6H0R | pdb_00006h0r

X-ray structure of SRS2 fragment of Rgs4 3' UTR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.237 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6H0R

This is version 1.2 of the entry. See complete history

Literature

Staufen2-mediated RNA recognition and localization requires combinatorial action of multiple domains.

Heber, S.Gaspar, I.Tants, J.N.Gunther, J.Moya, S.M.F.Janowski, R.Ephrussi, A.Sattler, M.Niessing, D.

(2019) Nat Commun 10: 1659-1659

  • DOI: https://doi.org/10.1038/s41467-019-09655-3
  • Primary Citation Related Structures: 
    6H0R

  • PubMed Abstract: 

    Throughout metazoans, Staufen (Stau) proteins are core factors of mRNA localization particles. They consist of three to four double-stranded RNA binding domains (dsRBDs) and a C-terminal dsRBD-like domain. Mouse Staufen2 (mStau2)-like Drosophila Stau (dmStau) contains four dsRBDs. Existing data suggest that only dsRBDs 3-4 are necessary and sufficient for mRNA binding. Here, we show that dsRBDs 1 and 2 of mStau2 bind RNA with similar affinities and kinetics as dsRBDs 3 and 4. While RNA binding by these tandem domains is transient, all four dsRBDs recognize their target RNAs with high stability. Rescue experiments in Drosophila oocytes demonstrate that mStau2 partially rescues dmStau-dependent mRNA localization. In contrast, a rescue with mStau2 bearing RNA-binding mutations in dsRBD1-2 fails, confirming the physiological relevance of our findings. In summary, our data show that the dsRBDs 1-2 play essential roles in the mRNA recognition and function of Stau-family proteins of different species.


  • Organizational Affiliation
    • Institute of Pharmaceutical Biotechnology, 89081 Ulm University, Ulm, Germany.

Macromolecule Content 

  • Total Structure Weight: 21.47 kDa 
  • Atom Count: 1,421 
  • Modeled Residue Count: 62 
  • Deposited Residue Count: 62 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
SRS2 fragment of Rgs4 3' UTR, RNA (31-MER)
A, B
31Rattus norvegicus
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BA

Query on BA



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.237 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.02α = 90
b = 32.39β = 103.47
c = 46.37γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Derived calculations