7K7G

nucleosome and Gal4 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation.

Guan, R.Lian, T.Zhou, B.R.He, E.Wu, C.Singleton, M.Bai, Y.

(2021) Nat Commun 12: 1763-1763

  • DOI: 10.1038/s41467-021-21985-9
  • Primary Citation of Related Structures:  
    7K79, 7K78, 7K7G

  • PubMed Abstract: 
  • Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner ...

    Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. The CBF3core specifically recognizes the nucleosomal CCG motif through the Gal4 domain while allosterically altering the DNA conformation. Cryo-EM, modeling, and mutational studies reveal that the CBF3core forms dynamic interactions with core histones H2B and CENP-A in the CEN3 nucleosome. Our results provide insights into the structure of the budding yeast centromeric nucleosome and the mechanism of its assembly, which have implications for analogous processes of human centromeric nucleosome formation.


    Organizational Affiliation

    Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. baiyaw@mail.nih.gov.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3A, E136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHT1YBR010WYBR0201HHT2SIN2YNL031CN2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHF1YBR009CYBR0122HHF2YNL030WN2752
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A.1C, G132Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTA1H2A1SPT11YDR225WYD9934.10
UniProt
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B.1D, H131Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTB1H2B1SPT12YDR224CYD9934.09C
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Centromere DNA-binding protein complex CBF3 subunit BK [auth M]48Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEP3CBF3CBF3BCSL1YMR168CYM8520.17C
UniProt
Find proteins for P40969 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (147-MER)I147Saccharomyces cerevisiae
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (147-MER)J147Saccharomyces cerevisiae
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
L [auth M], MZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2020-09-22 
  • Released Date: 2021-03-31 
  • Deposition Author(s): Ruifang, G., Yawen, B.

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release