6GYP

Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Architecture of the CBF3-centromere complex of the budding yeast kinetochore.

Yan, K.Zhang, Z.Yang, J.McLaughlin, S.H.Barford, D.

(2018) Nat. Struct. Mol. Biol. 25: 1103-1110

  • DOI: 10.1038/s41594-018-0154-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are ...

    Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are associated with the centromere-specific nucleosome Cse4. Deposition of Cse4 at CEN loci is dependent on the CBF3 complex that engages CDEIII to direct Cse4 nucleosomes to CDEII. To understand how CBF3 recognizes CDEIII and positions Cse4, we determined a cryo-EM structure of a CBF3-CEN complex. CBF3 interacts with CEN DNA as a head-to-head dimer that includes the whole of CDEIII and immediate 3' regions. Specific CEN-binding of CBF3 is mediated by a Cep3 subunit of one of the CBF3 protomers that forms major groove interactions with the conserved and essential CCG and TGT motifs of CDEIII. We propose a model for a CBF3-Cse4-CEN complex with implications for understanding CBF3-directed deposition of the Cse4 nucleosome at CEN loci.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Centromere DNA-binding protein complex CBF3 subunit B
B
608Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CEP3 (CBF3, CBF3B, CSL1)
Find proteins for P40969 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40969
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Centromere DNA-binding protein complex CBF3 subunit C
A
478Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CTF13 (CBF3C)
Find proteins for P35203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P35203
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Centromere DNA-binding protein complex CBF3 subunit B
C
564Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CEP3 (CBF3, CBF3B, CSL1)
Find proteins for P40969 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40969
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Suppressor of kinetochore protein 1
D
194Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SKP1 (CBF3D)
Find proteins for P52286 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SKP1
Go to UniProtKB:  P52286
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Centromere DNA-binding protein complex CBF3 subunit A
E
956Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CBF2 (CBF3A, CEP2, CTF14, NDC10)
Find proteins for P32504 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32504
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLN
Query on GLN

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Download CCD File 
B
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
ASN
Query on ASN

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Download CCD File 
B
ASPARAGINE
C4 H8 N2 O3
DCXYFEDJOCDNAF-REOHCLBHSA-N
 Ligand Interaction
PHE
Query on PHE

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Download CCD File 
B
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
THR
Query on THR

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Download CCD File 
B
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
 Ligand Interaction
ARG
Query on ARG

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Download CCD File 
B
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
MET
Query on MET

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Download CCD File 
B
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
phenix.real_space_refinerefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMRC_UP_1201/6
Cancer Research UKUnited KingdomC576/A14109

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-19
    Type: Data collection, Database references