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- EMDB-4791: full-length bacterial polysaccharide co-polymerase - C1 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-4791
Titlefull-length bacterial polysaccharide co-polymerase - C1 symmetry
Map dataFull-length bacterial polysaccharide co-polymerase - C1 symmetry
Sample
  • Complex: Octameric bacterial polysaccharide co-polymerase complex
    • Protein or peptide: Bacterial polysaccharide co-polymerase
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWiseman B / Nitharwal RG / Hogbom M
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: Nat Commun / Year: 2021
Title: Structure of a full-length bacterial polysaccharide co-polymerase.
Authors: Benjamin Wiseman / Ram Gopal Nitharwal / Göran Widmalm / Martin Högbom /
Abstract: Lipopolysaccharides are important components of the bacterial cell envelope that among other things act as a protective barrier against the environment and toxic molecules such as antibiotics. One of ...Lipopolysaccharides are important components of the bacterial cell envelope that among other things act as a protective barrier against the environment and toxic molecules such as antibiotics. One of the most widely disseminated pathways of polysaccharide biosynthesis is the inner membrane bound Wzy-dependent pathway. Here we present the 3.0 Å structure of the co-polymerase component of this pathway, WzzB from E. coli solved by single-particle cryo-electron microscopy. The overall architecture is octameric and resembles a box jellyfish containing a large bell-shaped periplasmic domain with the 2-helix transmembrane domain from each protomer, positioned 32 Å apart, encircling a large empty transmembrane chamber. This structure also reveals the architecture of the transmembrane domain, including the location of key residues for the Wzz-family of proteins and the Wzy-dependent pathway present in many Gram-negative bacteria, explaining several of the previous biochemical and mutational studies and lays the foundation for future investigations.
History
DepositionApr 10, 2019-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4791.png

Downloads & links

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Map

FileDownload / File: emd_4791.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull-length bacterial polysaccharide co-polymerase - C1 symmetry
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: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.7160566 - 1.7335296
Average (Standard dev.)0.0044566365 (±0.038793348)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.000424.000424.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.7161.7340.004

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Supplemental data

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Sample components

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Entire : Octameric bacterial polysaccharide co-polymerase complex

EntireName: Octameric bacterial polysaccharide co-polymerase complex
Components
  • Complex: Octameric bacterial polysaccharide co-polymerase complex
    • Protein or peptide: Bacterial polysaccharide co-polymerase

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Supramolecule #1: Octameric bacterial polysaccharide co-polymerase complex

SupramoleculeName: Octameric bacterial polysaccharide co-polymerase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria) / Recombinant strain: C41
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Bacterial polysaccharide co-polymerase

MacromoleculeName: Bacterial polysaccharide co-polymerase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
SequenceString: MRVENNNVSG QNHDPEQIDL IDLLVQLWRG KMTIIISVIV AIALAIGYLA VAKEKWTSTA IITQPDVGQI AGYNNAMNVI YGQAAPKVSD LQETLIGRFS SAFSALAETL DNQEEREKLT IEPSVKNQQL PLTVSYVGQT AEGAQMKLAQ YIQQVDDKVN QELEKDLKDN ...String:
MRVENNNVSG QNHDPEQIDL IDLLVQLWRG KMTIIISVIV AIALAIGYLA VAKEKWTSTA IITQPDVGQI AGYNNAMNVI YGQAAPKVSD LQETLIGRFS SAFSALAETL DNQEEREKLT IEPSVKNQQL PLTVSYVGQT AEGAQMKLAQ YIQQVDDKVN QELEKDLKDN IALGRKNLQD SLRTQEVVAQ EQKDLRIRQI QEALQYANQA QVTKPQIQQT GEDITQDTLF LLGSEALESM IKHEATRPLV FSPNYYQTRQ NLLDIESLKV DDLDIHAYRY VMKPMLPIRR DSPKKAITLI LAVLLGGMVG AGIVLGRNAL RNYNAKEFRV PGSHHHHHHH H

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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

Concentration3.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Details: 40 seconds at 20 mA
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: 2347 / 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
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: 90297
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 52378
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 2)
FSC plot (resolution estimation)

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