9I2R | pdb_00009i2r

Wzc-K540M-3YE MgADP C8


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9I2R

This is version 1.0 of the entry. See complete history

Literature

Molecular basis for the phosphorylation of bacterial tyrosine kinase Wzc.

Yang, Y.Batista, M.Clarke, B.R.Agyare-Tabbi, M.R.Song, H.Kuehfuss, N.M.Le Bas, A.Robinson, C.V.Whitfield, C.Stansfeld, P.J.Naismith, J.H.Liu, J.

(2025) Nat Commun 16: 3437-3437

  • DOI: https://doi.org/10.1038/s41467-025-58693-7
  • Primary Citation Related Structures: 
    9EXO, 9EXP, 9EXQ, 9EXR, 9I2Q, 9I2R

  • PubMed Abstract: 

    The regulation of polymerisation and translocation of biomolecules is fundamental. Wzc, an integral cytoplasmic membrane tyrosine autokinase protein serves as the master regulator of the biosynthesis and export of many bacterial capsular polysaccharides and exopolysaccharides. Such polysaccharides play essential roles in infection, defence, and some are important industrial products. Wzc comprises a large periplasmic domain, two transmembrane helices and a C-terminal cytoplasmic kinase domain with a tyrosine-rich tail. Wzc regulates polymerisation functions through cycling the formation and dissociation of an octameric complex, driven by changes in the phosphorylation status of the tyrosine-rich tail. E. coli Wzc serves a model for a wider family of polysaccharide co-polymerases. Here, we determine structures of intermediate states with different extents of phosphorylation. Structural and computational data reveal the pre-ordering of the tyrosine-rich tail, the molecular basis underlying the unidirectionality of phosphorylation events, and the underlying structural dynamics on how phosphorylation status is transmitted.


  • Organizational Affiliation
    • Structural Biology, The Rosalind Franklin Institute, Harwell Campus, Didcot, UK.

Macromolecule Content 

  • Total Structure Weight: 647.37 kDa 
  • Atom Count: 31,160 
  • Modeled Residue Count: 4,040 
  • Deposited Residue Count: 5,816 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative transmembrane protein Wzc
A, B, C, D, E
A, B, C, D, E, F, G, H
727Escherichia coliMutation(s): 1 
Gene Names: wzc
UniProt
Find proteins for Q9X4B9 (Escherichia coli)
Explore Q9X4B9 
Go to UniProtKB:  Q9X4B9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X4B9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release