25SB | pdb_000025sb

CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS059


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Shiga Toxin Neutralization by Human Antibodies Targeting Canonical Receptor-Binding and Non-Canonical Assembly Sites.

Ke, J.Li, X.Wang, X.Huang, Z.Xue, S.Liu, Y.Pan, J.Hu, G.Wang, Y.Wang, C.Chen, S.

(2026) Adv Sci (Weinh) : e77402-e77402

  • DOI: https://doi.org/10.1002/advs.77402
  • Primary Citation Related Structures: 
    25RG, 25SB

  • PubMed Abstract: 

    Shiga toxin-producing Escherichia coli (STEC) infections cause severe systemic complications, yet targeted antitoxin therapeutics remain an unmet clinical need. Here, we isolated a panel of human monoclonal antibodies (mAbs) targeted at STEC toxin and characterized two potent neutralizing candidates, RDS045 and RDS059. The cryo-electron microscopy structure of the human mAb RDS059 in complex with the Shiga toxin 1a B subunit (Stx1aB) reveals that RDS059 recognizes the surface-exposed loop of Stx1aB, whereby it directly competes with the host glycolipid globotriaosylceramide (Gb3) to block toxin-cell engagement. In contrast, RDS045 binds a non-canonical quaternary epitope at the pentameric interface of Stx1aB, acting as an interprotomer clamp via an extensive hydrogen-bonding and cation-π interaction network. Both antibodies confer robust protection in cellular assays and an in vivo murine Stx1a challenge model. Collectively, this work defines two distinct molecular blueprints for Shiga toxin receptor blockade and assembly interference, establishing mechanistic frameworks for the development of STEC therapeutics.


  • Organizational Affiliation
    • Division of Nephrology, Department of Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 273.43 kDa 
  • Atom Count: 19,240 
  • Modeled Residue Count: 2,560 
  • Deposited Residue Count: 2,560 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Shiga toxin subunit BA,
D,
G [auth E],
J [auth F],
M [auth G]
71Escherichia coli O157:H7Mutation(s): 0 
Gene Names: stx1
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of RDS059 FabB,
E [auth H],
H [auth I],
K [auth J],
N [auth K]
227Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of RDS059 FabC,
F [auth L],
I [auth M],
L [auth N],
O
214Homo sapiensMutation(s): 0 
Entity Groups
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Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-26
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references