Structural Basis for Recognition of the mRNA Class II AU-Rich Element by the Tandem Zinc Finger Domain of TIS11d

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d.

Hudson, B.P.Martinez-Yamout, M.A.Dyson, H.J.Wright, P.E.

(2004) Nat Struct Mol Biol 11: 257-264

  • DOI: https://doi.org/10.1038/nsmb738
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The tandem zinc finger (TZF) domain of the protein TIS11d binds to the class II AU-rich element (ARE) in the 3' untranslated region (3' UTR) of target mRNAs and promotes their deadenylation and degradation. The NMR structure of the TIS11d TZF domain bound to the RNA sequence 5'-UUAUUUAUU-3' comprises a pair of novel CCCH fingers of type CX(8)CX(5)CX(3)H separated by an 18-residue linker. The two TIS11d zinc fingers bind in a symmetrical fashion to adjacent 5'-UAUU-3' subsites on the single-stranded RNA via a combination of electrostatic and hydrogen-bonding interactions, with intercalative stacking between conserved aromatic side chains and the RNA bases. Sequence specificity in RNA recognition is achieved by a network of intermolecular hydrogen bonds, mostly between TIS11d main-chain functional groups and the Watson-Crick edges of the bases. The TIS11d structure provides insights into the RNA-binding functions of this large family of CCCH zinc finger proteins.

  • Organizational Affiliation

    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.


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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrate response factor 2B [auth A]70Homo sapiensMutation(s): 0 
Gene Names: ZFP36L2BRF2TIS11DERF2
UniProt & NIH Common Fund Data Resources
Find proteins for P47974 (Homo sapiens)
Explore P47974 
Go to UniProtKB:  P47974
GTEx:  ENSG00000152518 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47974
Sequence Annotations
  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*UP*AP*UP*UP*UP*AP*UP*U)-3')A [auth D]9N/A
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations