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- PDB-8r0f: Capsid structure of Giardiavirus (GLV) HP strain -

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Basic information

Entry
Database: PDB / ID: 8r0f
TitleCapsid structure of Giardiavirus (GLV) HP strain
ComponentsCapsid protein
KeywordsVIRUS / Giardia parasite / dsRNA virus / capsid structure / cryo / Totiviridae / Giardia lambia virus (GLV)
Function / homologyCapsid protein
Function and homology information
Biological speciesGiardia lamblia virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsWang, H. / Gianluca, M. / Munke, A. / Hassan, M.M. / Lalle, M. / Okamoto, K.
Funding support Sweden, Norway, 3items
OrganizationGrant numberCountry
Swedish Research Council2018-03387 Sweden
Swedish Research Council2018-00421 Sweden
Norwegian Research Council324266 Norway
CitationJournal: 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
DepositionOct 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
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Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Capsid protein
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)206,9632
Polymers206,9632
Non-polymers00
Water00
1
B: Capsid protein
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)12,417,758120
Polymers12,417,758120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein


Mass: 103481.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia virus / References: UniProt: A0A8F6AHR5
Has protein modificationN

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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: Giardia lamblia virus / Type: VIRUS
Details: GLV isolated from Giardia duodenalis isolates HP-1 from a human patient.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Giardia lamblia virus / Strain: HP-1
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Giardia intestinalis / Strain: HP-1
Virus shellName: Capsid / Diameter: 450 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4 / Details: 1 x PBS (-)
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified GLV-HP particles
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28342 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 6S2C

6s2c


Accession code: 6S2C / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413209
ELECTRON MICROSCOPYf_angle_d0.66818040
ELECTRON MICROSCOPYf_dihedral_angle_d5.6571793
ELECTRON MICROSCOPYf_chiral_restr0.0462030
ELECTRON MICROSCOPYf_plane_restr0.0062304

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