1FXL

CRYSTAL STRUCTURE OF HUD AND AU-RICH ELEMENT OF THE C-FOS RNA

• PDB DOI:  https://doi.org/10.2210/pdb1FXL/pdb
• NAKB: 1FXL

• Classification: TRANSCRIPTION/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-09-26 Released: 2001-02-05 
• Deposition Author(s): Wang, X., Hall, T.M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Structural basis for recognition of AU-rich element RNA by the HuD protein.

Wang, X., Tanaka Hall, T.M.

(2001) Nat Struct Biol 8: 141-145

• PubMed: 11175903 
• DOI: https://doi.org/10.1038/84131
• Primary Citation of Related Structures:  
  1FXL, 1G2E


• PubMed Abstract: 
  

Hu proteins bind to adenosine-uridine (AU)-rich elements (AREs) in the 3' untranslated regions of many short-lived mRNAs, thereby stabilizing them. Here we report the crystal structures of the first two RNA recognition motif (RRM) domains of the HuD protein in complex with an 11-nucleotide fragment of a class I ARE (the c-fos ARE; to 1.8 A), and with an 11-nucleotide fragment of a class II ARE (the tumor necrosis factor alpha ARE; to 2.3 A). These structures reveal a consensus RNA recognition sequence that suggests a preference for pyrimidine-rich sequences and a requirement for a central uracil residue in the clustered AUUUA repeats found in class II AREs. Comparison to structures of other RRM domain-nucleic acid complexes reveals two base recognition pockets in all the structures that interact with bases using residues in conserved ribonucleoprotein motifs and at the C-terminal ends of RRM domains. Different conformations of nucleic acid can be bound by RRM domains by using different combinations of base recognition pockets and multiple RRM domains.

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Organizational Affiliation: 

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.28 kDa 
• Atom Count: 1,690 
• Modelled Residue Count: 176 
• Deposited Residue Count: 176 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD	B [auth A]	167	Homo sapiens	Mutation(s): 0  Gene Names: ELAVL4, HUD, PNEM
UniProt & NIH Common Fund Data Resources
Find proteins for P26378 (Homo sapiens) Explore P26378  Go to UniProtKB:  P26378
PHAROS:  P26378

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.31	α = 90
b = 99.38	β = 106.4
c = 33.34	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-05 
Deposition Author(s): Wang, X., Hall, T.M.T.

Revision History  

• Version 1.0: 2001-02-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance