5MU3 | pdb_00005mu3

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 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5MU3

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 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.

Macromolecule Content 

  • Total Structure Weight: 97.48 kDa 
  • Atom Count: 6,464 
  • Modeled Residue Count: 745 
  • Deposited Residue Count: 842 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CJY0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Sequence Annotations
Expand
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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 2 21 21
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

View Full Validation Report



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