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

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Basic information

Entry
Database: PDB / ID: 25rg
TitleCyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS045
Components
  • Heavy chain of RDS045 Fab
  • Light chain of RDS045 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 / host cell Golgi apparatus / extracellular region / Shiga toxin subunit B
Function and homology information
Biological speciesShigella dysenteriae (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsChen, S.D. / Li, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising RDS045(pentamer)
Authors: Chen, S.D. / Li, X.
History
DepositionApr 15, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shiga toxin subunit B
B: Heavy chain of RDS045 Fab
C: Light chain of RDS045 Fab
D: Shiga toxin subunit B
H: Heavy chain of RDS045 Fab
L: Light chain of RDS045 Fab
E: Shiga toxin subunit B
I: Heavy chain of RDS045 Fab
M: Light chain of RDS045 Fab
F: Shiga toxin subunit B
J: Heavy chain of RDS045 Fab
N: Light chain of RDS045 Fab
G: Shiga toxin subunit B
K: Heavy chain of RDS045 Fab
O: Light chain of RDS045 Fab


Theoretical massNumber of molelcules
Total (without water)275,77815
Polymers275,77815
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: 8031.012 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella dysenteriae (bacteria) / Gene: stxB, SDY_1390 / Production host: Escherichia coli (E. coli) / References: UniProt: Q32GM0
#2: Antibody
Heavy chain of RDS045 Fab


Mass: 23474.154 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 RDS045 Fab


Mass: 23650.344 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 and RDS045 Fab / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 8
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
IDNameVersionCategoryImage processing-ID
1cryoSPARCparticle selection1
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction1
14cryoSPARCparticle selection2
19cryoSPARC3D reconstruction2
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.5FSC 0.143 CUT-OFF825199125RGPOINT
22.5FSC 0.143 CUT-OFF825199125RGPOINT
32.5FSC 0.143 CUT-OFF825199225RGPOINT
42.5FSC 0.143 CUT-OFF825199225RGPOINT
RefinementHighest resolution: 2.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00419805
ELECTRON MICROSCOPYf_angle_d0.56226955
ELECTRON MICROSCOPYf_dihedral_angle_d11.7017055
ELECTRON MICROSCOPYf_chiral_restr0.0453065
ELECTRON MICROSCOPYf_plane_restr0.0053460

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