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- PDB-5ykz: The crystal structure of Penaeus vannamei nodavirus P-domain (P21) -

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Basic information

Entry
Database: PDB / ID: 5ykz
TitleThe crystal structure of Penaeus vannamei nodavirus P-domain (P21)
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / viral capsid protein
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.17 Å
AuthorsChen, N.C. / Yoshimura, M. / Lin, C.C. / Guan, H.H. / Chuankhayan, P. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology105-2311-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
DepositionOct 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)25,1162
Polymers25,1162
Non-polymers00
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-13 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.600, 53.192, 46.072
Angle α, β, γ (deg.)90.00, 109.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein / Capsid


Mass: 12558.083 Da / Num. of mol.: 2 / Fragment: UNP residues 250-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus vannamei nodavirus / Production host: Escherichia coli (E. coli) / References: UniProt: A5H7Q8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 30%(w/v) Polyethylene glycol 4,000, 100mM MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.17→30 Å / Num. obs: 65509 / % possible obs: 99.1 % / Redundancy: 4.6 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.088 / Rsym value: 0.077 / Net I/σ(I): 17.9
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 4.3 % / CC1/2: 0.859 / Rpim(I) all: 0.22 / Rrim(I) all: 0.467 / Rsym value: 0.41 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.17→22.5 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.563 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16984 2910 4.7 %RANDOM
Rwork0.15069 ---
obs0.15159 58534 94.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.767 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.04 Å2
2---0.17 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.17→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 0 414 2095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021707
X-RAY DIFFRACTIONr_bond_other_d0.0010.021646
X-RAY DIFFRACTIONr_angle_refined_deg2.1171.9652330
X-RAY DIFFRACTIONr_angle_other_deg0.89633806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1615224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07626.20758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.69215280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.703152
X-RAY DIFFRACTIONr_chiral_restr0.1440.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3441.475902
X-RAY DIFFRACTIONr_mcbond_other1.3021.472901
X-RAY DIFFRACTIONr_mcangle_it1.7992.2171124
X-RAY DIFFRACTIONr_mcangle_other1.8042.221125
X-RAY DIFFRACTIONr_scbond_it2.9431.728805
X-RAY DIFFRACTIONr_scbond_other2.9431.728805
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.242.5061207
X-RAY DIFFRACTIONr_long_range_B_refined6.26415.2132191
X-RAY DIFFRACTIONr_long_range_B_other5.80313.2541921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.172→1.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 142 -
Rwork0.189 2989 -
obs--65.42 %

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