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 

wwPDB Validation 3D Report Full Report


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.Mol.Biol. 8: 968-973

  • DOI: 10.1038/nsb1101-968
  • Primary Citation of Related Structures:  

  • 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 homo ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Restrictocin
A, B
149Aspergillus restrictusMutation(s): 0 
Gene Names: ret
EC: 3.1.27.-
Find proteins for P67876 (Aspergillus restrictus)
Go to UniProtKB:  P67876
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23))-3'C18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*GP*GP*AP*AP*CP*CP*GP*GP*AP*GP*CP*GP*C)-3'F13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
31-mer SRD RNA analogD31N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
C, D, F
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
A23
Query on A23
C
RNA LINKINGC10 H13 N5 O9 P2A
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RNAKd: 1000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.400α = 90.00
b = 109.700β = 97.80
c = 40.000γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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