1BOS

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.226
R-Value Work: 0.170
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/bi971806n
Primary Citation of 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.

Organizational Affiliation

Department of Biochemistry, University of Alberta, Edmonton, Canada.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHIGA-LIKE TOXIN I B SUBUNIT	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69179
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain AC [auth R] SDF format, chain BC [auth T] SDF format, chain RB [auth C] SDF format, chain SB [auth E] SDF format, chain UB [auth I] SDF format, chain WB [auth K] SDF format, chain XB [auth L] SDF format, chain YB [auth N] SDF format, chain ZB [auth P] SDF format, chain TB [auth G] SDF format, chain VB [auth J] MOL2 format, chain AC [auth R] MOL2 format, chain BC [auth T] MOL2 format, chain RB [auth C] MOL2 format, chain SB [auth E] MOL2 format, chain UB [auth I] MOL2 format, chain WB [auth K] MOL2 format, chain XB [auth L] MOL2 format, chain YB [auth N] MOL2 format, chain ZB [auth P] MOL2 format, chain TB [auth G] MOL2 format, chain VB [auth J]	AC [auth R] BC [auth T] RB [auth C] SB [auth E] TB [auth G] 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		Interactions Focus chain AC [auth R] Focus chain BC [auth T] Focus chain RB [auth C] Focus chain SB [auth E] Focus chain TB [auth G] Focus chain UB [auth I] Focus chain VB [auth J] Focus chain WB [auth K] Focus chain XB [auth L] Focus chain YB [auth N] Focus chain ZB [auth P] Interactions & Density Focus chain AC [auth R] Focus chain BC [auth T] Focus chain RB [auth C] Focus chain SB [auth E] Focus chain TB [auth G] Focus chain UB [auth I] Focus chain VB [auth J] Focus chain WB [auth K] Focus chain XB [auth L] Focus chain YB [auth N] Focus chain ZB [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.226
R-Value Work: 0.170
R-Value Observed: 0.170
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1999-02-02

Deposition Author(s):

Revision History (Full details and data files)

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

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Help and Resources

1BOS

SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3