H2O/10% D2Oxfd_sample90% H2O/10% D2O1:2 sample of 13C,15N enriched to unlabeled (natural abundance) protein. This sample used to identify the dimer interface in PALB2cc using 13C filtered NOESY experiments ( pulse sequence: noesyhsqcgpwgx13d)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMPALB2cc[U-100% 13C; U-100% 15N]1
20 mMMESnatural abundance1
200 mMsodium chloridenatural abundance1
5 mMCalcium Chloridenatural abundance1
10 mMDTTnatural abundance1
10 %DSSnatural abundance1
0.02 %sodium azidenatural abundance1
1 v/vPALB2cc[U-100% 13C; U-100% 15N]2
2 v/vunlabeled PALB2ccnatural abundance2
20 mMMESnatural abundance2
200 mMsodium chloridenatural abundance2
5 mMCalcium Chloridenatural abundance2
10 mMDTTnatural abundance2
0.02 %sodium azidenatural abundance2
10 %DSSnatural abundance2
Sample conditionsIonic strength: 200 mM / Label: Conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 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
TopSpinBruker Biospincollection
SparkyGoddardpeak picking
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PINEBahrami, Markley, Assadi, and Eghbalniachemical 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
XEASYBartels et al.chemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 8 / Details: molecular dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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