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- EMDB-4798: full-length bacterial polysaccharide co-polymerase - C8 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-4798
Titlefull-length bacterial polysaccharide co-polymerase - C8 symmetry
Map datafull-length bacterial polysaccharide co-polymerase - C8 symmetry
Sample
  • Complex: Octameric bacterial polysaccharide co-polymerase complex
    • Protein or peptide: Chain length determinant protein
Keywordsmembrane protein / enzyme / polysaccharide / co-polymerase
Function / homologyPolysaccharide chain length determinant N-terminal domain / Chain length determinant protein / : / lipopolysaccharide biosynthetic process / protein tyrosine kinase activity / plasma membrane / Chain length determinant protein
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWiseman B / Nitharwal RG
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-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing 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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  • Surface view with fitted model
  • Atomic models: PDB-6rbg
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4798.png

Downloads & links

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Map

FileDownload / File: emd_4798.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull-length bacterial polysaccharide co-polymerase - C8 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-1.9880177 - 3.7666101
Average (Standard dev.)0.0036973557 (±0.0611758)
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/NZ-225-225-225
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.9883.7670.004

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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: Chain length determinant protein

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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)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Chain length determinant protein

MacromoleculeName: Chain length determinant protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 38.370621 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
SequenceString: MRVENNNVSG QNHDPEQIDL IDLLVQLWRG KMTIIISVIV AIALAIGYLA VAKEKWTSTA IITQPDVGQI AGYNNAMNVI YGQAAPKVS DLQETLIGRF SSAFSALAET LDNQEEREKL TIEPSVKNQQ LPLTVSYVGQ TAEGAQMKLA QYIQQVDDKV N QELEKDLK ...String:
MRVENNNVSG QNHDPEQIDL IDLLVQLWRG KMTIIISVIV AIALAIGYLA VAKEKWTSTA IITQPDVGQI AGYNNAMNVI YGQAAPKVS DLQETLIGRF SSAFSALAET LDNQEEREKL TIEPSVKNQQ LPLTVSYVGQ TAEGAQMKLA QYIQQVDDKV N QELEKDLK DNIALGRKNL QDSLRTQEVV AQEQKDLRIR QIQEALQYAN QAQVTKPQIQ QTGEDITQDT LFLLGSEALE SM IKHEATR PLVFSPNYYQ TRQNLLDIES LKVDDLDIHA YRYVMKPMLP IRRDSPKKAI TLILAVLLGG MVGAGIVLGR NAL RNYNAK EFRVPGSHHH HHHHH

UniProtKB: Chain length determinant 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

Concentration3.5 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
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 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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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87
Output model

PDB-6rbg:
full-length bacterial polysaccharide co-polymerase

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