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- PDB-1n5o: Structural consequences of a cancer-causing BRCA1-BRCT missense m... -

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Entry
Database: PDB / ID: 1n5o
TitleStructural consequences of a cancer-causing BRCA1-BRCT missense mutation
ComponentsBreast cancer type 1 susceptibility protein
KeywordsANTITUMOR PROTEIN / BRCA1 / BRCT / missense mutation / protein folding / Breast Cancer
Function / homology
Function and homology information


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 / negative regulation of centriole replication / sex-chromosome dosage compensation ...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 / negative regulation of centriole replication / sex-chromosome dosage compensation / random inactivation of X chromosome / ubiquitin-modified histone reader activity / nuclear ubiquitin ligase complex / chordate embryonic development / cellular response to indole-3-methanol / gamma-tubulin ring complex / negative regulation of intracellular estrogen receptor signaling pathway / DNA strand resection involved in replication fork processing / negative regulation of fatty acid biosynthetic process / homologous recombination / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / protein K6-linked ubiquitination / lateral element / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / RNA polymerase binding / DNA damage tolerance / DNA repair complex / centrosome cycle / 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 / intracellular membraneless organelle / HDR through Single Strand Annealing (SSA) / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to RAD51 / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / negative regulation of cell cycle / negative regulation of reactive oxygen species metabolic process / positive regulation of vascular endothelial growth factor production / Presynaptic phase of homologous DNA pairing and strand exchange / 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 / tubulin binding / Meiotic synapsis / positive regulation of DNA repair / cellular response to ionizing radiation / male germ cell nucleus / chromosome segregation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / negative regulation of cell growth / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / Meiotic recombination / Metalloprotease DUBs / 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 / KEAP1-NFE2L2 pathway / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / Neddylation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / protein ubiquitination / nuclear body / chromatin remodeling / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase 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 / DNA 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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. ...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 / 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 / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Breast cancer type 1 susceptibility protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWilliams, R.S. / Glover, J.N.M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural consequences of a cancer-causing BRCA1-BRCT missense mutation
Authors: Williams, R.S. / Glover, J.N.M.
History
DepositionNov 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Breast cancer type 1 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8084
Polymers24,5571
Non-polymers2513
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.535, 114.535, 121.527
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Breast cancer type 1 susceptibility protein


Mass: 24557.232 Da / Num. of mol.: 1 / Fragment: BRCT (residues 1646-1859) / Mutation: M1775R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P38398
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 4.68 Å3/Da / Density % sol: 73.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: ammonium sulphate, cobalt chloride, MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
21.4 Mammonium sulfate1reservoir
3100 mMMES1reservoirpH6.7
410 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0093 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12024 / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 99.3 % / Num. measured all: 100697 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1jnx

1jnx


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.883 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29777 825 6.9 %RANDOM
Rwork0.27364 ---
all0.27538 12035 --
obs0.27538 11141 99.43 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.131 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å22.32 Å20 Å2
2--4.63 Å20 Å2
3----6.95 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 11 59 1618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221595
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9392174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2563204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36715265
X-RAY DIFFRACTIONr_chiral_restr0.1310.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021180
X-RAY DIFFRACTIONr_nbd_refined0.1910.3767
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.5190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.335
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4760.55
X-RAY DIFFRACTIONr_mcbond_it0.4591.51028
X-RAY DIFFRACTIONr_mcangle_it0.87521646
X-RAY DIFFRACTIONr_scbond_it1.1153567
X-RAY DIFFRACTIONr_scangle_it1.9674.5528
LS refinement shellResolution: 2.802→2.874 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.416 47
Rwork0.34 797
Refinement TLS params.Method: refined / Origin x: 24.4148 Å / Origin y: 58.579 Å / Origin z: 36.9806 Å
111213212223313233
T0.9456 Å20.3635 Å2-0.038 Å2-0.1397 Å2-0.0131 Å2--0.2846 Å2
L9.155 °2-8.6102 °22.226 °2-10.8928 °20.0072 °2--2.8182 °2
S1.4927 Å °0.4582 Å °0.2388 Å °-2.5477 Å °-1.2966 Å °0.2426 Å °0.0049 Å °-0.0545 Å °-0.1961 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1649 - 1859
2X-RAY DIFFRACTION1X301
3X-RAY DIFFRACTION1X201 - 202
4X-RAY DIFFRACTION1X1 - 59
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.273
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.857

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