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- PDB-6ab6: Cryo-EM structure of T=3 Penaeus vannamei nodavirus -

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Basic information

Entry
Database: PDB / ID: 6ab6
TitleCryo-EM structure of T=3 Penaeus vannamei nodavirus
ComponentsCapsid proteinCapsid
KeywordsVIRUS LIKE PARTICLE / Nodaviridae / shrimp nodavirus
Function / homologyIcosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / Capsid protein
Function and homology information
Biological speciesPenaeus vannamei nodavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen, N.C. / Miyazaki, N. / Yoshimura, M. / Guan, H.H. / Lin, C.C. / Iwasaki, K. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)105-2311-B-213-001-MY3 Taiwan
CitationJournal: Commun Biol / Year: 2019
Title: The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi ...Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi Nakagawa / Sunney I Chan / Chun-Jung Chen /
Abstract: Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity ...Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of  = 3 and  = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in  = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic -terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls  = 3 and  = 1 assemblies. Increasing the /-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.
History
DepositionJul 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0279
Polymers120,7873
Non-polymers2406
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,261,618540
Polymers7,247,190180
Non-polymers14,428360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area7910 Å2
ΔGint-86 kcal/mol
Surface area43810 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 605 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)605,13545
Polymers603,93315
Non-polymers1,20230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 726 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)726,16254
Polymers724,71918
Non-polymers1,44336
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein / Capsid


Mass: 40262.168 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus vannamei nodavirus / Production host: Escherichia coli (E. coli) / References: UniProt: A5H7Q8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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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: Penaeus vannamei nodavirus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Penaeus vannamei nodavirus
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Litopenaeus vannamei
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESHEPES1
2300 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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 FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2750 nm / Nominal defocus min: 1250 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2806
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.5CTF correction
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 42751
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8596 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0077395
ELECTRON MICROSCOPYf_angle_d0.86510113
ELECTRON MICROSCOPYf_dihedral_angle_d8.5194433
ELECTRON MICROSCOPYf_chiral_restr0.0611229
ELECTRON MICROSCOPYf_plane_restr0.0071295

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