+Open data
-Basic information
Entry | Database: PDB / ID: 6rju | ||||||
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Title | C-terminal domain of TssA protein from T6SS of Escherichia coli. | ||||||
Components | Putative type VI secretion protein | ||||||
Keywords | TRANSPORT PROTEIN / T6SS / E. coli / TssA / cap | ||||||
Function / homology | Type VI secretion system-associated, VCA0119 / Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A0119, VasJ / ImpA, N-terminal / ImpA, N-terminal, type VI secretion system / Putative type VI secretion protein Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Nazarov, S. / Shneider, M. / Basler, M. / Leiman, P. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of TssA protein from Type VI secretion system of E. coli. Authors: Nazarov, S. / Demurtas, D. / Shneider, M. / Basler, M. / Leiman, P. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6rju.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rju.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rju_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6rju_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6rju_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 6rju_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/6rju ftp://data.pdbj.org/pub/pdb/validation_reports/rj/6rju | HTTPS FTP |
-Related structure data
Related structure data | 4906MUC M: map data used to model this data U: unfit; in different coordinate system*YM C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 59159.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NCTC12950_00920 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A376XSV1 |
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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: C-terminal domain of T6SS protein TssA. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.634 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: Leica EM GP2 |
-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 / Cs: 2.7 mm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3269 |
EM imaging optics | Energyfilter name: GIF Quantum LS |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 667861 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: D6 (2x6 fold dihedral) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52370 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4YO5 Pdb chain-ID: A / Pdb chain residue range: 388-474 |