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- PDB-1l0b: Crystal Structure of rat Brca1 tandem-BRCT region -

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Basic information

Entry
Database: PDB / ID: 1l0b
TitleCrystal Structure of rat Brca1 tandem-BRCT region
ComponentsBRCA1
KeywordsUNKNOWN FUNCTION / TANDEM-BRCT / THREE-HELIX BUNDLE
Function / homology
Function and homology information


HDR through Single Strand Annealing (SSA) / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / G2/M DNA damage checkpoint / : / : / : / 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 Single Strand Annealing (SSA) / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / G2/M DNA damage checkpoint / : / : / : / Resolution of D-loop Structures through Holliday Junction Intermediates / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / : / : / : / : / : / mitotic G2 DNA damage checkpoint signaling => GO:0007095 / HDR through Homologous Recombination (HRR) / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / : / : / regulation of cell cycle => GO:0051726 / : / Metalloprotease DUBs / SUMOylation of DNA damage response and repair proteins / Regulation of TP53 Activity through Phosphorylation / BRCA1-BARD1 complex / BRCA1-A complex / negative regulation of intracellular estrogen receptor signaling pathway / : / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / lateral element / dosage compensation by inactivation of X chromosome / protein K6-linked ubiquitination / mitotic G2/M transition checkpoint / postreplication repair / RNA polymerase binding / centrosome cycle / response to ionizing radiation / response to lipid / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / protein autoubiquitination / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / condensed chromosome / positive regulation of DNA repair / response to nutrient / : / condensed nuclear chromosome / positive regulation of protein ubiquitination / chromosome segregation / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / brain development / fatty acid biosynthetic process / positive regulation of protein import into nucleus / response to estrogen / ubiquitin-protein transferase activity / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / response to estradiol / chromosome / cellular response to tumor necrosis factor / damaged DNA binding / transcription coactivator activity / transcription cis-regulatory region binding / protein ubiquitination / mitochondrial matrix / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site ...Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Breast cancer type 1 susceptibility protein homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsJoo, W.S. / Jeffrey, P.D. / Cantor, S.B. / Finnin, M.S. / Livingston, D.M. / Pavletich, N.P.
CitationJournal: Genes Dev. / Year: 2002
Title: Structure of the 53BP1 BRCT region bound to p53 and its comparison to the Brca1 BRCT structure.
Authors: Joo, W.S. / Jeffrey, P.D. / Cantor, S.B. / Finnin, M.S. / Livingston, D.M. / Pavletich, N.P.
History
DepositionFeb 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 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 / 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: BRCA1


Theoretical massNumber of molelcules
Total (without water)26,1051
Polymers26,1051
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.512, 58.722, 65.327
Angle α, β, γ (deg.)90.00, 111.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BRCA1


Mass: 26104.854 Da / Num. of mol.: 1 / Fragment: tandem-BRCT region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O54952
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris-hydrochloride, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1reservoirpH8.5
2150 mM1reservoirNaCl
318 %(w/v)PEG80001reservoir
45 mMdithiothreitol1reservoir
575 mg/mlprotein1drop
610 mMsodium HEPES1droppH7.5
7150 mM1dropNaCl
85 mMdithiothreitol1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
31031
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.928
SYNCHROTRONNSLS X9A21.051
SYNCHROTRONNSLS X9A31.051
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 13, 2001
MARRESEARCH2CCDApr 28, 2001
MARRESEARCH3CCDApr 28, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rh-coated SiSINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
3Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9281
21.0511
ReflectionResolution: 2.1→15 Å / Num. obs: 17223 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.18 Å
Reflection
*PLUS
% possible obs: 97 % / Num. measured all: 55198 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.457

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→15 Å / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 0 177 1700
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 12529 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.203 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.61
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Rfactor Rfree: 0.341 / Rfactor Rwork: 0.262 / Rfactor obs: 0.262

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