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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 / 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 / response to X-ray / ATP-dependent activity, acting on DNA / 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 / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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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Details

Has protein modificationY

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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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