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- PDB-1miu: Structure of a BRCA2-DSS1 complex -

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Basic information

Entry
Database: PDB / ID: 1miu
TitleStructure of a BRCA2-DSS1 complex
Components
  • Breast Cancer type 2 susceptibility protein
  • Deleted in split hand/split foot protein 1
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) / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / BRCA2-MAGE-D1 complex / HDR through Homologous Recombination (HRR) / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / nuclear ubiquitin ligase complex ...HDR through MMEJ (alt-NHEJ) / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / BRCA2-MAGE-D1 complex / HDR through Homologous Recombination (HRR) / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / nuclear ubiquitin ligase complex / chordate embryonic development / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / lateral element / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / integrator complex / telomere maintenance via recombination / regulation of DNA damage checkpoint / gamma-tubulin binding / proteasome regulatory particle, lid subcomplex / DNA repair complex / oocyte maturation / response to UV-C / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / 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 / Cross-presentation of soluble exogenous antigens (endosomes) / 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 / Somitogenesis / Impaired BRCA2 binding to RAD51 / hematopoietic stem cell proliferation / female gonad development / male meiosis I / replication fork processing / hemopoiesis / 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 / chromosome organization / proteasome assembly / mRNA export from nucleus / positive regulation of mitotic cell cycle / proteasome complex / DNA damage response, signal transduction by p53 class mediator / secretory granule / regulation of cytokinesis / Regulation of activated PAK-2p34 by proteasome mediated degradation / stem cell proliferation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / cellular response to ionizing radiation / response to gamma radiation / nucleotide-excision repair / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / double-strand break repair via homologous recombination / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / brain development / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / HDR through Homologous Recombination (HRR) / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs
Similarity search - Function
Topoisomerase I; Chain A, domain 4 / Topoisomerase I; Chain A, domain 4 - #10 / BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / : / : / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower ...Topoisomerase I; Chain A, domain 4 / Topoisomerase I; Chain A, domain 4 - #10 / 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 / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / 26S proteasome complex subunit SEM1 / Breast cancer type 2 susceptibility protein homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsYang, H. / Jeffrey, P.D. / Miller, J. / Kinnucan, E. / Sun, Y. / Thoma, N.H. / Zheng, N. / Chen, P.L. / Lee, W.H. / Pavletich, N.P.
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 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Deleted in split hand/split foot protein 1
A: Breast Cancer type 2 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6387
Polymers91,6352
Non-polymers1,0035
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-146 kcal/mol
Surface area38000 Å2
MethodPISA
2
B: Deleted in split hand/split foot protein 1
A: Breast Cancer type 2 susceptibility protein
hetero molecules

B: Deleted in split hand/split foot protein 1
A: Breast Cancer type 2 susceptibility protein
hetero molecules

B: Deleted in split hand/split foot protein 1
A: Breast Cancer type 2 susceptibility protein
hetero molecules

B: Deleted in split hand/split foot protein 1
A: Breast Cancer type 2 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,55228
Polymers366,5418
Non-polymers4,01220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area35510 Å2
ΔGint-629 kcal/mol
Surface area142040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.509, 228.271, 81.715
Angle α, β, γ (deg.)90, 90, 90
Int Tables number21
Space group name H-MC222

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Components

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


Mass: 8284.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60896
#2: Protein Breast Cancer type 2 susceptibility protein / BRCA2


Mass: 83350.562 Da / Num. of mol.: 1 / Fragment: Residues 2378-3115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97929
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Hg

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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: 4.08 Å3/Da / Density % sol: 69.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, Tris-HCl, CaCL2, NaCl, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 %(w/v)PEG40001reservoir
2100 mMTris-HCl1reservoir
350 mM1reservoirCaCl2
475 mM1reservoirNaCl
510 mMdithiothreitol1reservoirpH8.0
620 mg/mlprotein1drop
720 mMTris-HCl1drop
8150 mM1dropNaCl
910 mMdithiothreitol1droppH8.0

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2001
RadiationMonochromator: Si(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. obs: 27074 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.046
Reflection shellResolution: 3.1→3.21 Å / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 25 Å / Redundancy: 5 % / Num. measured all: 136363 / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.31 1265 Random
Rwork0.256 --
all0.26 26000 -
obs0.26 26000 -
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5648 0 5 0 5653
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d1.8
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor all: 0.26 / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.8

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