2CJK | pdb_00002cjk

Structure of the RNA binding domain of Hrp1 in complex with RNA

• PDB DOI: https://doi.org/10.2210/pdb2CJK/pdb
• NAKB: 2CJK

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


• Deposited: 2006-04-04 Released: 2006-06-28 
• Deposition Author(s): Perez-Canadillas, J.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 25 
• Selection Criteria: COMPARISON BETWEEN ENERGY- ORDERED RMSD PROFILES AND TOTAL ENERGY 

Literature

Grabbing the message: structural basis of mRNA 3'UTR recognition by Hrp1.

Perez-Canadillas, J.M.

(2006) EMBO J 25: 3167-3178

• PubMed: 16794580 
• DOI: https://doi.org/10.1038/sj.emboj.7601190
• Primary Citation Related Structures: 
  2CJK


• PubMed Abstract: 
  

  The recognition of specific signals encoded within the 3'-untranslated region of the newly transcribed mRNA triggers the assembly of a multiprotein machine that modifies its 3'-end. Hrp1 recognises one of such signals, the so-called polyadenylation enhancement element (PEE), promoting the recruitment of other polyadenylation factors in yeast. The molecular bases of this interaction are revealed here by the solution structure of a complex between Hrp1 and an oligonucleotide mimicking the PEE. Six consecutive bases (AUAUAU) are specifically recognised by two RNA-binding domains arranged in tandem. Both protein and RNA undergo significant conformational changes upon complex formation with a concomitant large surface burial of RNA bases. Key aspects of RNA specificity can be explained by the presence of intermolecular aromatic-aromatic contacts and hydrogen bonds. Altogether, the Hrp1-PEE structure represents one of the first steps towards understanding of the assembly of the cleavage and polyadenylation machinery at the atomic level.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, Medical Research Council, Cambridge, UK. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.56 kDa 
• Atom Count: 1,507 
• Modeled Residue Count: 175 
• Deposited Residue Count: 175 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 4	A	167	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q99383 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q99383  Go to UniProtKB:  Q99383

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*UP*AP*UP*AP*UP*AP*UP*AP)-3'	B	8	Saccharomyces cerevisiae

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 25 
• Selection Criteria: COMPARISON BETWEEN ENERGY- ORDERED RMSD PROFILES AND TOTAL ENERGY 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-28 
Deposition Author(s): Perez-Canadillas, J.M.

Revision History  

• Version 1.0: 2006-06-28
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-05-02
  Changes: Data collection, Database references
• Version 1.4: 2024-05-15
  Changes: Data collection, Database references