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- PDB-1n0w: Crystal structure of a RAD51-BRCA2 BRC repeat complex -

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Basic information

Entry
Database: PDB / ID: 1n0w
TitleCrystal structure of a RAD51-BRCA2 BRC repeat complex
Components
  • ARTIFICIAL GLY-SER-MSE-GLY PEPTIDE
  • Breast cancer type 2 susceptibility protein
  • DNA repair protein RAD51 homolog 1
  • peptide linker
KeywordsGENE REGULATION/ANTITUMOR PROTEIN / DNA repair / homologous recombination / breast cancer susceptibility / RecA-like ATPase / protein complex / GENE REGULATION-ANTITUMOR PROTEIN COMPLEX
Function / homology
Function and homology information


BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / presynaptic intermediate filament cytoskeleton / mitotic recombination-dependent replication fork processing / cellular response to camptothecin / chromosome organization involved in meiotic cell cycle / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / positive regulation of DNA ligation / Impaired BRCA2 translocation to the nucleus ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / presynaptic intermediate filament cytoskeleton / mitotic recombination-dependent replication fork processing / cellular response to camptothecin / chromosome organization involved in meiotic cell cycle / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / positive regulation of DNA ligation / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to hydroxyurea / replication-born double-strand break repair via sister chromatid exchange / lateral element / telomere maintenance via recombination / DNA recombinase assembly / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / regulation of DNA damage checkpoint / mitotic recombination / Impaired BRCA2 binding to PALB2 / DNA strand invasion / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / DNA strand exchange activity / reciprocal meiotic recombination / DNA repair complex / 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) / response to UV-C / oocyte maturation / Resolution of D-loop Structures through Holliday Junction Intermediates / single-stranded DNA helicase activity / inner cell mass cell proliferation / ATP-dependent DNA damage sensor activity / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / regulation of double-strand break repair via homologous recombination / nuclear chromosome / female gonad development / replication fork processing / male meiosis I / DNA unwinding involved in DNA replication / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ATP-dependent activity, acting on DNA / interstrand cross-link repair / DNA polymerase binding / condensed chromosome / positive regulation of mitotic cell cycle / meiotic cell cycle / regulation of cytokinesis / condensed nuclear chromosome / secretory granule / male germ cell nucleus / cellular response to ionizing radiation / nucleotide-excision repair / response to gamma radiation / regulation of protein phosphorylation / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / brain development / PML body / Meiotic recombination / cellular senescence / double-strand break repair / site of double-strand break / single-stranded DNA binding / spermatogenesis / double-stranded DNA binding / DNA recombination / protease binding / chromosome, telomeric region / mitochondrial matrix / DNA repair / centrosome / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / identical protein binding
Similarity search - Function
: / 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 / Tower ...: / 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 / 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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Breast cancer type 2 susceptibility protein / DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsPellegrini, L. / Yu, D.S. / Lo, T. / Anand, S. / Lee, M. / Blundell, T.L. / Venkitaraman, A.R.
CitationJournal: Nature / Year: 2002
Title: Insights into DNA recombination from the structure of a RAD51-BRCA2 complex
Authors: Pellegrini, L. / Yu, D.S. / Lo, T. / Anand, S. / Lee, M. / Blundell, T.L. / Venkitaraman, A.R.
History
DepositionOct 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 25, 2016Group: Source and taxonomy
Revision 1.4Jan 22, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999SEQUENCE All chains in the entry are part of an engineered, chimeric protein construct. In the ...SEQUENCE All chains in the entry are part of an engineered, chimeric protein construct. In the construct, the amino-to-carboxyl order of the chains is: C-B-L-A. Chain C is a GSMG sequence that comes from the expression vector, B is the BRCA2 BRC repeat, L is the TGSTGSTGSTGSMG sequence linking chains B and A, and chain A is the RAD51 ATpase domain. Chain C appears as a separate entity because the two initial residues of chain B, 1517-8, are not visible in the density map. Likewise, the linker is not visible in the density map, with the exception of the first three residues:TGS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD51 homolog 1
B: Breast cancer type 2 susceptibility protein
L: peptide linker
C: ARTIFICIAL GLY-SER-MSE-GLY PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,82311
Polymers32,4534
Non-polymers3707
Water4,450247
1
A: DNA repair protein RAD51 homolog 1
B: Breast cancer type 2 susceptibility protein
hetero molecules

C: ARTIFICIAL GLY-SER-MSE-GLY PEPTIDE

L: peptide linker


Theoretical massNumber of molelcules
Total (without water)32,82311
Polymers32,4534
Non-polymers3707
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
Buried area3740 Å2
ΔGint-33 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.30, 59.14, 77.20
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains one biological unit, constituted by one chain A, one chain B and one chain C

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA repair protein RAD51 homolog 1 / RAD51 / hRAD51 / HsRAD51


Mass: 26855.346 Da / Num. of mol.: 1 / Fragment: ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD51 / Plasmid: pGAT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06609

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Protein/peptide , 3 types, 3 molecules BLC

#2: Protein/peptide Breast cancer type 2 susceptibility protein / BRCA2 BRC4 REPEAT SEQUENCE


Mass: 3966.598 Da / Num. of mol.: 1 / Fragment: BRC repeat type 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA2 / Plasmid: pGAT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51587
#3: Protein/peptide peptide linker


Mass: 1234.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: this peptide links the BRCA2 to the RAD51 / Plasmid: pGAT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#4: Protein/peptide ARTIFICIAL GLY-SER-MSE-GLY PEPTIDE


Mass: 397.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: this peptide comes from the expression vector and is linked to the N-terminus of BRCA2
Plasmid: pGAT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 4 types, 254 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.95 % / Description: Freidel pairs were used.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: ETHYLENE GLYCOL, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
Conc.: 25 % / Common name: ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792, 0.90831
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2002
RadiationMonochromator: channel - cut Si monochromator + cylindrical grazing incidence mirror
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.908311
ReflectionResolution: 1.7→24.85 Å / Num. obs: 55746 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 23.5
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 6.5 / Rsym value: 0.321 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 29143 / Num. measured all: 204230
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→24.85 Å / Data cutoff high absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined against the peak Se K edge wavelength dataset. Selenomethionine residues (residue name MSE) were used in the refinement, and are present in the deposited coordinate ...Details: The structure was refined against the peak Se K edge wavelength dataset. Selenomethionine residues (residue name MSE) were used in the refinement, and are present in the deposited coordinate file. Freidel pairs were used.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1529 5 %RANDOM
Rwork0.191 ---
obs-55746 99.9 %-
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 22 247 2225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.23
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 24.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.229

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