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- EMDB-72377: Staphylococcal Enterotoxin C in complex with NB C107 and NB C112 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72377
TitleStaphylococcal Enterotoxin C in complex with NB C107 and NB C112
Map data
Sample
  • Complex: HSA-nb33-nb77-nb125-N42 complex
    • Protein or peptide: Enterotoxin type C-2
    • Protein or peptide: NB C107
    • Protein or peptide: NB C112
  • Ligand: ZINC ION
KeywordsNanobody / VHH / IMMUNE SYSTEM
Function / homology
Function and homology information


toxin activity / extracellular region / metal ion binding
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / Enterotoxin
Similarity search - Domain/homology
Enterotoxin type C-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Staphylococcus aureus (bacteria) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHang W / Kim J / Taylor DJ / Shi Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM154832 United States
CitationJournal: Nat Commun / Year: 2026
Title: Multivalent nanobodies for potent and broad neutralization of Staphylococcus aureus toxins.
Authors: Yong Joon Jeffrey Kim / Nicholas R Walton / Wei Huang / Madison Lee / Yufei Xiang / Zhe Sang / Chaya Sussman / Sarah K L Moore / Derek J Taylor / Kong Chen / Jaime L Hook / John K McCormick / Yi Shi /
Abstract: Staphylococcus aureus is a leading cause of lethal bacteremia and pneumonia, which are driven by potent virulence factors such as T-cell superantigens and alpha hemolysin. S. aureus has among the ...Staphylococcus aureus is a leading cause of lethal bacteremia and pneumonia, which are driven by potent virulence factors such as T-cell superantigens and alpha hemolysin. S. aureus has among the highest rates of antibiotic resistance, yet no vaccines or alternative therapies are available. Here, we developed a repertoire of potent, high-affinity nanobodies (Nbs) targeting key toxins in S. aureus infection, including Hla and superantigens SEB, SEC, and TSST-1. Comprehensive cryo-EM and AlphaFold3 analyses of these Nbs, which were elicited with clinical cocktail vaccines, revealed diverse neutralizing epitopes and mechanisms that provide insights for immunotherapy and vaccine strategies. Guided by these findings, we engineered stable, multivalent, and multifunctional Nb constructs. These constructs included an aerosolizable trimeric Nb with enhanced neutralization activity against Hla and SEC, and a decameric Nb-IgG-Fc fusion construct with pM or better potencies against a wide range of major toxins in S. aureus sepsis (SEB, SEC, TSST-1, and Hla). These multifunctional Nbs demonstrated protective activity in murine models of pneumonia and sepsis, underscoring their potential as versatile immunotherapies that address the complex virulence of S. aureus. Our work lays a foundation for precision immunotherapies beyond current treatment options to combat complex bacterial infections with multiple virulence mechanisms.
History
DepositionAug 27, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72377.png

Downloads & links

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Map

FileDownload / File: emd_72377.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.52769184 - 0.9012732
Average (Standard dev.)-0.00006460184 (±0.016515251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72377_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72377_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 : HSA-nb33-nb77-nb125-N42 complex

EntireName: HSA-nb33-nb77-nb125-N42 complex
Components
  • Complex: HSA-nb33-nb77-nb125-N42 complex
    • Protein or peptide: Enterotoxin type C-2
    • Protein or peptide: NB C107
    • Protein or peptide: NB C112
  • Ligand: ZINC ION

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Supramolecule #1: HSA-nb33-nb77-nb125-N42 complex

SupramoleculeName: HSA-nb33-nb77-nb125-N42 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Enterotoxin type C-2

MacromoleculeName: Enterotoxin type C-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 27.278646 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PDPTPDELHK SSEFTGTMGN MKYLYDDHYV SATKVMSVDK FLAHDLIYNI SDKKLKNYDK VKTELLNEDL AKKYKDEVVD VYGSNYYVN CYFSSKDNVG KVTGGKTCMY GGITKHEGNH FDNGNLQNVL IRVYENKRNT ISFEVQTDKK SVTAQELDIK A RNFLINKK ...String:
PDPTPDELHK SSEFTGTMGN MKYLYDDHYV SATKVMSVDK FLAHDLIYNI SDKKLKNYDK VKTELLNEDL AKKYKDEVVD VYGSNYYVN CYFSSKDNVG KVTGGKTCMY GGITKHEGNH FDNGNLQNVL IRVYENKRNT ISFEVQTDKK SVTAQELDIK A RNFLINKK NLYEFNSSPY ETGYIKFIEN NGNTFWYDMM PAPGDKFDQS KYLMMYNDNK TVDSKSVKIE VHLTTKNG

UniProtKB: Enterotoxin type C-2

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Macromolecule #2: NB C107

MacromoleculeName: NB C107 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.440784 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG LVQPGGSLRL SCAPSGSTSG IYASGWYRQV PGKPQEWLAD ISRGGSTKYA DSVKGRFTIS RDNAKNTVYL QMNSLKPED TATYYCRVID TLGAEYRGQG TQVTVSS

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Macromolecule #3: NB C112

MacromoleculeName: NB C112 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.691323 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCTASERMYG IEMGWFRQAP GKERELVAAI TWSGVVSHLQ ESVKGRFTIS RDNPKKTVYL QMNSLKPED TATYYCAGHR LQWASGYTRH DYGSWGQGTQ VTVSS

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 189726
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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