[English] 日本語
Yorodumi
- PDB-3k16: Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k16
TitleCrystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus
Components
  • Breast cancer type 1 susceptibility protein
  • phospho peptide
KeywordsISOMERASE / BRCA1 / BRCT domain / DNA damage response / phospho peptide interactions / Abraxas / Alternative initiation / Cell cycle / Disease mutation / DNA damage / DNA repair / DNA-binding / Fatty acid biosynthesis / Ligase / Lipid synthesis / Metal-binding / Nucleus / Phosphoprotein / Tumor suppressor / Ubl conjugation pathway / Zinc-finger
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 / random inactivation of X chromosome / negative regulation of centriole replication / sex-chromosome dosage compensation / 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 / random inactivation of X chromosome / negative regulation of centriole replication / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / 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 / postreplication repair / DNA repair complex / RNA polymerase binding / centrosome cycle / 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 / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / negative regulation of gene expression via chromosomal CpG island methylation / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA-binding transcription activator activity / 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 / localization / 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 / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / negative regulation of cell growth / Metalloprotease DUBs / Meiotic recombination / fatty acid biosynthetic process / ubiquitin-protein transferase activity / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / double-strand break repair / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / cellular response to tumor necrosis factor / Neddylation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / nuclear body / transcription cis-regulatory region binding / regulation of cell cycle / 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
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 / molecular replacement / Resolution: 3 Å
AuthorsCampbell, S.J. / Edwards, R.A. / Glover, J.N.
CitationJournal: Structure / Year: 2010
Title: Comparison of the Structures and Peptide Binding Specificities of the BRCT Domains of MDC1 and BRCA1
Authors: Campbell, S.J. / Edwards, R.A. / Glover, J.N.
History
DepositionSep 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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.pdbx_leaving_atom_flag / _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
A: Breast cancer type 1 susceptibility protein
B: phospho peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2734
Polymers25,1792
Non-polymers942
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-25 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.337, 114.337, 123.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

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


Mass: 24648.449 Da / Num. of mol.: 1 / Fragment: BRCT Domain / Mutation: D1840T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Plasmid: pLM1-CD6 / 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: 530.464 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Sequence occurs naturally in humans in the Abraxas/CCDC98 protein. Synthesized by the Alberta Peptide Institute.
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.67 Å3/Da / Density % sol: 73.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Li2SO4, Tris-HCl, NiCl2, pH 8.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2008
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.95→38.66 Å / Num. obs: 10632 / % possible obs: 99.6 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.084 / Χ2: 0.989 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.0610.70.6759840.642196.1
3.06-3.1817.80.46610480.6621100
3.18-3.3221.10.33910320.7031100
3.32-3.521.70.22710430.7791100
3.5-3.7221.60.15410460.9131100
3.72-421.50.10610581.0511100
4-4.4121.40.08810661.2741100
4.41-5.0420.90.08110661.3161100
5.04-6.3520.70.06911011.1991100
6.35-5018.90.04311881.091199.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.24 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.94 Å38.67 Å
Translation2.94 Å38.67 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38.66 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.287 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.771 / SU B: 38.12 / SU ML: 0.327 / SU R Cruickshank DPI: 0.557 / SU Rfree: 0.375 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.557 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 480 4.8 %RANDOM
Rwork0.224 ---
obs0.227 10051 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 114.09 Å2 / Biso mean: 57.243 Å2 / Biso min: 22.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.21 Å20 Å2
2---0.42 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 3→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 2 6 1738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221774
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9442406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1695213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.79223.7882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.77415.049304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3741511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211332
X-RAY DIFFRACTIONr_mcbond_it1.2291.51072
X-RAY DIFFRACTIONr_mcangle_it2.33221746
X-RAY DIFFRACTIONr_scbond_it3.2993702
X-RAY DIFFRACTIONr_scangle_it5.5334.5660
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 34 -
Rwork0.322 680 -
all-714 -
obs--99.44 %
Refinement TLS params.Method: refined / Origin x: -18.919 Å / Origin y: 48.8269 Å / Origin z: -4.003 Å
111213212223313233
T0.0549 Å20.0147 Å20.0267 Å2-0.4555 Å20.0939 Å2--0.0341 Å2
L14.6258 °22.8701 °2-1.3389 °2-2.9684 °2-0.9515 °2--1.4052 °2
S-0.116 Å °1.4749 Å °0.1349 Å °-0.2535 Å °0.066 Å °-0.1855 Å °0.2517 Å °-0.2305 Å °0.05 Å °

+
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://pdbjlvh1.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