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- PDB-3j06: CryoEM Helical Reconstruction of TMV -

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Basic information

Entry
Database: PDB / ID: 3j06
TitleCryoEM Helical Reconstruction of TMV
Components
  • 5'-R(P*AP*UP*G)-3'
  • Coat protein
KeywordsVIRUS / RNA
Function / homology
Function and homology information


helical viral capsid / structural molecule activity / identical protein binding
Similarity search - Function
Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / Capsid protein
Similarity search - Component
Biological speciesTobacco mosaic virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGe, P. / Zhou, Z.H.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Hydrogen-bonding networks and RNA bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches.
Authors: Peng Ge / Z Hong Zhou /
Abstract: Helical assemblies such as filamentous viruses, flagella, and F-actin represent an important category of structures in biology. As the first discovered virus, tobacco mosaic virus (TMV) was at the ...Helical assemblies such as filamentous viruses, flagella, and F-actin represent an important category of structures in biology. As the first discovered virus, tobacco mosaic virus (TMV) was at the center of virus research. Previously, the structure of TMV was solved at atomic detail by X-ray fiber diffraction but only for its dormant or high-calcium-concentration state, not its low-calcium-concentration state, which is relevant to viral assembly and disassembly inside host cells. Here we report a helical reconstruction of TMV in its calcium-free, metastable assembling state at 3.3 Å resolution by cryo electron microscopy, revealing both protein side chains and RNA bases. An atomic model was built de novo showing marked differences from the high-calcium, dormant-state structure. Although it could be argued that there might be inaccuracies in the latter structure derived from X-ray fiber diffraction, these differences can be interpreted as conformational changes effected by calcium-driven switches, a common regulatory mechanism in plant viruses. Our comparisons of the structures of the low- and high-calcium states indicate that hydrogen bonds formed by Asp116 and Arg92 in the place of the calcium ion of the dormant (high-calcium) state might trigger allosteric changes in the RNA base-binding pockets of the coat protein. In turn, the coat protein-RNA interactions in our structure favor an adenine-X-guanine (A*G) motif over the G*A motif of the dormant state, thus offering an explanation underlying viral assembly initiation by an AAG motif.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2012Group: Refinement description
Revision 1.3Jul 18, 2018Group: Author supporting evidence / Data collection / Database references
Category: em_single_particle_entity / em_software / struct_ref_seq
Item: _em_software.image_processing_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5185
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coat protein
R: 5'-R(P*AP*UP*G)-3'


Theoretical massNumber of molelcules
Total (without water)18,5722
Polymers18,5722
Non-polymers00
Water0
1
A: Coat protein
R: 5'-R(P*AP*UP*G)-3'
x 49


Theoretical massNumber of molelcules
Total (without water)910,04098
Polymers910,04098
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation48
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 49 / Rise per n subunits: 1.408 Å / Rotation per n subunits: 22.035 °)

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Components

#1: Protein Coat protein


Mass: 17636.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tobacco mosaic virus / Strain: vulgare / References: UniProt: P69687
#2: RNA chain 5'-R(P*AP*UP*G)-3'


Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: viral RNA / Source: (natural) Tobacco mosaic virus / Strain: vulgare

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Tobacco Mosaic Virus (Vulgare) / Type: VIRUS / Details: 49 coat proteins in 3 turn right hand helix
Molecular weightValue: 37.8 MDa / Experimental value: NO
Details of virusHost category: PLANTAE (HIGHER PLANTS) / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Nicotiana tabacum
Buffer solutionName: Tris-buffered saline / pH: 7.4 / Details: 10 mM Tris, 130 mM sodium chloride
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10 mM Tris, 130 mM sodium chloride
Specimen supportDetails: 400 mesh Quantifoil 1.3/1.2 micro-meter
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 93 K / Humidity: 100 % / Details: 2 uL sample
Method: 10 second wait time, 1-2 second blot time, 1-2 second drain time, blot force 1

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jun 19, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 73000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Astigmatism: objective lens astigmatism was corrected at 250000x magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: SIDE ENTRY, EUCENTRIC / Specimen holder type: Eucentric / Temperature: 90 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 386
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: EMAN / Classification: refinement
EM software
IDNameCategory
1EMAN3D reconstruction
2IHRSR3D reconstruction
Helical symmertyAngular rotation/subunit: 22.035 ° / Axial rise/subunit: 1.407 Å / Axial symmetry: C1
3D reconstructionMethod: IHRSR / Resolution: 3.3 Å / Resolution method: OTHER / Nominal pixel size: 0.847 Å / Actual pixel size: 0.869 Å / Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 65 0 0 1275

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