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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: To Be Published
Title: Multivalent Nanobodies for Potent and Broad Neutralization of Staphylococcus aureus Toxins
Authors: Kim J / Huang W / Shi Y
History
DepositionAug 27, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 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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