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Basic information

Entry
Database: PDB / ID: 1t2v
TitleStructural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide
Components
  • BRCTide-7PS
  • Breast cancer type 1 susceptibility protein
KeywordsANTITUMOR PROTEIN / BRCT / BRCA1 / breast cancer / cell signaling / missense mutation / phosphopeptide
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 / negative regulation of centriole replication / sex-chromosome dosage compensation / random inactivation of X chromosome / 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 / negative regulation of centriole replication / sex-chromosome dosage compensation / random inactivation of X chromosome / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / chordate embryonic development / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / DNA strand resection involved in replication fork processing / homologous recombination / lateral element / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / DNA repair complex / centrosome cycle / postreplication repair / RNA polymerase binding / 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) / DNA-binding transcription activator activity / Impaired BRCA2 binding to RAD51 / negative regulation of gene expression via chromosomal CpG island methylation / intracellular membraneless organelle / response to ionizing radiation / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / 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 / protein autoubiquitination / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / Meiotic synapsis / positive regulation of DNA repair / 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 / G2/M DNA damage checkpoint / negative regulation of cell growth / HDR through Homologous Recombination (HRR) / Meiotic recombination / Metalloprotease DUBs / fatty acid biosynthetic process / positive regulation of angiogenesis / ubiquitin-protein transferase activity / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / p53 binding / double-strand break repair / cellular response to tumor necrosis factor / 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 / nuclear body / protein ubiquitination / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / 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 / zinc ion binding / nucleoplasm / identical protein 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: 3.3 Å
AuthorsWilliams, R.S. / Lee, M.S. / Hau, D.D. / Glover, J.N.M.
CitationJournal: 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.M.
History
DepositionApr 22, 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: Advisory / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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: Breast cancer type 1 susceptibility protein
F: BRCTide-7PS
G: BRCTide-7PS
H: BRCTide-7PS
I: BRCTide-7PS
J: BRCTide-7PS


Theoretical massNumber of molelcules
Total (without water)131,92110
Polymers131,92110
Non-polymers00
Water00
1
A: Breast cancer type 1 susceptibility protein
F: BRCTide-7PS


Theoretical massNumber of molelcules
Total (without water)26,3842
Polymers26,3842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-9 kcal/mol
Surface area11220 Å2
MethodPISA
2
B: Breast cancer type 1 susceptibility protein
G: BRCTide-7PS


Theoretical massNumber of molelcules
Total (without water)26,3842
Polymers26,3842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-9 kcal/mol
Surface area11490 Å2
MethodPISA
3
C: Breast cancer type 1 susceptibility protein
H: BRCTide-7PS


Theoretical massNumber of molelcules
Total (without water)26,3842
Polymers26,3842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-11 kcal/mol
Surface area10790 Å2
MethodPISA
4
D: Breast cancer type 1 susceptibility protein
I: BRCTide-7PS


Theoretical massNumber of molelcules
Total (without water)26,3842
Polymers26,3842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area11030 Å2
MethodPISA
5
E: Breast cancer type 1 susceptibility protein
J: BRCTide-7PS


Theoretical massNumber of molelcules
Total (without water)26,3842
Polymers26,3842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-8 kcal/mol
Surface area11220 Å2
MethodPISA
6
A: Breast cancer type 1 susceptibility protein
F: BRCTide-7PS

D: Breast cancer type 1 susceptibility protein
I: BRCTide-7PS


Theoretical massNumber of molelcules
Total (without water)52,7694
Polymers52,7694
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3660 Å2
ΔGint-28 kcal/mol
Surface area20600 Å2
MethodPISA
7
E: Breast cancer type 1 susceptibility protein
J: BRCTide-7PS

E: Breast cancer type 1 susceptibility protein
J: BRCTide-7PS


Theoretical massNumber of molelcules
Total (without water)52,7694
Polymers52,7694
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3250 Å2
ΔGint-29 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.117, 138.357, 198.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4

Dom-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA1649 - 18594 - 214
2BB1649 - 18594 - 214
3CC1649 - 18594 - 214
4DD1649 - 18564 - 211
5EE1649 - 18594 - 214

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Components

#1: Protein
Breast cancer type 1 susceptibility protein


Mass: 24531.234 Da / Num. of mol.: 5 / Fragment: BRCT DOMAIN 1646-1859
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: Protein/peptide
BRCTide-7PS


Mass: 1853.038 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: In vitro optimized phosphopeptide
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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / pH: 5.6
Details: PEG 4000 ammonium acetate, tri-sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.11
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 3.303→50 Å / Num. obs: 20289 / % possible obs: 99.9 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 11.1
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.814 / SU B: 31.291 / SU ML: 0.541 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: overall, with group TLS thermal parameters
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.669 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1016 5 %RANDOM
Rwork0.258 ---
obs0.261 19273 99.3 %-
all-20289 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å20 Å20 Å2
2---0.51 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8380 0 0 0 8380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218583
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9311716
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93451085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.21352
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026464
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1440.33680
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.5443
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.385
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it01.55470
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it028778
X-RAY DIFFRACTIONr_scbond_it033113
X-RAY DIFFRACTIONr_scangle_it04.52938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1398 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.30.5
2Bmedium positional0.330.5
3Cmedium positional0.270.5
4Dmedium positional0.340.5
5Emedium positional0.290.5
1Amedium thermal02
2Bmedium thermal02
3Cmedium thermal02
4Dmedium thermal02
5Emedium thermal02
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 78
Rwork0.263 1397
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)
17.4652-2.3594-1.37435.78190.46384.67620.138-0.30320.25080.1454-0.05160.0135-0.92170.1366-0.08640.5115-0.2221-0.02530.09670.00490.118474.986550.641238.534
26.67753.0281.91758.39343.17094.5337-0.0730.0327-0.1228-0.1052-0.0440.56770.07720.10260.1170.12490.121-0.02770.3943-0.03180.169335.025129.6948-2.2879
34.07891.4762-0.23849.72860.71835.20280.29090.1844-0.1827-0.33130.1168-0.2367-0.25190.6618-0.40770.21620.18550.01450.2732-0.08360.136551.92368.4195-16.848
49.08252.00825.16323.68671.15517.11420.30450.6778-0.4083-0.19210.23250.0288-0.01450.2921-0.5370.40920.1469-0.02160.3167-0.21140.479313.25818.856439.9385
55.7214-2.4776-2.89113.81732.3385.1116-0.11130.064-0.0617-0.03550.06920.009-0.1747-0.20720.04210.1743-0.0612-0.03730.1694-0.00770.089751.564931.879629.9912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1649 - 18594 - 214
2X-RAY DIFFRACTION1FF1 - 141 - 14
3X-RAY DIFFRACTION2BB1646 - 18591 - 214
4X-RAY DIFFRACTION2GG1 - 141 - 14
5X-RAY DIFFRACTION3CC1649 - 18594 - 214
6X-RAY DIFFRACTION3HH1 - 141 - 14
7X-RAY DIFFRACTION4DD1647 - 18562 - 211
8X-RAY DIFFRACTION4II1 - 111 - 11
9X-RAY DIFFRACTION5EE1649 - 18594 - 214
10X-RAY DIFFRACTION5JJ2 - 132 - 13

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