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- EMDB-80337: CyroEM structure of the complex between Shiga toxin Stx1a B subun... -

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Basic information

Entry
Database: EMDB / ID: EMD-80337
TitleCyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS059
Map data
Sample
  • Complex: Complex of shiga toxin 1a B subunit(Stx1aB) with RDS059 Fab
    • Protein or peptide: Shiga toxin subunit B
    • Protein or peptide: Heavy chain of RDS059 Fab
    • Protein or peptide: Light chain of RDS059 Fab
KeywordsShiga toxin / B subunit / Antibody / TOXIN/IMMUNE SYSTEM / 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 speciesHomo sapiens (human) / Escherichia coli O157:H7 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsChen SD / Li X
Funding support China, 1 items
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, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80337.png

Downloads & links

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Map

FileDownload / File: emd_80337.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 400 pix.
= 295.2 Å		0.74 Å/pix.
x 400 pix.
= 295.2 Å		0.74 Å/pix.
x 400 pix.
= 295.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.738 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.71
Minimum - Maximum-0.48233232 - 34.079884
Average (Standard dev.)0.01646118 (±0.71692944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 295.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80337_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80337_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of shiga toxin 1a B subunit(Stx1aB) with RDS059 Fab

EntireName: Complex of shiga toxin 1a B subunit(Stx1aB) with RDS059 Fab
Components
  • Complex: Complex of shiga toxin 1a B subunit(Stx1aB) with RDS059 Fab
    • Protein or peptide: Shiga toxin subunit B
    • Protein or peptide: Heavy chain of RDS059 Fab
    • Protein or peptide: Light chain of RDS059 Fab

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Supramolecule #1: Complex of shiga toxin 1a B subunit(Stx1aB) with RDS059 Fab

SupramoleculeName: Complex of shiga toxin 1a B subunit(Stx1aB) with RDS059 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Shiga toxin subunit B

MacromoleculeName: Shiga toxin subunit B / type: protein_or_peptide / ID: 1 / Details: B subunit of Shiga toxin 1a (Stx1a) / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O157:H7 (bacteria)
Molecular weightTheoretical: 7.916908 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SMTPDCVTGK VEYTKYNDDD TFTVKVGDKE LFTNRWNLQS LLLSAQITGM TVTIKTNACH NGGGFSEVIF R

UniProtKB: Shiga toxin subunit B

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Macromolecule #2: Heavy chain of RDS059 Fab

MacromoleculeName: Heavy chain of RDS059 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.159906 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QLQLQESGPG LVKPSETLSL TCTVSGGSIS SSNYFWGWIR QPPGKGLEWI GSFYHSGTIY SSGTTFYSPS LRSRVTISVD TSKNQFSLQ LSSVTAADTA VYYCARDWGR YTPFDPWGHG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QLQLQESGPG LVKPSETLSL TCTVSGGSIS SSNYFWGWIR QPPGKGLEWI GSFYHSGTIY SSGTTFYSPS LRSRVTISVD TSKNQFSLQ LSSVTAADTA VYYCARDWGR YTPFDPWGHG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPK

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Macromolecule #3: Light chain of RDS059 Fab

MacromoleculeName: Light chain of RDS059 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.609887 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QSALTQPPSA SGSPGQSVTV SCTGTSSDVG NYNYVSWYQQ HPGKAPKLMI YEVTKRPSGV PDRFSGSKSG NTASLTVSGL QAEDEADYY CSSYAGSNNR VLFGGGTRLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSALTQPPSA SGSPGQSVTV SCTGTSSDVG NYNYVSWYQQ HPGKAPKLMI YEVTKRPSGV PDRFSGSKSG NTASLTVSGL QAEDEADYY CSSYAGSNNR VLFGGGTRLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPT

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 428491
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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