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- PDB-1iyj: STRUCTURE OF A BRCA2-DSS1 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1iyj
TitleSTRUCTURE OF A BRCA2-DSS1 COMPLEX
Components
  • Deleted in split hand/split foot protein 1
  • breast cancer susceptibility
KeywordsGENE REGULATION/ANTITUMOR PROTEIN / TUMOR SUPPRESSOR / BREAST CANCER SUSCEPTIBILITY / DNA-BINDING / GENE REGULATION-ANTITUMOR PROTEIN COMPLEX
Function / homology
Function and homology information


HDR through MMEJ (alt-NHEJ) / Resolution of D-loop Structures through Holliday Junction Intermediates / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / HDR through Homologous Recombination (HRR) / homologous chromosome orientation in meiotic metaphase I / BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / nuclear ubiquitin ligase complex / establishment of protein localization to telomere ...HDR through MMEJ (alt-NHEJ) / Resolution of D-loop Structures through Holliday Junction Intermediates / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / HDR through Homologous Recombination (HRR) / homologous chromosome orientation in meiotic metaphase I / BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / nuclear ubiquitin ligase complex / establishment of protein localization to telomere / chordate embryonic development / mitotic recombination-dependent replication fork processing / oocyte maturation / histone H4 acetyltransferase activity / DNA repair complex / mammary gland development / histone H3 acetyltransferase activity / inner cell mass cell proliferation / lateral element / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / gamma-tubulin binding / integrator complex / telomere maintenance via recombination / response to UV-C / proteasome regulatory particle, lid subcomplex / cellular response to type I interferon / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / female gonad development / 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) / hemopoiesis / Resolution of D-loop Structures through Holliday Junction Intermediates / male meiosis I / Impaired BRCA2 binding to RAD51 / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / replication fork processing / centrosome duplication / chromosome organization / response to X-ray / Presynaptic phase of homologous DNA pairing and strand exchange / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / multicellular organism growth / proteasome assembly / mRNA export from nucleus / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / SPOP-mediated proteasomal degradation of PD-L1(CD274) / positive regulation of mitotic cell cycle / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / response to nutrient / response to gamma radiation / secretory granule / proteasome complex / regulation of proteasomal protein catabolic process / DNA damage response, signal transduction by p53 class mediator / cellular response to ionizing radiation / regulation of cytokinesis / brain development / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / nucleotide-excision repair / proteasomal protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / cell population proliferation / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / intrinsic apoptotic signaling pathway in response to DNA damage / Defective CFTR causes cystic fibrosis / double-strand break repair via homologous recombination / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
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. / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Breast cancer type 2 susceptibility protein homolog / 26S proteasome complex subunit SEM1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPavletich, N.P. / Jeffrey, P.D. / Yang, H.J.
CitationJournal: Science / Year: 2002
Title: BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.
Authors: Yang, H. / Jeffrey, P.D. / Miller, J. / Kinnucan, E. / Sun, Y. / Thoma, N.H. / Zheng, N. / Chen, P.L. / Lee, W.H. / Pavletich, N.P.
History
DepositionAug 28, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deleted in split hand/split foot protein 1
B: breast cancer susceptibility
C: Deleted in split hand/split foot protein 1
D: breast cancer susceptibility


Theoretical massNumber of molelcules
Total (without water)200,0194
Polymers200,0194
Non-polymers00
Water00
1
A: Deleted in split hand/split foot protein 1
B: breast cancer susceptibility


Theoretical massNumber of molelcules
Total (without water)100,0092
Polymers100,0092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-27 kcal/mol
Surface area30920 Å2
MethodPISA
2
C: Deleted in split hand/split foot protein 1
D: breast cancer susceptibility


Theoretical massNumber of molelcules
Total (without water)100,0092
Polymers100,0092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-26 kcal/mol
Surface area30940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.314, 130.314, 192.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / DSS1


Mass: 8284.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60896
#2: Protein breast cancer susceptibility / BRCA2


Mass: 91724.828 Da / Num. of mol.: 2 / Fragment: residues 2335-3151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O35923

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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: 4.09 Å3/Da / Density % sol: 69.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Li2SO4, NH4OCOCH3, Bis-tris Propane, DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2001
RadiationMonochromator: Se(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Num. all: 41234 / Num. obs: 41234 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.4→3.52 Å / % possible all: 90.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 700 2 %random
Rwork0.244 ---
all0.248 33694 --
obs0.248 33694 --
Refinement stepCycle: LAST / Resolution: 3.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10092 0 0 0 10092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.55

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