+Open data
-Basic information
Entry | Database: PDB / ID: 6x64 | ||||||||||||||||||||||||
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Title | Legionella pneumophila Dot T4SS PR | ||||||||||||||||||||||||
Components | Type IV secretion system unknown protein fragment | ||||||||||||||||||||||||
Keywords | PROTEIN TRANSPORT / Secretion / Dot | ||||||||||||||||||||||||
Biological species | Legionella pneumophila (bacteria) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||||||||
Authors | Durie, C.L. / Sheedlo, M.J. / Chung, J.M. / Byrne, B.G. / Su, M. / Knight, T. / Swanson, M.S. / Lacy, D.B. / Ohi, M.D. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Elife / Year: 2020 Title: Structural analysis of the Dot/Icm type IV secretion system core complex. Authors: Clarissa L Durie / Michael J Sheedlo / Jeong Min Chung / Brenda G Byrne / Min Su / Thomas Knight / Michele Swanson / D Borden Lacy / Melanie D Ohi / Abstract: is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires' Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver ... is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires' Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver effector proteins into host cells. Compared to prototypical T4SSs, the Dot/Icm assembly is much larger, containing ~27 different components including a core complex reported to be composed of five proteins: DotC, DotD, DotF, DotG, and DotH. Using single particle cryo-electron microscopy (cryo-EM), we report reconstructions of the core complex of the Dot/Icm T4SS that includes a symmetry mismatch between distinct structural features of the outer membrane cap (OMC) and periplasmic ring (PR). We present models of known core complex proteins, DotC, DotD, and DotH, and two structurally similar proteins within the core complex, DotK and Lpg0657. This analysis reveals the stoichiometry and contact interfaces between the key proteins of the Dot/Icm T4SS core complex and provides a framework for understanding a complex molecular machine. | ||||||||||||||||||||||||
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 | 6x64.cif.gz | 429 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x64.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6x64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x64_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6x64_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6x64_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 6x64_validation.cif.gz | 87.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/6x64 ftp://data.pdbj.org/pub/pdb/validation_reports/x6/6x64 | HTTPS FTP |
-Related structure data
Related structure data | 22069MC 6x62C 6x65C 6x66C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 28102.492 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) Sequence details | The authors state that the sequences are unknown. The sample was imaged from a purification that ...The authors state that the sequences are unknown. The sample was imaged from a purification that was derived directly from L. pneumophila and the polymer chains could not be identified. | |
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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: Legionella pneumophila Dot T4SS PR / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Legionella pneumophila (bacteria) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 58.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 771806 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C18 (18 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6850 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.71 Å2 | ||||||||||||||||||||||||
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