[English] 日本語
Yorodumi
- PDB-5t59: Structure of the MIND Complex Shows a Regulatory Focus of Yeast K... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t59
TitleStructure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly
Components
  • KLLA0B13629p
  • KLLA0E05809p
  • KLLA0F02343p
KeywordsCELL CYCLE / kinetochore / complex / chromosome / segregation / MIND / Mis12
Function / homology
Function and homology information


MIS12/MIND type complex / centromeric DNA binding / kinetochore assembly / mitotic spindle organization / chromosome segregation / kinetochore / mitotic cell cycle / cell division / protein-containing complex binding / nucleus
Similarity search - Function
Kinetochore-associated protein Nnf1 / Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like ...Kinetochore-associated protein Nnf1 / Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
KLLA0F02343p / Kinetochore-associated protein / KLLA0B13629p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.405 Å
AuthorsDimitrova, Y. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C.
CitationJournal: Cell / Year: 2016
Title: Structure of the MIND Complex Defines a Regulatory Focus for Yeast Kinetochore Assembly.
Authors: Dimitrova, Y.N. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KLLA0F02343p
B: KLLA0E05809p
C: KLLA0B13629p
D: KLLA0F02343p
E: KLLA0E05809p
F: KLLA0B13629p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0108
Polymers61,5966
Non-polymers4152
Water59433
1
A: KLLA0F02343p
B: KLLA0E05809p
C: KLLA0B13629p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0054
Polymers30,7983
Non-polymers2071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: KLLA0F02343p
E: KLLA0E05809p
F: KLLA0B13629p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0054
Polymers30,7983
Non-polymers2071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.400, 91.700, 95.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTrimer confirmed by gel filtration

-
Components

#1: Protein KLLA0F02343p


Mass: 13870.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues Asn0 and Ala1 are left over from the TEV cleavage site. Mtw1 starts at residue Thr2.
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_F02343g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CLK3
#2: Protein KLLA0E05809p


Mass: 12100.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_E05809g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CPD1
#3: Protein/peptide KLLA0B13629p


Mass: 4826.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_B13629g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CVA1
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CHES, pH 9.0, 18-30 % PEG 3000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.405→66.17 Å / Num. obs: 16798 / % possible obs: 56.5 % / Redundancy: 3.6 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.405→66.168 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.39
RfactorNum. reflection% reflection
Rfree0.2905 836 4.98 %
Rwork0.2492 --
obs0.2513 16798 63.61 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 2.405→66.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 26 33 3834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053852
X-RAY DIFFRACTIONf_angle_d0.6185180
X-RAY DIFFRACTIONf_dihedral_angle_d6.5243356
X-RAY DIFFRACTIONf_chiral_restr0.037591
X-RAY DIFFRACTIONf_plane_restr0.004660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.405-2.55570.4277140.375260X-RAY DIFFRACTION6
2.5557-2.75310.424460.3391926X-RAY DIFFRACTION22
2.7531-3.03010.3491280.32312368X-RAY DIFFRACTION57
3.0301-3.46860.30852040.30344093X-RAY DIFFRACTION98
3.4686-4.36990.25912190.23114113X-RAY DIFFRACTION98
4.3699-66.19260.28852250.21994202X-RAY DIFFRACTION96

+
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