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- EMDB-53598: CPS translocon Wza_C1 -

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Open data


ID or keywords:

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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: To Be Published
Title: CPS translocon Wza_C1
Authors: Yuan B / Heinz DW
History
DepositionMay 11, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53598.png

Downloads & links

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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 °

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Supplemental data

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Half map: #1

Fileemd_53598_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_53598_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 : Wza octamer

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

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Supramolecule #1: Wza octamer

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

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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

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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

Concentration2 mg/mL
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: 0.5 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: 3.0 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)

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