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Yorodumi- EMDB-5948: Three-dimensional structure of a protozoal dsRNA virus that infec... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5948 | |||||||||
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Title | Three-dimensional structure of a protozoal dsRNA virus that infects enteric pathogen Giardia lamblia | |||||||||
Map data | Icosahedral reconstruction of giardiavirus | |||||||||
Sample |
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Keywords | Giardia lamblia virus / protozoal virus / dsRNA virus / icosahedral image reconstruction / cryoTEM / infects Giardia lamblia | |||||||||
Biological species | Giardia lamblia virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
Authors | Janssen ME / Takagi Y / Parent KN / Cardone G / Fichorova RN / Nibert ML / Baker TS | |||||||||
Citation | Journal: J Virol / Year: 2015 Title: Three-dimensional structure of a protozoal double-stranded RNA virus that infects the enteric pathogen Giardia lamblia. Authors: Mandy E W Janssen / Yuko Takagi / Kristin N Parent / Giovanni Cardone / Max L Nibert / Timothy S Baker / Abstract: Giardia lamblia virus (GLV) is a small, nonenveloped, nonsegmented double-stranded RNA (dsRNA) virus infecting Giardia lamblia, the most common protozoan pathogen of the human intestine and a major ...Giardia lamblia virus (GLV) is a small, nonenveloped, nonsegmented double-stranded RNA (dsRNA) virus infecting Giardia lamblia, the most common protozoan pathogen of the human intestine and a major agent of waterborne diarrheal disease worldwide. GLV (genus Giardiavirus) is a member of family Totiviridae, along with several other groups of protozoal or fungal viruses, including Leishmania RNA viruses and Trichomonas vaginalis viruses. Interestingly, GLV is more closely related than other Totiviridae members to a group of recently discovered metazoan viruses that includes penaeid shrimp infectious myonecrosis virus (IMNV). Moreover, GLV is the only known protozoal dsRNA virus that can transmit efficiently by extracellular means, also like IMNV. In this study, we used transmission electron cryomicroscopy and icosahedral image reconstruction to examine the GLV virion at an estimated resolution of 6.0 Å. Its outermost diameter is 485 Å, making it the largest totivirus capsid analyzed to date. Structural comparisons of GLV and other totiviruses highlighted a related "T=2" capsid organization and a conserved helix-rich fold in the capsid subunits. In agreement with its unique capacity as a protozoal dsRNA virus to survive and transmit through extracellular environments, GLV was found to be more thermoresistant than Trichomonas vaginalis virus 1, but no specific protein machinery to mediate cell entry, such as the fiber complexes in IMNV, could be localized. These and other structural and biochemical findings provide a basis for future work to dissect the cell entry mechanism of GLV into a "primitive" (early-branching) eukaryotic host and an important enteric pathogen of humans. IMPORTANCE: Numerous pathogenic bacteria, including Corynebacterium diphtheriae, Salmonella enterica, and Vibrio cholerae, are infected with lysogenic bacteriophages that contribute significantly to ...IMPORTANCE: Numerous pathogenic bacteria, including Corynebacterium diphtheriae, Salmonella enterica, and Vibrio cholerae, are infected with lysogenic bacteriophages that contribute significantly to bacterial virulence. In line with this phenomenon, several pathogenic protozoa, including Giardia lamblia, Leishmania species, and Trichomonas vaginalis are persistently infected with dsRNA viruses, and growing evidence indicates that at least some of these protozoal viruses can likewise enhance the pathogenicity of their hosts. Understanding of these protozoal viruses, however, lags far behind that of many bacteriophages. Here, we investigated the dsRNA virus that infects the widespread enteric parasite Giardia lamblia. Using electron cryomicroscopy and icosahedral image reconstruction, we determined the virion structure of Giardia lamblia virus, obtaining new information relating to its assembly, stability, functions in cell entry and transcription, and similarities and differences with other dsRNA viruses. The results of our study set the stage for further mechanistic work on the roles of these viruses in protozoal virulence. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5948.map.gz | 143.2 MB | EMDB map data format | |
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Header (meta data) | emd-5948-v30.xml emd-5948.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_5948.png | 401 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5948 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5948 | HTTPS FTP |
-Validation report
Summary document | emd_5948_validation.pdf.gz | 79.1 KB | Display | EMDB validaton report |
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Full document | emd_5948_full_validation.pdf.gz | 78.2 KB | Display | |
Data in XML | emd_5948_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5948 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5948 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5948.map.gz / Format: CCP4 / Size: 808.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Icosahedral reconstruction of giardiavirus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : GLV virion
Entire | Name: GLV virion |
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Components |
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-Supramolecule #1000: GLV virion
Supramolecule | Name: GLV virion / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1 |
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-Supramolecule #1: Giardia lamblia virus
Supramolecule | Name: Giardia lamblia virus / type: virus / ID: 1 / Name.synonym: GLV / NCBI-ID: 29255 / Sci species name: Giardia lamblia virus / Sci species strain: WBI / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: GLV |
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Host (natural) | Organism: Giardia intestinalis (eukaryote) / Strain: WBI / synonym: PROTOZOA |
Virus shell | Shell ID: 1 / Diameter: 485 Å / T number (triangulation number): 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.2 / Details: 50 mM HEPES, 500 mM NaCl, 20 mM MgCl2 |
Grid | Details: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot 5 sec before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 90 K / Max: 96 K / Average: 93 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification. |
Date | Apr 18, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 101 / Average electron dose: 25 e/Å2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 58050 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.41 µm / Nominal defocus min: 0.78 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Particles were selected and preprocessed using RobEM. Image reconstruction was performed using Auto3DEM. |
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CTF correction | Details: robem |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Software - Name: auto3dem Details: Particles were selected and preprocessed using RobEM. Number images used: 14125 |