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


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

Download SDF File 
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

Download SDF File 
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