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- EMDB-66859: Colanic acid polysaccharide related protein structures -

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Basic information

Entry
Database: EMDB / ID: EMD-66859
TitleColanic acid polysaccharide related protein structures
Map data
Sample
  • Complex: dual complex of colanic acid polysaccharide transport channel Wza and Wzc
    • Protein or peptide: Tyrosine-protein kinase wzc
    • Protein or peptide: Putative polysaccharide export protein Wza
Keywordsprotein transporter complex / PROTEIN TRANSPORT
Function / homology
Function and homology information


colanic acid metabolic process / Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / polysaccharide transmembrane transporter activity / colanic acid biosynthetic process / polysaccharide transport / polysaccharide biosynthetic process / peptidyl-tyrosine autophosphorylation / porin activity / pore complex / monoatomic ion transport ...colanic acid metabolic process / Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / polysaccharide transmembrane transporter activity / colanic acid biosynthetic process / polysaccharide transport / polysaccharide biosynthetic process / peptidyl-tyrosine autophosphorylation / porin activity / pore complex / monoatomic ion transport / cell outer membrane / protein tyrosine kinase activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Outer-membrane lipoprotein Wza, C-terminal domain / Outer-membrane lipoprotein Wza C-terminal domain / Polysaccharide export protein / : / Polysaccharide biosynthesis/export protein / 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 ...Outer-membrane lipoprotein Wza, C-terminal domain / Outer-membrane lipoprotein Wza C-terminal domain / Polysaccharide export protein / : / Polysaccharide biosynthesis/export protein / 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 / : / : / SLBB domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Putative polysaccharide export protein Wza / Tyrosine-protein kinase wzc
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsYihua H / Yanlong H
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2026
Title: Architecture of the Wza-Wzc complex that mediates colanic acid translocation across the cell envelope in Gram-negative bacteria.
Authors: Jiao Liu / Yanlong Han / Guanxue Huang / Manfeng Zhang / Junlei Du / Haizhen Zhou / Dahua Chen / Yihua Huang /
Abstract: The Wzx/Wzy-dependent pathway is a highly conserved mechanism for bacterial polysaccharide biosynthesis. This pathway is exemplified by the assembly and export of colanic acid mediated by the Wza-Wzc ...The Wzx/Wzy-dependent pathway is a highly conserved mechanism for bacterial polysaccharide biosynthesis. This pathway is exemplified by the assembly and export of colanic acid mediated by the Wza-Wzc complex. While recent structural investigations have yielded valuable insights into the molecular basis of colanic acid biosynthesis, the overall architecture of the Wza-Wzc complex and the regulatory mechanism of colanic acid export remain incompletely understood. Here, we report cryo-electron microscopy (cryo-EM) structures of the Wza-Wzc complex from E. coli K12 in two functionally states: the autophosphorylated wild-type (Wza-Wzc) state and the non-phosphorylated (Wza-Wzc) state. Both structures reveal that Wza and Wzc assemble into a continuous channel spanning the entire bacterial cell envelope, indicating that phosphorylation of Wzc does not disassemble the intact export channel. Relative to Wza-Wzc, the octameric periplasmic domain of Wzc in Wza-Wzc undergoes a significant conformational rearrangement. This rearrangement reduces constriction region's diameter and confers a negatively charged property to the interior of the Wzc octamer, which is proposed to inhibit colanic acid export. Collectively, these structural findings confirm that the Wza-Wzc complex forms a colanic acid export channel throughout Wzc's phosphorylation-dephosphorylation cycle, advancing our mechanistic understanding of the Wzx/Wzy-dependent polysaccharide biosynthesis pathway in Gram-negative bacteria.
History
DepositionOct 31, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66859.png

Downloads & links

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Map

FileDownload / File: emd_66859.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 720 pix.
= 590.4 Å		0.82 Å/pix.
x 720 pix.
= 590.4 Å		0.82 Å/pix.
x 720 pix.
= 590.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.295
Minimum - Maximum-1.5328063 - 2.8143969
Average (Standard dev.)0.00024946654 (±0.05592984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 590.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66859_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_66859_half_map_2.map
Projections & Slices
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Sample components

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Entire : dual complex of colanic acid polysaccharide transport channel Wza...

EntireName: dual complex of colanic acid polysaccharide transport channel Wza and Wzc
Components
  • Complex: dual complex of colanic acid polysaccharide transport channel Wza and Wzc
    • Protein or peptide: Tyrosine-protein kinase wzc
    • Protein or peptide: Putative polysaccharide export protein Wza

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Supramolecule #1: dual complex of colanic acid polysaccharide transport channel Wza...

SupramoleculeName: dual complex of colanic acid polysaccharide transport channel Wza and Wzc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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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 (strain K12) (bacteria)
Molecular weightTheoretical: 79.489852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 QPDVLKPKKG 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

UniProtKB: Tyrosine-protein kinase wzc

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Macromolecule #2: Putative polysaccharide export protein Wza

MacromoleculeName: Putative polysaccharide export protein Wza / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 42.225082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSMMKSKMK LMPLLVSVTL ISGCTVLPGS NMSTMGKDVI KQQDADFDLD KMVNVYPLTP RLIDQLRPRP NVARPNMTLE SEIANYQYR VGPGDVLNVT VWDHPELTTP AGQYRSSSDT GNWVQPDGTM FYPYIGKVHV VGKTLAEIRS DITGRLATYI A DPQVDVNI ...String:
MGSMMKSKMK LMPLLVSVTL ISGCTVLPGS NMSTMGKDVI KQQDADFDLD KMVNVYPLTP RLIDQLRPRP NVARPNMTLE SEIANYQYR VGPGDVLNVT VWDHPELTTP AGQYRSSSDT GNWVQPDGTM FYPYIGKVHV VGKTLAEIRS DITGRLATYI A DPQVDVNI AAFRSQKAYI SGQVNKSGQQ AITNVPLTIL DAINAAGGLT DTADWRNVVL THNGREERIS LQALMQNGDL NQ NRLLYPG DILYVPRNDD LKVFVMGEVK KQSTLKMDFS GMTLTEALGN AEGIDMTTSN ASGIFVIRPL KGEGGRNGKI ANI YQLDMS DATSLVMATE FRLQPYDVVY VTTAPVSRWN RLINQLLPTI SGVRYMTDTA SDIHNW

UniProtKB: Putative polysaccharide export protein Wza

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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: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 96000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65188
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

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