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- EMDB-9705: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbe... -

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Basic information

Entry
Database: EMDB / ID: EMD-9705
TitleCryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii extra small virus (XSV) VLP
Map dataThe cryo-EM map of XSV-VLP
Sample
  • Virus: Viruses
    • Protein or peptide: Capsid protein of giant freshwater prawn Macrobrachium rosenbergii extra small virus
Function / homologyviral nucleocapsid / Nucleocapsid protein CP17
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
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)MOST 103-2321-B-001-048, MOST 104-2321-B-001-019, MOST 105-2321-B-001-009, MOST 106-0210-01-15-02, MOST 106-0210-01-15-04, MOST 107-0210-01-19-01, MOST 107-0210-01-19-02 Taiwan
Academia Sinica (Taiwan)Grand Challenge project, Nanoscience program, Thematic program AS-103-TP-B12 Taiwan
CitationJournal: To Be Published
Title: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii extra small virus (XSV) VLP
Authors: Wang CH / Lin HH / Wu YY / Chang WH
History
DepositionNov 9, 2018-
Header (metadata) releaseJul 17, 2019-
Map releaseJul 17, 2019-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jja
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6jja
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9705.png

Downloads & links

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Map

FileDownload / File: emd_9705.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM map of XSV-VLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.38343602 - 0.58749646
Average (Standard dev.)0.0014456568 (±0.03443572)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-159-159-159
Dimensions320320320
Spacing320320320
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8550.8550.855
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z273.600273.600273.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-159-159-159
NC/NR/NS320320320
D min/max/mean-0.3830.5870.001

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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 extra small virus

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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: 1.146 MDa
Virus shellShell ID: 1 / Name: nucleocapsid protein CP17 / Diameter: 188.0 Å / T number (triangulation number): 1

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

MacromoleculeName: Capsid protein of giant freshwater prawn Macrobrachium rosenbergii extra small virus
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Macrobrachium rosenbergii nodavirus / Strain: Taiwan
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MNKRINNNRR TMRSRRGRGR TMGSNLIPYA NSPVPIPYTP PVTPVTVIGN PRKTTWIDID LSSEESGIYT LTVGSYRNRI TKLGPSKPNF IIEKVAAYAA PGDYKVVLND FKTGIQVVDE GSYAHRAAAG ILYPPAAQMF YGISATGTLN TITTTAKDPV PVVRALVTYW DSEQ

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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

Concentration10 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: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe XSV-VLPs was purified by 10-25% sucrose density gradient

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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 / Number real images: 998 / Average exposure time: 20.0 sec. / Average electron dose: 100.0 e/Å2
Details: Images were collected in movie-mode with 65 frames within 5 second
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.03 µm / Calibrated defocus min: 0.51 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: 10755
CTF correctionSoftware: (Name: RELION (ver. 2.0), Gctf)
Startup modelType of model: NONE / Details: ab initio 3D model reconstruction by cryoSPARC
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 10755
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 2.0), cryoSPARC (ver. 2))
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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