1BOS | pdb_00001bos

SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR

• PDB DOI: https://doi.org/10.2210/pdb1BOS/pdb

• Classification: TOXIN
• Organism(s): Phage h30, Enterobacteria phage H-19B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-01-13 Released: 1999-02-02 
• Deposition Author(s): Ling, H., Boodhoo, A., Hazes, B., Cummings, M.D., Armstrong, G.D., Brunton, J.L., Read, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structure of the shiga-like toxin I B-pentamer complexed with an analogue of its receptor Gb3.

Ling, H., Boodhoo, A., Hazes, B., Cummings, M.D., Armstrong, G.D., Brunton, J.L., Read, R.J.

(1998) Biochemistry 37: 1777-1788

• PubMed: 9485303 
• DOI: https://doi.org/10.1021/bi971806n
• Primary Citation Related Structures: 
  1BOS


• PubMed Abstract: 
  

  Shiga-like toxin I (SLT-I) is a virulence factor of Escherichia coli strains that cause disease in humans. Like other members of the Shiga toxin family, it consists of an enzymatic (A) subunit and five copies of a binding subunit (the B-pentamer). The B-pentamer binds to a specific glycolipid, globotriaosylceramide (Gb3), on the surface of target cells and thereby plays a crucial role in the entry of the toxin. Here we present the crystal structure at 2.8 A resolution of the SLT-I B-pentamer complexed with an analogue of the Gb3 trisaccharide. The structure reveals a surprising density of binding sites, with three trisaccharide molecules bound to each B-subunit monomer of 69 residues. All 15 trisaccharides bind to one side of the B-pentamer, providing further evidence that this side faces the cell membrane. The structural model is consistent with data from site-directed mutagenesis and binding of carbohydrate analogues, and allows the rational design of therapeutic Gb3 analogues that block the attachment of toxin to cells.

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Organizational Affiliation: 
• Department of Biochemistry, University of Alberta, Edmonton, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 178.08 kDa 
• Atom Count: 12,767 
• Modeled Residue Count: 1,380 
• Deposited Residue Count: 1,380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHIGA-LIKE TOXIN I B SUBUNIT	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	69	Phage h30, Enterobacteria phage H-19B This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for P69179 (Enterobacteria phage H19B) Explore P69179  Go to UniProtKB:  P69179

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	AA [auth a], AB [auth 0], CA [auth c], CB [auth 2], EA [auth e], EB [auth 4], FA [auth f], FB [auth 5], GA [auth g], HA [auth h], HB [auth 7], IA [auth i], IB [auth 8], JA [auth j], JB [auth 9], KA [auth k], KB [auth AA], LB [auth BA], MA [auth m], MB [auth CA], OA [auth o], OB [auth EA], PA [auth p], PB [auth FA], RA [auth r], SA [auth s], TA [auth t], U, VA [auth v], W, X, XA [auth x], ZA [auth z]	3		N/A
Glycosylation Resources
GlyTouCan: G00059MO GlyCosmos: G00059MO GlyGen: G00059MO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose	BA [auth b], BB [auth 1], DA [auth d], DB [auth 3], GB [auth 6], LA [auth l], NA [auth n], NB [auth DA], QA [auth q], QB [auth GA], UA [auth u], V, WA [auth w], Y, YA [auth y], Z	2		N/A
Glycosylation Resources
GlyTouCan: G67988RO GlyCosmos: G67988RO GlyGen: G67988RO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL	AC [auth R], BC [auth T], RB [auth C], SB [auth E], TB [auth G], UB [auth I], VB [auth J], WB [auth K], XB [auth L], YB [auth N], ZB [auth P]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.5	α = 90
b = 97.7	β = 90
c = 164.2	γ = 90

Software Package:

Software Name	Purpose
XENGEN	data collection
XENGEN	data reduction
X-PLOR	model building
X-PLOR	refinement
XENGEN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-02 
Deposition Author(s): Ling, H., Boodhoo, A., Hazes, B., Cummings, M.D., Armstrong, G.D., Brunton, J.L., Read, R.J.

Revision History  

• Version 1.0: 1999-02-02
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Advisory, Data collection, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-08-09
  Changes: Advisory, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Data collection, Structure summary