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- PDB-1t29: Crystal structure of the BRCA1 BRCT repeats bound to a phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 1t29
TitleCrystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide
Components
  • BACH1 phosphorylated peptide
  • Breast cancer type 1 susceptibility protein
KeywordsSIGNALING PROTEIN / BRCA1 / BRCT repeats / BACH1 / phosphopeptide recognition / breast cancer
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-B complex / BRCA1-A 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-B complex / BRCA1-A complex / BRCA1-C complex / spermatogonial cell division / negative regulation of centriole replication / Cytosolic iron-sulfur cluster assembly / random inactivation of X chromosome / ubiquitin-modified histone reader activity / gamma-tubulin ring complex / negative regulation of intracellular estrogen receptor signaling pathway / chordate embryonic development / cellular response to indole-3-methanol / double-strand break repair involved in meiotic recombination / DNA strand resection involved in replication fork processing / nuclear ubiquitin ligase complex / homologous recombination / negative regulation of fatty acid biosynthetic process / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / lateral element / mitotic G2/M transition checkpoint / regulation of DNA damage checkpoint / protein-DNA covalent cross-linking repair / Impaired BRCA2 binding to PALB2 / XY body / DNA 5'-3' helicase / DNA repair complex / RNA polymerase binding / DNA damage tolerance / protein K6-linked ubiquitination / centrosome cycle / HDR through Single Strand Annealing (SSA) / seminiferous tubule development / response to ionizing radiation / 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) / negative regulation of gene expression via chromosomal CpG island methylation / Resolution of D-loop Structures through Holliday Junction Intermediates / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / Impaired BRCA2 binding to RAD51 / negative regulation of cell cycle / negative regulation of reactive oxygen species metabolic process / spermatid development / positive regulation of vascular endothelial growth factor production / Presynaptic phase of homologous DNA pairing and strand exchange / ubiquitin ligase complex / regulation of DNA repair / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / SUMOylation of DNA damage response and repair proteins / protein autoubiquitination / DNA damage checkpoint signaling / Meiotic synapsis / positive regulation of DNA repair / replication fork / DNA helicase activity / male germ cell nucleus / cellular response to ionizing radiation / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / chromosome segregation / tubulin binding / negative regulation of cell growth / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / double-strand break repair via homologous recombination / Meiotic recombination / HDR through Homologous Recombination (HRR) / cellular response to tumor necrosis factor / intrinsic apoptotic signaling pathway in response to DNA damage / Metalloprotease DUBs / fatty acid biosynthetic process / positive regulation of angiogenesis / p53 binding / ubiquitin-protein transferase activity / KEAP1-NFE2L2 pathway / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / 4 iron, 4 sulfur cluster binding / Neddylation / Processing of DNA double-strand break ends / nuclear membrane / 5'-3' DNA helicase activity / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / regulation of cell cycle / transcription cis-regulatory region binding
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 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShiozaki, E.N. / Gu, L. / Yan, N. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure of the BRCT repeats of BRCA1 bound to a BACH1 phosphopeptide: implications for signaling.
Authors: Shiozaki, E.N. / Gu, L. / Yan, N. / Shi, Y.
History
DepositionApr 20, 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 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Residue THR 1816 and residue GLU 1817 chain A are not linked. Distance of C-N bond is 3.29A.

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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: BACH1 phosphorylated peptide


Theoretical massNumber of molelcules
Total (without water)26,2092
Polymers26,2092
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-8 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.177, 63.177, 105.532
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: BRCT repeats of BRCA1 (residues 1646-1859)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38398
#2: Protein/peptide BACH1 phosphorylated peptide


Mass: 1677.770 Da / Num. of mol.: 1 / Fragment: residues 985-998 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide occurs naturally in humans
References: UniProt: Q9BX63
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.43 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. all: 11334 / Num. obs: 11209 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 40 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 0.179 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JNX

1jnx


Resolution: 2.3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 1106 random
Rwork0.252 --
obs0.252 11145 -
all-11292 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.634 Å2-1.589 Å20 Å2
2---0.634 Å20 Å2
3---1.268 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 0 235 2009
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.69
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4sep.par

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