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Yorodumi- PDB-7ovb: L. pneumophila Type IV Coupling Complex (T4CC) with density for D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ovb | |||||||||
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Title | L. pneumophila Type IV Coupling Complex (T4CC) with density for DotY N-terminal and middle domains | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Type IV Coupling Complex / T4CC / Type IV Secretion System / T4SS / Membrane protein complex / Membrane complex / DotY / DotZ / DotL / DotM / DotN / IcmSW / Legionella | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.61 Å | |||||||||
Authors | Mace, K. / Meir, A. / Lukoyanova, N. / Waksman, G. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Mol Microbiol / Year: 2022 Title: Proteins DotY and DotZ modulate the dynamics and localization of the type IVB coupling complex of Legionella pneumophila. Authors: Kevin Macé / Amit Meir / Natalya Lukoyanova / Luying Liu / David Chetrit / Manuela K Hospenthal / Craig R Roy / Gabriel Waksman / Abstract: Legionella pneumophila is an opportunistic pathogen infecting alveolar macrophages and protozoa species. Legionella utilizes a Type IV Secretion System (T4SS) to translocate over 300 effector ...Legionella pneumophila is an opportunistic pathogen infecting alveolar macrophages and protozoa species. Legionella utilizes a Type IV Secretion System (T4SS) to translocate over 300 effector proteins into its host cell. In a recent study, we have isolated and solved the cryo-EM structure of the Type IV Coupling Complex (T4CC), a large cytoplasmic determinant associated with the inner membrane that recruits effector proteins for delivery to the T4SS for translocation. The T4CC is composed of a DotLMNYZ hetero-pentameric core from which the flexible IcmSW module flexibly protrudes. The DotY and DotZ proteins were newly reported members of this complex and their role remained elusive. In this study, we observed the effect of deleting DotY and DotZ on T4CC stability and localization. Furthermore, we found these two proteins are co-dependent, whereby the deletion of DotY resulted in DotZ absence from the coupling complex, and vice versa. Additional cryo-EM data analysis revealed the dynamic movement of the IcmSW module is modified by the DotY/Z proteins. We therefore determined the likely function of DotY and DotZ and revealed their importance on T4CC function. | |||||||||
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 | 7ovb.cif.gz | 260.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ovb.ent.gz | 201.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ovb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ovb_validation.pdf.gz | 904.1 KB | Display | wwPDB validaton report |
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Full document | 7ovb_full_validation.pdf.gz | 939.8 KB | Display | |
Data in XML | 7ovb_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 7ovb_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/7ovb ftp://data.pdbj.org/pub/pdb/validation_reports/ov/7ovb | HTTPS FTP |
-Related structure data
Related structure data | 13083MC 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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1 |
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-Components
-Protein , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 87600.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Gene: icmO, lpg0446 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZYC6 |
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#2: Protein | Mass: 43858.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Gene: icmP, lpg0445 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZYC7 |
#3: Protein | Mass: 23762.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Gene: icmJ, lpg0455 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZYB7 |
#4: Protein | Mass: 33887.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Gene: lpg1549 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZV91 |
#5: Protein | Mass: 25550.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Gene: lpg0294 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZYR7 |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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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: T4CC pentameric core complex with DotY middle domain / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL |
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Source (natural) | Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) |
Source (recombinant) | Organism: Legionella pneumophila (bacteria) |
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: 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: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 183397 / Symmetry type: POINT |