[English] 日本語
Yorodumi
- PDB-3fa2: Crystal Structure of the BRCA1 Associated Ring Domain (BARD1) Tan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fa2
TitleCrystal Structure of the BRCA1 Associated Ring Domain (BARD1) Tandem BRCT Domains
ComponentsBRCA1-associated RING domain protein 1
KeywordsPROTEIN BINDING / BARD1 / BRCA1 / BRCT / BRCA1 C-terminal Domain / Tandem / ANK repeat / Disease mutation / Metal-binding / Nucleus / Zinc-finger
Function / homology
Function and homology information


negative regulation of mRNA 3'-end processing / 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 / nuclear ubiquitin ligase complex ...negative regulation of mRNA 3'-end processing / 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 / nuclear ubiquitin ligase complex / ubiquitin-modified histone reader activity / DNA strand resection involved in replication fork processing / homologous recombination / tissue homeostasis / protein K6-linked ubiquitination / Impaired BRCA2 binding to PALB2 / regulation of phosphorylation / regulation of DNA damage checkpoint / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / 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) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / ubiquitin ligase complex / regulation of DNA repair / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / kinase binding / Metalloprotease DUBs / cytoplasmic ribonucleoprotein granule / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / UCH proteinases / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / nuclear speck / protein ubiquitination / positive regulation of apoptotic process / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA damage response / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein homodimerization activity / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / BRCT domain / 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. ...BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / BRCT domain / 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. / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / 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
PHOSPHATE ION / BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFox III, D. / Le Trong, I. / Stenkamp, R.E. / Klevit, R.E.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the BRCA1 Associated Ring Domain (BARD1) Tandem BRCT Domains
Authors: Fox III, D. / Le Trong, I. / Stenkamp, R.E. / Klevit, R.E.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BRCA1-associated RING domain protein 1
B: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4817
Polymers50,0122
Non-polymers4695
Water1,58588
1
A: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1933
Polymers25,0061
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2884
Polymers25,0061
Non-polymers2823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.979, 67.466, 86.783
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein BRCA1-associated RING domain protein 1 / BARD-1


Mass: 25005.881 Da / Num. of mol.: 2 / Fragment: Tandem BRCT Domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARD1 / Plasmid: pET151D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99728
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES 15% w/v PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 12, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 28268 / % possible obs: 82.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 39.37 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.063 / Net I/σ(I): 16.77
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 1.22 / Num. unique all: 1032 / Rsym value: 0.696 / % possible all: 30.4

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NTE CHAIN A

2nte


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 20.585 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.299 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29772 1255 5 %RANDOM
Rwork0.22237 ---
obs0.22605 23629 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.983 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å2-1.85 Å2
2---2.37 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 27 88 3410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223424
X-RAY DIFFRACTIONr_bond_other_d0.0040.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9694625
X-RAY DIFFRACTIONr_angle_other_deg0.8323.0015889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26423.356149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55315626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9951523
X-RAY DIFFRACTIONr_chiral_restr0.0740.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02693
X-RAY DIFFRACTIONr_nbd_refined0.1990.2747
X-RAY DIFFRACTIONr_nbd_other0.1870.22390
X-RAY DIFFRACTIONr_nbtor_refined0.180.21607
X-RAY DIFFRACTIONr_nbtor_other0.0830.21746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1810.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.24
X-RAY DIFFRACTIONr_mcbond_it0.6871.52643
X-RAY DIFFRACTIONr_mcbond_other0.1181.5825
X-RAY DIFFRACTIONr_mcangle_it0.83923305
X-RAY DIFFRACTIONr_scbond_it1.26731657
X-RAY DIFFRACTIONr_scangle_it1.7514.51316
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 79 -
Rwork0.289 1210 -
obs--65.87 %

+
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