[English] 日本語
Yorodumi
- PDB-3n7n: Structure of Csm1/Lrs4 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n7n
TitleStructure of Csm1/Lrs4 complex
Components
  • Monopolin complex subunit CSM1
  • Monopolin complex subunit LRS4
KeywordsREPLICATION / meiosis / rDNA
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 / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / homologous chromosome segregation ...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 / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / homologous chromosome segregation / replication-born double-strand break repair via sister chromatid exchange / rDNA heterochromatin formation / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle / nuclear envelope / nucleolus / identical protein binding / nucleus
Similarity search - Function
Monopolin complex subunit Lrs4/Mde4 / Monopolin complex subunit LRS4 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 ...Monopolin complex subunit Lrs4/Mde4 / Monopolin complex subunit LRS4 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Aspartate Aminotransferase, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Monopolin complex subunit CSM1 / Monopolin complex subunit LRS4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.9 Å
AuthorsCorbett, K.D. / Harrison, S.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: The Monopolin Complex Crosslinks Kinetochore Components to Regulate Chromosome-Microtubule Attachments.
Authors: Corbett, K.D. / Yip, C.K. / Ee, L.S. / Walz, T. / Amon, A. / Harrison, S.C.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Monopolin complex subunit CSM1
B: Monopolin complex subunit CSM1
C: Monopolin complex subunit CSM1
D: Monopolin complex subunit CSM1
E: Monopolin complex subunit LRS4
F: Monopolin complex subunit LRS4


Theoretical massNumber of molelcules
Total (without water)109,5876
Polymers109,5876
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.624, 152.624, 118.794
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein
Monopolin complex subunit CSM1 / Chromosome segregation in meiosis protein 1


Mass: 21776.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CSM1, SPO86, YCR086W, YCR86W / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P25651
#2: Protein Monopolin complex subunit LRS4 / Loss of rDNA silencing protein 4


Mass: 11240.796 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-102, delta 38-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: D9461.25, LRS4, YDR439W / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q04087

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 120 mM MgCl2, 16% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
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: Apr 16, 2009 / Details: mirrors
RadiationMonochromator: side-bounce cryogenically cooled 220 silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. all: 6644 / Num. obs: 6644 / % possible obs: 43.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rsym value: 0.066 / Net I/σ(I): 12.6
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.464 / % possible all: 5.8

-
Processing

Software
NameVersionClassification
CNS1.3refinement
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
ADSCQuantumdata collection
RefinementResolution: 3.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.355 321 2.2 %
Rwork0.333 6321 -
obs-6642 44.5 %
Solvent computationBsol: 318.578 Å2
Displacement parametersBiso max: 500 Å2 / Biso mean: 358.075 Å2 / Biso min: 87.4 Å2
Baniso -1Baniso -2Baniso -3
1-103.662 Å20 Å20 Å2
2--103.662 Å20 Å2
3----207.325 Å2
Refinement stepCycle: LAST / Resolution: 3.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5496 0 0 0 5496
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_d1.544
X-RAY DIFFRACTIONc_mcbond_it52.27875
X-RAY DIFFRACTIONc_scbond_it61.339100
X-RAY DIFFRACTIONc_mcangle_it81.254100
X-RAY DIFFRACTIONc_scangle_it87.737125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.040.264750.349391X-RAY DIFFRACTION6.5
4.04-4.20.486660.2919135X-RAY DIFFRACTION9.6
4.2-4.390.390350.3631183X-RAY DIFFRACTION12.8
4.39-4.620.4562140.4165243X-RAY DIFFRACTION17.5
4.62-4.910.3998180.3458336X-RAY DIFFRACTION24.2
4.91-5.290.3605240.3767474X-RAY DIFFRACTION33.6
5.29-5.820.4715380.4221723X-RAY DIFFRACTION51.2
5.82-6.660.4941730.42271312X-RAY DIFFRACTION92
6.66-8.390.4305730.381388X-RAY DIFFRACTION96.6
8.39-500.2953650.29781436X-RAY DIFFRACTION94.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

+
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