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- EMDB-10129: Cryo-EM structure of TMV in water -

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Basic information

Entry
Database: EMDB / ID: EMD-10129
TitleCryo-EM structure of TMV in water
Map dataB-factor sharpened and locally filtered
Sample
  • Virus: Tobacco mosaic virus (strain vulgare)
    • Protein or peptide: Capsid proteinCapsid
    • RNA: RNA (5'-R(P*GP*AP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: water
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 / identical protein binding / Capsid protein
Function and homology information
Biological speciesTMV (virus) / Tobacco mosaic virus (strain vulgare)
Methodhelical reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsWeis F / Beckers M / Sachse C
CitationJournal: EMBO Rep / Year: 2019
Title: Elucidation of the viral disassembly switch of tobacco mosaic virus.
Authors: Felix Weis / Maximilian Beckers / Iris von der Hocht / Carsten Sachse /
Abstract: Stable capsid structures of viruses protect viral RNA while they also require controlled disassembly for releasing the viral genome in the host cell. A detailed understanding of viral disassembly ...Stable capsid structures of viruses protect viral RNA while they also require controlled disassembly for releasing the viral genome in the host cell. A detailed understanding of viral disassembly processes and the involved structural switches is still lacking. This process has been extensively studied using tobacco mosaic virus (TMV), and carboxylate interactions are assumed to play a critical part in this process. Here, we present two cryo-EM structures of the helical TMV assembly at 2.0 and 1.9 Å resolution in conditions of high Ca concentration at low pH and in water. Based on our atomic models, we identify the conformational details of the disassembly switch mechanism: In high Ca /acidic pH environment, the virion is stabilized between neighboring subunits through carboxyl groups E95 and E97 in close proximity to a Ca binding site that is shared between two subunits. Upon increase in pH and lower Ca levels, mutual repulsion of the E95/E97 pair and Ca removal destabilize the network of interactions between adjacent subunits at lower radius and release the switch for viral disassembly.
History
DepositionJul 16, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sae
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6sae
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10129.png

Downloads & links

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Map

FileDownload / File: emd_10129.map.gz / Format: CCP4 / Size: 437.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened and locally filtered
Voxel sizeX=Y=Z: 0.638 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.03
Minimum - Maximum-0.069113284 - 0.1624072
Average (Standard dev.)0.00001562518 (±0.007037313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions486486486
Spacing486486486
CellA=B=C: 310.068 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6380.6380.638
M x/y/z486486486
origin x/y/z0.0000.0000.000
length x/y/z310.068310.068310.068
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS486486486
D min/max/mean-0.0690.1620.000

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Supplemental data

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Mask #1

Fileemd_10129_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Confidence map

Fileemd_10129_additional.map
AnnotationConfidence map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 1

Fileemd_10129_half_map_1.map
AnnotationHalfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 2

Fileemd_10129_half_map_2.map
AnnotationHalfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tobacco mosaic virus (strain vulgare)

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

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Supramolecule #1: Tobacco mosaic virus (strain vulgare)

SupramoleculeName: Tobacco mosaic virus (strain vulgare) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 12243 / Sci species name: Tobacco mosaic virus (strain vulgare) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Nicotiana tabacum (common tobacco)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1
Details: Residues 154-158 are flexible and were not modelled.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: TMV (virus) / Strain: vulgare
Molecular weightTheoretical: 17.531463 KDa
SequenceString:
(ACE)SYSITTPSQ FVFLSSAWAD PIELINLCTN ALGNQFQTQQ ARTVVQRQFS EVWKPSPQVT VRFPDSDFKV YRYNAV LDP LVTALLGAFD TRNRIIEVEN QANPTTAETL DATRRVDDAT VAIRSAINNL IVELIRGTGS YNRSSFESSS GLVWTSG PA T

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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: 1
Source (natural)Organism: TMV (virus)
Molecular weightTheoretical: 958.66 Da
SequenceString:
GAA

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 92 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration22 mg/mL
BufferpH: 7 / Details: pure water
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Details: Pelco Easyglow, factory settings
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.35 µm / Nominal defocus min: 0.15 µm / Nominal magnification: 215000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-20 / Number grids imaged: 1 / Number real images: 62 / Average exposure time: 5.0 sec. / Average electron dose: 30.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 21709 / Software - Name: SPRING
CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4udv

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3)
Final reconstructionApplied symmetry - Helical parameters - Δz: 1.406 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.038 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 21598

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Atomic model buiding 1

Initial modelPDB ID:

4udv

Output model

PDB-6sae:
Cryo-EM structure of TMV in water

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