1QI7 | pdb_00001qi7

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

• PDB DOI: https://doi.org/10.2210/pdb1QI7/pdb

• Classification: HYDROLASE
• Organism(s): Saponaria officinalis
• Mutation(s): No 


• Deposited: 1999-06-08 Released: 2000-06-05 
• Deposition Author(s): Savino, C., Federici, L., Ippoliti, R., Lendaro, E., Tsernoglou, D.

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 10745075 
• DOI: https://doi.org/10.1016/s0014-5793(00)01325-9
• Primary Citation 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 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.

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 28.72 kDa 
• Atom Count: 2,135 
• Modeled Residue Count: 253 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (N-GLYCOSIDASE)	A	253	Saponaria officinalis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P20656 (Saponaria officinalis) Explore P20656  Go to UniProtKB:  P20656

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

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

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.53	α = 90
b = 67.53	β = 90
c = 119.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-06-05 
Deposition Author(s): Savino, C., Federici, L., Ippoliti, R., Lendaro, E., Tsernoglou, D.

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
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description