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- PDB-25sb: CyroEM structure of the complex between Shiga toxin Stx1a B subun... -

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Basic information

Entry
Database: PDB / ID: 25sb
TitleCyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS059
Components
  • Heavy chain of RDS059 Fab
  • Light chain of RDS059 Fab
  • Shiga toxin subunit B
KeywordsTOXIN/IMMUNE SYSTEM / Shiga toxin / B subunit / Antibody / TOXIN-IMMUNE SYSTEM complex
Function / homologyShiga-like toxin, beta subunit / Shiga-like toxin beta subunit / symbiont-mediated hemolysis of host erythrocyte / Enterotoxin / toxin activity / extracellular region / Shiga toxin subunit B
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsChen, S.D. / Li, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv Sci (Weinh) / Year: 2026
Title: Structural Basis of Shiga Toxin Neutralization by Human Antibodies Targeting Canonical Receptor-Binding and Non-Canonical Assembly Sites.
Authors: Jianting Ke / Xin Li / Xiaoli Wang / Zhaoxia Huang / Shaojie Xue / Yuyang Liu / Jing Pan / Guowei Hu / Yayu Wang / Cheng Wang / Shoudeng Chen /
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 ...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.
History
DepositionApr 16, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Shiga toxin subunit B
B: Heavy chain of RDS059 Fab
C: Light chain of RDS059 Fab
D: Shiga toxin subunit B
H: Heavy chain of RDS059 Fab
L: Light chain of RDS059 Fab
E: Shiga toxin subunit B
I: Heavy chain of RDS059 Fab
M: Light chain of RDS059 Fab
F: Shiga toxin subunit B
J: Heavy chain of RDS059 Fab
N: Light chain of RDS059 Fab
G: Shiga toxin subunit B
K: Heavy chain of RDS059 Fab
O: Light chain of RDS059 Fab


Theoretical massNumber of molelcules
Total (without water)273,43415
Polymers273,43415
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Shiga toxin subunit B


Mass: 7916.908 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: B subunit of Shiga toxin 1a (Stx1a) / Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: stx1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WZI6
#2: Antibody
Heavy chain of RDS059 Fab


Mass: 24159.906 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody
Light chain of RDS059 Fab


Mass: 22609.887 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of shiga toxin 1a B subunit(Stx1aB) with RDS059 Fab
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.4 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 428491 / Symmetry type: POINT
RefinementHighest resolution: 2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00419725
ELECTRON MICROSCOPYf_angle_d0.64326925
ELECTRON MICROSCOPYf_dihedral_angle_d11.1586965
ELECTRON MICROSCOPYf_chiral_restr0.0463060
ELECTRON MICROSCOPYf_plane_restr0.0053440

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