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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24005 | |||||||||||||||
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Title | Legionella pneumophila Dot/Icm T4SS OMC | |||||||||||||||
![]() | Reconstruction of the Legionella pneumophila Dot/Icm T4SS OMC | |||||||||||||||
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Function / homology | ![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
![]() | Sheedlo MJ / Durie CL / Swanson M / Lacy DB / Ohi MD | |||||||||||||||
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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 44.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
Images | ![]() | 83.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mudMC ![]() 7mucC ![]() 7mueC ![]() 7muqC ![]() 7musC ![]() 7muvC ![]() 7muwC ![]() 7muyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of the Legionella pneumophila Dot/Icm T4SS OMC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Legionella pneumophila Dot/Icm T4SS OMC
+Supramolecule #1: Legionella pneumophila Dot/Icm T4SS OMC
+Macromolecule #1: DotC
+Macromolecule #2: DotD
+Macromolecule #3: Type IV secretion protein IcmK
+Macromolecule #4: Inner membrane lipoprotein YiaD
+Macromolecule #5: Outer membrane protein, OmpA family protein
+Macromolecule #6: DUF2807 domain-containing protein
+Macromolecule #7: Neurogenic locus notch
+Macromolecule #8: Unknown protein fragment
+Macromolecule #9: DotF
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84886 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7mud: |