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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10045 | |||||||||
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Title | Inner membrane ring of the Shigella type 3 secretion system | |||||||||
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![]() | The periplasmic inner membrane ring of the Shigella type 3 secretion system: Protein MxiG / Lipoprotein MxiJ | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Lunelli M / Kamprad A | |||||||||
Funding support | 2 items
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![]() | ![]() Title: Cryo-EM structure of the Shigella type III needle complex. Authors: Michele Lunelli / Antje Kamprad / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / Michael Kolbe / ![]() Abstract: The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram- ...The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram-negative bacterial pathogens. This system is composed of a membrane-embedded basal body and an extracellular needle that deliver effector proteins into host cells. High-resolution structures of the T3SS from different organisms and infection stages are needed to understand the underlying molecular mechanisms of effector translocation. Here, we present the cryo-electron microscopy structure of the isolated Shigella T3SS needle complex. The inner membrane (IM) region of the basal body adopts 24-fold rotational symmetry and forms a channel system that connects the bacterial periplasm with the export apparatus cage. The secretin oligomer adopts a heterogeneous architecture with 16- and 15-fold cyclic symmetry in the periplasmic N-terminal connector and C-terminal outer membrane ring, respectively. Two out of three IM subunits bind the secretin connector via a β-sheet augmentation. The cryo-EM map also reveals the helical architecture of the export apparatus core, the inner rod, the needle and their intervening interfaces. | |||||||||
Validation Report | ![]() ![]() ![]() ![]() | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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FSC (resolution estimation) |
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Header (meta data in XML format) |
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Images |
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Masks (Map data of sub-region, etc) |
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Others |
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Archive directory |
-Related structure data
Related structure data | ![]() 6rwxCM ![]() 6rwkC ![]() 6rwyC C: citing same article ( M: atomic model generated by this map |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38369 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Masked C24 map of inner membrane ring of...
File | emd_10045_additional.map | ||||||||||||
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Annotation | Masked C24 map of inner membrane ring of Shigella type 3 secretion system, post-processed, sharpened (b=-128) and filtered at 3.2 A. Used for model building and refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map
File | emd_10045_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map
File | emd_10045_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map | ||||||||||||
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Density Histograms |
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Sample components
-Entire The periplasmic inner membrane ring of the Shigella type 3 secret...
Entire | Name: The periplasmic inner membrane ring of the Shigella type 3 secretion system Details: Focused reconstruction from isolated needle complexes of the Shigella type 3 secretion system Number of components: 3 |
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-Component #1: protein, The periplasmic inner membrane ring of the Shigella type...
Protein | Name: The periplasmic inner membrane ring of the Shigella type 3 secretion system Details: Focused reconstruction from isolated needle complexes of the Shigella type 3 secretion system Recombinant expression: No |
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Source | Species: ![]() ![]() |
Source (natural) | Location in cell: Membrane |
-Component #2: protein, Protein MxiG
Protein | Name: Protein MxiG / Number of Copies: 24 / Recombinant expression: No |
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Mass | Theoretical: 43.053844 kDa |
Source | Species: ![]() ![]() |
-Component #3: protein, Lipoprotein MxiJ
Protein | Name: Lipoprotein MxiJ / Number of Copies: 24 / Recombinant expression: No |
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Mass | Theoretical: 27.542055 kDa |
Source | Species: ![]() ![]() |
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | pH: 8 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 % Details: Sample applied on grid 5 ul, incubation time 5 min on ice, then moved into Vitrobot and 5 ul sample applied again. Blot time: 2 sec Blot force: -2 Drain time: 0 sec. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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![]() | Microscope: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 101179 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: FEI TITAN KRIOS AUTOGRID HOLDER |
Camera | Detector: FEI FALCON II (4k x 4k) |
-Image acquisition
Image acquisition | Number of digital images: 5238 |
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