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- EMDB-2801: Negative stain electron microscopy reconstruction of the wild typ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2801 | |||||||||
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Title | Negative stain electron microscopy reconstruction of the wild type tip complex from the type III secretion system of Shigella flexneri | |||||||||
![]() | Negative stain electron microscopy reconstruction of the wild type tip complex and needle of the type III secretion system from Shigella flexneri. | |||||||||
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![]() | Tip complex / type III secretion system / Shigella flexneri / wild type | |||||||||
Function / homology | effector-mediated activation of programmed cell death in host / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / extracellular region / Invasin IpaD![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.0 Å | |||||||||
![]() | Cheung M / Shen D / Makino F / Kato T / Roehrich D / Martinez-Argudo I / Walker ML / Murillo I / Liu X / Pain M ...Cheung M / Shen D / Makino F / Kato T / Roehrich D / Martinez-Argudo I / Walker ML / Murillo I / Liu X / Pain M / Brown J / Frazer G / Mantell J / Mina P / Todd T / Sessions RB / Namba K / Blocker AJ | |||||||||
![]() | Journal: Proc Natl Acad Sci U S A / Year: 2008 Title: What's the point of the type III secretion system needle? Authors: Ariel J Blocker / Janet E Deane / Andreas K J Veenendaal / Pietro Roversi / Julie L Hodgkinson / Steven Johnson / Susan M Lea / ![]() Abstract: Recent work by several groups has significantly expanded our knowledge of the structure, regulation of assembly, and function of components of the extracellular portion of the type III secretion ...Recent work by several groups has significantly expanded our knowledge of the structure, regulation of assembly, and function of components of the extracellular portion of the type III secretion system (T3SS) of Gram-negative bacteria. This perspective presents a structure-informed analysis of functional data and discusses three nonmutually exclusive models of how a key aspect of T3SS biology, the sensing of host cells, may be performed. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.5 KB 17.5 KB | Display Display | ![]() |
Images | ![]() | 32.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d3eMC ![]() 2802C ![]() 2803C ![]() 2804C ![]() 2805C ![]() 2806C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain electron microscopy reconstruction of the wild type tip complex and needle of the type III secretion system from Shigella flexneri. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Wild type conformation of the tip complex from the type III secre...
Entire | Name: Wild type conformation of the tip complex from the type III secretion system of Shigella flexneri, bound to the needle |
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Components |
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-Supramolecule #1000: Wild type conformation of the tip complex from the type III secre...
Supramolecule | Name: Wild type conformation of the tip complex from the type III secretion system of Shigella flexneri, bound to the needle type: sample / ID: 1000 Details: Tip complexes were analysed from purified needle complexes and therefore when still bound to the needle tip Oligomeric state: Five subunits of the tip complex bound to fifty subunits of the needle Number unique components: 2 |
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Molecular weight | Theoretical: 680 KDa |
-Supramolecule #1: Tip complex
Supramolecule | Name: Tip complex / type: organelle_or_cellular_component / ID: 1 / Number of copies: 1 / Oligomeric state: Heteropentameric / Recombinant expression: Yes |
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Ref GO | 0: GO:0030257 |
Ref INTERPRO | 0: IPR006135 |
Source (natural) | Organism: ![]() Location in cell: Extracellular component of membrane embedded complex |
Molecular weight | Theoretical: 210 KDa |
Recombinant expression | Organism: ![]() |
-Supramolecule #2: Needle
Supramolecule | Name: Needle / type: organelle_or_cellular_component / ID: 2 / Number of copies: 1 / Oligomeric state: helical polymer / Recombinant expression: Yes |
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Ref GO | 0: GO:0030257 |
Ref INTERPRO | 0: IPR006135 |
Source (natural) | Organism: ![]() Location in cell: Extracellular component of membrane embedded complex |
Molecular weight | Theoretical: 470 KDa |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 Details: 0.1% (w/v) DDM, 150 mM NaCl, 25 mM Tris pH 8, 5 mM EDTA |
Staining | Type: NEGATIVE Details: Carbon coating mica sheets were submerged in a drop of 0.01% (w/v) DDM until the carbon sheet partially detached from the mica. The mica was then submerged in the sample for 5 s, then ...Details: Carbon coating mica sheets were submerged in a drop of 0.01% (w/v) DDM until the carbon sheet partially detached from the mica. The mica was then submerged in the sample for 5 s, then submerged in a drop of water for 5 s. The mica was then placed onto the surface of a drop of 1% uranyl acetate and allowed to sink, causing the carbon to float on the surface of the drop. After 10 s, the carbon sheet was adsorbed onto a grid. |
Grid | Details: 300 mesh copper grid with a thin carbon film to which the specimen was adsorbed to |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Alignment procedure | Legacy - Astigmatism: Thon rings visualised at 50-100,000 times magnification using the fast FT and corrected accordingly Legacy - Electron beam tilt params: 0 |
Date | Aug 31, 2011 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 300 / Average electron dose: 9 e/Å2 / Camera length: 460 / Od range: 3.56 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 70754 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.4 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: FEI single tilt holder / Specimen holder model: SIDE ENTRY, EUCENTRIC |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: ![]() |
Details | Residues comprising the N domain were removed. The 10 residues at the C terminus (not resolved in the crystal structure) were built into an alpha helix |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-4d3e: |