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Yorodumi- PDB-6x6l: Cryo-EM Structure of CagX and CagY within the dCag3 Helicobacter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x6l | ||||||||||||||||||||||||
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Title | Cryo-EM Structure of CagX and CagY within the dCag3 Helicobacter pylori PR | ||||||||||||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / T4SS / Secretion | ||||||||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||||||||
Biological species | Helicobacter pylori (bacteria) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||||||||||||||
Authors | Sheedlo, M.J. / Chung, J.M. / Sawhney, N. / Durie, C.L. / Cover, T.L. / Ohi, M.D. / Lacy, D.B. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Elife / Year: 2020 Title: Cryo-EM reveals species-specific components within the Cag type IV secretion system core complex. Authors: Michael J Sheedlo / Jeong Min Chung / Neha Sawhney / Clarissa L Durie / Timothy L Cover / Melanie D Ohi / D Borden Lacy / Abstract: The pathogenesis of -associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The Cag T4SS includes a large membrane-spanning core ...The pathogenesis of -associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The Cag T4SS includes a large membrane-spanning core complex containing five proteins, organized into an outer membrane cap (OMC), a periplasmic ring (PR) and a stalk. Here, we report cryo-EM reconstructions of a core complex lacking Cag3 and an improved map of the wild-type complex. We define the structures of two unique species-specific components (Cag3 and CagM) and show that Cag3 is structurally similar to CagT. Unexpectedly, components of the OMC are organized in a 1:1:2:2:5 molar ratio (CagY:CagX:CagT:CagM:Cag3). CagX and CagY are components of both the OMC and the PR and bridge the symmetry mismatch between these regions. These results reveal that assembly of the T4SS core complex is dependent on incorporation of interwoven species-specific components. | ||||||||||||||||||||||||
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 | 6x6l.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6x6l.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6x6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x6l_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6x6l_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6x6l_validation.xml.gz | 137.3 KB | Display | |
Data in CIF | 6x6l_validation.cif.gz | 201.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/6x6l ftp://data.pdbj.org/pub/pdb/validation_reports/x6/6x6l | HTTPS FTP |
-Related structure data
Related structure data | 22077MC 6x6jC 6x6kC 6x6sC 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: 60607.324 Da / Num. of mol.: 17 / Source method: isolated from a natural source Source: (natural) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / References: UniProt: O25263 #2: Protein | Mass: 219748.641 Da / Num. of mol.: 17 / Source method: isolated from a natural source Source: (natural) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / References: UniProt: O25262 Has protein modification | 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: Helicobacter pylori dCag3 Cag T4SS PR / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Helicobacter pylori (bacteria) |
Buffer solution | pH: 7 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 59.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10477 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.9 Å2 | ||||||||||||||||||||||||
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