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- EMDB-80320: CyroEM structure of the complex between Shiga toxin Stx1a B subun... -

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Basic information

Entry
Database: EMDB / ID: EMD-80320
TitleCyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS045
Map data
Sample
  • Complex: Complex of Shiga toxin 1a B subunit and RDS045 Fab
    • Protein or peptide: Shiga toxin subunit B
    • Protein or peptide: Heavy chain of RDS045 Fab
    • Protein or peptide: Light chain of RDS045 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 / host cell Golgi apparatus / extracellular region / Shiga toxin subunit B
Function and homology information
Biological speciesHomo sapiens (human) / Shigella dysenteriae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsChen SD / Li X
Funding support China, 1 items
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 SD / Li X
History
DepositionApr 15, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80320.png

Downloads & links

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Map

FileDownload / File: emd_80320.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.738 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-0.5811936 - 33.709361999999999
Average (Standard dev.)0.006705803 (±0.62411714)
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: #2

Fileemd_80320_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_80320_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Shiga toxin 1a B subunit and RDS045 Fab

EntireName: Complex of Shiga toxin 1a B subunit and RDS045 Fab
Components
  • Complex: Complex of Shiga toxin 1a B subunit and RDS045 Fab
    • Protein or peptide: Shiga toxin subunit B
    • Protein or peptide: Heavy chain of RDS045 Fab
    • Protein or peptide: Light chain of RDS045 Fab

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Supramolecule #1: Complex of Shiga toxin 1a B subunit and RDS045 Fab

SupramoleculeName: Complex of Shiga toxin 1a B subunit and RDS045 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 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Shigella dysenteriae (bacteria)
Molecular weightTheoretical: 8.031012 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTPDCVTGKV EYTKYNDDDT FTVKVGDKEL FTNRWNLQSL LLSAQITGMT VTIKTNACHN GGGFSEVIFR GSG

UniProtKB: Shiga toxin subunit B

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Macromolecule #2: Heavy chain of RDS045 Fab

MacromoleculeName: Heavy chain of RDS045 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.474154 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKTSGYSFT DYYIHWIRQA PGQGLEWMGW INPNSGHTDF AHNFQGRVIM TRDTSISTAS MELSGLTSD DTAVYYCTRV PGITEVDEDF WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
QVQLVQSGAE VKKPGASVKV SCKTSGYSFT DYYIHWIRQA PGQGLEWMGW INPNSGHTDF AHNFQGRVIM TRDTSISTAS MELSGLTSD DTAVYYCTRV PGITEVDEDF WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EP

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Macromolecule #3: Light chain of RDS045 Fab

MacromoleculeName: Light chain of RDS045 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.650344 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EIVLTQSPAT LSLSPGDRAT FSCRASQTVS GYLAWYQQKP GQAPRLLIYD ASNRATGIPA RFSGSGSGTE FTLTISSLEP EDVAVYYCQ HRSNWPLMCT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
EIVLTQSPAT LSLSPGDRAT FSCRASQTVS GYLAWYQQKP GQAPRLLIYD ASNRATGIPA RFSGSGSGTE FTLTISSLEP EDVAVYYCQ HRSNWPLMCT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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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: 8
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 #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 825199
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 825199
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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