[English] 日本語
Yorodumi
- EMDB-53598: CPS translocon Wza_C1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53598
TitleCPS translocon Wza_C1
Map data
Sample
  • Complex: Wza octamer
    • Protein or peptide: Putative polysaccharide export protein Wza
Keywordscapsular polysaccharide / TRANSPORT PROTEIN
Function / homology
Function and homology information


colanic acid metabolic process / polysaccharide transmembrane transporter activity / polysaccharide transport / polysaccharide biosynthetic process / porin activity / pore complex / monoatomic ion transport / cell outer 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 / : / SLBB domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Putative polysaccharide export protein Wza
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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

-
Structure visualization

Supplemental images

emd_53598.png

Downloads & links

-
Map

FileDownload / File: emd_53598.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 232.96 Å		0.91 Å/pix.
x 256 pix.
= 232.96 Å		0.91 Å/pix.
x 256 pix.
= 232.96 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: 0.1
Minimum - Maximum-0.80057335 - 1.0954021
Average (Standard dev.)0.0011920972 (±0.049282607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 232.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_53598_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_53598_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Wza octamer

EntireName: Wza octamer
Components
  • Complex: Wza octamer
    • Protein or peptide: Putative polysaccharide export protein Wza

-
Supramolecule #1: Wza octamer

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

-
Macromolecule #1: Putative polysaccharide export protein Wza

MacromoleculeName: Putative polysaccharide export protein Wza / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 43.873832 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MMKSKMKLMP LLVSVTLISG CTVLPGSNMS TMGKDVIKQQ DADFDLDKMV NVYPLTPRLI DQLRPRPNVA RPNMTLESEI ANYQYRVGP GDVLNVTVWD HPELTTPAGQ YRSSSDTGNW VQPDGTMFYP YIGKVHVVGK TLAEIRSDIT GRLATYIADP Q VDVNIAAF ...String:
MMKSKMKLMP LLVSVTLISG CTVLPGSNMS TMGKDVIKQQ DADFDLDKMV NVYPLTPRLI DQLRPRPNVA RPNMTLESEI ANYQYRVGP GDVLNVTVWD HPELTTPAGQ YRSSSDTGNW VQPDGTMFYP YIGKVHVVGK TLAEIRSDIT GRLATYIADP Q VDVNIAAF RSQKAYISGQ VNKSGQQAIT NVPLTILDAI NAAGGLTDTA DWRNVVLTHN GREERISLQA LMQNGDLNQN RL LYPGDIL YVPRNDDLKV FVMGEVKKQS TLKMDFSGMT LTEALGNAEG IDMTTSNASG IFVIRPLKGE GGRNGKIANI YQL DMSDAT SLVMATEFRL QPYDVVYVTT APVSRWNRLI NQLLPTISGV RYMTDTASDI HNWENLYFQS WSHPQFEK

UniProtKB: Putative polysaccharide export protein Wza

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 0.5 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125938
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more