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- EMDB-10130: Cryo-EM structure of TMV with Ca2+ at low pH -

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Basic information

Entry
Database: EMDB / ID: EMD-10130
TitleCryo-EM structure of TMV with Ca2+ at low pH
Map dataB-factor sharpened and locally filtered
Sample
  • Virus: Tobacco mosaic virus (strain vulgare)
    • Protein or peptide: Capsid protein
    • RNA: RNA (5'-R(P*GP*AP*A)-3')
  • Ligand: CALCIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsTMV / virus assembly/disassembly / Ca2+ switch / Caspar carboxylates / VIRUS
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 speciesTobacco mosaic virus (strain vulgare) / Tobacco mosaic virus (vulgare)
Methodhelical reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsWeis F / Beckers M
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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sag
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6sag
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10130.png

Downloads & links

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Map

FileDownload / File: emd_10130.map.gz / Format: CCP4 / Size: 437.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened and locally filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 486 pix.
= 310.068 Å		0.64 Å/pix.
x 486 pix.
= 310.068 Å		0.64 Å/pix.
x 486 pix.
= 310.068 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.638 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.0638554 - 0.14728498
Average (Standard dev.)0.00001341234 (±0.0069958675)
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-0.0640.1470.000

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Supplemental data

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Mask #1

Fileemd_10130_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Confidence map

Fileemd_10130_additional.map
AnnotationConfidence map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap1

Fileemd_10130_half_map_1.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap 1

Fileemd_10130_half_map_2.map
Annotationhalfmap 1
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 protein
    • RNA: RNA (5'-R(P*GP*AP*A)-3')
  • Ligand: CALCIUM ION
  • 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: Tobacco mosaic virus (strain vulgare) / 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

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: 1
Source (natural)Organism: Tobacco mosaic virus (vulgare)
Molecular weightTheoretical: 958.66 Da
SequenceString:
GAA

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: MAGNESIUM ION

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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 71 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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

Concentration1.1 mg/mL
BufferpH: 5.2
Component:
ConcentrationFormulaName
0.1 MNaOAcsodium acetate
20.0 mMCaCl2calcium chloride
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
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 197 / Average exposure time: 4.0 sec. / Average electron dose: 41.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.35000000000000003 µm / Nominal defocus min: 0.15 µm / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.405 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.036 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 15216
Segment selectionNumber selected: 16170 / Software - Name: SPRING
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4udv

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial modelPDB ID:

4udv


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6sag:
Cryo-EM structure of TMV with Ca2+ at low pH

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