+Open data
-Basic information
Entry | Database: PDB / ID: 7p0z | |||||||||||||||
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Title | 2.43 A Mycobacterium marinum EspB. | |||||||||||||||
Components | ESX-1 secretion-associated protein EspB | |||||||||||||||
Keywords | PROTEIN TRANSPORT / Cryo-EM / EspB / ESX-1 / Preferential orientation | |||||||||||||||
Function / homology | : / ESX-1 secretion-associated protein EspB, PPE domain / ESX-1 secretion-associated protein EspB, PE domain / ESX-1 secreted protein B PE domain / PPE superfamily / extracellular region / ESX-1 secretion-associated protein EspB Function and homology information | |||||||||||||||
Biological species | Mycobacterium marinum (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.43 Å | |||||||||||||||
Authors | Gijsbers, A. / Zhang, Y. / Vinciauskaite, V. / Siroy, A. / Ye, G. / Tria, G. / Mathew, A. / Sanchez-Puig, N. / Lopez-Iglesias, C. / Peters, P.J. / Ravelli, R.B.G. | |||||||||||||||
Funding support | Netherlands, European Union, Mexico, 4items
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Citation | Journal: Curr Res Struct Biol / Year: 2021 Title: Priming mycobacterial ESX-secreted protein B to form a channel-like structure. Authors: Abril Gijsbers / Vanesa Vinciauskaite / Axel Siroy / Ye Gao / Giancarlo Tria / Anjusha Mathew / Nuria Sánchez-Puig / Carmen López-Iglesias / Peter J Peters / Raimond B G Ravelli / Abstract: ESX-1 is a major virulence factor of , a secretion machinery directly involved in the survival of the microorganism from the immune system defence. It disrupts the phagosome membrane of the host cell ...ESX-1 is a major virulence factor of , a secretion machinery directly involved in the survival of the microorganism from the immune system defence. It disrupts the phagosome membrane of the host cell through a contact-dependent mechanism. Recently, the structure of the inner-membrane core complex of the homologous ESX-3 and ESX-5 was resolved; however, the elements involved in the secretion through the outer membrane or those acting on the host cell membrane are unknown. Protein substrates might form this missing element. Here, we describe the oligomerisation process of the ESX-1 substrate EspB, which occurs upon cleavage of its C-terminal region and is favoured by an acidic environment. Cryo-electron microscopy data shows that quaternary structure of EspB is conserved across slow growing species, but not in the fast growing . EspB assembles into a channel with dimensions and characteristics suitable for the transit of ESX-1 substrates, as shown by the presence of another EspB trapped within. Our results provide insight into the structure and assembly of EspB, and suggests a possible function as a structural element of ESX-1. | |||||||||||||||
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 | 7p0z.cif.gz | 291.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p0z.ent.gz | 232.1 KB | Display | PDB format |
PDBx/mmJSON format | 7p0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p0z_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7p0z_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7p0z_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 7p0z_validation.cif.gz | 76.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/7p0z ftp://data.pdbj.org/pub/pdb/validation_reports/p0/7p0z | HTTPS FTP |
-Related structure data
Related structure data | 13153MC 7p13C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 31274.275 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria) Strain: ATCC BAA-535 / M / Gene: espB, MMAR_5457 / Plasmid: pAG10 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HNQ9 |
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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: Heptamer of EspB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.21 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: Mycobacterium marinum (bacteria) / Strain: BAA-535 | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: pAG10 | |||||||||||||||
Buffer solution | pH: 5.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 8.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS Details: Basic direct alignments were done as well as astigmatism and coma alignment using AutoCTF |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: -2000 nm / Nominal defocus min: -1250 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 90 K |
Image recording | Average exposure time: 1.8 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2421 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 5760 / Height: 4092 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 435505 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 45.53 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4XXX Pdb chain-ID: A / Accession code: 4XXX / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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