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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4975 | ||||||||||||
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Title | Haemonchus galactose containing glycoprotein complex | ||||||||||||
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Function / homology | ![]() metalloendopeptidase activity / membrane => GO:0016020 / aspartic-type endopeptidase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||||||||
![]() | Scarff CA / Thompson RF / Newlands GFJ / Jamson H / Kennaway C / da Silva VJ / Rabelo EM / Song CF / Trinick J / Smith WD / Muench SP | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 107.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.5 KB 19.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.9 KB | Display | ![]() |
Images | ![]() | 120.1 KB | ||
Masks | ![]() | 184 MB | ![]() | |
Others | ![]() ![]() ![]() | 107.3 MB 145.4 MB 145 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 341.9 KB | Display | ![]() |
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Full document | ![]() | 341.1 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rowMC ![]() 4976C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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-Additional map: #1
File | emd_4975_additional.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_4975_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_4975_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Haemonchus galactose containing glycoprotein complex
Entire | Name: Haemonchus galactose containing glycoprotein complex |
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Components |
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-Supramolecule #1: Haemonchus galactose containing glycoprotein complex
Supramolecule | Name: Haemonchus galactose containing glycoprotein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Multi-protease complex |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Putative zinc metallopeptidase
Macromolecule | Name: Putative zinc metallopeptidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 86.819812 KDa |
Sequence | String: 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 |
-Macromolecule #2: Parasite pepsinogen
Macromolecule | Name: Parasite pepsinogen / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.310469 KDa |
Sequence | String: 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 |
-Macromolecule #3: Cysteine Protease
Macromolecule | Name: Cysteine Protease / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.31549 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 62.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
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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Refinement | Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-6row: |