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- EMDB-45748: Cryo-EM structure of human claudin-4 complex with Clostridium per... -

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Basic information

Entry
Database: EMDB / ID: EMD-45748
TitleCryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin
Map data
Sample
  • Complex: Human claudin-4 complex with Clostridium perfringens enterotoxin
    • Protein or peptide: Claudin-4
    • Protein or peptide: Heat-labile enterotoxin B chain
Keywordsclaudin / enterotoxin / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of metallopeptidase activity / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / apicolateral plasma membrane / tight junction / regulation of cell morphogenesis / positive regulation of wound healing / renal absorption / chloride channel activity ...positive regulation of metallopeptidase activity / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / apicolateral plasma membrane / tight junction / regulation of cell morphogenesis / positive regulation of wound healing / renal absorption / chloride channel activity / chloride channel complex / lateral plasma membrane / bicellular tight junction / establishment of skin barrier / basal plasma membrane / response to progesterone / female pregnancy / circadian rhythm / transmembrane signaling receptor activity / cell-cell junction / toxin activity / cell adhesion / positive regulation of cell migration / apical plasma membrane / structural molecule activity / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Claudin-4 / Claudin / Claudin, conserved site / Claudin family signature. / Clostridium enterotoxin / Clostridium enterotoxin / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily
Similarity search - Domain/homology
Claudin-4 / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesother entries (others) / Homo sapiens (human) / Clostridium perfringens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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
CitationJournal: To Be Published
Title: Cryo-EM Structures of Clostridium perfringens Enterotoxin Bound to its Human Receptor, Claudin-4
Authors: Vecchio AJ / Kossiakoff AA / Erramilli SK / Rathnayake SS
History
DepositionJul 15, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45748.png

Downloads & links

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Map

FileDownload / File: emd_45748.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 252 pix.
= 326.088 Å		1.29 Å/pix.
x 252 pix.
= 326.088 Å		1.29 Å/pix.
x 252 pix.
= 326.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.19084787 - 0.49007356
Average (Standard dev.)0.0009384884 (±0.009878351)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions252252252
Spacing252252252
CellA=B=C: 326.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45748_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_45748_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 : Human claudin-4 complex with Clostridium perfringens enterotoxin

EntireName: Human claudin-4 complex with Clostridium perfringens enterotoxin
Components
  • Complex: Human claudin-4 complex with Clostridium perfringens enterotoxin
    • Protein or peptide: Claudin-4
    • Protein or peptide: Heat-labile enterotoxin B chain

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

SupramoleculeName: Human claudin-4 complex with Clostridium perfringens enterotoxin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: 2-protein complex
Source (natural)Organism: other entries (others)
Molecular weightTheoretical: 55 KDa

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Macromolecule #1: Claudin-4

MacromoleculeName: Claudin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.234332 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GSMASMGLQV MGIALAVLGW LAVMLCCALP MWRVTAFIGS NIVTSQTIWE GLWMNCVVQS TGQMQCKVYD SLLALPQDLQ AARALVIIS IIVAALGVLL SVVGGKCTNC LEDESAKAKT MIVAGVVFLL AGLMVIVPVS WTAHNIIQDF YNPLVASGQK R EMGASLYV ...String:
GSMASMGLQV MGIALAVLGW LAVMLCCALP MWRVTAFIGS NIVTSQTIWE GLWMNCVVQS TGQMQCKVYD SLLALPQDLQ AARALVIIS IIVAALGVLL SVVGGKCTNC LEDESAKAKT MIVAGVVFLL AGLMVIVPVS WTAHNIIQDF YNPLVASGQK R EMGASLYV GWAASGLLLL GGGLLCCNCP PRTDKPYSAK YSAARSAAAS NYV

UniProtKB: Claudin-4

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Macromolecule #2: Heat-labile enterotoxin B chain

MacromoleculeName: Heat-labile enterotoxin B chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 33.000582 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: TPINITNSNS NLSDGLYVID KGDGWILGEP SVVSSQILNP NETGTFSQSL TKSKEVSINV NFSVGFTSEF IQASVEYGFG ITIGEQNTI ERSVSTTAGP NEYVYYKVYA TYRKYQAIRI SHGNISDDGS IYKLTGIWLS KTSADSLGNI DQGSLIETGE R CVLTVPST ...String:
TPINITNSNS NLSDGLYVID KGDGWILGEP SVVSSQILNP NETGTFSQSL TKSKEVSINV NFSVGFTSEF IQASVEYGFG ITIGEQNTI ERSVSTTAGP NEYVYYKVYA TYRKYQAIRI SHGNISDDGS IYKLTGIWLS KTSADSLGNI DQGSLIETGE R CVLTVPST DIEKEILDLA AATERLNLTD ALNSNPAGNL YDWRSSNSYP WTQKLNLHLT ITATGQKYRI LASKIVDFNI YS NNFNNLV KLEQSLGDGV KDHYVDISLD AGQYVLVMKA NSSYSGNYPY SILFQKFGLV PR

UniProtKB: Heat-labile enterotoxin B chain

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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

Concentration8.0 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHepes pH 7.4
100.0 mMNaClNaCl
0.003 %LMNG

Details: 20 mM Hepes pH 7.4, 100 mM NaCl, and 0.003% LMNG
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
Details: glow-discharged for 60 seconds at 15 mA using a Pelco easiGlow (Ted Pella Inc) instrument.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7100 / 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 129000
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

Particle selectionNumber selected: 2504188
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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 44683
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7kp4

source_name: PDB, initial_model_type: experimental model

8u5f

source_name: PDB, initial_model_type: experimental model
SoftwareName: UCSF Chimera
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9cmh:
Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin

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