1JBR

Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.238 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping.

Yang, X., Gerczei, T., Glover, L.T., Correll, C.C.

(2001) Nat Struct Biol 8: 968-973

  • DOI: 10.1038/nsb1101-968
  • Primary Citation of Related Structures:  
    1JBR, 1JBS, 1JBT

  • PubMed Abstract: 

    • The cytotoxin sarcin disrupts elongation factor binding and protein synthesis by specifically cleaving one phosphodiester bond in ribosomes. To elucidate the molecular basis of toxin action, we determined three cocrystal structures of the sarcin homolog restrictocin bound to different analogs that mimic the target sarcin/ricin loop (SRL) structure of the rat 28S rRNA ...

    The cytotoxin sarcin disrupts elongation factor binding and protein synthesis by specifically cleaving one phosphodiester bond in ribosomes. To elucidate the molecular basis of toxin action, we determined three cocrystal structures of the sarcin homolog restrictocin bound to different analogs that mimic the target sarcin/ricin loop (SRL) structure of the rat 28S rRNA. In these structures, restrictocin contacts the bulged-G motif and an unfolded form of the tetraloop of the SRL RNA. In one structure, toxin loops guide selection of the target site by contacting the base critical for recognition (G4319) and the surrounding S-shaped backbone. In another structure, base flipping of the tetraloop enables cleavage by placing the target nucleotide in the active site with the nucleophile nearly inline for attack on the scissile bond. These structures provide the first views of how a site-specific protein endonuclease recognizes and cleaves a folded RNA substrate.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637 USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RestrictocinD [auth A],
E [auth B]		149Aspergillus restrictusMutation(s): 0 
Gene Names: ret
EC: 3.1.27
UniProt
Find proteins for P67876 (Aspergillus restrictus)
Explore P67876 
Go to UniProtKB:  P67876
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67876
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23))-3'A [auth C]18N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*GP*AP*AP*CP*CP*GP*GP*AP*GP*CP*GP*C)-3'B [auth F]13N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
31-mer SRD RNA analogC [auth D]31N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
RNA PDBBind:  1JBR Kd: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.4α = 90
b = 109.7β = 97.8
c = 40γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance