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

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Basic information

Entry
Database: PDB / ID: 3pxe
TitleImpact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K
Components
  • Breast cancer type 1 susceptibility protein
  • phospho peptide
KeywordsPROTEIN BINDING / BRCA1 protein / Missense / phosphopeptide recognition / BRCT domain / Phospho-peptide binding / 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 / chordate embryonic development / nuclear ubiquitin ligase complex / 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 / 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 / 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: 2.85 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: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Breast cancer type 1 susceptibility protein
B: Breast cancer type 1 susceptibility protein
C: Breast cancer type 1 susceptibility protein
D: Breast cancer type 1 susceptibility protein
E: phospho peptide
F: phospho peptide
G: phospho peptide
H: phospho peptide


Theoretical massNumber of molelcules
Total (without water)102,9508
Polymers102,9508
Non-polymers00
Water28816
1
A: Breast cancer type 1 susceptibility protein
E: phospho peptide


Theoretical massNumber of molelcules
Total (without water)25,7382
Polymers25,7382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-9 kcal/mol
Surface area11030 Å2
MethodPISA
2
B: Breast cancer type 1 susceptibility protein
F: phospho peptide


Theoretical massNumber of molelcules
Total (without water)25,7382
Polymers25,7382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-8 kcal/mol
Surface area11140 Å2
MethodPISA
3
C: Breast cancer type 1 susceptibility protein
G: phospho peptide


Theoretical massNumber of molelcules
Total (without water)25,7382
Polymers25,7382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-9 kcal/mol
Surface area11340 Å2
MethodPISA
4
D: Breast cancer type 1 susceptibility protein
H: phospho peptide


Theoretical massNumber of molelcules
Total (without water)25,7382
Polymers25,7382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-8 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.820, 131.050, 180.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 24531.301 Da / Num. of mol.: 4 / Fragment: BRCT domain, UNP residues 1646-1859 / Mutation: E1836K
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: Protein/peptide
phospho peptide


Mass: 1206.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Peptide derived from BRCA1 partner BACH1.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM MES 0.15M (NH4)2SO4 26% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.85→44.37 Å / Num. all: 31218 / Num. obs: 31218 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.85-2.9173.6
2.9-3196.7
3-6197.5
6-44.37196.8

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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: 2.85→44.363 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 30.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 1561 5 %
Rwork0.2202 --
obs0.2226 31205 96.12 %
all-31205 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.016 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-38.4433 Å2-0 Å2-0 Å2
2---16.319 Å2-0 Å2
3----22.1243 Å2
Refinement stepCycle: LAST / Resolution: 2.85→44.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6815 0 0 16 6831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076979
X-RAY DIFFRACTIONf_angle_d1.0789492
X-RAY DIFFRACTIONf_dihedral_angle_d14.972485
X-RAY DIFFRACTIONf_chiral_restr0.0681074
X-RAY DIFFRACTIONf_plane_restr0.0051199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.94210.39091200.35772293X-RAY DIFFRACTION83
2.9421-3.04720.40581430.34362702X-RAY DIFFRACTION97
3.0472-3.16920.34481410.30432686X-RAY DIFFRACTION98
3.1692-3.31340.37461440.28462725X-RAY DIFFRACTION98
3.3134-3.4880.25241420.25722708X-RAY DIFFRACTION97
3.488-3.70640.29221430.23092718X-RAY DIFFRACTION98
3.7064-3.99240.25221440.21212728X-RAY DIFFRACTION97
3.9924-4.39390.23931440.18812729X-RAY DIFFRACTION98
4.3939-5.02890.22041440.16382752X-RAY DIFFRACTION98
5.0289-6.3330.26321450.20152742X-RAY DIFFRACTION97
6.333-44.36830.23071510.20062861X-RAY DIFFRACTION97
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)
13.30280.58311.26941.31230.25411.9895-0.11360.3407-0.08810.02690.04030.0216-0.0745-0.182-0.00080.2634-0.10330.04030.45150.01710.2329-1.6773-14.8793-39.3337
22.5662-1.24920.62142.83680.03611.2751-0.065-0.0218-0.10380.7496-0.11470.04280.36720.08740.00030.5367-0.1299-0.01940.48970.03720.44863.1192-15.9708-28.0535
30.03480.00190.08550.2588-0.15110.2082-0.1882-0.34460.04211.8967-0.00540.09250.6444-0.1774-0.0030.746-0.1058-0.0310.7890.01410.69899.5752-9.5731-20.766
42.26560.03061.6052.5597-0.14211.58510.19530.42140.7953-0.3905-0.1901-0.4249-0.44760.1360.00030.4841-0.0388-0.05960.47050.14230.684319.40512.2735-35.2009
53.2471.25371.72171.41070.47911.96850.84770.18610.68630.3193-0.4198-0.9941-0.60630.42250.0121-0.0746-0.1013-0.3610.11130.12860.331729.5737-2.0627-31.1902
61.86790.7926-0.24781.42590.09611.92530.0691-0.0985-0.16080.2146-0.16580.13480.0016-0.41180.00010.61790.061-0.04420.45070.03990.4295-11.414514.7515.4919
71.3985-0.97190.16591.3906-1.2471.5082-0.1042-0.08380.34990.2348-0.2288-0.264-0.61880.04350.00020.2621-0.015-0.0950.3177-0.00920.3399-3.093517.5484-2.4608
80.30940.2923-0.10130.3110.01060.28860.02690.01710.5525-0.4168-0.648-0.2143-0.28420.7142-0.00240.6186-0.02640.01390.77040.05250.6032-2.08219.1308-14.1841
93.33051.6568-0.15613.04471.15252.2489-0.16540.0156-0.0032-0.3436-0.25560.3728-0.7081-0.76560.00030.45660.0726-0.10560.6225-0.0430.379-18.86687.8969-20.6256
103.2593-0.3806-0.52082.24731.34553.75180.01460.43180.055-0.1386-0.1680.3690.8122-0.01630.00040.2716-0.0611-0.10060.3757-0.0210.14-11.37180.8201-26.4148
111.22110.83490.8231.2642-0.18761.6844-0.0610.1680.3413-0.0717-0.1777-0.3963-0.09740.48280.00040.48910.0006-0.04910.55730.08230.8181-6.535257.8826-27.7166
121.09440.8202-0.24041.29610.45540.58910.04340.5702-0.0741-0.07130.0131-0.48030.6330.0656-0.00010.63710.1054-0.05510.43660.08030.4986-12.60647.7789-30.3615
130.43550.08570.25020.264-0.12810.2819-0.08030.566-0.2949-1.76990.07380.58051.422-0.259-0.00260.9442-0.1727-0.21140.74910.06711.018-20.911140.8968-26.1356
142.01730.33560.63013.44950.35752.9875-0.444-0.19570.44041.09220.48640.013-0.2797-0.2161-0.00020.85910.099-0.20390.47830.010.6544-19.470946.2222-5.795
151.64110.8895-1.18414.0776-1.01532.6738-0.5225-0.51670.09570.81490.2775-0.1150.1545-0.41990.00080.96960.1402-0.15760.482-0.04220.5365-16.740734.7513-3.7858
161.339-1.1552-0.94551.17570.45171.13021.15510.38440.82250.2797-0.4164-0.8382-0.81940.2810.00161.0010.03720.15360.6960.23941.27922.254168.205920.7678
170.50310.4981-0.24140.3431-0.1076-0.0310.25830.25280.4117-0.31690.0669-0.9138-0.65270.6805-0.00040.43880.05890.36690.73050.25041.40199.024558.328618.8782
180.0689-0.0811-0.12290.13180.15520.18180.1368-0.04860.6133-0.77060.0829-1.9651-0.69830.6950.00470.96810.17280.40750.9860.07451.36598.166646.750617.5392
192.6277-0.50751.45242.9636-0.40770.8624-0.13490.0922-0.12840.0376-0.5240.8454-0.2094-0.7218-0.00110.42920.04760.15880.5615-0.16710.9446-10.61545.05724.7639
201.7695-1.74821.18361.947-0.72181.3694-0.41980.0082-0.81571.2075-0.20770.72120.5557-0.5009-0.00090.86420.02390.47370.5303-0.07810.9431-6.682236.830732.6916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1647:1684
2X-RAY DIFFRACTION2chain A and resid 1685:1741
3X-RAY DIFFRACTION3chain A and resid 1742:1753
4X-RAY DIFFRACTION4chain A and resid 1754:1803
5X-RAY DIFFRACTION5chain A and resid 1804:1859
6X-RAY DIFFRACTION6chain B and resid 1647:1684
7X-RAY DIFFRACTION7chain B and resid 1685:1741
8X-RAY DIFFRACTION8chain B and resid 1742:1753
9X-RAY DIFFRACTION9chain B and resid 1754:1803
10X-RAY DIFFRACTION10chain B and resid 1804:1859
11X-RAY DIFFRACTION11chain C and resid 1647:1684
12X-RAY DIFFRACTION12chain C and resid 1685:1741
13X-RAY DIFFRACTION13chain C and resid 1742:1753
14X-RAY DIFFRACTION14chain C and resid 1754:1803
15X-RAY DIFFRACTION15chain C and resid 1804:1859
16X-RAY DIFFRACTION16chain D and resid 1649:1684
17X-RAY DIFFRACTION17chain D and resid 1685:1741
18X-RAY DIFFRACTION18chain D and resid 1742:1753
19X-RAY DIFFRACTION19chain D and resid 1754:1803
20X-RAY DIFFRACTION20chain D and resid 1804:1859

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