4WX8

Crystal structure of binary complex Gon7-Pcc1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex.

Zhang, W.Collinet, B.Graille, M.Daugeron, M.C.Lazar, N.Libri, D.Durand, D.van Tilbeurgh, H.

(2015) Nucleic Acids Res 43: 3358-3372

  • DOI: 10.1093/nar/gkv155
  • Primary Citation of Related Structures:  
    4WW5, 4WW7, 4WW9, 4WWA, 4WX8, 4WXA, 4XAH

  • PubMed Abstract: 
  • The yeast KEOPS protein complex comprising Kae1, Bud32, Cgi121, Pcc1 and Gon7 is responsible for the essential tRNA threonylcarbamoyladenosine (t(6)A) modification. Deletion of genes coding for the KEOPS subunits also affects telomere elongation and transcriptional regulation ...

    The yeast KEOPS protein complex comprising Kae1, Bud32, Cgi121, Pcc1 and Gon7 is responsible for the essential tRNA threonylcarbamoyladenosine (t(6)A) modification. Deletion of genes coding for the KEOPS subunits also affects telomere elongation and transcriptional regulation. In the present work, the crystal structure of Bud32/Cgi121 in complex with ADP revealed that ADP is bound in the catalytic site of Bud32 in a canonical manner characteristic of Protein Kinase A (PKA) family proteins. We found that Gon7 forms a stable heterodimer with Pcc1 and report the crystal structure of the Pcc1-Gon7 heterodimer. Gon7 interacts with the same Pcc1 region engaged in the archaeal Pcc1 homodimer. We further show that yeast KEOPS, unlike its archaeal counterpart, exists as a heteropentamer in which Gon7, Pcc1, Kae1, Bud32 and Cgi121 also adopt a linear arrangement. We constructed a model of yeast KEOPS that provides structural insight into the role of Gon7. The model also revealed the presence of a highly positively charged crater surrounding the entrance of Kae1 that likely binds tRNA.


    Organizational Affiliation

    Institut de Biologie Intégrative de la Cellule, UMR 9198, CNRS, Université de Paris Sud XI, Bâtiment 430, 91405 Orsay, France herman.van-tilbeurgh@u-psud.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit PCC1A, B, C94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PCC1YKR095W-A
UniProt
Find proteins for Q3E833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E833 
Go to UniProtKB:  Q3E833
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3E833
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit GON7D, E, F123Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GON7LDB6PCC2YJL184WJ0420
UniProt
Find proteins for P46984 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46984 
Go to UniProtKB:  P46984
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46984
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.1α = 90
b = 102.5β = 111.8
c = 88.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SHELXDEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references