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- EMDB-80645: Colanic acid polysaccharide related protein structures -

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Basic information

Entry
Database: EMDB / ID: EMD-80645
TitleColanic acid polysaccharide related protein structures
Map data
Sample
  • Complex: Wza-Wzc complex
    • Protein or peptide: Tyrosine-protein kinase wzc
    • Protein or peptide: Putative polysaccharide export protein Wza
KeywordsComplex / 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 K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
Authorsjiao L / 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
DepositionApr 29, 2026-
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_80645.png

Downloads & links

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Map

FileDownload / File: emd_80645.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. 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: 0.32
Minimum - Maximum-2.139481 - 3.4518085
Average (Standard dev.)0.0005303938 (±0.075812005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 492.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80645_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_80645_half_map_2.map
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Sample components

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Entire : Wza-Wzc complex

EntireName: Wza-Wzc complex
Components
  • Complex: Wza-Wzc complex
    • Protein or peptide: Tyrosine-protein kinase wzc
    • Protein or peptide: Putative polysaccharide export protein Wza

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Supramolecule #1: Wza-Wzc complex

SupramoleculeName: Wza-Wzc complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 42.644277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: CAVVYTFFAT PIYSADALVQ IEQNSGNSLV QDIGSALANK PPASDAEIQL IRSRLVLGKT VDDLDLDIAV SKNTFPIFGA GWDRLMGRQ NETVKVTTFN RPKEMADQVF TLNVLDNKNY TLSSDGGFSA RGQAGQMLKK EGVTLMVEAI HASPGSEFTV T KYSTLGMI ...String:
CAVVYTFFAT PIYSADALVQ IEQNSGNSLV QDIGSALANK PPASDAEIQL IRSRLVLGKT VDDLDLDIAV SKNTFPIFGA GWDRLMGRQ NETVKVTTFN RPKEMADQVF TLNVLDNKNY TLSSDGGFSA RGQAGQMLKK EGVTLMVEAI HASPGSEFTV T KYSTLGMI NQLQNSLTVT ENGKDAGVLS LTYTGEDREQ IRDILNSIAR NYQEQNIERK SAEASKSLAF LAQQLPEVRS RL DVAENKL NAFRQDKDSV DLPLEAKAVL DSMVNIDAQL NELTFKEAEI SKLYTKVHPA YRTLLEKRQA LEDEKAKLNG RVT AMPKTQ QEIVRLTRDV ESGQQVYMQL LNKEQELKIT EASTVGDVRI VDPAITQPGV LKPKKGLII

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 K-12 (bacteria)
Molecular weightTheoretical: 39.756898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: CTVLPGSNMS TMGKDVIKQQ DADFDLDKMV NVYPLTPRLI DQLRPRPNVA RPNMTLESEI ANYQYRVGPG DVLNVTVWDH PELTTPAGQ YRSSSDTGNW VQPDGTMFYP YIGKVHVVGK TLAEIRSDIT GRLATYIADP QVDVNIAAFR SQKAYISGQV N KSGQQAIT ...String:
CTVLPGSNMS TMGKDVIKQQ DADFDLDKMV NVYPLTPRLI DQLRPRPNVA RPNMTLESEI ANYQYRVGPG DVLNVTVWDH PELTTPAGQ YRSSSDTGNW VQPDGTMFYP YIGKVHVVGK TLAEIRSDIT GRLATYIADP QVDVNIAAFR SQKAYISGQV N KSGQQAIT NVPLTILDAI NAAGGLTDTA DWRNVVLTHN GREERISLQA LMQNGDLNQN RLLYPGDILY VPRNDDLKVF VM GEVKKQS TLKMDFSGMT LTEALGNAEG IDMTTSNASG IFVIRPLKGE GGRNGKIANI YQLDMSDATS LVMATEFRLQ PYD VVYVTT APVSRWNRLI NQLLPTISGV RYMTDTASDI HNW

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 TALOS
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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16148
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

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