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

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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 protein
    • RNA: RNA (5'-R(P*GP*AP*A)-3')
Keywordscryo-EM / single particle reconstruction / Tobacco mosaic virus / helical reconstruction / ESRF / Titan Krios / K2 Summit / VIRAL PROTEIN
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: Acta Crystallogr D Struct Biol / Year: 2019
Title: CM01: a facility for cryo-electron microscopy at the European Synchrotron.
Authors: Eaazhisai Kandiah / Thierry Giraud / Alejandro de Maria Antolinos / Fabien Dobias / Gregory Effantin / David Flot / Michael Hons / Guy Schoehn / Jean Susini / Olof Svensson / Gordon A ...Authors: Eaazhisai Kandiah / Thierry Giraud / Alejandro de Maria Antolinos / Fabien Dobias / Gregory Effantin / David Flot / Michael Hons / Guy Schoehn / Jean Susini / Olof Svensson / Gordon A Leonard / Christoph Mueller-Dieckmann /
Abstract: Recent improvements in direct electron detectors, microscope technology and software provided the stimulus for a `quantum leap' in the application of cryo-electron microscopy in structural biology, ...Recent improvements in direct electron detectors, microscope technology and software provided the stimulus for a `quantum leap' in the application of cryo-electron microscopy in structural biology, and many national and international centres have since been created in order to exploit this. Here, a new facility for cryo-electron microscopy focused on single-particle reconstruction of biological macromolecules that has been commissioned at the European Synchrotron Radiation Facility (ESRF) is presented. The facility is operated by a consortium of institutes co-located on the European Photon and Neutron Campus and is managed in a similar fashion to a synchrotron X-ray beamline. It has been open to the ESRF structural biology user community since November 2017 and will remain open during the 2019 ESRF-EBS shutdown.
History
DepositionMay 2, 2019-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing 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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 384.12 Å		1.07 Å/pix.
x 360 pix.
= 384.12 Å		1.07 Å/pix.
x 360 pix.
= 384.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
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 protein
    • 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

UniProtKB: Capsid protein

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

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Image processing

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
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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