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- PDB-4y18: Structure of BRCA1 BRCT domains in complex with Abraxas double ph... -

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Basic information

Entry
Database: PDB / ID: 4y18
TitleStructure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide
Components
  • BRCA1-A complex subunit Abraxas
  • Breast cancer type 1 susceptibility protein
KeywordsANTITUMOR PROTEIN / DNA damage response / BRCT / phosphopeptide / ligase-peptide complex
Function / homology
Function and homology information


Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / sex-chromosome dosage compensation / attachment of spindle microtubules to kinetochore ...Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / sex-chromosome dosage compensation / attachment of spindle microtubules to kinetochore / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / lateral element / homologous recombination / DNA strand resection involved in replication fork processing / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / postreplication repair / DNA repair complex / RNA polymerase binding / centrosome cycle / 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 / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to RAD51 / DNA-binding transcription activator activity / response to ionizing radiation / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / polyubiquitin modification-dependent protein binding / mitotic spindle assembly / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / protein autoubiquitination / SUMOylation of DNA damage response and repair proteins / regulation of DNA repair / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / Meiotic synapsis / positive regulation of DNA repair / tubulin binding / male germ cell nucleus / chromosome segregation / cellular response to ionizing radiation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / negative regulation of cell growth / Metalloprotease DUBs / Meiotic recombination / fatty acid biosynthetic process / positive regulation of angiogenesis / ubiquitin-protein transferase activity / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / double-strand break repair / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to tumor necrosis factor / chromatin organization / chromosome / Neddylation / Processing of DNA double-strand break ends / microtubule binding / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / nuclear body / regulation of cell cycle / transcription cis-regulatory region binding / protein ubiquitination / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / 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
Similarity search - Function
FAM175 family, BRCA1-A complex, Abraxas 1 subunit / BRCA1-A complex subunit Abraxas 1 MPN domain / FAM175 family / 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) ...FAM175 family, BRCA1-A complex, Abraxas 1 subunit / BRCA1-A complex subunit Abraxas 1 MPN domain / FAM175 family / 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 / MPN domain / MPN domain profile. / 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 / BRCA1-A complex subunit Abraxas 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWu, Q. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust093167/Z/10/Z United Kingdom
CitationJournal: Mol.Cell / Year: 2016
Title: Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites.
Authors: Wu, Q. / Paul, A. / Su, D. / Mehmood, S. / Foo, T.K. / Ochi, T. / Bunting, E.L. / Xia, B. / Robinson, C.V. / Wang, B. / Blundell, T.L.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Breast cancer type 1 susceptibility protein
B: Breast cancer type 1 susceptibility protein
C: Breast cancer type 1 susceptibility protein
D: Breast cancer type 1 susceptibility protein
E: Breast cancer type 1 susceptibility protein
F: Breast cancer type 1 susceptibility protein
G: Breast cancer type 1 susceptibility protein
H: Breast cancer type 1 susceptibility protein
I: BRCA1-A complex subunit Abraxas
J: BRCA1-A complex subunit Abraxas
K: BRCA1-A complex subunit Abraxas
L: BRCA1-A complex subunit Abraxas
M: BRCA1-A complex subunit Abraxas
N: BRCA1-A complex subunit Abraxas
O: BRCA1-A complex subunit Abraxas
P: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)217,64016
Polymers217,64016
Non-polymers00
Water181
1
A: Breast cancer type 1 susceptibility protein
I: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)27,2052
Polymers27,2052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Breast cancer type 1 susceptibility protein
B: Breast cancer type 1 susceptibility protein
I: BRCA1-A complex subunit Abraxas
J: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)54,4104
Polymers54,4104
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-25 kcal/mol
Surface area22030 Å2
MethodPISA
3
B: Breast cancer type 1 susceptibility protein
J: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)27,2052
Polymers27,2052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Breast cancer type 1 susceptibility protein
K: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)27,2052
Polymers27,2052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Breast cancer type 1 susceptibility protein
K: BRCA1-A complex subunit Abraxas

E: Breast cancer type 1 susceptibility protein
M: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)54,4104
Polymers54,4104
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area3520 Å2
ΔGint-27 kcal/mol
Surface area22040 Å2
MethodPISA
6
D: Breast cancer type 1 susceptibility protein
L: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)27,2052
Polymers27,2052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
D: Breast cancer type 1 susceptibility protein
L: BRCA1-A complex subunit Abraxas

F: Breast cancer type 1 susceptibility protein
N: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)54,4104
Polymers54,4104
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area3240 Å2
ΔGint-24 kcal/mol
Surface area21570 Å2
MethodPISA
8
E: Breast cancer type 1 susceptibility protein
M: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)27,2052
Polymers27,2052
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
F: Breast cancer type 1 susceptibility protein
N: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)27,2052
Polymers27,2052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
G: Breast cancer type 1 susceptibility protein
O: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)27,2052
Polymers27,2052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
G: Breast cancer type 1 susceptibility protein
H: Breast cancer type 1 susceptibility protein
O: BRCA1-A complex subunit Abraxas
P: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)54,4104
Polymers54,4104
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-24 kcal/mol
Surface area21370 Å2
MethodPISA
12
H: Breast cancer type 1 susceptibility protein
P: BRCA1-A complex subunit Abraxas


Theoretical massNumber of molelcules
Total (without water)27,2052
Polymers27,2052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.819, 183.726, 190.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Breast cancer type 1 susceptibility protein / RING finger protein 53


Mass: 25796.668 Da / Num. of mol.: 8 / Fragment: BRCT domains, UNP residues 1646-1859
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Production host: Escherichia coli (E. coli)
References: UniProt: P38398, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide
BRCA1-A complex subunit Abraxas / Coiled-coil domain-containing protein 98 / Protein FAM175A


Mass: 1408.280 Da / Num. of mol.: 8 / Fragment: UNP residues 399-409 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6UWZ7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, Ammonium Sulphate, PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.5→95.3 Å / Num. obs: 39170 / % possible obs: 99.82 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 16.4
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5572 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T15

1t15


Resolution: 3.5→95.255 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2975 1961 5.01 %
Rwork0.2326 --
obs0.2355 39160 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→95.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13975 0 0 1 13976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714312
X-RAY DIFFRACTIONf_angle_d0.919493
X-RAY DIFFRACTIONf_dihedral_angle_d13.515111
X-RAY DIFFRACTIONf_chiral_restr0.0312184
X-RAY DIFFRACTIONf_plane_restr0.0032478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.58750.34091300.31942563X-RAY DIFFRACTION98
3.5875-3.68450.35541420.29372627X-RAY DIFFRACTION100
3.6845-3.7930.3441360.28992620X-RAY DIFFRACTION100
3.793-3.91540.29091360.2822640X-RAY DIFFRACTION100
3.9154-4.05530.35441400.26612607X-RAY DIFFRACTION100
4.0553-4.21770.29331400.24222638X-RAY DIFFRACTION100
4.2177-4.40970.30571400.24262648X-RAY DIFFRACTION100
4.4097-4.64210.32391370.23842635X-RAY DIFFRACTION100
4.6421-4.9330.26491410.22832627X-RAY DIFFRACTION100
4.933-5.31380.25511390.21242676X-RAY DIFFRACTION100
5.3138-5.84850.26631460.21842665X-RAY DIFFRACTION100
5.8485-6.69460.31261320.24082694X-RAY DIFFRACTION100
6.6946-8.43370.28381470.2132721X-RAY DIFFRACTION100
8.4337-95.29020.29691550.19692838X-RAY DIFFRACTION100

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