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- EMDB-18792: Capsid structure of Giardiavirus (GLV) CAT strain -

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Basic information

Entry
Database: EMDB / ID: EMD-18792
TitleCapsid structure of Giardiavirus (GLV) CAT strain
Map dataFull map of GLV-CAT capsid
Sample
  • Virus: Giardia lamblia virus
    • Protein or peptide: Capsid protein
KeywordsGiardia parsite / dsRNA virus / capsid structure / Totiviridae / Giardia lambia virus (GLV) / VIRUS
Function / homologyCapsid protein
Function and homology information
Biological speciesGiardia lamblia virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang H / Gianluca M / Munke A / Hassan MM / Lalle M / Okamoto K
Funding support Sweden, Norway, 3 items
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, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18792.png

Downloads & links

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Map

FileDownload / File: emd_18792.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map of GLV-CAT capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 640 pix.
= 678.4 Å		1.06 Å/pix.
x 640 pix.
= 678.4 Å		1.06 Å/pix.
x 640 pix.
= 678.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.3521256 - 2.9467044
Average (Standard dev.)0.023335572 (±0.14959416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 678.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of GLV-CAT capsid

Fileemd_18792_half_map_1.map
AnnotationHalf map A of GLV-CAT capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of GLV-CAT capsid

Fileemd_18792_half_map_2.map
AnnotationHalf map B of GLV-CAT capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Giardia lamblia virus

EntireName: Giardia lamblia virus
Components
  • Virus: Giardia lamblia virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Giardia lamblia virus

SupramoleculeName: Giardia lamblia virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: GLV isolated from G. duodenalis isolates CAT-1 from a cat
NCBI-ID: 29255 / Sci species name: Giardia lamblia virus / Sci species strain: CAT-1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Giardia intestinalis (eukaryote) / Strain: CAT-1
Virus shellShell ID: 1 / Name: Capsid / Diameter: 450.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Giardia lamblia virus
Molecular weightTheoretical: 103.492406 KDa
SequenceString: PENITLDTLN TQNDYEETHG ESPEVPKASI APAGRQNVPV LQQNQENKDN HALGGSEDAK DEREIRFSAI KTLYNYYSEG PSTPIMPHL VNRLRGLDAL AKIDATLTKV DMNAAYIFAL RPTFPYSYGY KQRFSNRRLT TSAVCYARTG LSSFLTVNKT Y TSNSPLKG ...String:
PENITLDTLN TQNDYEETHG ESPEVPKASI APAGRQNVPV LQQNQENKDN HALGGSEDAK DEREIRFSAI KTLYNYYSEG PSTPIMPHL VNRLRGLDAL AKIDATLTKV DMNAAYIFAL RPTFPYSYGY KQRFSNRRLT TSAVCYARTG LSSFLTVNKT Y TSNSPLKG GSRGWPIFNV GVSPHVAEPH MRTLSPIGLE VFSQNLATFS KTLLTASSKV FTQSLYTADI LSIFGEVFLP HV MQPVSNY TPILVRALLA LIHILGPGSG NCSLSSSIFE SSIPQFFTVS HSTNMSNRTR YCLHTWSAYK DMFRNGIPPQ STL PPTLAP EGSSARVLIP AALVTSPMFP WLLALVSSGP QFFLYSKDAS INTVDIGSRG RITSPIPDVA NLDLHRLWNL FRFD GHRYI DVVIVGVDRD YVWPYQNGVY VHGGKGPNGT DNYGNADVHD GIGTIFSSFN DNVNVQTSDL ILGLLTLWNH ITTTY ATEE EVTMAIKIAA AFALVYPVQP IVYSGCPRAF QSHTSYYQPS SENCYTTDTA EVKSTWDTVE LSVQVNNAMV LGMTLP FGQ PTVSSAQWFN NIDKAEISMF KVGNLPLQNL DYLSLDMMEF YAPTTGQLYD IRSDNLILSA HRTVNLGIGY TALADFF AY LASVPAQSFY HDRMVTSPIS KQTYSVYERF IERFVDDFVG WDRCDLFNLD TLLAAKRIAG VASSPIPWHC SLQRCPLP I IMHYTGLHFG QEHITVRDVA GVEGLQQIVM RNDQGKIVVD ALGTAAPSRL AVKLDWSRLS AWYSDTTCAI PLSDRVMEI INYAAIWDPT QERRATGFVY TYFSPNFLSS FNASEPIFNT SINLTPPYDD TSHTVIQNLS MPQMLSFDPY YESTFYVVSA DNEWIPTSG PAWKVPYLEN VVKRSGRRLL AELRIASNNG SGDRTFLDDV

UniProtKB: Capsid protein

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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

Concentration1.0 mg/mL
BufferpH: 7.4 / Details: 1 x PBS (-)
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified GLV-CAT particles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

30538

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5804
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

6s2c


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8r0g:
Capsid structure of Giardiavirus (GLV) CAT strain

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