6HU6

Structure of ARF1 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of Staufen1 in complex with a physiological RNA sheds light on substrate selectivity.

Lazzaretti, D.Bandholz-Cajamarca, L.Emmerich, C.Schaaf, K.Basquin, C.Irion, U.Bono, F.

(2018) Life Sci Alliance 1: e201800187-e201800187

  • DOI: https://doi.org/10.26508/lsa.201800187
  • Primary Citation of Related Structures:  
    6HTU, 6HU6

  • PubMed Abstract: 

    During mRNA localization, RNA-binding proteins interact with specific structured mRNA localization motifs. Although several such motifs have been identified, we have limited structural information on how these interact with RNA-binding proteins. Staufen proteins bind structured mRNA motifs through dsRNA-binding domains (dsRBD) and are involved in mRNA localization in Drosophila and mammals. We solved the structure of two dsRBDs of human Staufen1 in complex with a physiological dsRNA sequence. We identified interactions between the dsRBDs and the RNA sugar-phosphate backbone and direct contacts of conserved Staufen residues to RNA bases. Mutating residues mediating nonspecific backbone interactions only affected Staufen function in Drosophila when in vitro binding was severely reduced. Conversely, residues involved in base-directed interactions were required in vivo even when they minimally affected in vitro binding. Our work revealed that Staufen can read sequence features in the minor groove of dsRNA and suggests that these influence target selection in vivo.


  • Organizational Affiliation

    Max Planck Institute for Developmental Biology, Tübingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (19-MER)19Homo sapiens
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (19-MER)B [auth E]19Homo sapiens
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*AP*GP*UP*GP*CP*CP*AP*GP*A)-3')C [auth B]10Homo sapiens
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*UP*GP*GP*UP*AP*CP*UP*C)-3')D [auth F]9Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.803α = 90
b = 43.803β = 90
c = 452.087γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany310957
German Research FoundationGermanyBO3588/2-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references