4C0B

Structure of wild-type Clp1p-Pcf11p (454 -563) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for ATP loss by Clp1p in a G135R mutant protein.

Dupin, A.F.Fribourg, S.

(2014) Biochimie 101: 203-207

  • DOI: https://doi.org/10.1016/j.biochi.2014.01.017
  • Primary Citation of Related Structures:  
    4C0B, 4C0H

  • PubMed Abstract: 

    Pcf11p and Clp1p form a heterodimer and are subunits of the Cleavage Factor IA (CF IA), a complex that is involved in the maturation of the 3'-end of mRNAs in Saccharomyces cerevisiae. The role of Clp1p protein in polyadenylation remains elusive, as does the need for ATP binding by Clp1p. In order to obtain structural details at atomic resolution of point mutants of Clp1p, we solved the crystal structure of Clp1-1p (G135R) point mutant complexed with Pcf11p (454-563) domain. The Clp1-1p-Pcf11p structure provides the atomic details for ATP loss while the point mutation preserves intact the Pcf11p interaction surface of Clp1p. This provides a rationale for the absence of phenotype in the yeast clp1-1 strain. Additionally, the structure allows for the description of an extended binding interface of Pcf11p with Clp1p which is likely to be S. cerevisiae specific.


  • Organizational Affiliation

    Univ. Bordeaux, IECB, F-33607 Pessac, France; INSERM, U869, F-33077 Pessac, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
A, B
446Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q08685 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08685 
Go to UniProtKB:  Q08685
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08685
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PCF11P
C, D
110Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39081 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39081 
Go to UniProtKB:  P39081
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39081
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.352α = 90
b = 95.41β = 90
c = 182.142γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description