9R6A | pdb_00009r6a

CPS secretion pathway Wza-Wzc (Conf 3)

PDB DOI: https://doi.org/10.2210/pdb9R6A/pdb
EM Map EMD-53608: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli B
Mutation(s): Yes

Deposited: 2025-05-11 Released: 2026-03-04
Deposition Author(s): Yuan, B., Heinz, D.W.
Funding Organization(s): Helmholtz Association

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Molecular insights into the capsular polysaccharide transporter Wza-Wzc complex.

Yuan, B., Sieben, C., Raj, P., Rietschel, T., Hennell James, R., Gatzemeier, A., Jansch, L., Marlovits, T.C., Heinz, D.W.

(2026) Nat Commun 17: 1436-1436

PubMed: 41644548 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-69136-2
Primary Citation Related Structures:
9R60, 9R61, 9R62, 9R63, 9R64, 9R65, 9R66, 9R67, 9R68, 9R69, 9R6A, 9R6B, 9R6C

PubMed Abstract:
Capsular polysaccharides (CPS) are key virulence determinants, constituting the protective capsule that surrounds bacterial pathogens. Here, we present the complete cryo-EM structure of Gram-negative bacterial CPS secretion machinery formed by the E. coli K12 Wza-Wzc complex. The structure reveals an elongated, continuous channel spanning the entire envelope that facilitates CPS secretion. Multiple structural snapshots of the ADP-bound Wza-Wzc complex capture intermediate conformations of the double membrane assembly, highlighting its remarkable intrinsic dynamics. In-depth analysis of the isolated Wza translocon and Wzc co-polymerase, reveals mechanistic details of both complex formation and CPS transport. We further uncover the jellyroll domain of Wzc as a CPS-binding module, likely guiding CPS repeat units into a proposed Wzc-Wzy polymerization platform. Collectively, this work provides structural and functional insights into CPS synthesis and transport, advancing our understanding of bacterial capsule formation and virulence mechanisms.

Organizational Affiliation

Department of Molecular Structural Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany. biao.yuan@helmholtz-hzi.de.

Macromolecule Content

Total Structure Weight: 1,006.86 kDa
Atom Count: 64,248
Modeled Residue Count: 8,248
Deposited Residue Count: 9,056
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative polysaccharide export protein Wza	A, B, C, D, E A, B, C, D, E, F, G, H	394	Escherichia coli K-12	Mutation(s): 0 Gene Names: wza, b2062, JW2047
UniProt
Find proteins for P0A930 (Escherichia coli (strain K12)) Explore P0A930 Go to UniProtKB: P0A930
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A930
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase wzc	I, J, K, L, M I, J, K, L, M, N, O, P	738	Escherichia coli K-12	Mutation(s): 1 Gene Names: wzc, b2060, JW2045 EC: 2.7.10
UniProt
Find proteins for P76387 (Escherichia coli (strain K12)) Explore P76387 Go to UniProtKB: P76387
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P76387
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain X [auth P] SDF format, chain W [auth O] SDF format, chain V [auth N] SDF format, chain U [auth M] SDF format, chain T [auth L] SDF format, chain S [auth K] SDF format, chain R [auth J] SDF format, chain Q [auth I] MOL2 format, chain X [auth P] MOL2 format, chain W [auth O] MOL2 format, chain V [auth N] MOL2 format, chain U [auth M] MOL2 format, chain T [auth L] MOL2 format, chain S [auth K] MOL2 format, chain R [auth J] MOL2 format, chain Q [auth I] mmCIF format, chain X [auth P] mmCIF format, chain W [auth O] mmCIF format, chain V [auth N] mmCIF format, chain U [auth M] mmCIF format, chain T [auth L] mmCIF format, chain S [auth K] mmCIF format, chain R [auth J] mmCIF format, chain Q [auth I]	Q [auth I] R [auth J] S [auth K] T [auth L] U [auth M] Q [auth I], R [auth J], S [auth K], T [auth L], U [auth M], V [auth N], W [auth O], X [auth P]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Q [auth I] Focus chain R [auth J] Focus chain S [auth K] Focus chain T [auth L] Focus chain U [auth M] Focus chain V [auth N] Focus chain W [auth O] Focus chain X [auth P] Interactions & Density Focus chain Q [auth I] Focus chain R [auth J] Focus chain S [auth K] Focus chain T [auth L] Focus chain U [auth M] Focus chain V [auth N] Focus chain W [auth O] Focus chain X [auth P]