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- EMDB-52864: CryoEM structure of a synthetic antibody, COP-2, in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52864
TitleCryoEM structure of a synthetic antibody, COP-2, in complex with the C-terminal domain of Clostridium perfringens Enterotoxin
Map data
Sample
  • Complex: Complex of synthetic antibody COP-2 and the C-terminal domain of Clostridium perfringens Enterotoxin
    • Protein or peptide: Heat-labile enterotoxin B chain
    • Protein or peptide: COP-2 antibody heavy chain
    • Protein or peptide: COP-2 antibody light chain
Keywordsclostridium / COP-2 / toxin
Function / homologyClostridium enterotoxin / Clostridium enterotoxin / toxin activity / extracellular region / Heat-labile enterotoxin B chain
Function and homology information
Biological speciesClostridium perfringens (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsPacesa M / Goldbach N / Vecchio AJ / Correia BE
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: CryoEM structure of synthetic antibody, COP-2, in complex with the C-terminal domain of Clostridium perfringens Enterotoxin
Authors: Goldbach N / Ogbu CP / Kapoor S / Pacesa M / Correia BE / Vecchio AJ
History
DepositionFeb 21, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52864.png

Downloads & links

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Map

FileDownload / File: emd_52864.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 420 pix.
= 239.4 Å		0.57 Å/pix.
x 420 pix.
= 239.4 Å		0.57 Å/pix.
x 420 pix.
= 239.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0506
Minimum - Maximum-0.11950238 - 0.266405
Average (Standard dev.)0.000050643863 (±0.0051255617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 239.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52864_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52864_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_52864_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of synthetic antibody COP-2 and the C-terminal domain of ...

EntireName: Complex of synthetic antibody COP-2 and the C-terminal domain of Clostridium perfringens Enterotoxin
Components
  • Complex: Complex of synthetic antibody COP-2 and the C-terminal domain of Clostridium perfringens Enterotoxin
    • Protein or peptide: Heat-labile enterotoxin B chain
    • Protein or peptide: COP-2 antibody heavy chain
    • Protein or peptide: COP-2 antibody light chain

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Supramolecule #1: Complex of synthetic antibody COP-2 and the C-terminal domain of ...

SupramoleculeName: Complex of synthetic antibody COP-2 and the C-terminal domain of Clostridium perfringens Enterotoxin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium perfringens (bacteria)

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Macromolecule #1: Heat-labile enterotoxin B chain

MacromoleculeName: Heat-labile enterotoxin B chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 15.114945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTDIEKEIL DLAAATERLN LTDALNSNPA GNLYDWRSSN SYPWTQKLNL HLTITATGQK YRILASKIVD FNIYSNNFNN LVKLEQSLG DGVKDHYVDI SLDAGQYVLV MKANSSYSGN YPYSILFQKF GLVPR

UniProtKB: Heat-labile enterotoxin B chain

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Macromolecule #2: COP-2 antibody heavy chain

MacromoleculeName: COP-2 antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 27.79908 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFNFSSSSI HWVRQAPGKG LEWVASISSY SGYTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARYWSWY NSSHYIYSAL DYWGQGTLVT VSSASTKGPS V FPLAPSSK ...String:
MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFNFSSSSI HWVRQAPGKG LEWVASISSY SGYTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARYWSWY NSSHYIYSAL DYWGQGTLVT VSSASTKGPS V FPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HK PSNTKVD KKVEPKSCDK THT

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Macromolecule #3: COP-2 antibody light chain

MacromoleculeName: COP-2 antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.053135 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKKNIAFLLA SMFVFSIATN AYASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQSYEWA PVTFGQGTKV EIKRTVAAPS VFIFPPSDSQ LKSGTASVVC L LNNFYPRE ...String:
MKKNIAFLLA SMFVFSIATN AYASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQSYEWA PVTFGQGTKV EIKRTVAAPS VFIFPPSDSQ LKSGTASVVC L LNNFYPRE AKVQWKVDNA LQSGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87280
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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