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- PDB-1t15: Crystal Structure of the Brca1 BRCT Domains in Complex with the P... -

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Basic information

Entry
Database: PDB / ID: 1t15
TitleCrystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase
Components
  • BRCA1 interacting protein C-terminal helicase 1
  • Breast cancer type 1 susceptibility protein
KeywordsANTITUMOR PROTEIN / Protein-Peptide Complex
Function / homology
Function and homology information


meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / chiasma assembly / catalytic activity, acting on a nucleic acid / histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / 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 ...meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / chiasma assembly / catalytic activity, acting on a nucleic acid / histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / 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 / spermatogonial cell division / negative regulation of centriole replication / sex-chromosome dosage compensation / Cytosolic iron-sulfur cluster assembly / random inactivation of X chromosome / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / ubiquitin-modified histone reader activity / chordate embryonic development / negative regulation of intracellular estrogen receptor signaling pathway / cellular response to indole-3-methanol / gamma-tubulin ring complex / negative regulation of fatty acid biosynthetic process / DNA strand resection involved in replication fork processing / homologous recombination / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / seminiferous tubule development / protein K6-linked ubiquitination / lateral element / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / DNA 5'-3' helicase / protein-DNA covalent cross-linking repair / mitotic G2/M transition checkpoint / centrosome cycle / RNA polymerase binding / postreplication repair / DNA repair complex / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / intracellular membraneless organelle / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / negative regulation of cell cycle / negative regulation of reactive oxygen species metabolic process / Presynaptic phase of homologous DNA pairing and strand exchange / positive regulation of vascular endothelial growth factor production / spermatid development / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of DNA repair / protein autoubiquitination / cellular response to ionizing radiation / tubulin binding / Meiotic synapsis / DNA helicase activity / positive regulation of DNA repair / DNA damage checkpoint signaling / replication fork / double-strand break repair via homologous recombination / male germ cell nucleus / nucleotide-excision repair / chromosome segregation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / HDR through Homologous Recombination (HRR) / negative regulation of cell growth / G2/M DNA damage checkpoint / Metalloprotease DUBs / RING-type E3 ubiquitin transferase / Meiotic recombination / KEAP1-NFE2L2 pathway / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / ubiquitin-protein transferase activity / fatty acid biosynthetic process / cellular response to tumor necrosis factor / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / double-strand break repair / Neddylation / Processing of DNA double-strand break ends / chromosome / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / Regulation of TP53 Activity through Phosphorylation / nuclear membrane / damaged DNA binding / transcription coactivator activity
Similarity search - Function
Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 ...Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Breast cancer type 1 susceptibility protein / Fanconi anemia group J protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsClapperton, J.A. / Manke, I.A. / Lowery, D.M. / Ho, T. / Haire, L.F. / Yaffe, M.B. / Smerdon, S.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer
Authors: Clapperton, J.A. / Manke, I.A. / Lowery, D.M. / Ho, T. / Haire, L.F. / Yaffe, M.B. / Smerdon, S.J.
History
DepositionApr 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Breast cancer type 1 susceptibility protein
B: BRCA1 interacting protein C-terminal helicase 1


Theoretical massNumber of molelcules
Total (without water)25,4932
Polymers25,4932
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.837, 65.837, 93.075
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Breast cancer type 1 susceptibility protein


Mass: 24531.234 Da / Num. of mol.: 1 / Fragment: BCRT 1, BCRT 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1 / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38398
#2: Protein/peptide BRCA1 interacting protein C-terminal helicase 1


Mass: 961.929 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: GenBank: 14042978, UniProt: Q9BX63*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5
Details: PEG 8000, Ammonium Sulphate, MES, pH 6.5, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→15 Å / Num. all: 20529 / Num. obs: 19219 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5
Reflection shellResolution: 1.85→1.93 Å / % possible all: 76.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 972 5.1 %Random
Rwork0.206 ---
all-20484 --
obs-18242 --
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 0 156 1906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.35

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