9S8L | pdb_00009s8l

Structure of E. coli WbaP in complex with a megabody in presence of UDP-Gal

PDB DOI: https://doi.org/10.2210/pdb9S8L/pdb
EM Map EMD-54664: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Escherichia coli, Lama glama
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2025-08-05 Released: 2026-07-01
Deposition Author(s): Weckener, M., Le Bas, A., Ward, P.N., Naismith, J.H.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9S8L

This is version 1.0 of the entry. See complete history.

Literature

Structural and functional studies of the polytopic phosphoglycosyltransferase WbaP in E. coli

Weckener, M., Le Bas, A., Ward, P.N., Naismith, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 229.33 kDa
Atom Count: 9,016
Modeled Residue Count: 1,104
Deposited Residue Count: 2,042
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP	A, B	497	Escherichia coli	Mutation(s): 0 Gene Names: wbaP
UniProt
Find proteins for Q9X4C0 (Escherichia coli) Explore Q9X4C0 Go to UniProtKB: Q9X4C0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X4C0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody	C, D	524	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDU (Subject of Investigation/LOI) Query on GDU Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	GALACTOSE-URIDINE-5'-DIPHOSPHATE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-ABVWGUQPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	220526/Z/20/Z
Wellcome Trust	United Kingdom	100209/Z/12/Z

Revision History (Full details and data files)

Version 1.0: 2026-07-01
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.