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Open data
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Basic information
Entry | Database: PDB / ID: 3j6d | ||||||
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Title | Model of the PrgH-PrgK periplasmic rings | ||||||
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![]() | STRUCTURAL PROTEIN / Bacterial secression macromolecular assemblies | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.7 Å | ||||||
![]() | Bergeron, J.R.C. / Strynadka, N.C.J. | ||||||
![]() | ![]() Title: Three-dimensional model of Salmonella's needle complex at subnanometer resolution. Authors: Oliver Schraidt / Thomas C Marlovits / ![]() Abstract: Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core ...Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core structure, the needle complex (NC), is a ~3.5 megadalton-sized, oligomeric, membrane-embedded complex. Analyzing cryo-electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly. | ||||||
History |
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Remark 0 | THIS ENTRY 3J6D CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-1875) DETERMINED ...THIS ENTRY 3J6D CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-1875) DETERMINED ORIGINALLY BY AUTHORS: O.SCHRAIDT, T.C.MARLOVITS |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1875M ![]() 2mkyC ![]() 4oycC ![]() 4w4mC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 44509.367 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: prgH, STM2874 / Production host: ![]() ![]() #2: Protein | Mass: 28245.287 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SEETLT22_01090 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: PrgH-PrgK periplasmic rings / Type: COMPLEX |
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Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 93000 X |
Image recording | Film or detector model: GENERIC CCD |
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Processing
EM software |
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Symmetry | Point symmetry: C24 (24 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 11.7 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 37171 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--EM-guided symmetrical modeling | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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