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- EMDB-4928: Cryo-EM reconstruction of TMV coat protein -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-4928
TitleCryo-EM reconstruction of TMV coat protein
Map data
Sample
  • Virus: Tobacco mosaic virus
    • Protein or peptide: Capsid proteinCapsid
    • RNA: RNA (5'-R(P*GP*AP*A)-3')
Function / homologyTobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesTobacco mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKandiah E / Effantin G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM reconstruction of TMV coat protein
Authors: Kandiah E / Mueller-Dieckmann C / Effantin G / Schoehn G / Hons M / Leonard G
History
DepositionMay 2, 2019-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_4928.png

Downloads & links

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Map

FileDownload / File: emd_4928.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.067 Å
Density
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.1419214 - 0.35838932
Average (Standard dev.)0.000548363 (±0.011957242)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.12003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tobacco mosaic virus

EntireName: Tobacco mosaic virus
Components
  • Virus: Tobacco mosaic virus
    • Protein or peptide: Capsid proteinCapsid
    • RNA: RNA (5'-R(P*GP*AP*A)-3')

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Supramolecule #1: Tobacco mosaic virus

SupramoleculeName: Tobacco mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12242 / Sci species name: Tobacco mosaic virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Tobacco mosaic virus
Molecular weightTheoretical: 17.091998 KDa
SequenceString:
SYSITTPSQF VFLSSAWADP IELINLCTNA LGNQFQTQQA RTVVQRQFSE VWKPSPQVTV RFPDSDFKVY RYNAVLDPLV TALLGAFDT RNRIIEVENQ ANPTTAETLD ATRRVDDATV AIRSAINNLI VELIRGTGSY NRSSFESSSG LVWT

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Macromolecule #2: RNA (5'-R(P*GP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*GP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 24
Source (natural)Organism: Tobacco mosaic virus
Molecular weightTheoretical: 958.66 Da
SequenceString:
GAA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 1.41 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.04 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109763

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