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- EMDB-16073: Full-length bacterial polysaccharide co-polymerase WzzE from E. c... -

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Basic information

Entry
Database: EMDB / ID: EMD-16073
TitleFull-length bacterial polysaccharide co-polymerase WzzE from E. coli. C8 symmetry
Map dataC8 symmetrized map of the E. coli polysaccharide co-polymerase WzzE
Sample
  • Complex: Bacterial Polysaccharide Co-polymerase WzzE
    • Protein or peptide: polysaccharide co-polymerase WzzE
KeywordsComplex / Lipopolysaccharide / bacterial polysaccharide co-polymerase / MEMBRANE PROTEIN
Function / homologyECA polysaccharide chain length modulation protein WzzE / enterobacterial common antigen biosynthetic process / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / : / protein tyrosine kinase activity / plasma membrane / ECA polysaccharide chain length modulation protein
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWiseman B / Hogbom M
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research Council2017-04018 Sweden
Knut and Alice Wallenberg Foundation2017.0275 Sweden
Knut and Alice Wallenberg Foundation2019.0436 Sweden
CitationJournal: Commun Biol / Year: 2023
Title: Alternating L4 loop architecture of the bacterial polysaccharide co-polymerase WzzE.
Authors: Benjamin Wiseman / Göran Widmalm / Martin Högbom /
Abstract: Lipopolysaccharides such as the enterobacterial common antigen are important components of the enterobacterial cell envelope that act as a protective barrier against the environment and are often ...Lipopolysaccharides such as the enterobacterial common antigen are important components of the enterobacterial cell envelope that act as a protective barrier against the environment and are often polymerized by the inner membrane bound Wzy-dependent pathway. By employing cryo-electron microscopy we show that WzzE, the co-polymerase component of this pathway that is responsible for the length modulation of the enterobacterial common antigen, is octameric with alternating up-down conformations of its L4 loops. The alternating up-down nature of these essential loops, located at the top of the periplasmic bell, are modulated by clashing helical faces between adjacent protomers that flank the L4 loops around the octameric periplasmic bell. This alternating arrangement and a highly negatively charged binding face create a dynamic environment in which the polysaccharide chain is extended, and suggest a ratchet-type mechanism for polysaccharide elongation.
History
DepositionNov 1, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16073.png

Downloads & links

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Map

FileDownload / File: emd_16073.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC8 symmetrized map of the E. coli polysaccharide co-polymerase WzzE
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.2219096 - 0.65569514
Average (Standard dev.)0.0010228201 (±0.01764607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A for C8 symmetrized map of...

Fileemd_16073_half_map_1.map
AnnotationHalf map A for C8 symmetrized map of the E. coli polysaccharide co-polymerase WzzE
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B for C8 symmetrized map of...

Fileemd_16073_half_map_2.map
AnnotationHalf map B for C8 symmetrized map of the E. coli polysaccharide co-polymerase WzzE
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacterial Polysaccharide Co-polymerase WzzE

EntireName: Bacterial Polysaccharide Co-polymerase WzzE
Components
  • Complex: Bacterial Polysaccharide Co-polymerase WzzE
    • Protein or peptide: polysaccharide co-polymerase WzzE

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Supramolecule #1: Bacterial Polysaccharide Co-polymerase WzzE

SupramoleculeName: Bacterial Polysaccharide Co-polymerase WzzE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Homo octameric complex
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: polysaccharide co-polymerase WzzE

MacromoleculeName: polysaccharide co-polymerase WzzE / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTQPMPGKPA EDAENELDIR GLFRTLWAGK LWIIGMGLAF ALIALAYTFF ARQEWSSTAI TDRPTVNMLG GYYSQQQFLR NLDVRSNMA SADQPSVMDE AYKEFVMQLA SWDTRREFWL QTDYYKQRMV GNSKADAALL DEMINNIQFI PGDFTRAVND S VKLIAETA ...String:
MTQPMPGKPA EDAENELDIR GLFRTLWAGK LWIIGMGLAF ALIALAYTFF ARQEWSSTAI TDRPTVNMLG GYYSQQQFLR NLDVRSNMA SADQPSVMDE AYKEFVMQLA SWDTRREFWL QTDYYKQRMV GNSKADAALL DEMINNIQFI PGDFTRAVND S VKLIAETA PDANNLLRQY VAFASQRAAS HLNDELKGAW AARTIQMKAQ VKRQEEVAKA IYDRRMNSIE QALKIAEQHN IS RSATDVP AEELPDSEMF LLGRPMLQAR LENLQAVGPA FDLDYDQNRA MLNTLNVGPT LDPRFQTYRY LRTPEEPVKR DSP RRAFLM IMWGIVGGLI GAGVALTRRC SKEFRVPGSH HHHHHHH

UniProtKB: ECA polysaccharide chain length modulation protein

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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

Concentration3.0 mg/mL
BufferpH: 8
GridModel: C-flat-2/2 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 5111 / Average electron dose: 52.0 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: 3.2 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 578253
Startup modelType of model: INSILICO MODEL
In silico model: initial models were made using cryoSPARC's ab initio reconstruction job
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C8 (8 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 197015
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 150000 / Software - Name: cryoSPARC (ver. 3)
FSC plot (resolution estimation)

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