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- PDB-9s8l: Structure of E. coli WbaP in complex with a megabody in presence ... -

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Basic information

Entry
Database: PDB / ID: 9s8l
TitleStructure of E. coli WbaP in complex with a megabody in presence of UDP-Gal
Components
  • Megabody
  • UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP
KeywordsTRANSFERASE / membrane protein / cell wall / oligosaccharides
Function / homology
Function and homology information


phosphotransferase activity, for other substituted phosphate groups / polysaccharide biosynthetic process / plasma membrane
Similarity search - Function
Undecaprenyl-phosphate galactose phosphotransferase, WbaP / Exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase / CoA-binding domain / Bacterial sugar transferase / Bacterial sugar transferase
Similarity search - Domain/homology
GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWeckener, M. / Le Bas, A. / Ward, P.N. / Naismith, J.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust220526/Z/20/Z United Kingdom
Wellcome Trust100209/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: Structural and functional studies of the polytopic phosphoglycosyltransferase WbaP in E. coli
Authors: Weckener, M. / Le Bas, A. / Ward, P.N. / Naismith, J.H.
History
DepositionAug 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP
B: UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP
C: Megabody
D: Megabody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,3266
Polymers228,1934
Non-polymers1,1332
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP


Mass: 57521.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: wbaP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q9X4C0
#2: Antibody Megabody


Mass: 56575.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): wk6(su-)
#3: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of dimeric WbaP with 2 megabody moleculesCOMPLEX#1-#20RECOMBINANT
2WbaPORGANELLE OR CELLULAR COMPONENT#11RECOMBINANT
3MegabodyORGANELLE OR CELLULAR COMPONENT#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
33NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli (E. coli)562
22Escherichia coli (E. coli)562C43(DE3)
33Escherichia coli (E. coli)562wk6(su-)
Buffer solutionpH: 8
Details: 20 mM Tris-HCl pH 8.0; 150 mM NaCl; 2 mM beta-mercaptoethanol; 0.001% LMNG
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: grids were Glow discharged twice at 30mA for 30sec each.
Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2293857
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225535 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 9S7S

9s7s


Accession code: 9S7S / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029243
ELECTRON MICROSCOPYf_angle_d0.45312536
ELECTRON MICROSCOPYf_dihedral_angle_d7.0431328
ELECTRON MICROSCOPYf_chiral_restr0.0361390
ELECTRON MICROSCOPYf_plane_restr0.0031530

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