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- PDB-2ing: X-ray Structure of the BRCA1 BRCT mutant M1775K -

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Basic information

Entry
Database: PDB / ID: 2ing
TitleX-ray Structure of the BRCA1 BRCT mutant M1775K
ComponentsBreast cancer type 1 susceptibility protein
KeywordsDNA BINDING PROTEIN / Zinc-finger / DNA-binding / DNA repair / Disease mutation / Phosphorylation
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 / negative regulation of intracellular estrogen receptor signaling pathway ...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 / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / homologous recombination / lateral element / XY body / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / dosage compensation by inactivation of X chromosome / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to PALB2 / : / 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 / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / DNA-binding transcription activator activity / intracellular non-membrane-bounded organelle / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / localization / regulation of DNA repair / protein autoubiquitination / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of DNA repair / Meiotic synapsis / 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 / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / negative regulation of cell growth / Metalloprotease DUBs / Meiotic recombination / ubiquitin-protein transferase activity / fatty acid biosynthetic process / positive regulation of angiogenesis / 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 / chromosome / Neddylation / cellular response to tumor necrosis factor / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / protein ubiquitination / nuclear body / transcription cis-regulatory region binding / regulation of cell cycle / 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 / RNA 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsBirrane, G. / Soni, A. / Ladias, J.A.A.
CitationJournal: Eur.J.Hum.Genet. / Year: 2008
Title: Pathogenicity of the BRCA1 missense variant M1775K is determined by the disruption of the BRCT phosphopeptide-binding pocket: a multi-modal approach.
Authors: Tischkowitz, M. / Hamel, N. / Carvalho, M.A. / Birrane, G. / Soni, A. / van Beers, E.H. / Joosse, S.A. / Wong, N. / Novak, D. / Quenneville, L.A. / Grist, S.A. / Nederlof, P.M. / Goldgar, D. ...Authors: Tischkowitz, M. / Hamel, N. / Carvalho, M.A. / Birrane, G. / Soni, A. / van Beers, E.H. / Joosse, S.A. / Wong, N. / Novak, D. / Quenneville, L.A. / Grist, S.A. / Nederlof, P.M. / Goldgar, D.E. / Tavtigian, S.V. / Monteiro, A.N. / Ladias, J.A. / Foulkes, W.D.
History
DepositionOct 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_label_seq_id / _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 1.4Aug 30, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,5924
Polymers24,3411
Non-polymers2513
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
X: Breast cancer type 1 susceptibility protein
hetero molecules

X: Breast cancer type 1 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1848
Polymers48,6822
Non-polymers5026
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area2470 Å2
ΔGint-81 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.340, 114.340, 119.878
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 24340.973 Da / Num. of mol.: 1 / Fragment: BRCT1, BRCT2 / Mutation: M1775K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Plasmid: pMAL-c2x / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 4.67 Å3/Da / Density % sol: 73.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 1.4M Ammonium sulfate, 20mM Cobalt chloride, 100mM 2-(N-Morpholino) ethanesulfonic acid, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→30 Å / Num. obs: 5744 / % possible obs: 99.9 % / Redundancy: 27.5 % / Rmerge(I) obs: 0.093 / Χ2: 1.054 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.6-3.7328.90.535551.0091100
3.73-3.8828.70.3575460.9841100
3.88-4.0528.70.2625591.152199.8
4.05-4.2728.50.2085561.091100
4.27-4.5428.50.1485621.1651100
4.54-4.8928.20.1295651.0831100
4.89-5.3827.90.1115721.083199.8
5.38-6.1527.40.0985801.0351100
6.15-7.7526.60.0795971.0041100
7.75-5022.80.0546520.917199.2

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.87 Å41.37 Å
Translation3.87 Å41.37 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N5O

1n5o


Resolution: 3.6→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 103.603 / SU ML: 0.682 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.292 / ESU R Free: 0.642 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.302 501 8.8 %RANDOM
Rwork0.247 ---
obs0.251 5678 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 148.161 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.55 Å20 Å2
2---1.1 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 3.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 11 0 1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221718
X-RAY DIFFRACTIONr_bond_other_d0.0020.021160
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9462329
X-RAY DIFFRACTIONr_angle_other_deg0.95532820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3695205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72123.5978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.69615296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4641511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021869
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02353
X-RAY DIFFRACTIONr_nbd_refined0.2830.2570
X-RAY DIFFRACTIONr_nbd_other0.2180.21355
X-RAY DIFFRACTIONr_nbtor_refined0.2070.2865
X-RAY DIFFRACTIONr_nbtor_other0.0960.2955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.235
LS refinement shellResolution: 3.6→3.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 36 -
Rwork0.392 374 -
obs-410 99.76 %
Refinement TLS params.Method: refined / Origin x: 18.647 Å / Origin y: 48.226 Å / Origin z: 3.867 Å
111213212223313233
T-0.9717 Å2-0.1477 Å2-0.0631 Å2-0.111 Å2-0.7346 Å2---0.6903 Å2
L23.2434 °2-4.0678 °2-2.2069 °2-5.6322 °22.0872 °2--5.6025 °2
S0.5766 Å °-2.9547 Å °0.3596 Å °0.9229 Å °-0.4543 Å °0.7603 Å °0.22 Å °1.2426 Å °-0.1224 Å °
Refinement TLS groupSelection: ALL

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