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Yorodumi- PDB-9cmi: Cryo-EM structure of human claudin-4 complex with Clostridium per... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cmi | |||||||||
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Title | Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin, sFab COP-1, and Nanobody | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / claudin / Fab / enterotoxin / nanobody | |||||||||
Function / homology | Function and homology information paracellular transport / 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 / regulation of cell morphogenesis / tight junction / chloride channel activity / positive regulation of wound healing ...paracellular transport / 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 / regulation of cell morphogenesis / tight junction / chloride channel activity / positive regulation of wound healing / renal absorption / chloride channel complex / bicellular tight junction / lateral plasma membrane / 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 | |||||||||
Biological species | Homo sapiens (human) Clostridium perfringens (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
Authors | Vecchio, A.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Cryo-EM Structures of Clostridium perfringens Enterotoxin Bound to its Human Receptor, Claudin-4 Authors: Vecchio, A.J. / Kossiakoff, A.A. / Erramilli, S.K. / Rathnayake, S.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cmi.cif.gz | 213.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cmi.ent.gz | 164.1 KB | Display | PDB format |
PDBx/mmJSON format | 9cmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cmi_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 9cmi_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 9cmi_validation.xml.gz | 47.4 KB | Display | |
Data in CIF | 9cmi_validation.cif.gz | 69.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/9cmi ftp://data.pdbj.org/pub/pdb/validation_reports/cm/9cmi | HTTPS FTP |
-Related structure data
Related structure data | 45749MC 9cmhC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 22234.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLDN4, CPER, CPETR1, WBSCR8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14493 |
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#2: Protein | Mass: 33000.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Trypsin treated CpE / Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01558 |
-Antibody , 3 types, 3 molecules HKL
#3: Antibody | Mass: 28064.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#4: Antibody | Mass: 13175.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#5: Antibody | Mass: 25794.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 2 types, 3 molecules
#6: Chemical | ChemComp-AV0 / |
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#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human claudin-4 complex with Clostridium perfringens enterotoxin, sFab COP-1, and Nanobody Type: COMPLEX / Details: 5-protein complex / Entity ID: #1-#5 / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.12 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: synthetic construct (others) | ||||||||||||||||||||
Source (recombinant) | Organism: synthetic construct (others) | ||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: 20 mM Hepes pH 7.4, 100 mM NaCl, and 0.003% LMNG | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: glow-discharged for 30 seconds at 20 W using a Solarus 950 (Gatan) plasma cleaner Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6774 |
EM imaging optics | Energyfilter name: GIF Bioquantum |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5766325 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 431680 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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