8T53 | pdb_00008t53

S. enterica WbaP in a styrene maleic acid liponanoparticle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8T53

This is version 1.1 of the entry. See complete history

Literature

Mapping the architecture of the initiating phosphoglycosyl transferase from S. enterica O-antigen biosynthesis in a liponanoparticle.

Dodge, G.J.Anderson, A.J.He, Y.Liu, W.Viner, R.Imperiali, B.

(2024) Elife 12

  • DOI: https://doi.org/10.7554/eLife.91125
  • Primary Citation Related Structures: 
    8T53

  • PubMed Abstract: 

    Bacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have untapped potential as therapeutic targets. The localization of many glycoconjugate biosynthesis enzymes to the membrane represents a significant challenge for expressing, purifying, and characterizing these enzymes. Here, we leverage cutting-edge detergent-free methods to stabilize, purify, and structurally characterize WbaP, a phosphoglycosyl transferase (PGT) from the Salmonella enterica (LT2) O-antigen biosynthesis. From a functional perspective, these studies establish WbaP as a homodimer, reveal the structural elements responsible for dimerization, shed light on the regulatory role of a domain of unknown function embedded within WbaP, and identify conserved structural motifs between PGTs and functionally unrelated UDP-sugar dehydratases. From a technological perspective, the strategy developed here is generalizable and provides a toolkit for studying other classes of small membrane proteins embedded in liponanoparticles beyond PGTs.


  • Organizational Affiliation
    • Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.

Macromolecule Content 

  • Total Structure Weight: 122.77 kDa 
  • Atom Count: 6,660 
  • Modeled Residue Count: 796 
  • Deposited Residue Count: 1,056 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Undecaprenyl-phosphate galactose phosphotransferase
A, B
528Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: rfbPSTM2082
EC: 2.7.8.6
Membrane Entity: Yes 
UniProt
Find proteins for P26406 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P26406 
Go to UniProtKB:  P26406
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26406
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134576
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131627
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM039334

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Database references