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- EMDB-9706: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbe... -

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Basic information

Entry
Database: EMDB / ID: EMD-9706
TitleCryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty VLP
Map dataCryo-EM map of MrNV semi-empty VLP
Sample
  • Virus: Viruses
    • Protein or peptide: Capsid protein of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV)
Function / homologyViral coat protein subunit / Capsid protein alpha
Function and homology information
Biological speciesMacrobrachium rosenbergii nodavirus / Viruses
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang CH / Lin HH / Wu YY / Chang WH
CitationJournal: To Be Published
Title: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty VLP
Authors: Wang CH / Lin HH / Wu YY / Chang WH
History
DepositionNov 9, 2018-
Header (metadata) releaseMay 1, 2019-
Map releaseMay 1, 2019-
UpdateMay 1, 2019-
Current statusMay 1, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0774999
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0774999
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jjc
  • Surface level: 0.0774999
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6jjc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9706.png

Downloads & links

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Map

FileDownload / File: emd_9706.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of MrNV semi-empty VLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 450 pix.
= 461.7 Å		1.03 Å/pix.
x 450 pix.
= 461.7 Å		1.03 Å/pix.
x 450 pix.
= 461.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.026 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0774999 / Movie #1: 0.0774999
Minimum - Maximum-0.14252177 - 0.2829151
Average (Standard dev.)0.0017783724 (±0.015802428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-224-224-224
Dimensions450450450
Spacing450450450
CellA=B=C: 461.7 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0261.0261.026
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z461.700461.700461.700
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-224-224-224
NC/NR/NS450450450
D min/max/mean-0.1430.2830.002

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Supplemental data

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Sample components

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Entire : Viruses

EntireName: Viruses
Components
  • Virus: Viruses
    • Protein or peptide: Capsid protein of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV)

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Supramolecule #1: Viruses

SupramoleculeName: Viruses / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10239 / Sci species name: Viruses / Sci species strain: Taiwan / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli BL21 (bacteria)
Host systemOrganism: Macrobrachium rosenbergii nodavirus
Molecular weightTheoretical: 7.452 MDa
Virus shellShell ID: 1 / Name: capsid protein [Macrobrachium rosenbergii nodavirus] / Diameter: 400.0 Å / T number (triangulation number): 3

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Macromolecule #1: Capsid protein of giant freshwater prawn Macrobrachium rosenbergi...

MacromoleculeName: Capsid protein of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Macrobrachium rosenbergii nodavirus
SequenceString: MARGKQNSNQ IQNNSNANGK RRKRNRRNRN PQTVPNFNPI VAKPTVAPLQ TNIRSARSDV NAITVLNGSD FLTTVKVRGS NNLIDSKSRI LVKQPISASS FLGTRISGLS QFWERYRWHK AAVRYVPAVP NTLACQLIGY IDTDPLDDPN VILDVDQLLR QATSQVGARQ ...String:
MARGKQNSNQ IQNNSNANGK RRKRNRRNRN PQTVPNFNPI VAKPTVAPLQ TNIRSARSDV NAITVLNGSD FLTTVKVRGS NNLIDSKSRI LVKQPISASS FLGTRISGLS QFWERYRWHK AAVRYVPAVP NTLACQLIGY IDTDPLDDPN VILDVDQLLR QATSQVGARQ WNFSDTTTIP LIVRRDDQLY YTGQDKENVR FSQQGVFYLL QVTTLLNISG EAITNDLISG SLYLDWVCGF SMPQINPSPV EVSQLTYNAD TIGNWVPPTE LKQTYTQDIT GLKPNSKFII IPYMDRVSSE VLQKCTITCN EVDAVGSISY SDTSAIKCDG YILFQANSIG EATFTLVTDY QGAVDPKPYQ YRIIRAIVGN N

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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

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
50.0 mMTris
50.0 mMNaCl
1.0 mMCaCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 270 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 93.0 K / Max: 103.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 37.0 e/Å2
Details: Images were collected in movie-mode with 30 frames within 3 second
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus min: 0.45 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.37 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 19049
CTF correctionSoftware: (Name: Gctf, RELION (ver. 2.0))
Startup modelType of model: NONE / Details: ab initio 3D model reconstruction using cryoSPARC
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 19049
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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