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- PDB-30wc: Structure of E. coli WbaP in complex with a megabody in the prese... -

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Basic information

Entry
Database: PDB / ID: 30wc
TitleStructure of E. coli WbaP in complex with a megabody in the presence of UDP-Gal processed in C2 symmetry
Components
  • Megabody
  • Undecaprenyl-phosphate galactose phosphotransferase WbaP
KeywordsMEMBRANE PROTEIN / cell wall / oligosaccharides / transferase
Function / homologyGALACTOSE-URIDINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWeckener, M. / Le Bas, A. / Ward, P.N. / Harrison, P.J. / 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. / Harrison, P.J. / Naismith, J.H.
History
DepositionMay 14, 2026Deposition 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: 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

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Assembly

Deposited unit
A: Undecaprenyl-phosphate galactose phosphotransferase WbaP
B: Undecaprenyl-phosphate galactose phosphotransferase WbaP
C: Megabody
D: Megabody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,1846
Polymers228,0514
Non-polymers1,1332
Water00
1


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

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Components

#1: Protein Undecaprenyl-phosphate galactose phosphotransferase WbaP


Mass: 57450.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: wbaP, HMV95_22310 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A6D1CLM9
#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 modificationN

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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

ComponentName: Complex of dimeric WbaP with 2 megabody molecules / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Details: 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM beta-merecaptoethanol, 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 30 mM for 30s 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
1cryoSPARC5particle selection
2PHENIX2.1rc2_6040model refinement
3EPUimage acquisition
5cryoSPARC5CTF correction
10cryoSPARC5initial Euler assignment
11cryoSPARC5final Euler assignment
12cryoSPARCclassification
13cryoSPARC53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5021937
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 492904 / Symmetry type: POINT
Atomic model buildingSource name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 128.92 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00249233
ELECTRON MICROSCOPYf_angle_d0.520612518
ELECTRON MICROSCOPYf_chiral_restr0.03731381
ELECTRON MICROSCOPYf_plane_restr0.0041534
ELECTRON MICROSCOPYf_dihedral_angle_d4.34041231

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