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Yorodumi- PDB-7yl9: Cryo-EM structure of complete transmembrane channel E289A mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yl9 | |||||||||
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Title | Cryo-EM structure of complete transmembrane channel E289A mutant Vibrio cholerae Cytolysin | |||||||||
Components | Hemolysin | |||||||||
Keywords | TOXIN / Vibrio cholerae Cytolysin (VCC) / Pore forming toxin (PFT) / cryo-EM / membrane / transmembrane channel / mutant PFT | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Mondal, A.K. / Sengupta, N. / Singh, M. / Biswas, R. / Lata, K. / Lahiri, I. / Dutta, S. / Chattopadhyay, K. | |||||||||
Funding support | India, 2items
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Citation | Journal: J.Biol.Chem. Title: Cryo-EM structure of complete transmembrane channel E289A mutant Vibrio cholerae Cytolysin Authors: Mondal, A.K. / Sengupta, N. / Singh, M. / Biswas, R. / Lata, K. / Lahiri, I. / Dutta, S. / Chattopadhyay, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yl9.cif.gz | 674.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yl9.ent.gz | 565.2 KB | Display | PDB format |
PDBx/mmJSON format | 7yl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/7yl9 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/7yl9 | HTTPS FTP |
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-Related structure data
Related structure data | 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
#1: Protein | Mass: 65717.258 Da / Num. of mol.: 7 / Mutation: E289A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: hlyA_3, hlyA_2, D6U24_17690, ERS013199_02025, ERS013202_03387 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H6SZL4 |
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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: Liposome embedded form of complete transmembrane channel VCC with E289A mutation Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 7500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42124 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||
Atomic model building | PDB-ID: 3O44 |