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- EMDB-18791: Capsid structure of Giardiavirus (GLV) HP strain -

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Basic information

Entry
Database: EMDB / ID: EMD-18791
TitleCapsid structure of Giardiavirus (GLV) HP strain
Map dataFull 3D reconstruction of GLV-HP capsid.
Sample
  • Virus: Giardia lamblia virus
    • Protein or peptide: Capsid proteinCapsid
KeywordsGiardia parasite / dsRNA virus / capsid structure / cryo / Totiviridae / Giardia lambia virus (GLV) / VIRUS
Function / homologyCapsid protein
Function and homology information
Biological speciesGiardia lamblia virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.14 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: To Be Published
Title: Capsid structure of Giardiavirus (GLV) HP strain
Authors: Wang H / Gianluca M / Munke A / Hassan MM / Lalle M / Okamoto K
History
DepositionOct 31, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18791.png

Downloads & links

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Map

FileDownload / File: emd_18791.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull 3D reconstruction of GLV-HP capsid.
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.68
Minimum - Maximum-3.3936827 - 5.5469723
Average (Standard dev.)0.021851333 (±0.22716478)
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 the 3D reconstruction of GLV-HP capsid.

Fileemd_18791_half_map_1.map
AnnotationHalf map A of the 3D reconstruction of GLV-HP capsid.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the 3D reconstruction of GLV-HP capsid.

Fileemd_18791_half_map_2.map
AnnotationHalf map B of the 3D reconstruction of GLV-HP 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 proteinCapsid

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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 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
Host (natural)Organism: Giardia intestinalis (eukaryote) / Strain: HP-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: 103.48132 KDa
SequenceString: 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

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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-HP particles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

30538

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28342

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

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