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- PDB-1mje: STRUCTURE OF A BRCA2-DSS1-SSDNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1mje
TitleSTRUCTURE OF A BRCA2-DSS1-SSDNA COMPLEX
Components
  • 5'-D(P*TP*TP*TP*TP*TP*T)-3'
  • Deleted in split hand/split foot protein 1
  • breast cancer 2
KeywordsGENE REGULATION/ANTITUMOR PROTEIN/DNA / TUMOR SUPPRESSOR / BREAST CANCER SUSCEPTIBILITY / DNA-BINDING / GENE REGULATION-ANTITUMOR PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


HDR through MMEJ (alt-NHEJ) / homologous chromosome orientation in meiotic metaphase I / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / inner cell mass cell proliferation / Resolution of D-loop Structures through Holliday Junction Intermediates / BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / HDR through Homologous Recombination (HRR) / establishment of protein localization to telomere ...HDR through MMEJ (alt-NHEJ) / homologous chromosome orientation in meiotic metaphase I / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / inner cell mass cell proliferation / Resolution of D-loop Structures through Holliday Junction Intermediates / BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / HDR through Homologous Recombination (HRR) / establishment of protein localization to telomere / mammary gland development / chordate embryonic development / mitotic recombination-dependent replication fork processing / oocyte maturation / histone H3 acetyltransferase activity / histone H4 acetyltransferase activity / female gonad development / nuclear ubiquitin ligase complex / lateral element / gamma-tubulin binding / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / male meiosis I / integrator complex / DNA repair complex / telomere maintenance via recombination / response to UV-C / transcription export complex 2 / proteasome regulatory particle, lid subcomplex / multicellular organism growth / response to X-ray / chromosome organization / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / cellular response to type I interferon / Cross-presentation of soluble exogenous antigens (endosomes) / regulation of DNA damage checkpoint / Somitogenesis / 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 / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / mRNA export from nucleus / proteasome assembly / positive regulation of mitotic cell cycle / response to gamma radiation / proteasome complex / secretory granule / replication fork processing / regulation of proteasomal protein catabolic process / cellular response to ionizing radiation / regulation of cytokinesis / DNA damage response, signal transduction by p53 class mediator / brain development / intrinsic apoptotic signaling pathway in response to DNA damage / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / 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 / double-strand break repair via homologous recombination / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / nucleotide-excision repair / 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 / Regulation of RUNX3 expression and activity / Autodegradation of the E3 ubiquitin ligase COP1 / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / 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 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / cellular senescence
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
: / DNA / 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 / MOLECULAR REPLACEMENT / Resolution: 3.5 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 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE RESIDUES 2793-2879 OF THE BRCA2 CHAIN WERE REMOVED PROTEOLYTICALLY. RESIDUES 3087 AND 3089 ...SEQUENCE RESIDUES 2793-2879 OF THE BRCA2 CHAIN WERE REMOVED PROTEOLYTICALLY. RESIDUES 3087 AND 3089 ARE COVALENTLY BOUND. 3088 WAS SKIPPED IN THE NUMBERING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(P*TP*TP*TP*TP*TP*T)-3'
B: Deleted in split hand/split foot protein 1
A: breast cancer 2


Theoretical massNumber of molelcules
Total (without water)83,0483
Polymers83,0483
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.866, 198.866, 200.047
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422

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Components

#1: DNA chain 5'-D(P*TP*TP*TP*TP*TP*T)-3'


Mass: 1780.199 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: 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
#3: Protein breast cancer 2 / BRCA2


Mass: 72983.172 Da / Num. of mol.: 1
Fragment: sequence database residues 2378-2792, 2880-3113 (residues 2793-2879 removed)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 17973451, UniProt: P97929*PLUS

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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: 5.95 Å3/Da / Density % sol: 79.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Sodium Acetate, Sodium Citrate, NaCl, DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Acetate11
2Sodium Citrate11
3NaCl11
4DTT11
5NaCl12

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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: 3.5→25 Å / Num. all: 24950 / Num. obs: 24950 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.5→3.62 Å / % possible all: 99.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2783 565 random 2.5%
Rwork0.2448 --
all-22508 -
obs-22508 -
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5077 121 0 0 5198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_d1.98

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