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- EMDB-53601: CPS co-polymerase Wzc_C4 -

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Basic information

Entry
Database: EMDB / ID: EMD-53601
TitleCPS co-polymerase Wzc_C4
Map data
Sample
  • Complex: WzcK540M octamer
    • Protein or peptide: Tyrosine-protein kinase wzc
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsCapsular polysaccharide secretion pathway / TRANSPORT PROTEIN
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / colanic acid biosynthetic process / polysaccharide biosynthetic process / peptidyl-tyrosine autophosphorylation / protein tyrosine kinase activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase Wzc, N-terminal domain / Tyrosine kinase, G-rich domain / G-rich domain on putative tyrosine kinase / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / AAA domain / AAA domain / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tyrosine-protein kinase wzc
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYuan B / Heinz DW
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: Nat Commun / Year: 2026
Title: Molecular insights into the capsular polysaccharide transporter Wza-Wzc complex.
Authors: Biao Yuan / Christian Sieben / Prateek Raj / Tina Rietschel / Rory Hennell James / Anja Gatzemeier / Lothar Jänsch / Thomas C Marlovits / Dirk W Heinz /
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 ...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.
History
DepositionMay 11, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53601.png

Downloads & links

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Map

FileDownload / File: emd_53601.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.2227072 - 0.33656022
Average (Standard dev.)0.0005514527 (±0.010132679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 327.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53601_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53601_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : WzcK540M octamer

EntireName: WzcK540M octamer
Components
  • Complex: WzcK540M octamer
    • Protein or peptide: Tyrosine-protein kinase wzc
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: WzcK540M octamer

SupramoleculeName: WzcK540M octamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Tyrosine-protein kinase wzc

MacromoleculeName: Tyrosine-protein kinase wzc / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 81.557086 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MTEKVKQHAA PVTGSDEIDI GRLVGTVIEA RWWVIGITTV FALCAVVYTF FATPIYSADA LVQIEQNSGN SLVQDIGSAL ANKPPASDA EIQLIRSRLV LGKTVDDLDL DIAVSKNTFP IFGAGWDRLM GRQNETVKVT TFNRPKEMAD QVFTLNVLDN K NYTLSSDG ...String:
MTEKVKQHAA PVTGSDEIDI GRLVGTVIEA RWWVIGITTV FALCAVVYTF FATPIYSADA LVQIEQNSGN SLVQDIGSAL ANKPPASDA EIQLIRSRLV LGKTVDDLDL DIAVSKNTFP IFGAGWDRLM GRQNETVKVT TFNRPKEMAD QVFTLNVLDN K NYTLSSDG GFSARGQAGQ MLKKEGVTLM VEAIHASPGS EFTVTKYSTL GMINQLQNSL TVTENGKDAG VLSLTYTGED RE QIRDILN SIARNYQEQN IERKSAEASK SLAFLAQQLP EVRSRLDVAE NKLNAFRQDK DSVDLPLEAK AVLDSMVNID AQL NELTFK EAEISKLYTK VHPAYRTLLE KRQALEDEKA KLNGRVTAMP KTQQEIVRLT RDVESGQQVY MQLLNKEQEL KITE ASTVG DVRIVDPAIT QPGVLKPKKG LIILGAIILG LMLSIVGVLL RSLFNRGIES PQVLEEHGIS VYASIPLSEW QKARD SVKT IKGIKRYKQS QLLAVGNPTD LAIEAIRSLR TSLHFAMMQA QNNVLMMTGV SPSIGMTFVC ANLAAVISQT NKRVLL IDC DMRKGYTHEL LGTNNVNGLS EILIGQGDIT TAAKPTSIAK FDLIPRGQVP PNPSELLMSE RFAELVNWAS KNYDLVL ID TPPILAVTDA AIVGRHVGTT LMVARYAVNT LKEVETSLSR FEQNGIPVKG VILNSIFRRA SAYQDYGYYE YEYKSDAK S SGENLYFQGW SHPQFEK

UniProtKB: Tyrosine-protein kinase wzc

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128284
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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