[English] 日本語
Yorodumi
- PDB-2i3s: Bub3 complex with Bub1 GLEBS motif -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i3s
TitleBub3 complex with Bub1 GLEBS motif
Components
  • Cell cycle arrest protein
  • Checkpoint serine/threonine-protein kinase
KeywordsCELL CYCLE / WD40 protein / beta-propeller / GLEBS motif / mitotic spindle checkpoint
Function / homology
Function and homology information


bub1-bub3 complex / Inactivation of APC/C via direct inhibition of the APC/C complex / mitotic DNA integrity checkpoint signaling / mitotic checkpoint complex / centromere complex assembly / sister chromatid biorientation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore ...bub1-bub3 complex / Inactivation of APC/C via direct inhibition of the APC/C complex / mitotic DNA integrity checkpoint signaling / mitotic checkpoint complex / centromere complex assembly / sister chromatid biorientation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / positive regulation of protein autoubiquitination / mitotic spindle assembly checkpoint signaling / ubiquitin binding / macroautophagy / kinetochore / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
Mad3/Bub1 homology region 2 / Mad3/BUB1 homology region 2 / Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Mad3/Bub1 homology region 2 / Mad3/BUB1 homology region 2 / Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Cell cycle arrest protein BUB3 / Checkpoint serine/threonine-protein kinase BUB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLarsen, N.A. / Harrison, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural analysis of Bub3 interactions in the mitotic spindle checkpoint.
Authors: Larsen, N.A. / Al-Bassam, J. / Wei, R.R. / Harrison, S.C.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the spindle assembly checkpoint protein Bub3.
Authors: Larsen, N.A. / Harrison, S.C.
History
DepositionAug 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 2, 2014Group: Source and taxonomy
Revision 1.4Aug 30, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell cycle arrest protein
B: Checkpoint serine/threonine-protein kinase
C: Cell cycle arrest protein
D: Checkpoint serine/threonine-protein kinase
E: Cell cycle arrest protein
F: Checkpoint serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)131,7146
Polymers131,7146
Non-polymers00
Water11,602644
1
A: Cell cycle arrest protein
B: Checkpoint serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)43,9052
Polymers43,9052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-16 kcal/mol
Surface area16090 Å2
MethodPISA
2
C: Cell cycle arrest protein
D: Checkpoint serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)43,9052
Polymers43,9052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-16 kcal/mol
Surface area15550 Å2
MethodPISA
3
E: Cell cycle arrest protein
F: Checkpoint serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)43,9052
Polymers43,9052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-15 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.656, 79.181, 142.582
Angle α, β, γ (deg.)90.00, 98.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly consists of a single heterodimer of Bub3 and Bub1 GLEBS peptide. There are 3 heterodimers in the asymmetric unit.

-
Components

#1: Protein Cell cycle arrest protein


Mass: 39554.633 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BUB3, YOR026W, OR26.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P26449
#2: Protein/peptide Checkpoint serine/threonine-protein kinase / Bub1 GLEBS motif


Mass: 4349.952 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Chemically synthesized peptide. / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P41695, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 18% PEG 3K 200 mM NaCl 100 mM Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 79711 / % possible obs: 90.6 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Rsym value: 0.054
Reflection shellResolution: 1.9→1.97 Å / % possible all: 68.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U4C

1u4c


Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 3811 Random
Rwork0.219 --
all0.221 75071 -
obs0.221 75071 -
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8798 0 0 644 9442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.72

+
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