9GEK | pdb_00009gek

Structure of the FAST1-FAST2-RAP module from human FASTKD4 by carrier-driven crystallisation with maltose binding protein from E. coli.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.241 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

The Vsr-like protein FASTKD4 regulates the stability and polyadenylation of the MT-ND3 mRNA.

Yang, X.Stentenbach, M.Hughes, L.A.Siira, S.J.Lau, K.Hothorn, M.Martinou, J.C.Rackham, O.Filipovska, A.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkae1261
  • Primary Citation of Related Structures:  
    9GEK

  • PubMed Abstract: 

    Expression of the compact mitochondrial genome is regulated by nuclear encoded, mitochondrially localized RNA-binding proteins (RBPs). RBPs regulate the lifecycles of mitochondrial RNAs from transcription to degradation by mediating RNA processing, maturation, stability and translation. The Fas-activated serine/threonine kinase (FASTK) family of RBPs has been shown to regulate and fine-tune discrete aspects of mitochondrial gene expression. Although the roles of specific targets of FASTK proteins have been elucidated, the molecular mechanisms of FASTK proteins in mitochondrial RNA metabolism remain unclear. Therefore, we resolved the structure of FASTKD4 at atomic level that includes the RAP domain and the two FAST motifs, creating a positively charged cavity resembling that of the very short patch repair endonuclease. Our biochemical studies show that FASTKD4 binds the canonical poly(A) tail of MT-ND3 enabling its maturation and translation. The in vitro role of FASTKD4 is consistent with its loss in cells that results in decreased MT-ND3 polyadenylation, which destabilizes this messenger RNA in mitochondria.


  • Organizational Affiliation
    • Department of Molecular Cell Biology, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,FAST kinase domain-containing protein 4,FAST kinase domain-containing protein 4725Homo sapiensMutation(s): 1 
Gene Names: malEZ5632ECs5017TBRG4CPR2FASTKD4KIAA0948
UniProt & NIH Common Fund Data Resources
Find proteins for Q969Z0 (Homo sapiens)
Explore Q969Z0 
Go to UniProtKB:  Q969Z0
PHAROS:  Q969Z0
GTEx:  ENSG00000136270 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ969Z0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download Ideal Coordinates CCD File 
B [auth A]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
FRU
Query on FRU

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A]
beta-D-fructofuranose
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
GLC
Query on GLC

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.058α = 90
b = 88.315β = 90
c = 114.809γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references