5MU3

Crystal structure of Ctf19-Mcm21 kinetochore assembly bound with Ctf19-Mcm21 binding motif of central kinetochore subunit Okp1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis for inner kinetochore configuration through RWD domain-peptide interactions.

Schmitzberger, F.Richter, M.M.Gordiyenko, Y.Robinson, C.V.Dadlez, M.Westermann, S.

(2017) EMBO J 36: 3458-3482

  • DOI: https://doi.org/10.15252/embj.201796636
  • Primary Citation of Related Structures:  
    5MU3

  • PubMed Abstract: 

    Kinetochores are dynamic cellular structures that connect chromosomes to microtubules. They form from multi-protein assemblies that are evolutionarily conserved between yeasts and humans. One of these assemblies-COMA-consists of subunits Ame1 CENP-U , Ctf19 CENP-P , Mcm21 CENP-O and Okp1 CENP-Q A description of COMA molecular organization has so far been missing. We defined the subunit topology of COMA, bound with inner kinetochore proteins Nkp1 and Nkp2, from the yeast Kluyveromyces lactis , with nanoflow electrospray ionization mass spectrometry, and mapped intermolecular contacts with hydrogen-deuterium exchange coupled to mass spectrometry. Our data suggest that the essential Okp1 subunit is a multi-segmented nexus with distinct binding sites for Ame1, Nkp1-Nkp2 and Ctf19-Mcm21. Our crystal structure of the Ctf19-Mcm21 RWD domains bound with Okp1 shows the molecular contacts of this important inner kinetochore joint. The Ctf19-Mcm21 binding motif in Okp1 configures a branch of mitotic inner kinetochores, by tethering Ctf19-Mcm21 and Chl4 CENP-N -Iml3 CENP-L Absence of this motif results in dependence on the mitotic checkpoint for viability.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA florian.schmitzberger@uni-due.de.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Central kinetochore subunit MCM21
A, D
189Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: MCM21KLLA0B10142g
UniProt
Find proteins for Q6CVQ9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CVQ9 
Go to UniProtKB:  Q6CVQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CVQ9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Central kinetochore subunit CTF19165Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: CTF19KLLA0D07612g
UniProt
Find proteins for Q6CRN7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CRN7 
Go to UniProtKB:  Q6CRN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CRN7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Central kinetochore subunit Okp1
C, F
67Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_F15136g
UniProt
Find proteins for Q6CJY0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CJY0 
Go to UniProtKB:  Q6CJY0
Entity Groups  
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UniProt GroupQ6CJY0
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Central kinetochore subunit CTF19165Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: CTF19KLLA0D07612g
UniProt
Find proteins for Q6CRN7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CRN7 
Go to UniProtKB:  Q6CRN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CRN7
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
E
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.342α = 90
b = 105.476β = 90
c = 122.982γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Boehringer IngelheimAustria--
Howard Hughes Medical InstituteUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2018-11-21
    Changes: Data collection, Derived calculations
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description