[English] 日本語
Yorodumi- EMDB-1215: Assembly of the inner rod determines needle length in the type II... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1215 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Assembly of the inner rod determines needle length in the type III secretion injectisome. | |||||||||
Map data | Type III Secretion Complex from an prgJ-mutant strain from Salmonella typhimurium | |||||||||
Sample |
| |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | Marlovits TC / Kubori T / Lara-Tejero M / Thomas D / Unger VM / Galan JE | |||||||||
Citation | Journal: Nature / Year: 2006 Title: Assembly of the inner rod determines needle length in the type III secretion injectisome. Authors: Thomas C Marlovits / Tomoko Kubori / María Lara-Tejero / Dennis Thomas / Vinzenz M Unger / Jorge E Galán / Abstract: Assembly of multi-component supramolecular machines is fundamental to biology, yet in most cases, assembly pathways and their control are poorly understood. An example is the type III secretion ...Assembly of multi-component supramolecular machines is fundamental to biology, yet in most cases, assembly pathways and their control are poorly understood. An example is the type III secretion machine, which mediates the transfer of bacterial virulence proteins into host cells. A central component of this nanomachine is the needle complex or injectisome, an organelle associated with the bacterial envelope that is composed of a multi-ring base, an inner rod, and a protruding needle. Assembly of this organelle proceeds in sequential steps that require the reprogramming of the secretion machine. Here we provide evidence that, in Salmonella typhimurium, completion of the assembly of the inner rod determines the size of the needle substructure. Assembly of the inner rod, which is regulated by the InvJ protein, triggers conformational changes on the cytoplasmic side of the injectisome, reprogramming the secretion apparatus to stop secretion of the needle protein. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1215.map.gz | 12.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1215-v30.xml emd-1215.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | 1215.gif | 4.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1215 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1215 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_1215.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Type III Secretion Complex from an prgJ-mutant strain from Salmonella typhimurium | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Type III Secretion Complex from an prgJ-mutant strain of Salmonel...
Entire | Name: Type III Secretion Complex from an prgJ-mutant strain of Salmonella typhimurium |
---|---|
Components |
|
-Supramolecule #1000: Type III Secretion Complex from an prgJ-mutant strain of Salmonel...
Supramolecule | Name: Type III Secretion Complex from an prgJ-mutant strain of Salmonella typhimurium type: sample / ID: 1000 / Oligomeric state: 20 / Number unique components: 3 |
---|---|
Molecular weight | Theoretical: 2.64 MDa |
-Macromolecule #1: PrgH
Macromolecule | Name: PrgH / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) synonym: Salmonella / Location in cell: Membrane |
Molecular weight | Experimental: 44 MDa |
Recombinant expression | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
-Macromolecule #2: PrgK
Macromolecule | Name: PrgK / type: protein_or_peptide / ID: 2 / Number of copies: 20 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) synonym: Salmonella / Location in cell: Membrane |
Molecular weight | Experimental: 28 MDa |
Recombinant expression | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
-Macromolecule #3: InvG
Macromolecule | Name: InvG / type: protein_or_peptide / ID: 3 / Number of copies: 20 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) synonym: Salmonella / Location in cell: Membrane |
Molecular weight | Experimental: 60 MDa |
Recombinant expression | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 10mM Tris-HCl 500mM NaCl 0.2% LDAO |
---|---|
Grid | Details: 400 mesh Cu/Rh |
Vitrification | Cryogen name: ETHANE / Method: Blot for 15 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Alignment procedure | Legacy - Astigmatism: 200 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 47 / Average electron dose: 10 e/Å2 / Od range: 0.8 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side-entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: phase flipping, each particle |
---|---|
Final reconstruction | Applied symmetry - Point group: C20 (20 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC-5, MRC / Details: supervised projection matching procedure |