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- PDB-7muq: Reconstruction of the Legionella pneumophila Dot/Icm T4SS 3DVA Map 1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7muq | |||||||||||||||
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Title | Reconstruction of the Legionella pneumophila Dot/Icm T4SS 3DVA Map 1 | |||||||||||||||
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![]() | TRANSLOCASE / Dot/Icm / Secretion / T4SS | |||||||||||||||
Function / homology | ![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||||||||
![]() | Sheedlo, M.J. / Durie, C.L. / Swanson, M. / Lacy, D.B. / Ohi, M.D. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM reveals new species-specific proteins and symmetry elements in the Dot/Icm T4SS. Authors: Michael J Sheedlo / Clarissa L Durie / Jeong Min Chung / Louise Chang / Jacquelyn Roberts / Michele Swanson / Dana Borden Lacy / Melanie D Ohi / ![]() ![]() Abstract: is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins ... is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 Å resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly, the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 4.7 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 24018MC ![]() 7mucC ![]() 7mudC ![]() 7mueC ![]() 7musC ![]() 7muvC ![]() 7muwC ![]() 7muyC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 9 types, 174 molecules AGGgHgBGBgIgJgCGKgLgDGCgMgAgVGWGEGXGYGZGFGDgGGEgFgHGIGJGKGLG...
#1: Protein | Mass: 107911.891 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 34162.441 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 29729.969 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 17860.678 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 38958.926 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 21096.492 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 27582.047 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 36095.367 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 13598.854 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Unknown protein ... , 2 types, 31 molecules GUHUIUJUKULUMUAUBUCUDUEUFUGXDXHXIXJXKXLXMXVXWXXXYXZXAXBXCXEXFX
#10: Protein/peptide | Mass: 783.958 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein/peptide | Mass: 4103.049 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Details
Sequence details | The protein fragment sequence could not be directly identified as the sample was purified from a ...The protein fragment sequence could not be directly identified as the sample was purified from a native source. |
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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 |
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Sample preparation
Component | Name: Legionella pneumophila Dot/Icm T4SS C1 / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79720 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL |