9F9U | pdb_00009f9u

Crystal structure of Saccharolobus solfataricus NusA2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.236 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Archaeal NusA2 is the ancestor of ribosomal protein eS7 in eukaryotes.

Phung, D.K.Pilotto, S.Matelska, D.Blombach, F.Pinotsis, N.Hovan, L.Gervasio, F.L.Werner, F.

(2025) Structure 33: 149

  • DOI: https://doi.org/10.1016/j.str.2024.10.019
  • Primary Citation of Related Structures:  
    9F9U

  • PubMed Abstract: 

    N-utilization substance A (NusA) is a regulatory factor with pleiotropic functions in gene expression in bacteria. Archaea encode two conserved small proteins, NusA1 and NusA2, with domains orthologous to the two RNA binding K Homology (KH) domains of NusA. Here, we report the crystal structures of NusA2 from Sulfolobus acidocaldarius and Saccharolobus solfataricus obtained at 3.1 Å and 1.68 Å, respectively. NusA2 comprises an N-terminal zinc finger followed by two KH-like domains lacking the GXXG signature. Despite the loss of the GXXG motif, NusA2 binds single-stranded RNA. Mutations in the zinc finger domain compromise the structural integrity of NusA2 at high temperatures and molecular dynamics simulations indicate that zinc binding provides an energy barrier preventing the domain from reaching unfolded states. A structure-guided phylogenetic analysis of the KH-like domains supports the notion that the NusA2 clade is ancestral to the ribosomal protein eS7 in eukaryotes, implying a potential role of NusA2 in translation.


  • Organizational Affiliation
    • RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor NusA170Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: SSO0172
UniProt
Find proteins for Q980V4 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q980V4 
Go to UniProtKB:  Q980V4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ980V4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.236 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.467α = 90
b = 72.813β = 111.95
c = 41.746γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
SHELXDEphasing
ARP/wARPmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom207446/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Database references, Structure summary
  • Version 1.2: 2025-01-15
    Changes: Database references