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- EMDB-41915: Cryo-EM structure of human claudin-4 complex with Clostridium per... -

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Basic information

Entry
Database: EMDB / ID: EMD-41915
TitleCryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain and sFab COP-1
Map data
Sample
  • Complex: Human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain and sFab COP-1
    • Protein or peptide: Claudin-4CLDN4
    • Protein or peptide: Heat-labile enterotoxin B chain
    • Protein or peptide: COP-1 sFab Light Chain
    • Protein or peptide: COP-1 sFab Heavy Chain
  • Ligand: Lauryl Maltose Neopentyl Glycol
KeywordsClaudin / Fab / Toxin / 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 / apicolateral plasma membrane / bicellular tight junction assembly / regulation of cell morphogenesis / tight junction / chloride channel activity / positive regulation of wound healing / renal absorption ...positive regulation of metallopeptidase activity / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / apicolateral plasma membrane / bicellular tight junction assembly / regulation of cell morphogenesis / tight junction / chloride channel activity / positive regulation of wound healing / renal absorption / chloride channel complex / lateral plasma membrane / bicellular tight junction / establishment of skin barrier / basal plasma membrane / response to progesterone / female pregnancy / circadian rhythm / cell-cell junction / transmembrane signaling receptor activity / 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 speciesHomo sapiens (human) / Clostridium perfringens (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 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: To be published
Title: Cryo-EM structures of a synthetic antibody against 22 kDa claudin-4 reveal its complex with Clostridium perfringens enterotoxin
Authors: 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 12, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41915.png

Downloads & links

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Map

FileDownload / File: emd_41915.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.507 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.031891707 - 0.08482177
Average (Standard dev.)0.00014671533 (±0.003031392)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 259.584 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41915_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41915_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: #1

Fileemd_41915_half_map_2.map
Projections & Slices
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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 and sFab COP-1
Components
  • Complex: Human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain and sFab COP-1
    • Protein or peptide: Claudin-4CLDN4
    • Protein or peptide: Heat-labile enterotoxin B chain
    • Protein or peptide: COP-1 sFab Light Chain
    • Protein or peptide: COP-1 sFab Heavy Chain
  • Ligand: Lauryl Maltose Neopentyl Glycol

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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 and sFab COP-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Assembled complex of 4 proteins (Fab is 2 proteins) expressed from insect cells and E coli
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 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: 22.613852 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASMGLQVMG IALAVLGWLA VMLCCALPMW RVTAFIGSNI VTSQTIWEGL WMNCVVQSTG QMQCKVYDSL LALPQDLQAA RALVIISII VAALGVLLSV VGGKCTNCLE DESAKAKTMI VAGVVFLLAG LMVIVPVSWT AHNIIQDFYN PLVASGQKRE M GASLYVGW ...String:
MASMGLQVMG IALAVLGWLA VMLCCALPMW RVTAFIGSNI VTSQTIWEGL WMNCVVQSTG QMQCKVYDSL LALPQDLQAA RALVIISII VAALGVLLSV VGGKCTNCLE DESAKAKTMI VAGVVFLLAG LMVIVPVSWT AHNIIQDFYN PLVASGQKRE M GASLYVGW AASGLLLLGG GLLCCNCPPR TDKPYSAKYS AARSAAASNY VGLVPR

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: 14.044594 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GSDEILDLAA ATERLNLTDA LNSNPAGNLY DWRSSNSYPW TQKLNLHLTI TATGQKYRIL ASKIVDFNIY SNNFNNLVKL EQSLGDGVK DHYVDISLDA GQYVLVMKAN SSYSGNYPYS ILFQKF

UniProtKB: Heat-labile enterotoxin B chain

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Macromolecule #3: COP-1 sFab Light Chain

MacromoleculeName: COP-1 sFab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.258783 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: COP-1 sFab Heavy Chain

MacromoleculeName: COP-1 sFab Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 28.064498 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFNFSSSYI HWVRQAPGKG LEWVASISSS SGSTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARWFHPW WWWEYLFRGA IDYWGQGTLV TVSSASTKGP S VFPLAPSS ...String:
MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFNFSSSYI HWVRQAPGKG LEWVASISSS SGSTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARWFHPW WWWEYLFRGA IDYWGQGTLV TVSSASTKGP S VFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NH KPSNTKV DKKVEPKSCD KTHT

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Macromolecule #5: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 5 / Number of copies: 1 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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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

Concentration6 mg/mL
BufferpH: 7.4 / Details: 20 mM Hepes pH 7.4, 100 mM NaCl, and 0.003% LMNG
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 92000
Specialist opticsEnergy filter - Name: GIF Bioquantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1073 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 37586
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kp4

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 37296
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
Output model

PDB-8u5b:
Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain and sFab COP-1

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