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- EMDB-51321: Structure of IPNV L5 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-51321
TitleStructure of IPNV L5 capsid
Map data
Sample
  • Virus: Infectious pancreatic necrosis virus
    • Protein or peptide: Structural polyprotein
KeywordsSalmoid / Capsid / Birnavirus / Infectious pancreatic necrosis virus / IPNV / VIRUS
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding
Similarity search - Function
Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesInfectious pancreatic necrosis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsMunke A / Gamil A / Mikalsen A / Wang H / Evensen O / Okamoto K
Funding support Sweden, Norway, 6 items
OrganizationGrant numberCountry
Swedish Research Council2018-03387 Sweden
Swedish Research Council2023-01857 Sweden
Swedish Research Council2022-00236 Sweden
Swedish Research Council2018-00421 Sweden
Swedish Research Council2022-02347 Sweden
Norwegian Research Council324266 Norway
CitationJournal: To Be Published
Title: Structure of IPNV L5 capsid
Authors: Munke A / Gamil A / Mikalsen A / Wang H / Evensen O / Okamoto K
History
DepositionAug 13, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 8, 2025-
Current statusJan 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51321.png

Downloads & links

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Map

FileDownload / File: emd_51321.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 700 pix.
= 898.8 Å		1.28 Å/pix.
x 700 pix.
= 898.8 Å		1.28 Å/pix.
x 700 pix.
= 898.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.284 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.92
Minimum - Maximum-1.9112991 - 3.982858
Average (Standard dev.)0.03813521 (±0.23051384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-350-350-350
Dimensions700700700
Spacing700700700
CellA=B=C: 898.80005 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51321_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51321_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Infectious pancreatic necrosis virus

EntireName: Infectious pancreatic necrosis virus
Components
  • Virus: Infectious pancreatic necrosis virus
    • Protein or peptide: Structural polyprotein

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Supramolecule #1: Infectious pancreatic necrosis virus

SupramoleculeName: Infectious pancreatic necrosis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified from infected cell culture fluid / NCBI-ID: 11002 / Sci species name: Infectious pancreatic necrosis virus / Sci species strain: L5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / T number (triangulation number): 13

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Macromolecule #1: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Source (natural)Organism: Infectious pancreatic necrosis virus / Strain: L5
Molecular weightTheoretical: 55.724777 KDa
SequenceString: MNTNKATATY LKSIMLPETG PASIPDDITE RHILKQETSS YNLEVSESGS GILVCFPGAP GSRIGAHYRW NANQTGLEFD QWLETSQDL KKAFNYGRLI SRKYDIQSST LPAGLYALNG TLNAATFEGS LSEVESLTYN SLMSLTTNPQ DKVNNQLVTK G VTVLNLPT ...String:
MNTNKATATY LKSIMLPETG PASIPDDITE RHILKQETSS YNLEVSESGS GILVCFPGAP GSRIGAHYRW NANQTGLEFD QWLETSQDL KKAFNYGRLI SRKYDIQSST LPAGLYALNG TLNAATFEGS LSEVESLTYN SLMSLTTNPQ DKVNNQLVTK G VTVLNLPT GFDKPYVRLE DETPQGLQSM NGAKMRCTAA IAPRRYEIDL PSQRLPPVPA TGTLTTLYEG NADIVNSTTV TG DINFGLA RQPADETTFH FQLDFMGLDN DVPVVTVVSS ALATTDNHRG VSAKMTQSIP TENITKPITR VKLSYKINQQ TAI DNVATL GTMGPASVSF SSGNGNVPGV LRPITLVAYE KMTPLSILTV AGVSNYELIP NPELLKNMVT RYGKYDPEGL NYAK MILSH REELDIRTVW RTEEYKERTR VFNEITDFSS DLPTSKAWGW RDIVRGIRKV AAPVLSTLFP MAAPLIGMAD QFIGD LTKT NAAGGRYHSM AAGGRYKDVL ESWA

UniProtKB: Structural polyprotein

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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

Concentration1.08 mg/mL
BufferpH: 7.4 / Details: PBS (-)
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 27945 / Average electron dose: 26.8 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: 1.7 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: HELIUM
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 35498 / Details: including 12,898 dsRNA-genome filled particles
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 35498
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3.1)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: Predicted from sequence
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9gg2:
Structure of IPNV L5 capsid

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