1QI7

THE CRYSTAL STRUCTURE AT 2.0 A OF SAPORIN SO6, A RIBOSOME INACTIVATING PROTEIN FROM SAPONARIA OFFICINALIS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 

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This is version 1.3 of the entry. See complete history. 


Literature

The crystal structure of saporin SO6 from Saponaria officinalis and its interaction with the ribosome.

Savino, C., Federici, L., Ippoliti, R., Lendaro, E., Tsernoglou, D.

(2000) FEBS Lett 470: 239-243

  • DOI: 10.1016/s0014-5793(00)01325-9
  • Primary Citation of Related Structures:  
    1QI7

  • PubMed Abstract: 

    • The 2.0 A resolution crystal structure of the ribosome inactivating protein saporin (isoform 6) from seeds of Saponaria officinalis is presented. The fold typical of other plant toxins is conserved, despite some differences in the loop regions. The loop ...

    The 2.0 A resolution crystal structure of the ribosome inactivating protein saporin (isoform 6) from seeds of Saponaria officinalis is presented. The fold typical of other plant toxins is conserved, despite some differences in the loop regions. The loop between strands beta7 and beta8 in the C-terminal region which spans over the active site cleft appears shorter in saporin, suggesting an easier access to the substrate. Furthermore we investigated the molecular interaction between saporin and the yeast ribosome by differential chemical modifications. A contact surface inside the C-terminal region of saporin has been identified. Structural comparison between saporin and other ribosome inactivating proteins reveals that this region is conserved and represents a peculiar motif involved in ribosome recognition.

    Organizational Affiliation: 

    Department of Biochemical Sciences and CNR Centre for Molecular Biology, University of Rome 'La Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (N-GLYCOSIDASE) A253Saponaria officinalisMutation(s): 0 
Gene Names: SAP6
EC: 3.2.2.22
Find proteins for P20656 (Saponaria officinalis)
Explore P20656 
Go to UniProtKB:  P20656
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.53α = 90
b = 67.53β = 90
c = 119.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-05
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description