2XS2

Crystal structure of the RRM domain of mouse Deleted in azoospermia-like in complex with RNA, UUGUUCUU

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Kinked beta-strands mediate high-affinity recognition of mRNA targets by the germ-cell regulator DAZL.

Jenkins, H.T., Malkova, B., Edwards, T.A.

(2011) Proc Natl Acad Sci U S A 108: 18266-18271

  • DOI: 10.1073/pnas.1105211108
  • Primary Citation of Related Structures:  
    2XS2, 2XS5, 2XS7, 2XSF

  • PubMed Abstract: 

    • A defect in germ-cell (sperm and oocyte) development is the leading cause of male and female infertility. Control of translation through the binding of deleted in azoospermia (DAZ)-like (DAZL) to the 3'-UTRs of mRNAs, via a highly conserved RNA recognition motif (RRM), has been shown to be essential in germ-cell development ...

    A defect in germ-cell (sperm and oocyte) development is the leading cause of male and female infertility. Control of translation through the binding of deleted in azoospermia (DAZ)-like (DAZL) to the 3'-UTRs of mRNAs, via a highly conserved RNA recognition motif (RRM), has been shown to be essential in germ-cell development. Crystal structures of the RRM from murine DAZL (Dazl), both alone and in complex with RNA sequences from the 3'-UTRs of mRNAs regulated by Dazl, reveal high-affinity sequence-specific recognition of a GUU triplet involving an extended, kinked, pair of β-strands. Recognition of the GUU triplet is maintained, whereas the identity and position of bases flanking this triplet varies. The Dazl RRM is thus able to recognize GUU triplets in different sequence contexts. Mutation of bases within the GUU triplet reduces the affinity of binding. Together with the demonstration that multiple Dazl RRMs can bind to a single RNA containing multiple GUU triplets, these structures suggest that the number of DAZL molecules bound to GUU triplets in the 3'-UTR provides a method for modulating the translation of a target RNA. The conservation of RNA binding and structurally important residues between members of the DAZ family, together with the demonstration that mutation of these residues severely impairs RNA binding, indicate that the mode of RNA binding revealed by these structures is conserved in proteins essential for gamete development from flies to humans.

    Organizational Affiliation: 

    Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DELETED IN AZOOSPERMIA-LIKEA102Mus musculusMutation(s): 1 
Gene Names: Dazl, Dazl1, Dazla
UniProt & NIH Common Fund Data Resources
Find proteins for Q64368 (Mus musculus)
Explore Q64368 
Go to UniProtKB:  Q64368
IMPC:  MGI:1342328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64368
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*UP*UP*GP*UP*UP*CP*UP*U)-3'B8Mus musculus
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.1α = 90
b = 52.06β = 90
c = 60.49γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2011-11-02
    Changes: Database references
  • Version 1.2: 2011-11-23
    Changes: Database references
  • Version 1.3: 2018-06-13
    Changes: Data collection, Database references