+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18791 | ||||||||||||
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Title | Capsid structure of Giardiavirus (GLV) HP strain | ||||||||||||
Map data | Full 3D reconstruction of GLV-HP capsid. | ||||||||||||
Sample |
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Keywords | Giardia parasite / dsRNA virus / capsid structure / cryo / Totiviridae / Giardia lambia virus (GLV) / VIRUS | ||||||||||||
Function / homology | Capsid protein Function and homology information | ||||||||||||
Biological species | Giardia lamblia virus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.14 Å | ||||||||||||
Authors | Wang H / Gianluca M / Munke A / Hassan MM / Lalle M / Okamoto K | ||||||||||||
Funding support | Sweden, Norway, 3 items
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Citation | Journal: PLoS Pathog / Year: 2024 Title: High-resolution comparative atomic structures of two Giardiavirus prototypes infecting G. duodenalis parasite. Authors: Han Wang / Gianluca Marucci / Anna Munke / Mohammad Maruf Hassan / Marco Lalle / Kenta Okamoto / Abstract: The Giardia lamblia virus (GLV) is a non-enveloped icosahedral dsRNA and endosymbiont virus that infects the zoonotic protozoan parasite Giardia duodenalis (syn. G. lamblia, G. intestinalis), which ...The Giardia lamblia virus (GLV) is a non-enveloped icosahedral dsRNA and endosymbiont virus that infects the zoonotic protozoan parasite Giardia duodenalis (syn. G. lamblia, G. intestinalis), which is a pathogen of mammals, including humans. Elucidating the transmission mechanism of GLV is crucial for gaining an in-depth understanding of the virulence of the virus in G. duodenalis. GLV belongs to the family Totiviridae, which infects yeast and protozoa intracellularly; however, it also transmits extracellularly, similar to the phylogenetically, distantly related toti-like viruses that infect multicellular hosts. The GLV capsid structure is extensively involved in the longstanding discussion concerning extracellular transmission in Totiviridae and toti-like viruses. Hence, this study constructed the first high-resolution comparative atomic models of two GLV strains, namely GLV-HP and GLV-CAT, which showed different intracellular localization and virulence phenotypes, using cryogenic electron microscopy single-particle analysis. The atomic models of the GLV capsids presented swapped C-terminal extensions, extra surface loops, and a lack of cap-snatching pockets, similar to those of toti-like viruses. However, their open pores and absence of the extra crown protein resemble those of other yeast and protozoan Totiviridae viruses, demonstrating the essential structures for extracellular cell-to-cell transmission. The structural comparison between GLV-HP and GLV-CAT indicates the first evidence of critical structural motifs for the transmission and virulence of GLV in G. duodenalis. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18791.map.gz | 936.1 MB | EMDB map data format | |
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Header (meta data) | emd-18791-v30.xml emd-18791.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_18791.png | 249.5 KB | ||
Filedesc metadata | emd-18791.cif.gz | 6 KB | ||
Others | emd_18791_half_map_1.map.gz emd_18791_half_map_2.map.gz | 925 MB 925 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18791 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18791 | HTTPS FTP |
-Validation report
Summary document | emd_18791_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_18791_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_18791_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | emd_18791_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18791 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18791 | HTTPS FTP |
-Related structure data
Related structure data | 8r0fMC 8r0gC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18791.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Full 3D reconstruction of GLV-HP capsid. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A of the 3D reconstruction of GLV-HP capsid.
File | emd_18791_half_map_1.map | ||||||||||||
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Annotation | Half map A of the 3D reconstruction of GLV-HP capsid. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of the 3D reconstruction of GLV-HP capsid.
File | emd_18791_half_map_2.map | ||||||||||||
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Annotation | Half map B of the 3D reconstruction of GLV-HP capsid. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Giardia lamblia virus
Entire | Name: Giardia lamblia virus |
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Components |
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-Supramolecule #1: Giardia lamblia virus
Supramolecule | Name: Giardia lamblia virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: GLV isolated from Giardia duodenalis isolates HP-1 from a human patient. NCBI-ID: 29255 / Sci species name: Giardia lamblia virus / Sci species strain: HP-1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Giardia intestinalis (eukaryote) / Strain: HP-1 |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 450.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Giardia lamblia virus |
Molecular weight | Theoretical: 103.48132 KDa |
Sequence | String: PENITFDTLN TQNDHEETYG ESPEVPKASI APAGRQNVPV LQQNQENEDN HALGGSEDAK DEREIQSSAI KTLYNYYSEG PSTPIMPHL VNRLRGLDAL AKVDATLSKV DMNAAYIFAL RPTFPYSYGY KQRFSNRRLT TSALCYARTG LSSFLTVDKT Y TSNSPLKG ...String: PENITFDTLN TQNDHEETYG ESPEVPKASI APAGRQNVPV LQQNQENEDN HALGGSEDAK DEREIQSSAI KTLYNYYSEG PSTPIMPHL VNRLRGLDAL AKVDATLSKV DMNAAYIFAL RPTFPYSYGY KQRFSNRRLT TSALCYARTG LSSFLTVDKT Y TSNSPLKG GSRGWPIFNV GVSPHVAEPH MRTLSPIGLE VFNLATSQFS KTLLTASSKV FTQSLYTADI LSIFGEVFLP HV MQPVSNY TPILVRALLA LIHILGSGSG NCSLSSSIFE SSIPQFLTIS HSTNMSNRTR YCLHTWSAYK DMFRNGIPPQ STF PPTLAP EGSSARILIP AALVTSPMFP WLLVLVSSGP QFFLYSKDAS INTVDIGSRG RITSPIPDVA HLDLHRLWNL FRFD GYRYI DVVIVGVDRD YVWPYQNGVY VHGGKGPKGT DNYENADVHD GIGTIFSSFN NNVNVQTSDL LLGLSTLWNH ITTTY ATEE EVTMAIKIAA AFALVYPVQP IVYSGCSRAL YNHTSYFQPS SENCYTTDTA EVKSTWDTVE LSVQVNNAMV LGMTLP FGQ PTVSSAQWFN NIDKAEISMF KVGNLPLQNL DYLSLDMMEF YAPTTGQLYD IRSDSLISSA HRTVNLGIGY TALADFF AY LASVPAQSFY HNRMVTSPIS KQAYSVYERF IERFIDDFVG WGRCDLFNLD TLLGAKRIAG VASSPIPWHC SLQRCPLP I IMHYTGLHFG QEHIRVRDVA GVEGLQQIVL RNDQGSIVLD ALGTAAPSRL AVKLDWSRLS AWYSDTTCAI PISDRVMEI VNYAAIWDPT QERRATGFVY TYFSPNFLSS FNVSEPIFNK TINLTPPYDD TSQTVIQNLS MPQMLSFDPY YESTFYVVSA DNEWVPTSG PAWKVPYLEN VVKRSGRRLL AELRIASNNG SGDRTFLDDV UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.4 / Details: 1 x PBS (-) |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | Purified GLV-HP particles |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28342 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |