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- EMDB-4976: Haemonchus sialylated galactose containing glycoprotein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4976
TitleHaemonchus sialylated galactose containing glycoprotein complex
Map dataHaemonchus sialylated galactose containing glycoprotein complex
Sample
  • Complex: Haemonchus sialylated galactose containing glycoprotein complex
Biological speciesHaemonchus contortus (barber pole worm)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsScarff CA / Thompson RF / Newlands GFJ / Jamson H / Kennaway C / da Silva VJ / Rabelo EM / Song CF / Trinick J / Smith WD / Muench SP
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust204825/Z/16/Z United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
Wellcome Trust096685/Z/11/Z United Kingdom
CitationJournal: PLoS Pathog / Year: 2020
Title: Structure of the protective nematode protease complex H-gal-GP and its conservation across roundworm parasites.
Authors: Charlotte A Scarff / Rebecca F Thompson / George F J Newlands / Alexander H Jamson / Christopher Kennaway / Vivian J da Silva / Elida M Rabelo / Chun-Feng Song / John Trinick / W David Smith ...Authors: Charlotte A Scarff / Rebecca F Thompson / George F J Newlands / Alexander H Jamson / Christopher Kennaway / Vivian J da Silva / Elida M Rabelo / Chun-Feng Song / John Trinick / W David Smith / Stephen P Muench /
Abstract: Roundworm parasite infections are a major cause of human and livestock disease worldwide and a threat to global food security. Disease control currently relies on anthelmintic drugs to which ...Roundworm parasite infections are a major cause of human and livestock disease worldwide and a threat to global food security. Disease control currently relies on anthelmintic drugs to which roundworms are becoming increasingly resistant. An alternative approach is control by vaccination and 'hidden antigens', components of the worm gut not encountered by the infected host, have been exploited to produce Barbervax, the first commercial vaccine for a gut dwelling nematode of any host. Here we present the structure of H-gal-GP, a hidden antigen from Haemonchus contortus, the Barber's Pole worm, and a major component of Barbervax. We demonstrate its novel architecture, subunit composition and topology, flexibility and heterogeneity using cryo-electron microscopy, mass spectrometry, and modelling. Importantly, we demonstrate that complexes with the same architecture are present in other Strongylid roundworm parasites including human hookworm. This suggests a common ancestry and the potential for development of a unified hidden antigen vaccine.
History
DepositionMay 13, 2019-
Header (metadata) releaseMar 25, 2020-
Map releaseMar 25, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.117
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.117
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4976.png

Downloads & links

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Map

FileDownload / File: emd_4976.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHaemonchus sialylated galactose containing glycoprotein complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 182 pix.
= 387.66 Å		2.13 Å/pix.
x 182 pix.
= 387.66 Å		2.13 Å/pix.
x 182 pix.
= 387.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117 / Movie #1: 0.117
Minimum - Maximum-0.18133898 - 0.54841423
Average (Standard dev.)0.0011765957 (±0.015845068)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions182182182
Spacing182182182
CellA=B=C: 387.66003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.132.132.13
M x/y/z182182182
origin x/y/z0.0000.0000.000
length x/y/z387.660387.660387.660
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS182182182
D min/max/mean-0.1810.5480.001

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Supplemental data

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Mask #1

Fileemd_4976_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Haemonchus sialylated galactose containing glycoprotein complex half map...

Fileemd_4976_half_map_1.map
AnnotationHaemonchus sialylated galactose containing glycoprotein complex half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Haemonchus sialylated galactose containing glycoprotein complex half map...

Fileemd_4976_half_map_2.map
AnnotationHaemonchus sialylated galactose containing glycoprotein complex half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Haemonchus sialylated galactose containing glycoprotein complex

EntireName: Haemonchus sialylated galactose containing glycoprotein complex
Components
  • Complex: Haemonchus sialylated galactose containing glycoprotein complex

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Supramolecule #1: Haemonchus sialylated galactose containing glycoprotein complex

SupramoleculeName: Haemonchus sialylated galactose containing glycoprotein complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Multi-protease complex
Source (natural)Organism: Haemonchus contortus (barber pole worm)
Molecular weightTheoretical: 500 KDa

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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

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 62.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 23186
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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