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- EMDB-9576: Cryo-EM structure of T=3 Penaeus vannamei nodavirus -

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Basic information

Entry
Database: EMDB / ID: EMD-9576
TitleCryo-EM structure of T=3 Penaeus vannamei nodavirus
Map data
Sample
  • Virus: Penaeus vannamei nodavirus
    • Protein or peptide: Capsid protein
  • Ligand: CALCIUM ION
KeywordsNodaviridae / shrimp nodavirus / VIRUS LIKE PARTICLE
Function / homologyIcosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / metal ion binding / Capsid protein
Function and homology information
Biological speciesPenaeus vannamei nodavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen NC / Miyazaki N
Funding support Taiwan, 1 items
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, 2018-
Header (metadata) releaseMar 13, 2019-
Map releaseMar 20, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.068
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.068
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ab6
  • Surface level: 0.068
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ab6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9576.png

Downloads & links

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Map

FileDownload / File: emd_9576.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.068 / Movie #1: 0.068
Minimum - Maximum-0.11609429 - 0.29195783
Average (Standard dev.)0.0023585588 (±0.013645462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 573.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z573.440573.440573.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-0.1160.2920.002

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Supplemental data

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Sample components

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Entire : Penaeus vannamei nodavirus

EntireName: Penaeus vannamei nodavirus
Components
  • Virus: Penaeus vannamei nodavirus
    • Protein or peptide: Capsid protein
  • Ligand: CALCIUM ION

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Supramolecule #1: Penaeus vannamei nodavirus

SupramoleculeName: Penaeus vannamei nodavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 430911 / Sci species name: Penaeus vannamei nodavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Litopenaeus vannamei (Pacific white shrimp)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Penaeus vannamei nodavirus
Molecular weightTheoretical: 40.262168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRKPNSNQN NNNNRGNGNG LRRVRGGRVS RRRVVINQSN QSMPVTSNGA PLQALTSYSR PNVNKISRLG PDSDFLTSVV AKASTSIVT PADRILVKQP LSASSFPGTR ITGLSSYWER YKWLSAVARY VPAVPNTVAC QFVMYIDTDP LDDPSNISDD N QIVRQAVS ...String:
MKRKPNSNQN NNNNRGNGNG LRRVRGGRVS RRRVVINQSN QSMPVTSNGA PLQALTSYSR PNVNKISRLG PDSDFLTSVV AKASTSIVT PADRILVKQP LSASSFPGTR ITGLSSYWER YKWLSAVARY VPAVPNTVAC QFVMYIDTDP LDDPSNISDD N QIVRQAVS QAGSNQFNFN TSKTVPLIVR ADNQYYYTGV DKQNLRFSLQ GILYIIQVTD LINFNGELIT QDLTCGSLFL DW LVNFSIP QINPTSLTDV RVDKAVNFIK PEVSGVAEIQ TVTGLSPSTS YLLTPAFLEQ NFQSEAGIYI LSATPVEGEG TIS INMDPT VTTVSGFIKV KTDTFGTFDL SVVLTTASKK QTTGFNIIAA TS

UniProtKB: Capsid protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMHEPESHEPES
300.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2806 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 42751
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 8596
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 5 / Avg.num./class: 6000 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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