+Open data
-Basic information
Entry | Database: PDB / ID: 8t53 | ||||||||||||
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Title | S. enterica WbaP in a styrene maleic acid liponanoparticle | ||||||||||||
Components | Undecaprenyl-phosphate galactose phosphotransferase | ||||||||||||
Keywords | TRANSFERASE / phosphoglycosyl transferase / liponanopaticle / SMALP / O-antigen / Salmonella enterica | ||||||||||||
Function / homology | Function and homology information undecaprenyl-phosphate galactose phosphotransferase / undecaprenyl-phosphate galactose phosphotransferase activity / phosphotransferase activity, for other substituted phosphate groups / O antigen biosynthetic process / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Dodge, G.J. / Imperiali, B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Elife / Year: 2024 Title: Mapping the architecture of the initiating phosphoglycosyl transferase from O-antigen biosynthesis in a liponanoparticle. Authors: Greg J Dodge / Alyssa J Anderson / Yi He / Weijing Liu / Rosa Viner / Barbara Imperiali / 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 ...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 (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. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t53.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t53.ent.gz | 123.3 KB | Display | PDB format |
PDBx/mmJSON format | 8t53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t53_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8t53_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8t53_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 8t53_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/8t53 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/8t53 | HTTPS FTP |
-Related structure data
Related structure data | 41042MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 61382.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: rfbP, STM2082 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 References: UniProt: P26406, undecaprenyl-phosphate galactose phosphotransferase |
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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 |
-Sample preparation
Component | Name: WbaP dimer embedded in a styrene maleic acid liponanoparticle Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.25 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C43 | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50.13 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4841 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1266538 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196663 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refine LS restraints |
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