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- PDB-3pxc: Impact of BRCA1 BRCT domain missense substitutions on phospho-pep... -

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Basic information

Entry
Database: PDB / ID: 3pxc
TitleImpact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1699Q
ComponentsBreast cancer type 1 susceptibility protein
KeywordsPROTEIN BINDING / BRCA1 protein / Missense / phosphopeptide recognition / BRCT tandem repeats / BACH1 Ctip Abraxas / nuclear protein
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
NICKEL (II) ION / Breast cancer type 1 susceptibility protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCoquelle, N. / Green, R. / Glover, J.N.M.
Citation
Journal: Biochemistry / Year: 2011
Title: Impact of BRCA1 BRCT Domain Missense Substitutions on Phosphopeptide Recognition.
Authors: Coquelle, N. / Green, R. / Glover, J.N.
#1: Journal: Cancer Res. / Year: 2010
Title: Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays.
Authors: Lee, M.S. / Green, R. / Marsillac, S.M. / Coquelle, N. / Williams, R.S. / Yeung, T. / Foo, D. / Hau, D.D. / Hui, B. / Monteiro, A.N. / Glover, J.N.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1.
Authors: Williams, R.S. / Lee, M.S. / Hau, D.D. / Glover, J.N.
#3: Journal: 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.
#4: Journal: J.Biol.Chem. / Year: 2003
Title: Structural consequences of a cancer-causing BRCA1-BRCT missense mutation.
Authors: Williams, R.S. / Glover, J.N.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)24,6573
Polymers24,5021
Non-polymers1552
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.620, 114.620, 122.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11X-8-

HOH

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Components

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


Mass: 24502.170 Da / Num. of mol.: 1 / Fragment: BRCT domain, UNP residues 1646-1859 / Mutation: R1699Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold
References: UniProt: P38398, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.73 Å3/Da / Density % sol: 73.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.8M Li2SO4 100mM Tris 5mM CaCl2 10mM NiCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11584 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2009
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11584 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 12036 / Num. obs: 12036 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 70.3 Å2 / Rsym value: 0.057 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.85199.8
2.85-2.9198.8
2.9-3199.2
3-3.2199.5
3.2-4199.1
4-20197.9

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N5O

1n5o


Resolution: 2.8→19.595 Å / SU ML: 0.39 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 602 5 %RANDOM
Rwork0.2278 ---
all0.2298 12034 --
obs0.2298 12034 99.18 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.708 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1378 Å20 Å20 Å2
2---0.1378 Å20 Å2
3---0.2756 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 6 13 1633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081657
X-RAY DIFFRACTIONf_angle_d1.1792255
X-RAY DIFFRACTIONf_dihedral_angle_d15.096582
X-RAY DIFFRACTIONf_chiral_restr0.071257
X-RAY DIFFRACTIONf_plane_restr0.005284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.08080.38111460.33382777X-RAY DIFFRACTION99
3.0808-3.52430.31721480.29572811X-RAY DIFFRACTION99
3.5243-4.43180.25981500.2262848X-RAY DIFFRACTION99
4.4318-19.59590.23431580.18472996X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5793-5.51831.0936.7018-0.64561.12510.36940.88611.2246-0.3939-0.6729-0.9350.44950.44710.34150.48590.32280.00620.68670.18940.50739.07550.390944.6967
25.4696-4.86161.5355.028-0.39850.30761.79662.2446-0.2381-1.7386-1.98510.12330.37990.09620.14681.00640.70970.01940.90820.04150.282133.84849.001634.1396
34.0448-3.7452.30293.8452-2.56532.07992.24282.39950.0739-2.9712-2.27890.22662.91041.1842-0.0442.02091.42910.20171.61950.17760.375127.114354.075726.4029
47.9472-6.39621.78689.0556-2.94886.9945-0.02220.1321.25810.4168-0.5924-0.3983-0.66320.2740.50320.45120.1164-0.10780.32690.12390.524818.985269.324438.5316
56.6303-7.14742.8962.6821-1.99656.35961.5280.9046-1.6041-1.8101-1.7143.13460.6411-0.0904-0.23760.55740.2461-0.34140.1796-0.11010.6419.032565.333134.9755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain X and resid 1649:1684
2X-RAY DIFFRACTION2chain X and resid 1685:1741
3X-RAY DIFFRACTION3chain X and resid 1742:1753
4X-RAY DIFFRACTION4chain X and resid 1754:1803
5X-RAY DIFFRACTION5chain X and resid 1804:1859

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