4CW7

Structure of the Fap7-Rps14 complex in complex with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Literature

RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis

Loc'h, J.Blaud, M.Rety, S.Lebaron, S.Deschamps, P.Bareille, J.Jombart, J.Robert-Paganin, J.Delbos, L.Chardon, F.Zhang, E.Charenton, C.Tollervey, D.Leulliot, N.

(2014) PLoS Biol 12: 01860

  • DOI: https://doi.org/10.1371/journal.pbio.1001860
  • Primary Citation of Related Structures:  
    4CVN, 4CW7

  • PubMed Abstract: 

    During biogenesis of the 40S and 60S ribosomal subunits, the pre-40S particles are exported to the cytoplasm prior to final cleavage of the 20S pre-rRNA to mature 18S rRNA. Amongst the factors involved in this maturation step, Fap7 is unusual, as it both interacts with ribosomal protein Rps14 and harbors adenylate kinase activity, a function not usually associated with ribonucleoprotein assembly. Human hFap7 also regulates Cajal body assembly and cell cycle progression via the p53-MDM2 pathway. This work presents the functional and structural characterization of the Fap7-Rps14 complex. We report that Fap7 association blocks the RNA binding surface of Rps14 and, conversely, Rps14 binding inhibits adenylate kinase activity of Fap7. In addition, the affinity of Fap7 for Rps14 is higher with bound ADP, whereas ATP hydrolysis dissociates the complex. These results suggest that Fap7 chaperones Rps14 assembly into pre-40S particles via RNA mimicry in an ATP-dependent manner. Incorporation of Rps14 by Fap7 leads to a structural rearrangement of the platform domain necessary for the pre-rRNA to acquire a cleavage competent conformation.


  • Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Faculté de Pharmacie, Sorbonne Paris Cité, Paris, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE ADENYLATE KINASE
A, C, E, G
191Pyrococcus abyssi GE5Mutation(s): 0 
EC: 2.7.4.3
UniProt
Find proteins for Q9UZK4 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9UZK4 
Go to UniProtKB:  Q9UZK4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UZK4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11
B, D, F, H
137Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
Find proteins for P62010 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore P62010 
Go to UniProtKB:  P62010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62010
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
I [auth A],
O [auth E]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
L [auth C],
R [auth G]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
M [auth C]
N [auth C]
P [auth E]
J [auth A],
K [auth A],
M [auth C],
N [auth C],
P [auth E],
Q [auth E],
S [auth G],
T [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.046α = 90
b = 143.079β = 90
c = 83.786γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Data collection, Database references, Structure summary