2MEX | pdb_00002mex

Structure of the tetrameric building block of the Salmonella Typhimurium PrgI Type three secretion system needle

• PDB DOI: https://doi.org/10.2210/pdb2MEX/pdb
• BMRB: 18276

• Classification: PROTEIN TRANSPORT
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-01 Released: 2013-12-25 
• Deposition Author(s): Loquet, A., Habenstein, B., Chevelkov, V., Giller, K., Becker, S., Lange, A.

---

Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 640 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Atomic structure and handedness of the building block of a biological assembly.

Loquet, A., Habenstein, B., Chevelkov, V., Vasa, S.K., Giller, K., Becker, S., Lange, A.

(2013) J Am Chem Soc 135: 19135-19138

• PubMed: 24328247 
• DOI: https://doi.org/10.1021/ja411362q
• Primary Citation Related Structures: 
  2MEX


• PubMed Abstract: 
  

  Noncovalent supramolecular assemblies possess in general several unique subunit-subunit interfaces.The basic building block of such an assembly consists of several subunits and contains all unique interfaces. Atomic-resolution structures of monomeric subunits are typically accessed by crystallography or solution NMR and fitted into electron microscopy density maps. However, the structure of the intact building block in the assembled state remains unknown with this hybrid approach. Here, we present the solid-state NMR atomic structure of the building block of the type III secretion system needle. The building block structure consists of a homotetrameric subunit complex with three unique supramolecular interfaces. Side-chain positions at the interfaces were solved at atomic detail. The high-resolution structure reveals unambiguously the helical handedness of the assembly, determined to be right-handed for the type III secretion system needle.Additionally, the axial rise per subunit could be extracted from the tetramer structure and independently validated by mass-per-length measurements.

---

Organizational Affiliation: 
• Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.46 kDa 
• Atom Count: 2,500 
• Modeled Residue Count: 320 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PrgI	A, B, C, D	80	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	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: 640 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Loquet, A., Habenstein, B., Chevelkov, V., Giller, K., Becker, S., Lange, A.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Database references, Experimental preparation
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references