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- EMDB-11908: N-terminally truncated WzzB from E.coli - C1 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-11908
TitleN-terminally truncated WzzB from E.coli - C1 symmetry
Map dataN-terminally truncated WzzB from E.coli - C1 symmetry
Sample
  • Complex: Octameric bacterial polysaccharide co-polymerase complex
    • Protein or peptide: Chain length determinant protein
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 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
DepositionOct 28, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.85
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.85
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11908.png

Downloads & links

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Map

FileDownload / File: emd_11908.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationN-terminally truncated WzzB from E.coli - C1 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 280 pix.
= 476. Å		1.7 Å/pix.
x 280 pix.
= 476. Å		1.7 Å/pix.
x 280 pix.
= 476. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.85 / Movie #1: 0.85
Minimum - Maximum-3.738507 - 3.9162214
Average (Standard dev.)0.0068460447 (±0.08771392)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 476.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z476.000476.000476.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-3.7393.9160.007

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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)
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria) / Recombinant strain: C41
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 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
SequenceString: MQIDLIDLLV QLWRGKMTII ISVIVAIALA IGYLAVAKEK WTSTAIITQP DVGQIAGYNN AMNVI YGQA APKVSDLQET LIGRFSSAFS ALAETLDNQE EREKLTIEPS VKNQQLPLTV SYVGQTAEGA QMKLAQYIQQ VDDKVN QEL EKDLKDNIAL GRKNLQDSLR ...String:
MQIDLIDLLV QLWRGKMTII ISVIVAIALA IGYLAVAKEK WTSTAIITQP DVGQIAGYNN AMNVI YGQA APKVSDLQET LIGRFSSAFS ALAETLDNQE EREKLTIEPS VKNQQLPLTV SYVGQTAEGA QMKLAQYIQQ VDDKVN QEL EKDLKDNIAL GRKNLQDSLR TQEVVAQEQK DLRIRQIQEA LQYANQAQVT KPQIQQTGED ITQDTLFLLG SEALESM IK HEATRPLVFS PNYYQTRQNL LDIESLKVDD LDIHAYRYVM KPMLPIRRDS PKKAITLILA VLLGGMVGAG IVLGRNAL R NYNAKEFRVP GSHHHHHHHH

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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: GOLD / 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: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2050 / Average electron dose: 50.0 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: 183973
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 76968
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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