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- PDB-5yl1: T=1 subviral particle of Penaeus vannamei nodavirus capsid protei... -

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Basic information

Entry
Database: PDB / ID: 5yl1
TitleT=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368)
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / Viral capsid protein
Function / homologyIcosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Viral coat protein subunit / viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesPenaeus vannamei nodavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 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 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 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 1.2Mar 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 1.3Mar 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6893
Polymers20,6091
Non-polymers802
Water0
1
A: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,241,360180
Polymers1,236,55060
Non-polymers4,809120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


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


  • icosahedral pentamer
  • 103 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)103,44715
Polymers103,0465
Non-polymers40110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 124 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)124,13618
Polymers123,6556
Non-polymers48112
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
6
A: Capsid protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 1.24 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,241,360180
Polymers1,236,55060
Non-polymers4,809120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)196.981, 200.319, 419.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.313223, -0.816078, -0.485704), (0.755963, 0.523816, -0.392604), (0.574815, -0.244202, 0.780995)10.78738, -58.44395, -40.4454
3generate(-0.798005, -0.564479, -0.211071), (0.407096, -0.246667, -0.879448), (0.444365, -0.78773, 0.426638)81.50555, -65.02394, -51.5602
4generate(-0.798005, 0.407096, 0.444365), (-0.564479, -0.246667, -0.78773), (-0.211071, -0.879448, 0.426638)114.42439, -10.64664, -17.98413
5generate(0.313223, 0.755963, 0.574815), (-0.816078, 0.523816, -0.244202), (-0.485704, -0.392604, 0.780995)64.05119, 29.54037, 13.88183
6generate(-0.986957, -0.006135, 0.160866), (-0.006135, -0.997115, -0.075663), (0.160866, -0.075663, 0.984072)109.83443, -1.74874, -8.97192
7generate(-0.221307, 0.762937, 0.607413), (-0.799195, -0.498821, 0.335358), (0.558847, -0.411225, 0.720128)93.03999, 59.52064, -42.6157
8generate(0.856583, 0.431911, 0.282345), (-0.434648, 0.30902, 0.845924), (0.278113, -0.847325, 0.452431)21.49657, 66.48878, -41.67945
9generate(0.757106, -0.541746, -0.365106), (0.583716, 0.31, 0.75045), (-0.293371, -0.781288, 0.550928)-5.92527, 9.52596, -7.45705
10generate(-0.382265, -0.812473, -0.440184), (0.848551, -0.497236, 0.180878), (-0.365834, -0.304375, 0.879501)48.67054, -32.64716, 12.75732
11generate(-0.999371, -0.035442, -0.001403), (-0.035442, 0.996244, 0.079001), (-0.001403, 0.079001, -0.996874)102.12416, 5.8902, -103.02187
12generate(-0.340625, 0.797342, 0.498218), (0.787433, 0.531479, -0.312216), (-0.513735, 0.285965, -0.808888)93.47163, -55.91181, -67.33521
13generate(0.782452, 0.573971, 0.241509), (0.468955, -0.287966, -0.834959), (-0.409696, 0.766572, -0.494486)23.04677, -65.85152, -56.87416
14generate(0.817805, -0.396864, -0.416766), (-0.550751, -0.329646, -0.766816), (0.166936, 0.85664, -0.488159)-11.82567, -10.19259, -86.09556
15generate(-0.283422, -0.773501, -0.566893), (-0.862485, 0.46404, -0.201957), (0.419275, 0.431698, -0.798652)37.04685, 34.14624, -114.61641
16generate(0.986328, 0.041576, -0.159463), (0.041576, -0.99913, -0.003338), (-0.159463, -0.003338, -0.987198)-7.56659, -0.45346, -94.37021
17generate(0.248709, -0.744201, -0.619927), (-0.744201, -0.556474, 0.369462), (-0.619927, 0.369462, -0.692235)7.09299, 58.52313, -55.9677
18generate(-0.84103, -0.441403, -0.312783), (-0.441403, 0.225613, 0.868483), (-0.312783, 0.868483, -0.384583)78.34312, 68.07468, -56.25018
19generate(-0.776906, 0.531514, 0.337506), (0.531514, 0.266313, 0.804096), (0.337506, 0.804096, -0.489407)107.71855, 15.00127, -94.82727
20generate(0.352463, 0.830011, 0.432263), (0.830011, -0.490619, 0.265281), (0.432263, 0.265281, -0.861844)54.62342, -27.35145, -118.38673
21generate(-0.096723, -0.043196, -0.994374), (0.993282, 0.05958, -0.099205), (0.06353, -0.997288, 0.037143)4.77945, -55.00573, -52.0015
22generate(-0.634531, 0.299134, -0.712663), (0.299134, -0.75516, -0.583311), (-0.712663, -0.583311, 0.389691)46.47844, -43.76051, 5.46704
23generate(-0.382265, 0.848551, -0.365834), (-0.812473, -0.497236, -0.304375), (-0.440184, 0.180878, 0.879501)50.97487, 27.19316, 16.10906
24generate(0.311453, 0.845779, -0.433191), (-0.805336, 0.47691, 0.352123), (0.504411, 0.239195, 0.829672)12.05482, 59.79972, -34.78234
25generate(0.487927, 0.294649, -0.82165), (0.310681, 0.821041, 0.478925), (0.815723, -0.488952, 0.309066)-16.49552, 8.99802, -76.87698
26generate(-0.064234, 0.118903, -0.990826), (-0.996651, -0.057995, 0.057652), (-0.050608, 0.991211, 0.12223)3.15292, 54.87668, -43.61297
27generate(-0.499775, 0.356665, -0.789313), (-0.322877, 0.768887, 0.551873), (0.803726, 0.530663, -0.269112)35.58521, 45.18312, -107.03281
28generate(-0.340625, 0.787433, -0.513735), (0.797342, 0.531479, 0.285965), (0.498218, -0.312216, -0.808888)41.27313, -25.55738, -118.49243
29generate(0.193276, 0.815901, -0.544931), (0.815901, -0.442129, -0.372596), (-0.544931, -0.372596, -0.751148)12.35617, -59.58385, -62.15504
30generate(0.364095, 0.402726, -0.83979), (-0.292847, -0.806444, -0.513701), (-0.884124, 0.432966, -0.175685)-11.20342, -9.87287, -15.87699
31generate(0.099588, -0.118163, 0.987988), (-0.994629, 0.016315, 0.102209), (-0.028197, -0.99286, -0.115903)97.08949, 57.00356, -55.21435
32generate(0.509777, -0.384435, 0.769635), (-0.240456, 0.795281, 0.556515), (-0.82602, -0.468761, 0.312976)65.11012, 41.18671, 7.19591
33generate(0.311453, -0.805336, 0.504411), (0.845779, 0.47691, 0.239195), (-0.433191, 0.352123, 0.829672)61.94899, -30.39502, 13.02314
34generate(-0.221307, -0.799195, 0.558847), (0.762937, -0.498821, -0.411225), (0.607413, 0.335358, 0.720128)91.97469, -58.81812, -45.78569
35generate(-0.352247, -0.374499, 0.857714), (-0.374499, -0.783484, -0.495887), (0.857714, -0.495887, 0.135731)113.69271, -4.80282, -87.95878
36generate(0.06137, 0.042456, 0.997212), (0.997998, -0.0179, -0.060656), (0.015275, 0.998938, -0.04347)99.37014, -53.18651, -55.53518
37generate(0.624529, -0.271364, 0.732342), (0.264198, -0.809008, -0.525076), (0.734957, 0.521409, -0.433555)57.21824, -38.92132, -111.99414
38generate(0.411437, -0.830648, 0.375157), (-0.830648, -0.511153, -0.220785), (0.375157, -0.220785, -0.900284)50.19501, 32.44724, -117.00377
39generate(-0.283422, -0.862485, 0.419275), (-0.773501, 0.46404, 0.431698), (-0.566893, -0.201957, -0.798652)88.00632, 62.29025, -63.64093
40generate(-0.499775, -0.322877, 0.803726), (0.356665, 0.768887, 0.530663), (-0.789313, 0.551873, -0.269112)118.39822, 9.36568, -25.65125
41generate(-0.096723, 0.993282, 0.06353), (-0.043196, 0.05958, -0.997288), (-0.994374, -0.099205, 0.037143)58.40211, -48.37681, 1.22722
42generate(0.757106, 0.583716, -0.293371), (-0.541746, 0.31, -0.781288), (-0.365106, 0.75045, 0.550928)-3.26208, -11.98914, -5.20381
43generate(0.509777, -0.240456, -0.82602), (-0.384435, 0.795281, -0.468761), (0.769635, 0.556515, 0.312976)-17.34405, -4.35125, -75.28415
44generate(-0.49691, -0.340256, -0.798314), (0.211338, 0.844782, -0.491609), (0.841675, -0.413, -0.347872)35.617, -36.01846, -112.16516
45generate(-0.871748, 0.422235, -0.248542), (0.422235, 0.390093, -0.818257), (-0.248542, -0.818257, -0.518346)82.43071, -63.22775, -64.87853
46generate(0.099588, -0.994629, -0.028197), (-0.118163, 0.016315, -0.99286), (0.987988, 0.102209, -0.115903)45.47162, -44.27782, -108.14899
47generate(-0.736917, -0.595388, 0.320104), (-0.595388, 0.347434, -0.724433), (0.320104, -0.724433, -0.610517)105.8164, -6.3494, -98.77692
48generate(-0.49691, 0.211338, 0.841675), (-0.340256, 0.844782, -0.413), (-0.798314, -0.491609, -0.347872)119.71711, -3.77755, -28.29252
49generate(0.487927, 0.310681, 0.815723), (0.294649, 0.821041, -0.488952), (-0.82165, 0.478925, 0.309066)67.96344, -40.11648, 5.89715
50generate(0.856583, -0.434648, 0.278113), (0.431911, 0.30902, -0.847325), (0.282345, 0.845924, 0.452431)22.07721, -65.14703, -43.45687
51generate(0.06137, 0.997998, 0.015275), (0.042456, -0.0179, 0.998938), (0.997212, -0.060656, -0.04347)47.83003, 50.30529, -104.73324
52generate(0.782452, 0.468955, -0.409696), (0.573971, -0.287966, 0.766572), (0.241509, -0.834959, -0.494486)-10.45272, 11.40699, -88.67282
53generate(0.364095, -0.292847, -0.884124), (0.402726, -0.806444, 0.432966), (-0.83979, -0.513701, -0.175685)-12.84936, 3.42419, -17.26956
54generate(-0.615546, -0.234623, -0.752366), (-0.234623, -0.856815, 0.459152), (-0.752366, 0.459152, 0.472361)43.95218, 37.38885, 10.79965
55generate(-0.802641, 0.563163, -0.196507), (-0.457282, -0.369468, 0.808941), (0.382963, 0.739149, 0.554075)81.4541, 66.36297, -43.25588
56generate(-0.064234, -0.996651, -0.050608), (0.118903, -0.057995, 0.991211), (-0.990826, 0.057652, 0.12223)52.68824, 46.03734, 5.29102
57generate(-0.802641, -0.457282, 0.382963), (0.563163, -0.369468, 0.739149), (-0.196507, 0.808941, 0.554075)112.2904, 10.61955, -13.71046
58generate(-0.376961, 0.321965, 0.868469), (0.321965, -0.833619, 0.448795), (0.868469, 0.448795, 0.210581)114.8683, 8.39262, -85.51776
59generate(0.624529, 0.264198, 0.734957), (-0.271364, -0.809008, 0.521409), (0.732342, -0.525076, -0.433555)56.85938, 42.43409, -110.89564
60generate(0.817805, -0.550751, 0.166936), (-0.396864, -0.329646, 0.85664), (-0.416766, -0.766816, -0.488159)18.42998, 65.69981, -54.77272

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Components

#1: Protein Capsid protein / Capsid


Mass: 20609.170 Da / Num. of mol.: 1
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.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris 8.0, 20%(w/v) Poly(acrylic acid sodium salt) 5100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.12→37.62 Å / Num. obs: 292229 / % possible obs: 99.7 % / Redundancy: 5 % / Rpim(I) all: 0.108 / Rrim(I) all: 0.244 / Net I/σ(I): 7.1
Reflection shellResolution: 3.12→3.23 Å / Redundancy: 5 % / CC1/2: 0.646 / Rpim(I) all: 0.428 / Rrim(I) all: 0.963 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→37.62 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.91 / SU B: 16.916 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22071 14413 5 %RANDOM
Rwork0.21953 ---
obs0.21959 274292 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.435 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 3.12→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 2 0 1456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021486
X-RAY DIFFRACTIONr_bond_other_d0.0040.021398
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9482031
X-RAY DIFFRACTIONr_angle_other_deg1.15933205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9085184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11924.70668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.57515235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.099158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211699
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02349
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_it2.8946.452739
X-RAY DIFFRACTIONr_mcbond_other2.8556.451738
X-RAY DIFFRACTIONr_mcangle_it4.1599.69922
X-RAY DIFFRACTIONr_mcangle_other4.1579.693923
X-RAY DIFFRACTIONr_scbond_it3.7396.694747
X-RAY DIFFRACTIONr_scbond_other3.7386.697748
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3189.9611110
X-RAY DIFFRACTIONr_long_range_B_refined7.22164.0186350
X-RAY DIFFRACTIONr_long_range_B_other7.2364.0186351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.119→3.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 931 -
Rwork0.345 17122 -
obs--84.42 %

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