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- EMDB-6999: Cryo-EM structure of T=1 Penaeus vannamei nodavirus -

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Basic information

Entry
Database: EMDB / Id: 6999
TitleCryo-EM structure of T=1 Penaeus vannamei nodavirus
Map data
SamplePenaeus vannamei nodavirus:
virus / Capsid proteinCapsid
Func homologyIcosahedral viral capsid protein, S domain / Viral coat protein subunit / Viral coat protein (S domain) / viral capsid / structural molecule activity / Capsid protein
Function and homology information
SourcePenaeus vannamei nodavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsChen NC / Miyazaki N / Yoshimura M / Guan HH / Lin CC / Iwasaki K / Chen CJ
CitationJournal: Commun Biol / Year: 2019
Title: The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
P-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.
Validation ReportPDB-ID: 6ab5

SummaryFull reportAbout validation report
DateDeposition: Jul 20, 2018 / Header (metadata) release: Mar 20, 2019 / Map release: Mar 20, 2019 / Last update: Mar 20, 2019

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Strvis

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0425
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0425
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ab5
  • Surface level: 0.0425
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ab5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_6999.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.12 Å/pix.
= 358.4 Å
320 pix
1.12 Å/pix.
= 358.4 Å
320 pix
1.12 Å/pix.
= 358.4 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
Contour Level:0.0425 (by author), 0.0425 (movie #1):
Minimum - Maximum-0.22813772 - 0.39708844
Average (Standard dev.)0.002641407 (0.01784026)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin-160.0-160.0-160.0
Limit159.0159.0159.0
Spacing320320320
CellA=B=C: 358.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.2280.3970.003

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Supplemental data

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Sample components

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Entire Penaeus vannamei nodavirus

EntireName: Penaeus vannamei nodavirus / Number of components: 2

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Component #1: virus, Penaeus vannamei nodavirus

VirusName: Penaeus vannamei nodavirus / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Penaeus vannamei nodavirus
Source (engineered)Expression System: Escherichia coli (E. coli)
Source (natural)Host Species: Litopenaeus vannamei (Pacific white shrimp)

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Component #2: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.262168 kDa
SourceSpecies: Penaeus vannamei nodavirus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 6 mg/ml / Ph: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 1250.0 - 2750.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2806

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 70543
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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