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- PDB-2kz3: Backbone 1H, 13C, and 15N Chemical Shift Assignments for human Ra... -

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Basic information

Entry
Database: PDB / ID: 2kz3
TitleBackbone 1H, 13C, and 15N Chemical Shift Assignments for human Rad51D from 1 to 83
ComponentsPutative uncharacterized protein RAD51L3
KeywordsUNKNOWN FUNCTION / Rad51D / Homologous Recombination
Function / homology
Function and homology information


Rad51B-Rad51C-Rad51D-XRCC2 complex / DNA strand invasion / telomere maintenance via recombination / Impaired BRCA2 binding to PALB2 / gamma-tubulin binding / reciprocal meiotic recombination / 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 ...Rad51B-Rad51C-Rad51D-XRCC2 complex / DNA strand invasion / telomere maintenance via recombination / Impaired BRCA2 binding to PALB2 / gamma-tubulin binding / reciprocal meiotic recombination / 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 / ATP-dependent DNA damage sensor activity / Presynaptic phase of homologous DNA pairing and strand exchange / ATP-dependent activity, acting on DNA / interstrand cross-link repair / telomere maintenance / replication fork / TP53 Regulates Transcription of DNA Repair Genes / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / single-stranded DNA binding / chromosome, telomeric region / regulation of cell cycle / DNA repair / centrosome / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / : / RAD51D, N-terminal domain / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA repair protein RAD51 homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsChoi, N. / Kim, Y.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2011
Title: Structural and functional characterization of the N-terminal domain of human Rad51D
Authors: Kim, Y.M. / Choi, B.S.
History
DepositionJun 11, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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 1.4May 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: Putative uncharacterized protein RAD51L3


Theoretical massNumber of molelcules
Total (without water)9,0711
Polymers9,0711
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative uncharacterized protein RAD51L3


Mass: 9070.666 Da / Num. of mol.: 1 / Fragment: UNP residues 1-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: C9JSQ7, UniProt: O75771*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1233D 1H-15N NOESY
1333D 1H-15N TOCSY
1423D (H)CCH-TOCSY
1523D 1H-13C NOESY
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HNCO
1913D H(CCO)NH
11013D C(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] human Rad51D_N-1, 1 mM [U-13C; U-15N] human Rad51D_N-2, 1 mM DTT-3, 0.02 % sodium azide-4, 1 mM [U-99% 13C; U-99% 15N] human Rad51D_N-5, 100% D2O100% D2O
21 mM [U-99% 13C; U-99% 15N] human Rad51D_N-6, 25 mM TRIS-7, 100 mM sodium chloride-8, 1 mM DTT-9, 0.02 % sodium azide-10, 100% D2O100% D2O
31 mM [U-99% 15N] human Rad51D_N-11, 25 mM TRIS-12, 100 mM sodium chloride-13, 1 mM DTT-14, 0.02 % sodium azide-15, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMhuman Rad51D_N-1[U-100% 15N]1
1 mMhuman Rad51D_N-2[U-13C; U-15N]1
1 mMDTT-31
0.02 %sodium azide-41
1 mMhuman Rad51D_N-5[U-99% 13C; U-99% 15N]1
1 mMhuman Rad51D_N-6[U-99% 13C; U-99% 15N]2
25 mMTRIS-72
100 mMsodium chloride-82
1 mMDTT-92
0.02 %sodium azide-102
1 mMhuman Rad51D_N-11[U-99% 15N]3
25 mMTRIS-123
100 mMsodium chloride-133
1 mMDTT-143
0.02 %sodium azide-153
Sample conditionsIonic strength: 100 / pH: 7.5 / Pressure: 1 atm / Temperature: 287 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: CYANA / Version: 2.1 / Developer: P.GUNTERT ET AL. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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