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- EMDB-4975: Haemonchus galactose containing glycoprotein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4975
TitleHaemonchus galactose containing glycoprotein complex
Map data
Sample
  • Complex: Haemonchus galactose containing glycoprotein complex
    • Protein or peptide: Putative zinc metallopeptidase
    • Protein or peptide: Parasite pepsinogen
    • Protein or peptide: Cysteine Protease
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) / Barber pole worm (barber pole worm)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6row
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4975.png

Downloads & links

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Map

FileDownload / File: emd_4975.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 364 pix.
= 387.66 Å		1.07 Å/pix.
x 364 pix.
= 387.66 Å		1.07 Å/pix.
x 364 pix.
= 387.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.05
Minimum - Maximum-0.13055639 - 0.3030045
Average (Standard dev.)0.0008251641 (±0.009447437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions364364364
Spacing364364364
CellA=B=C: 387.66003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z364364364
origin x/y/z0.0000.0000.000
length x/y/z387.660387.660387.660
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS364364364
D min/max/mean-0.1310.3030.001

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Supplemental data

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Mask #1

Fileemd_4975_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: #1

Fileemd_4975_additional.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_4975_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_4975_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Haemonchus galactose containing glycoprotein complex

EntireName: Haemonchus galactose containing glycoprotein complex
Components
  • Complex: Haemonchus galactose containing glycoprotein complex
    • Protein or peptide: Putative zinc metallopeptidase
    • Protein or peptide: Parasite pepsinogen
    • Protein or peptide: Cysteine Protease

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Supramolecule #1: Haemonchus galactose containing glycoprotein complex

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

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Macromolecule #1: Putative zinc metallopeptidase

MacromoleculeName: Putative zinc metallopeptidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Barber pole worm (barber pole worm)
Molecular weightTheoretical: 86.819812 KDa
SequenceString: NANRSKEWKN AANTLLFGLD ESVDPCEDFY GFTCNKFIER IDLDELGRGR FTTFSQAQLE VNSDIVKALE KVDVNDEKFS QTERITKAA FQSCVEYTLK DDRKASVNEL LQYISERFGG IPFLGQRVKG GCELYREMGR IEQQRALPTF MYTWVNVDHK N VSRNSYYI ...String:
NANRSKEWKN AANTLLFGLD ESVDPCEDFY GFTCNKFIER IDLDELGRGR FTTFSQAQLE VNSDIVKALE KVDVNDEKFS QTERITKAA FQSCVEYTLK DDRKASVNEL LQYISERFGG IPFLGQRVKG GCELYREMGR IEQQRALPTF MYTWVNVDHK N VSRNSYYI SQPTLPMPRE FYVLPQFAPE LDARTKAIEN VMKAFASDIL KDPSKYDKMI KTAAREVTQI EQKIAMASWP DD ELRNHEQ QYNPYELFAP SEGKIALQDA FPNIRFGKYI AGLMETATGG VPVSPVFIGD VIVTNPAYMG FLNTLFRQTN IQM NQYPFV NYIIVHMLFE DAEHLGDKYL RIAKDADYVT YAQRKGVGIT RSGRKYSRVF DERTDARMKC VDTITTYMPY GTGY VYVNS REDRDQVVED VKQQTELIMK TFLKKMLSTL SWMQGESYRR AEKKINEMHR NYGWPKKLFG DFKNFDTIDA YHRDD YYSI LEAYNNKTDK STAFYTILNI LRRGYENRES FRRKNETADR TNFLESPASV NAWYAPELNS LTLPFGILTS PHYDLQ FPK AFNFAGSGTV GGHELVHGFD DEGVQFDYDG SLADCSVYEC GWLEQKGKNG FKDMAQCVVT QYNAQCCPAK EGNVHCA NG AHTQGENIAD LGGLQASYNA YKEYIKMKGA EEMRLPGLEK FTPNQIFWIS YGYSWCAKET QSSLVKRLLT NPHSPNSC R VNQVLQDIPS FAKDFQCALG QKMYPPAEQR CKVW

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Macromolecule #2: Parasite pepsinogen

MacromoleculeName: Parasite pepsinogen / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Barber pole worm (barber pole worm)
Molecular weightTheoretical: 40.310469 KDa
SequenceString: VFPHPIYDYQ DTEYLAKITI GAPGQSFHVV LDTGSANLWI PDNICVNGRR GACRITTCDR GLVCEVLCHD KSCCEDDVDN PDEDNPCKG KSGFDSTQST SYAKITPKKY FEIVYGTGFA KGFLGNDTVR FGEEGNNKTL VVPGTVFGQA VQIGDPFANN P INGILGLG ...String:
VFPHPIYDYQ DTEYLAKITI GAPGQSFHVV LDTGSANLWI PDNICVNGRR GACRITTCDR GLVCEVLCHD KSCCEDDVDN PDEDNPCKG KSGFDSTQST SYAKITPKKY FEIVYGTGFA KGFLGNDTVR FGEEGNNKTL VVPGTVFGQA VQIGDPFANN P INGILGLG FRGLAQAGVT PPLQRAIDLK LVDPIFTVYM KQLGAKAKGQ DGGAFTYGGL DSVNCGQEIA YVDLTRPLYW QF KMEAFSA GYLSIRKGWE VISDTGTSFM GVPTAIADLV ADSYGGQYDE MFEIYTVDCN ATVTFGMTIG GKQYKIERKN LVL EEDKDS CMIAMTPLSS VGFGPQWILG APFIRQYCNI HDMRNNTIGF AEP

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Macromolecule #3: Cysteine Protease

MacromoleculeName: Cysteine Protease / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Barber pole worm (barber pole worm)
Molecular weightTheoretical: 28.31549 KDa
SequenceString: DPDIPENYDP RLIWPNCSSL FTIPDQANCG SCWAVSTAAA ISDRLCIASK GENQVFISSA DILSCCDTCG FGCDGGITFR AWEYFATKG SVSGGHFEAP NCCRPYYFHP CGQHGNDTFY GYCPRFAQTP FCRRKCRIGF NKSYAQDRIQ GKSFYTVDYS V PAIQREIM ...String:
DPDIPENYDP RLIWPNCSSL FTIPDQANCG SCWAVSTAAA ISDRLCIASK GENQVFISSA DILSCCDTCG FGCDGGITFR AWEYFATKG SVSGGHFEAP NCCRPYYFHP CGQHGNDTFY GYCPRFAQTP FCRRKCRIGF NKSYAQDRIQ GKSFYTVDYS V PAIQREIM TKGSVVGSYD VFTDFSHYKS GIYRHTGGKP DGRHAVRIIG WGKENGTDYW LIANSWHDDW GENGYFRMIR GI NDCGIEQ DITAGD

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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: 62.5 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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 110863
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsModels were generated using Phyre2, rigid body fitted in Chimera and then flexibly fitted into the map using MDFF in VMD.
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6row:
Haemonchus galactose containing glycoprotein complex

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