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- PDB-9gg2: Structure of IPNV L5 capsid -

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Basic information

Entry
Database: PDB / ID: 9gg2
TitleStructure of IPNV L5 capsid
ComponentsStructural polyprotein
KeywordsVIRUS / Salmoid / Capsid / Birnavirus / Infectious pancreatic necrosis virus / IPNV
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsMunke, A. / Gamil, A. / Mikalsen, A. / Wang, H. / Evensen, O. / Okamoto, K.
Funding support Sweden, Norway, 6items
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: J Virol / Year: 2025
Title: Structure of the T=13 capsid of infectious pancreatic necrosis virus (IPNV)-a salmonid birnavirus.
Authors: Anna Munke / Amr Ahmed Abdelrahim Gamil / Aase B Mikalsen / Han Wang / Øystein Evensen / Kenta Okamoto /
Abstract: Birnaviruses infect a broad range of vertebrate hosts, including fish and birds, and cause substantial economic losses in the fishery and livestock industries. The infectious pancreatic necrosis ...Birnaviruses infect a broad range of vertebrate hosts, including fish and birds, and cause substantial economic losses in the fishery and livestock industries. The infectious pancreatic necrosis virus (IPNV), an aquabirnavirus, specifically infects salmonids. While structures on T=1 subviral particles of the birnaviruses, including IPNV, have been studied, structural insights into the infectious T=13 particles have been limited to the infectious bursal disease virus (IBDV), an avibirnavirus. Determining the capsid structure of the T=13 particle of IPNV is crucial for advancing knowledge of its antigenicity, capsid assembly, and possible functional structures. Here, the capsid structure of the IPNV L5 strain has been determined at a resolution of 2.75 Å. The overall structure resembles the T=13 IBDV structure, with notable differences in the surface loops on the P domain of the VP2 capsid protein essential for antigenicity and virulence. Additionally, previously undescribed structural features have been identified, including the C-terminal regions of the VP2 subunits within the pentagonal assembly unit at each 5-fold axis, which interlock with adjacent VP2 subunits. This interlocking, together with class-averaged projections of triangular and pentagonal units, suggests that the pentagonal unit formation could be important for a correct T=13 particle assembly, preventing the formation of T=1 subviral particles. Furthermore, positively charged residues in obstructed capsid pores at each 5-fold axis are speculated to facilitate intraparticle genome synthesis of IPNV.IMPORTANCEAquabirnaviruses cause deadly infectious diseases in salmonid fish, posing significant challenges for both wild and farmed fish populations. The most prevalent aquabirnavirus worldwide is the infectious pancreatic necrosis virus, whose multifunctional capsid is critical to its infection, replication, and maturation. Previously, research has focused on the structure of the virus' non-infectious subviral capsid. In this study, however, the first structure of the large, infectious, and functional form of the capsid has been determined. This new capsid structure reveals functional motifs that were previously unclear in the non-infectious capsid. These motifs are believed to be essential for the virus' replication and particle assembly, making them promising targets for developing strategies to control virus proliferation.
History
DepositionAug 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural polyprotein
B: Structural polyprotein
C: Structural polyprotein
D: Structural polyprotein
E: Structural polyprotein
F: Structural polyprotein
G: Structural polyprotein
H: Structural polyprotein
I: Structural polyprotein
J: Structural polyprotein
K: Structural polyprotein
L: Structural polyprotein
M: Structural polyprotein


Theoretical massNumber of molelcules
Total (without water)724,42213
Polymers724,42213
Non-polymers00
Water00
1
A: Structural polyprotein
B: Structural polyprotein
C: Structural polyprotein
D: Structural polyprotein
E: Structural polyprotein
F: Structural polyprotein
G: Structural polyprotein
H: Structural polyprotein
I: Structural polyprotein
J: Structural polyprotein
K: Structural polyprotein
L: Structural polyprotein
M: Structural polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)43,465,326780
Polymers43,465,326780
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Structural polyprotein / PP


Mass: 55724.777 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Infectious pancreatic necrosis virus / Strain: L5
References: UniProt: A0A346FTX9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
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: Infectious pancreatic necrosis virus / Type: VIRUS / Details: Purified from infected cell culture fluid / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Infectious pancreatic necrosis virus / Strain: L5
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellTriangulation number (T number): 13
Buffer solutionpH: 7.4 / Details: PBS (-)
SpecimenConc.: 1.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 1700 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: HELIUM / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 26.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 27945

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3.1particle selection
4cryoSPARC4.3.1CTF correction
7Coot1.0.06model fitting
9cryoSPARC4.3.1initial Euler assignment
10cryoSPARC4.3.1final Euler assignment
11cryoSPARC4.3.1classification
12cryoSPARC4.3.13D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 35498 / Details: including 12,898 dsRNA-genome filled particles
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35498 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Predicted from sequence / Source name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00643324
ELECTRON MICROSCOPYf_angle_d0.74259025
ELECTRON MICROSCOPYf_dihedral_angle_d6.71226358
ELECTRON MICROSCOPYf_chiral_restr0.0496895
ELECTRON MICROSCOPYf_plane_restr0.0057676

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