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- PDB-2y9k: Three-dimensional model of Salmonella's needle complex at subnano... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y9k | ||||||
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Title | Three-dimensional model of Salmonella's needle complex at subnanometer resolution | ||||||
![]() | PROTEIN INVG | ||||||
![]() | PROTEIN TRANSPORT / TYPE III SECRETION SYSTEM / OUTER MEMBRANE RING / SECRETIN FAMILY / C15 FOLD | ||||||
Function / homology | ![]() type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / cell outer membrane / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.3 Å | ||||||
![]() | Schraidt, O. / Marlovits, T.C. | ||||||
![]() | ![]() 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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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 352.2 KB | Display | ![]() |
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PDB format | ![]() | 282.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 766.2 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 109.3 KB | Display | |
Data in CIF | ![]() | 134.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1871MC ![]() 1874C ![]() 1875C ![]() 2y9jC 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: 15616.915 Da / Num. of mol.: 15 / Fragment: N-TERMINAL DOMAIN, RESIDUES 34-170 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P35672 |
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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: NEEDLE COMPLEX / Type: COMPLEX |
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Buffer solution | pH: 7.5 / Details: 10mM Tris-HCl 0.5M NaCl 0.1% LDAO |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Cryogen name: ETHANE / Details: LIQUID 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 Details: ACUAL MAGNIFICATION AT CCD 112968, CAMERA PIXEL SIZE 15UM, 1.33 ANGSTROM PER PIXEL, DATA COLLECTED SEMI- AUTOMATICALLY USING POINT-2-POINT (DEVELOPED IN-HOUSE) |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 93000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm |
Specimen holder | Tilt angle min: 0 ° |
Image recording | Film or detector model: GENERIC GATAN (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: EACH CCD FRAME | ||||||||||||
Symmetry | Point symmetry: C15 (15 fold cyclic) | ||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 8.3 Å / Resolution method: FSC 0.5 CUT-OFF / Actual pixel size: 1.33 Å Details: RESOLUTION 8.3 ANGSTROM (0.5 FSC), 6.7 ANGSTROM (HALF BIT) SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1871. (DEPOSITION ID: 7820). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY FITTING | ||||||||||||
Atomic model building | PDB-ID: 3GR5 Accession code: 3GR5 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 8.3 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.3 Å
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