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- EMDB-41897: Cryo-EM structure of human claudin-4 complex with Clostridium per... -

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Basic information

Entry
Database: EMDB / ID: EMD-41897
TitleCryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-1, and Nanobody (Tight Mask)
Map dataMap from Tight Mask
Sample
  • Complex: Human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-1, and Nanobody
KeywordsClaudin / Fab / Toxin / Nanobody / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsVecchio AJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138368 United States
Citation
Journal: Commun Biol / Year: 2024
Title: Structural and biophysical insights into targeting of claudin-4 by a synthetic antibody fragment
Authors: Erramilli SK / Dominik PK / Ogbu CP / Kossiakoff AA / Vecchio AJ
#1: Journal: bioRxiv / Year: 2023
Title: Cryo-EM structures of a synthetic antibody against 22 kDa claudin-4 reveal its complex with
Authors: Erramilli SK / Dominik PK / Ogbu CP / Kossiakoff AA / Vecchio AJ
History
DepositionSep 11, 2023-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41897.png

Downloads & links

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Map

FileDownload / File: emd_41897.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap from Tight Mask
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 320.4 Å		1.07 Å/pix.
x 300 pix.
= 320.4 Å		1.07 Å/pix.
x 300 pix.
= 320.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.161523 - 3.6349695
Average (Standard dev.)0.00025575308 (±0.016944857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 320.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41897_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_41897_half_map_1.map
Annotationhalf B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_41897_half_map_2.map
Annotationhalf A
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 : Human claudin-4 complex with Clostridium perfringens enterotoxin ...

EntireName: Human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-1, and Nanobody
Components
  • Complex: Human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-1, and Nanobody

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Supramolecule #1: Human claudin-4 complex with Clostridium perfringens enterotoxin ...

SupramoleculeName: Human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-1, and Nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: Assembled complex of 5 proteins (Fab is 2 protein) expressed from insect cells and E coli
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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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

Concentration7 mg/mL
BufferpH: 7.4 / Details: 20 mM Hepes pH 7.4, 100 mM NaCl, and 0.003% LMNG
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5039 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kp4

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1126378
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7kp4


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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