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- PDB-6row: Haemonchus galactose containing glycoprotein complex -

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Basic information

Entry
Database: PDB / ID: 6row
TitleHaemonchus galactose containing glycoprotein complex
Components
  • Cysteine Protease
  • Parasite pepsinogen
  • Putative zinc metallopeptidase
KeywordsHYDROLASE / Multi-protease complex
Function / homology
Function and homology information


metalloendopeptidase activity / protein processing / lysosome / aspartic-type endopeptidase activity / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / Aspartic peptidase, N-terminal / A1 Propeptide / Pepsin-like domain ...Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / Aspartic peptidase, N-terminal / A1 Propeptide / Pepsin-like domain / Metallopeptidase, catalytic domain superfamily / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Putative zinc metallopeptidase / Parasite pepsinogen
Similarity search - Component
Biological speciesHaemonchus contortus (barber pole worm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsScarff, C.A. / Thompson, R.F. / Newlands, G.F.J. / Jamson, H. / Kennaway, C. / da Silva, V.J. / Rabelo, E.M. / Song, C.F. / Trinick, J. / Smith, W.D. / Muench, S.P.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust204825/Z/16/Z United Kingdom
Wellcome Trust096685/Z/11/Z United Kingdom
Wellcome Trust108466/Z/15/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, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Putative zinc metallopeptidase
B: Putative zinc metallopeptidase
C: Putative zinc metallopeptidase
D: Putative zinc metallopeptidase
E: Parasite pepsinogen
F: Parasite pepsinogen
G: Cysteine Protease


Theoretical massNumber of molelcules
Total (without water)456,2167
Polymers456,2167
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5840 Å2
ΔGint-16 kcal/mol
Surface area161110 Å2
MethodPISA

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Components

#1: Protein
Putative zinc metallopeptidase


Mass: 86819.812 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Haemonchus contortus (barber pole worm) / References: UniProt: O76751
#2: Protein Parasite pepsinogen


Mass: 40310.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Haemonchus contortus (barber pole worm) / References: UniProt: Q25037
#3: Protein Cysteine Protease


Mass: 28315.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haemonchus contortus (barber pole worm)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Haemonchus galactose containing glycoprotein complex / Type: COMPLEX / Details: Multi-protease complex / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Haemonchus contortus (barber pole worm)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 62.5 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110863 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Details: Models were generated using Phyre2, rigid body fitted in Chimera and then flexibly fitted into the map using MDFF in VMD.

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