3QSU

Structure of Staphylococcus aureus Hfq in complex with A7 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract.

Horstmann, N.Orans, J.Valentin-Hansen, P.Shelburne, S.A.Brennan, R.G.

(2012) Nucleic Acids Res 40: 11023-11035

  • DOI: https://doi.org/10.1093/nar/gks809
  • Primary Citation of Related Structures:  
    3QSU

  • PubMed Abstract: 

    Hfq is a post-transcriptional regulator that plays a key role in bacterial gene expression by binding AU-rich sequences and A-tracts to facilitate the annealing of sRNAs to target mRNAs and to affect RNA stability. To understand how Hfq from the Gram-positive bacterium Staphylococcus aureus (Sa) binds A-tract RNA, we determined the crystal structure of an Sa Hfq-adenine oligoribonucleotide complex. The structure reveals a bipartite RNA-binding motif on the distal face that is composed of a purine nucleotide-specificity site (R-site) and a non-discriminating linker site (L-site). The (R-L)-binding motif, which is also utilized by Bacillus subtilis Hfq to bind (AG)(3)A, differs from the (A-R-N) tripartite poly(A) RNA-binding motif of Escherichia coli Hfq whereby the Sa Hfq R-site strongly prefers adenosine, is more aromatic and permits deeper insertion of the adenine ring. R-site adenine-stacking residue Phe30, which is conserved among Gram-positive bacterial Hfqs, and an altered conformation about β3 and β4 eliminate the adenosine-specificity site (A-site) and create the L-site. Binding studies show that Sa Hfq binds (AU)(3)A ≈ (AG)(3)A ≥ (AC)(3)A > (AA)(3)A and L-site residue Lys33 plays a significant role. The (R-L) motif is likely utilized by Hfqs from most Gram-positive bacteria to bind alternating (A-N)(n) RNA.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA chaperone Hfq77Staphylococcus aureus subsp. aureus ECT-R 2Mutation(s): 0 
Gene Names: ECTR2_1161hfq
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')O [auth R],
P
7N/A
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 
AA [auth M]
BA [auth M]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth M],
BA [auth M],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth D],
GA [auth D],
HA [auth E],
IA [auth E],
JA [auth F],
KA [auth F],
LA [auth G],
MA [auth G],
NA [auth J],
OA [auth J],
PA [auth N],
Q [auth A],
QA [auth N],
R [auth A],
RA [auth S],
S [auth B],
SA [auth S],
T [auth B],
U [auth H],
V [auth H],
W [auth I],
X [auth I],
Y [auth K],
Z [auth K]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.397α = 90
b = 156.397β = 90
c = 34.646γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references
  • Version 1.2: 2012-12-12
    Changes: Database references
  • Version 1.3: 2013-06-19
    Changes: Derived calculations
  • Version 1.4: 2017-11-08
    Changes: Refinement description
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references, Derived calculations