- PDB-2mme: Hybrid structure of the Shigella flexneri MxiH Type three secreti... -
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Basic information
Entry
Database: PDB / ID: 2mme
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
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.
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
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
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Processing
3D reconstruction
Resolution: 7.7 Å / Symmetry type: HELICAL
Refinement step
Cycle: LAST
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
18763
0
0
0
18763
NMR software
Name
Developer
Classification
Sparky
Goddard
dataanalysis
Rosetta
refinement
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
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