[English] 日本語
Yorodumi
- PDB-6mj8: Structure of Candida glabrata Csm1:Mam1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mj8
TitleStructure of Candida glabrata Csm1:Mam1 complex
Components
  • Mam1
  • Monopolin complex subunit CSM1
KeywordsCELL CYCLE / monopolin / kinetochore
Function / homology
Function and homology information


microtubule site clamp / chromosome, centromeric core domain / monopolin complex / meiotic sister chromatid segregation / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / rDNA chromatin condensation / meiotic sister chromatid cohesion, centromeric / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle ...microtubule site clamp / chromosome, centromeric core domain / monopolin complex / meiotic sister chromatid segregation / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / rDNA chromatin condensation / meiotic sister chromatid cohesion, centromeric / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle / nuclear envelope / nucleolus / identical protein binding
Similarity search - Function
Monopolin complex, subunit Mam1 / Monopolin complex protein MAM1 / Aspartate Aminotransferase, domain 1 - #80 / Monopolin complex subunit Csm1/Pcs1, C-terminal / Csm1/Pcs1, C-terminal domain superfamily / Monopolin complex subunit Csm1/Pcs1 / Csm1 N-terminal domain / Chromosome segregation protein Csm1/Pcs1 / Csm1 N-terminal domain / Aspartate Aminotransferase, domain 1 ...Monopolin complex, subunit Mam1 / Monopolin complex protein MAM1 / Aspartate Aminotransferase, domain 1 - #80 / Monopolin complex subunit Csm1/Pcs1, C-terminal / Csm1/Pcs1, C-terminal domain superfamily / Monopolin complex subunit Csm1/Pcs1 / Csm1 N-terminal domain / Chromosome segregation protein Csm1/Pcs1 / Csm1 N-terminal domain / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Monopolin complex subunit CSM1 / Candida glabrata strain CBS138 chromosome G complete sequence / Candida glabrata strain CBS138 chromosome E complete sequence
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsSingh, N. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104141 United States
CitationJournal: Chromosoma / Year: 2019
Title: The molecular basis of monopolin recruitment to the kinetochore.
Authors: Plowman, R. / Singh, N. / Tromer, E.C. / Payan, A. / Duro, E. / Spanos, C. / Rappsilber, J. / Snel, B. / Kops, G.J.P.L. / Corbett, K.D. / Marston, A.L.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monopolin complex subunit CSM1
B: Monopolin complex subunit CSM1
C: Mam1
D: Mam1


Theoretical massNumber of molelcules
Total (without water)39,7054
Polymers39,7054
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-53 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.124, 58.639, 109.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Monopolin complex subunit CSM1


Mass: 13241.077 Da / Num. of mol.: 2 / Fragment: UNP residues 69-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: AO440_000897, AO440_004693 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W0CH22, UniProt: Q6FVN3*PLUS
#2: Protein Mam1


Mass: 6611.495 Da / Num. of mol.: 2 / Fragment: UNP residues 162-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0G03377g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FTD4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 0.6 M sodium chloride, 20% PEG4000, cryoprotectant: 20% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2013
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.03→55 Å / Num. obs: 6723 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.136 / Rrim(I) all: 0.358 / Net I/σ(I): 8.4
Reflection shellResolution: 3.03→3.2 Å / Rmerge(I) obs: 1.651 / Num. unique obs: 958 / Rpim(I) all: 0.714 / Rrim(I) all: 1.919

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3N4R

3n4r


Resolution: 3.03→54.915 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6
RfactorNum. reflection% reflection
Rfree0.2829 315 4.72 %
Rwork0.2712 --
obs0.272 6675 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.03→54.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 0 0 1944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051980
X-RAY DIFFRACTIONf_angle_d0.7632662
X-RAY DIFFRACTIONf_dihedral_angle_d14.9071208
X-RAY DIFFRACTIONf_chiral_restr0.042302
X-RAY DIFFRACTIONf_plane_restr0.006330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0301-3.20.33571460.30553120X-RAY DIFFRACTION99
3.8175-54.92450.2581690.25363240X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.4084 Å / Origin y: 7.5734 Å / Origin z: 12.409 Å
111213212223313233
T0.2677 Å2-0.0337 Å2-0.0393 Å2-0.3635 Å20.004 Å2--0.2381 Å2
L1.6948 °2-0.7868 °2-0.9192 °2-1.4791 °20.4639 °2--1.4843 °2
S-0.0654 Å °0.0503 Å °-0.0692 Å °-0.1034 Å °-0.1064 Å °-0.0602 Å °-0.0679 Å °-0.1071 Å °0.1407 Å °
Refinement TLS groupSelection details: all

+
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