Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Homo 29-mer - A29 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 257.08 kDa 
• Atom Count: 18125 
• Modelled Residue Count: 2320 
• Deposited Residue Count: 2320 
• Unique protein chains: 1

2LPZ

Atomic model of the Type-III Secretion System Needle

• PDB DOI: 10.2210/pdb2LPZ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-21 Released: 2012-05-16 
• Deposition Author(s): Loquet, A., Sgourakis, N.G., Gupta, R., Giller, K., Riedel, D., Goosmann, C., Griesinger, C., Kolbe, M.G., Baker, D., Becker, S., Lange, A.

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 1000000 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Literature

Atomic model of the type III secretion system needle.

Loquet, A., Sgourakis, N.G., Gupta, R., Giller, K., Riedel, D., Goosmann, C., Griesinger, C., Kolbe, M., Baker, D., Becker, S., Lange, A.

(2012) Nature 486: 276-279

• PubMed: 22699623 
• DOI: 10.1038/nature11079
• Primary Citation of Related Structures:  
  2LPZ


• PubMed Abstract: 
  

Pathogenic bacteria using a type III secretion system (T3SS) to manipulate host cells cause many different infections including Shigella dysentery, typhoid fever, enterohaemorrhagic colitis and bubonic plague. An essential part of the T3SS is a hollow needle-like protein filament through which effector proteins are injected into eukaryotic host cells. Currently, the three-dimensional structure of the needle is unknown because it is not amenable to X-ray crystallography and solution NMR, as a result of its inherent non-crystallinity and insolubility. Cryo-electron microscopy combined with crystal or solution NMR subunit structures has recently provided a powerful hybrid approach for studying supramolecular assemblies, resulting in low-resolution and medium-resolution models. However, such approaches cannot deliver atomic details, especially of the crucial subunit-subunit interfaces, because of the limited cryo-electron microscopic resolution obtained in these studies. Here we report an alternative approach combining recombinant wild-type needle production, solid-state NMR, electron microscopy and Rosetta modelling to reveal the supramolecular interfaces and ultimately the complete atomic structure of the Salmonella typhimurium T3SS needle. We show that the 80-residue subunits form a right-handed helical assembly with roughly 11 subunits per two turns, similar to that of the flagellar filament of S. typhimurium. In contrast to established models of the needle in which the amino terminus of the protein subunit was assumed to be α-helical and positioned inside the needle, our model reveals an extended amino-terminal domain that is positioned on the surface of the needle, while the highly conserved carboxy terminus points towards the lumen.

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Organizational Affiliation: 

Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein prgI	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, AA [auth a], BA [auth b], CA [auth c]	80	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: prgI, STM2873
UniProt
Find proteins for P41784 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P41784  Go to UniProtKB:  P41784

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 1000000 
• Conformers Submitted: 10 
• Selection Criteria: target function 
• OLDERADO: 2LPZ Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-21 
• Released Date: 2012-05-16 
Deposition Author(s): Loquet, A., Sgourakis, N.G., Gupta, R., Giller, K., Riedel, D., Goosmann, C., Griesinger, C., Kolbe, M.G., Baker, D., Becker, S., Lange, A.

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2012-06-27
  Changes: Database references
• Version 1.2: 2021-08-18
  Changes: Data collection, Database references, Experimental preparation, Refinement description