8Q84 | pdb_00008q84

Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules.

Muir, K.W.Batters, C.Dendooven, T.Yang, J.Zhang, Z.Burt, A.Barford, D.

(2023) Science 382: 1184-1190

  • DOI: https://doi.org/10.1126/science.adj8736
  • Primary Citation Related Structures: 
    8Q84, 8Q85

  • PubMed Abstract: 

    Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until biorientation is achieved. The structural basis for how kinetochore-mediated chromosome segregation is accomplished and regulated remains an outstanding question. In this work, we describe the cryo-electron microscopy structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. Complex assembly occurs through multiple interfaces, and a staple within Dam1 aids ring assembly. Perturbation of key interfaces suppresses yeast viability. Force-rupture assays indicated that this is a consequence of impaired kinetochore-microtubule attachment. The presence of error correction phosphorylation sites at Ndc80-Dam1 ring complex interfaces and the Dam1 staple explains how kinetochore-microtubule attachments are destabilized and reset.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.

Macromolecule Content 

  • Total Structure Weight: 713.54 kDa 
  • Atom Count: 21,802 
  • Modeled Residue Count: 3,115 
  • Deposited Residue Count: 6,235 
  • Unique protein chains: 12

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinetochore protein NDC80A,
C [auth F]
691Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NDC80
UniProt
Find proteins for P40460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinetochore protein NUF2B,
D [auth G]
451Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NUF2
UniProt
Find proteins for P33895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP33895
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit DAM1E [auth I],
O [auth U],
Y [auth e]
343Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DAM1
UniProt
Find proteins for P53267 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit DUO1F [auth J],
P [auth V]
247Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DUO1
UniProt
Find proteins for P53168 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP53168
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit DAD2G [auth K],
Q [auth W]
133Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DAD2
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit DAD1H [auth L],
R [auth X]
94Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DAD1
UniProt
Find proteins for Q12248 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit DAD4I [auth M],
S [auth Y]
72Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DAD4
UniProt
Find proteins for P69851 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit DAD3J [auth N],
T [auth Z]
94Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DAD3
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit SPC34K [auth O],
U [auth a]
295Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPC34
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit ASK1L [auth P],
V [auth b]
292Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ASK1
UniProt
Find proteins for P35734 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit HSK3M [auth Q],
W [auth c]
69Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HSK3
UniProt
Find proteins for P69852 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
DASH complex subunit SPC19N [auth R],
X [auth d]
165Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPC19
UniProt
Find proteins for Q03954 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev-4620-000

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomMC_UP_1201/6
Cancer Research UKUnited KingdomC576/A14109

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references