[English] 日本語
Yorodumi
- PDB-2nte: Crystal Structure of the BARD1 BRCT Domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nte
TitleCrystal Structure of the BARD1 BRCT Domains
ComponentsBRCA1-associated RING domain protein 1
KeywordsANTITUMOR PROTEIN / BRCT / RING FINGER / BRCA1 / ZINC-BINDING PROTEIN / UBIQUITIN LIGASE
Function / homology
Function and homology information


negative regulation of mRNA 3'-end processing / 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 / DNA strand resection involved in replication fork processing / homologous recombination ...negative regulation of mRNA 3'-end processing / 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 / DNA strand resection involved in replication fork processing / homologous recombination / tissue homeostasis / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / regulation of phosphorylation / 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 / regulation of DNA repair / ubiquitin ligase complex / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / kinase binding / Metalloprotease DUBs / cytoplasmic ribonucleoprotein granule / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / 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 / protein ubiquitination / nuclear speck / positive regulation of apoptotic process / protein heterodimerization activity / DNA repair / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / RNA binding / nucleoplasm / nucleus / metal ion binding / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / BRCT domain / 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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBirrane, G. / Varma, A.K. / Soni, A. / Ladias, J.A.A.
CitationJournal: Biochemistry / Year: 2007
Title: Crystal structure of the BARD1 BRCT domains.
Authors: Birrane, G. / Varma, A.K. / Soni, A. / Ladias, J.A.
History
DepositionNov 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
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_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: BRCA1-associated RING domain protein 1
B: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,81512
Polymers48,2062
Non-polymers60910
Water4,288238
1
A: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4216
Polymers24,1031
Non-polymers3185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3946
Polymers24,1031
Non-polymers2915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.441, 75.797, 116.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 24102.910 Da / Num. of mol.: 2 / Fragment: BRCT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARD1 / Plasmid: pET-6H / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q99728
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MES, 20% PEG 8K, 150mM Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9784 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2005 / Details: Dual Slits
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40185 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rsym value: 0.064 / Net I/σ(I): 30.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.402 / % possible all: 91.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.87 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.346 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24743 1910 5 %RANDOM
Rwork0.19618 ---
obs0.19871 36401 93.82 %-
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: 40.929 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 33 238 3653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223489
X-RAY DIFFRACTIONr_bond_other_d0.0020.022465
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.9724714
X-RAY DIFFRACTIONr_angle_other_deg0.98736001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7223.684152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01715626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5551522
X-RAY DIFFRACTIONr_chiral_restr0.1140.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02696
X-RAY DIFFRACTIONr_nbd_refined0.2240.2734
X-RAY DIFFRACTIONr_nbd_other0.2050.22488
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21684
X-RAY DIFFRACTIONr_nbtor_other0.090.21847
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5530.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5271.52644
X-RAY DIFFRACTIONr_mcbond_other0.3631.5840
X-RAY DIFFRACTIONr_mcangle_it1.8623402
X-RAY DIFFRACTIONr_scbond_it2.80831637
X-RAY DIFFRACTIONr_scangle_it3.914.51312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 108 -
Rwork0.25 2018 -
obs--72.02 %
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)
13.90021.0462-2.17642.93120.44894.94650.0879-0.24750.1542-0.0361-0.12420.0949-0.49030.20490.0363-0.2062-0.0570.0168-0.2139-0.0729-0.174118.0611.87738.003
22.03680.5311-1.81892.350.6895.46570.2583-0.18280.26770.0755-0.1609-0.0351-0.30780.1957-0.0974-0.2087-0.03340.0134-0.1812-0.0275-0.135122.242-2.42119.084
32.5671-0.43870.21915.5102-0.83913.51460.1082-0.1207-0.0665-0.1494-0.21320.17430.0695-0.09210.1051-0.2142-0.0108-0.0118-0.1926-0.0403-0.183417.017-13.09415.623
42.9379-0.002-0.81017.06543.34395.65770.17820.08690.3322-0.7416-0.32520.4495-0.6332-0.39480.1469-0.12140.048-0.054-0.2165-0.0333-0.107213.528-1.97312.082
51.69810.72092.28265.66884.44687.7337-0.13320.07310.1006-0.45070.00260.0378-1.05070.08680.1305-0.0317-0.06350.036-0.2493-0.0427-0.176841.0915.94410.614
61.5419-2.1093-1.21778.62367.556610.13790.0109-0.0572-0.02680.66050.7147-0.82850.22330.7315-0.7256-0.1145-0.0191-0.0974-0.0436-0.14010.028648.4725.99413.617
79.3922-0.1162.00544.078-0.15274.0986-0.04820.31130.3659-0.34560.0645-0.0581-0.26270.0107-0.0163-0.0766-0.01810.0027-0.19630.079-0.068535.351-0.712-10.474
85.0852-0.08470.13481.89260.19422.1506-0.0093-0.1525-0.10070.10370.0786-0.12590.0726-0.0599-0.0693-0.12090.0055-0.0006-0.18910.0154-0.122335.619-10.322-5.052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA568 - 6581 - 91
2X-RAY DIFFRACTION2AA659 - 70992 - 142
3X-RAY DIFFRACTION3AA710 - 739143 - 172
4X-RAY DIFFRACTION4AA740 - 777173 - 210
5X-RAY DIFFRACTION5BB569 - 6412 - 74
6X-RAY DIFFRACTION6BB642 - 66875 - 101
7X-RAY DIFFRACTION7BB669 - 715102 - 148
8X-RAY DIFFRACTION8BB716 - 777149 - 210

+
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