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Yorodumi- PDB-2mme: Hybrid structure of the Shigella flexneri MxiH Type three secreti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mme | ||||||
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Title | Hybrid structure of the Shigella flexneri MxiH Type three secretion system needle | ||||||
Components | MxiH | ||||||
Keywords | PROTEIN TRANSPORT / type-three secretion system / filamentous protein / helical assembly / Shigella flexneri / protein translocation / hybrid methods / Rosetta | ||||||
Function / homology | Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / type III protein secretion system complex / protein secretion by the type III secretion system / : / MxiH Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | SOLID-STATE NMR / ELECTRON MICROSCOPY / helical reconstruction / Rosetta fold-and-dock, Rosetta symmetric relax / cryo EM / Resolution: 7.7 Å | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Demers, J.P. / Habenstein, B. / Loquet, A. / Vasa, S.K. / Becker, S. / Baker, D. / Lange, A. / Sgourakis, N.G. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms. Authors: Takashi Fujii / Martin Cheung / Amandine Blanco / Takayuki Kato / Ariel J Blocker / Keiichi Namba / Abstract: Type III secretion systems of Gram-negative bacteria form injection devices that deliver effector proteins into eukaryotic cells during infection. They span both bacterial membranes and the ...Type III secretion systems of Gram-negative bacteria form injection devices that deliver effector proteins into eukaryotic cells during infection. They span both bacterial membranes and the extracellular space to connect with the host cell plasma membrane. Their extracellular portion is a needle-like, hollow tube that serves as a secretion conduit for effector proteins. The needle of Shigella flexneri is approximately 50-nm long and 7-nm thick and is made by the helical assembly of one protein, MxiH. We provide a 7-Å resolution 3D image reconstruction of the Shigella needle by electron cryomicroscopy, which resolves α-helices and a β-hairpin that has never been observed in the crystal and solution structures of needle proteins, including MxiH. An atomic model of the needle based on the 3D-density map, in comparison with that of the bacterial-flagellar filament, provides insights into how such a thin tubular structure is stably assembled by intricate intermolecular interactions. The map also illuminates how the needle-length control protein functions as a ruler within the central channel during export of MxiH for assembly at the distal end of the needle, and how the secretion-activation signal may be transduced through a conformational change of the needle upon host-cell contact. | ||||||
History |
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Remark 0 | THIS ENTRY 2MME CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-5352) DETERMINED ...THIS ENTRY 2MME CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-5352) DETERMINED ORIGINALLY BY AUTHORS: T.FUJII, M.CHEUNG, A.BLANCO, T.KATO, A.J.BLOCKER, K.NAMBA |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2mme.cif.gz | 6.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2mme.ent.gz | 5.9 MB | Display | PDB format |
PDBx/mmJSON format | 2mme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mme_validation.pdf.gz | 508 KB | Display | wwPDB validaton report |
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Full document | 2mme_full_validation.pdf.gz | 815.7 KB | Display | |
Data in XML | 2mme_validation.xml.gz | 247.9 KB | Display | |
Data in CIF | 2mme_validation.cif.gz | 441.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/2mme ftp://data.pdbj.org/pub/pdb/validation_reports/mm/2mme | HTTPS FTP |
-Related structure data
Related structure data | 5352M M: map data used to model this data |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9396.321 Da / Num. of mol.: 29 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: Serotype 6, BC-114 / Gene: mxiH / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XVY0 |
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-Experimental details
-Experiment
Experiment |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction | ||||||||||||
NMR experiment |
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-Sample preparation
Component | Name: Shigella flexneri MxiH Type three secretion system needle Type: COMPLEX |
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Buffer solution | pH: 7.4 / Details: 20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE |
Details | Contents: 20 mg [U-100% 13C; U-100% 15N] MxiH, wet / Solvent system: wet |
Sample | Units: % / Component: MxiH-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | pH: 5.5 / Pressure: ambient / Temperature: 278 K |
-Data collection
Microscopy | Model: JEOL 3200FSC / Date: Jul 2, 2008 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz |
-Processing
3D reconstruction | Resolution: 7.7 Å / Symmetry type: HELICAL | ||||||||||||
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Refinement step | Cycle: LAST
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NMR software |
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Refinement | Method: Rosetta fold-and-dock, Rosetta symmetric relax / Software ordinal: 2 Details: symmetric fragment-based Monte Carlo trials followed by full-atom refinement, symmetric refinement (relax) of backbone, sidechain, and rigid-body degrees of freedom | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 5000 / Conformers submitted total number: 10 |