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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: 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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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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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