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- PDB-8uvw: Crystal structure of RAD51-BRCA2 Cter complex -

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Basic information

Entry
Database: PDB / ID: 8uvw
TitleCrystal structure of RAD51-BRCA2 Cter complex
Components
  • Breast cancer type 2 susceptibility protein, DNA repair protein RAD51 homolog 1 fusion
  • DNA repair protein RAD51 homolog 1,Breast cancer type 2 susceptibility protein
KeywordsRECOMBINATION / Homologous recombination / DNA repair / DSB repair
Function / homology
Function and homology information


BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / chromosome organization involved in meiotic cell cycle / cellular response to camptothecin / DNA recombinase assembly / telomere maintenance via telomere lengthening ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / chromosome organization involved in meiotic cell cycle / cellular response to camptothecin / DNA recombinase assembly / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin / DNA strand invasion / cellular response to hydroxyurea / mitotic recombination / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / lateral element / DNA strand exchange activity / histone H4 acetyltransferase activity / replication-born double-strand break repair via sister chromatid exchange / histone H3 acetyltransferase activity / telomere maintenance via recombination / Impaired BRCA2 binding to PALB2 / regulation of DNA damage checkpoint / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / single-stranded DNA helicase activity / reciprocal meiotic recombination / DNA repair complex / oocyte maturation / response to UV-C / 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 / HDR through Single Strand Annealing (SSA) / ATP-dependent DNA damage sensor activity / regulation of double-strand break repair via homologous recombination / nuclear chromosome / Impaired BRCA2 binding to RAD51 / hematopoietic stem cell proliferation / female gonad development / Transcriptional Regulation by E2F6 / male meiosis I / replication fork processing / centrosome duplication / Presynaptic phase of homologous DNA pairing and strand exchange / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ATP-dependent activity, acting on DNA / response to X-ray / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / positive regulation of mitotic cell cycle / male germ cell nucleus / secretory granule / condensed nuclear chromosome / regulation of cytokinesis / meiotic cell cycle / cellular response to ionizing radiation / response to gamma radiation / nucleotide-excision repair / double-strand break repair via homologous recombination / cellular response to gamma radiation / brain development / PML body / Meiotic recombination / HDR through Homologous Recombination (HRR) / response to toxic substance / cellular senescence / double-strand break repair / single-stranded DNA binding / site of double-strand break / protease binding / double-stranded DNA binding / DNA recombination / spermatogenesis / chromosome, telomeric region / mitochondrial matrix / response to xenobiotic stimulus / DNA repair / centrosome / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding
Similarity search - Function
BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / : / : / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / BRCA2, OB2 ...BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / : / : / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / BRCA2, OB2 / BRCA2 TR2 domain / Tower / BRCA2 repeat / BRCA2, OB1 / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 / BRCA2 repeat profile. / DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Breast cancer type 2 susceptibility protein / DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsLongo, M.A. / Perera, R. / Tsai, C.-L. / Tainer, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA220430 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP180813 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F31CA142313 United States
CitationJournal: To Be Published
Title: Molecular Recognition of RAD51 by the BRCA2 Carboxy Terminal Domain
Authors: Longo, M.A. / Syed, M.A.
History
DepositionNov 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Breast cancer type 2 susceptibility protein, DNA repair protein RAD51 homolog 1 fusion
D: DNA repair protein RAD51 homolog 1,Breast cancer type 2 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5398
Polymers63,4282
Non-polymers1,1116
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-16 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.463, 98.551, 128.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules BD

#1: Protein Breast cancer type 2 susceptibility protein, DNA repair protein RAD51 homolog 1 fusion / Fanconi anemia group D1 protein / HsRAD51 / hRAD51 / RAD51 homolog A


Mass: 32212.562 Da / Num. of mol.: 1 / Mutation: C319S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA2, FACD, FANCD1, RAD51, RAD51A, RECA / Production host: Escherichia coli (E. coli) / References: UniProt: P51587, UniProt: Q06609
#2: Protein DNA repair protein RAD51 homolog 1,Breast cancer type 2 susceptibility protein / Fanconi anemia group D1 protein


Mass: 31215.408 Da / Num. of mol.: 1 / Mutation: S208E,A209D,C3287A,C3304A,C391S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD51, BRCA2, FACD, FANCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06609, UniProt: P51587

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Non-polymers , 4 types, 39 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% v/v 1,4-Dioxane 0.05 M MOPS pH 7.0 0.005 M Magnesium chloride hexahydrate 0.001 M Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.73→39.24 Å / Num. obs: 17974 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 2.73→2.86 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2352 / CC1/2: 0.34 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4924:000)refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→31.82 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2821 881 4.98 %
Rwork0.2479 --
obs0.2496 17681 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 70 34 4023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024073
X-RAY DIFFRACTIONf_angle_d0.4675495
X-RAY DIFFRACTIONf_dihedral_angle_d10.1731517
X-RAY DIFFRACTIONf_chiral_restr0.038625
X-RAY DIFFRACTIONf_plane_restr0.003702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.90.39621360.39292670X-RAY DIFFRACTION96
2.9-3.120.34881370.34232775X-RAY DIFFRACTION100
3.13-3.440.33461360.31912795X-RAY DIFFRACTION98
3.44-3.930.34351660.31782716X-RAY DIFFRACTION97
3.94-4.960.29661430.21512852X-RAY DIFFRACTION100
4.96-31.820.22621630.20732992X-RAY DIFFRACTION100

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