Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.20 kDa 
• Atom Count: 765 
• Modelled Residue Count: 79 
• Deposited Residue Count: 79 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1RGO

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

• PDB DOI: 10.2210/pdb1RGO/pdb
• NDB: 1RGO
• BMRB: 6005

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-11-12 Released: 2004-03-02 
• Deposition Author(s): Hudson, B.P., Martinez-Yamout, M.A., Dyson, H.J., Wright, P.E.

---

Experimental Data Snapshot

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

Literature

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

• PubMed: 14981510 
• DOI: 10.1038/nsmb738
• Primary Citation of Related Structures:  
  1RGO


• 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.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Butyrate response factor 2	B [auth A]	70	Homo sapiens	Mutation(s): 0  Gene Names: ZFP36L2, BRF2, TIS11D, ERF2, RNF162C
UniProt & NIH Common Fund Data Resources
Find proteins for P47974 (Homo sapiens) Explore P47974  Go to UniProtKB:  P47974
PHAROS:  P47974

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*AP*UP*UP*UP*AP*UP*U)-3')	A [auth D]	9	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1RGO Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-12 
• Released Date: 2004-03-02 
Deposition Author(s): Hudson, B.P., Martinez-Yamout, M.A., Dyson, H.J., Wright, P.E.

Revision History  

• 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