[English] 日本語
Yorodumi
- PDB-3pxc: Impact of BRCA1 BRCT domain missense substitutions on phospho-pep... -

+
Open data


ID or keywords:

Loading...

-
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


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 / postreplication repair / centrosome cycle / 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 / intracellular membraneless organelle / Impaired BRCA2 binding to RAD51 / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / 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 / 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) / Metalloprotease DUBs / Meiotic recombination / fatty acid biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / ubiquitin-protein transferase activity / 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 / Neddylation / chromosome / 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 / 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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