6UPH

Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history


Literature

Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 angstrom Resolution.

Migl, D.Kschonsak, M.Arthur, C.P.Khin, Y.Harrison, S.C.Ciferri, C.Dimitrova, Y.N.

(2020) Structure 28: 363-370.e3

  • DOI: 10.1016/j.str.2019.12.002
  • Primary Citation of Related Structures:  
    6UPH

  • PubMed Abstract: 
  • Kinetochores mediate chromosome segregation during cell division. They assemble on centromeric nucleosomes and capture spindle microtubules. In budding yeast, a kinetochore links a single nucleosome, containing the histone variant Cse4 CENP-A instead of H3, with a single microtubule ...

    Kinetochores mediate chromosome segregation during cell division. They assemble on centromeric nucleosomes and capture spindle microtubules. In budding yeast, a kinetochore links a single nucleosome, containing the histone variant Cse4 CENP-A instead of H3, with a single microtubule. Conservation of most kinetochore components from yeast to metazoans suggests that the yeast kinetochore represents a module of the more complex metazoan arrangements. We describe here a streamlined protocol for reconstituting a yeast centromeric nucleosome and a systematic exploration of cryo-grid preparation. These developments allowed us to obtain a high-resolution cryoelectron microscopy reconstruction. As suggested by previous work, fewer base pairs are in tight association with the histone octamer than there are in canonical nucleosomes. Weak binding of the end DNA sequences may contribute to specific recognition by other inner kinetochore components. The centromeric nucleosome structure and the strategies we describe will facilitate studies of many other aspects of kinetochore assembly and chromatin biochemistry.


    Organizational Affiliation

    Structural Biology, Genentech, South San Francisco, CA, USA. Electronic address: dimitrova.yoana@gene.com.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3-like centromeric protein CSE4A, E229Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSE4CSL2YKL049CYKL262
UniProt
Find proteins for P36012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P36012
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F118Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_E08647gKLLA0_E17601g
UniProt
Find proteins for Q6CMU6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Go to UniProtKB:  Q6CMU6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G145Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: HTA1KLLA0E17413gHTA2KLLA0F13332g
UniProt
Find proteins for Q6CK59 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B.1D, H147Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: HTB1KLLA0F13310g
UniProt
Find proteins for Q6CK60 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CK60 
Go to UniProtKB:  Q6CK60
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (119-MER)I147unidentified
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (119-MER)J147unidentified
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM62580
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.2: 2020-02-12
    Changes: Database references
  • Version 1.3: 2020-03-18
    Changes: Database references