[English] 日本語
Yorodumi
- PDB-1t2v: Structural basis of phospho-peptide recognition by the BRCT domai... -

+
Open data


ID or keywords:

Loading...

-
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


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-C complex / BRCA1-B complex / BRCA1-A 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-C complex / BRCA1-B complex / BRCA1-A complex / negative regulation of centriole replication / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / random inactivation of X chromosome / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / ubiquitin-modified histone reader activity / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / DNA strand resection involved in replication fork processing / homologous recombination / lateral element / protein K6-linked ubiquitination / Impaired BRCA2 binding to PALB2 / regulation of DNA damage checkpoint / XY body / mitotic G2/M transition checkpoint / postreplication repair / centrosome cycle / RNA polymerase binding / DNA repair complex / 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 / DNA-binding transcription activator activity / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / 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 / ubiquitin ligase complex / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein autoubiquitination / Meiotic synapsis / tubulin binding / positive regulation of DNA repair / male germ cell nucleus / cellular response to ionizing radiation / chromosome segregation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / negative regulation of cell growth / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / Meiotic recombination / Metalloprotease DUBs / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / ubiquitin-protein transferase activity / fatty acid biosynthetic process / 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 / nuclear body / regulation of cell cycle / transcription cis-regulatory region binding / protein ubiquitination / chromatin remodeling / 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
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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more