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Yorodumi- PDB-7b9f: Structure of the mycobacterial ESX-5 Type VII Secretion System he... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b9f | ||||||
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Title | Structure of the mycobacterial ESX-5 Type VII Secretion System hexameric pore complex | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Mycobacterial ESX-5 Type VII Secretion System | ||||||
Function / homology | Function and homology information hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium xenopi RIVM700367 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Chojnowski, G. / Ritter, C. / Beckham, K.S.H. / Mullapudi, E. / Rettel, M. / Savitski, M.M. / Mortensen, S.A. / Ziemianowicz, D. / Kosinski, J. / Wilmanns, M. | ||||||
Citation | Journal: Sci Adv / Year: 2021 Title: Structure of the mycobacterial ESX-5 type VII secretion system pore complex. Authors: Katherine S H Beckham / Christina Ritter / Grzegorz Chojnowski / Daniel S Ziemianowicz / Edukondalu Mullapudi / Mandy Rettel / Mikhail M Savitski / Simon A Mortensen / Jan Kosinski / Matthias Wilmanns / Abstract: The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation ...The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation machinery and the composition of the central secretion pore have remained unknown. Here, we present the high-resolution structure of the 2.1-megadalton ESX-5 core complex. Our structure captured a dynamic, secretion-competent conformation of the pore within a well-defined transmembrane section, sandwiched between two flexible protein layers at the cytosolic entrance and the periplasmic exit. We propose that this flexibility endows the ESX-5 machinery with large conformational plasticity required to accommodate targeted protein secretion. Compared to known secretion systems, a highly dynamic state of the pore may represent a fundamental principle of bacterial secretion machineries. | ||||||
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 | 7b9f.cif.gz | 300.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b9f.ent.gz | 214.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/7b9f ftp://data.pdbj.org/pub/pdb/validation_reports/b9/7b9f | HTTPS FTP |
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-Related structure data
Related structure data | 12103MC 7b7jC 7b9sC 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
#1: Protein | Mass: 44469.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium xenopi RIVM700367 (bacteria) Gene: MXEN_09224 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: I0RST0 | ||||
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#2: Protein | Mass: 53399.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium xenopi RIVM700367 (bacteria) Gene: MXEN_09214 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: I0RSS8 #3: Protein | | Mass: 152946.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium xenopi RIVM700367 (bacteria) Gene: MXEN_04114 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: I0RZI0 #4: Protein | | Mass: 53226.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium xenopi RIVM700367 (bacteria) Gene: MXEN_04109 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: I0RZH9 |
-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: Protomeric unit of the hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 0.357 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Mycobacterium xenopi RIVM700367 (bacteria) / Cellular location: membrane | ||||||||||||
Source (recombinant) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||||||||
Buffer solution | pH: 8 | ||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 283 K |
-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 FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 49.34 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 27873 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 731844 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL Details: Initial model was build into the map using ARP/wARP 8.1 web-service. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7B7J Accession code: 7B7J / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 128.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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