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- PDB-3j9s: Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstro... -

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Basic information

Entry
Database: PDB / ID: 3j9s
TitleSingle particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution
ComponentsIntermediate capsid protein VP6
KeywordsVIRAL PROTEIN / rotavirus / virus
Function / homology
Function and homology information


viral intermediate capsid / T=13 icosahedral viral capsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / metal ion binding
Similarity search - Function
Viral capsid alpha domain / Viral capsid alpha domain / Jelly Rolls - #170 / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls / Sandwich / Orthogonal Bundle ...Viral capsid alpha domain / Viral capsid alpha domain / Jelly Rolls - #170 / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Intermediate capsid protein VP6
Similarity search - Component
Biological speciesBovine rotavirus strain UK/G6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGrant, T. / Grigorieff, N.
CitationJournal: Elife / Year: 2015
Title: Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6.
Authors: Timothy Grant / Nikolaus Grigorieff /
Abstract: Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that ...Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using a 2.6 Å resolution single particle cryo-EM reconstruction of rotavirus VP6, determined from movies recorded with a total exposure of 100 electrons/Å(2), we obtained accurate measurements of optimal exposure values over a wide range of resolutions. At low and intermediate resolutions, our measured values are considerably higher than obtained previously for crystalline specimens, indicating that both images and movies should be collected with higher exposures than are generally used. We demonstrate a method of using our optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions. This 'high-exposure' technique should benefit cryo-EM work on all types of samples, especially those of relatively low-molecular mass.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jul 1, 2015Group: Derived calculations
Revision 1.3Sep 2, 2015Group: Database references
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Movie
  • Biological unit as complete point assembly
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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-6272
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
  • EMDB-6272
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intermediate capsid protein VP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0875
Polymers44,9061
Non-polymers1814
Water1,892105
1
A: Intermediate capsid protein VP6
hetero molecules

A: Intermediate capsid protein VP6
hetero molecules

A: Intermediate capsid protein VP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,26015
Polymers134,7173
Non-polymers54312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
2


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


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

#1: Protein Intermediate capsid protein VP6 / Rotavirus VP6


Mass: 44905.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine rotavirus strain UK/G6 / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: P04509, UniProt: P18610*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bovine rotavirus VP6 / Type: VIRUS
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: C-Flat 1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temp: 120 K / Humidity: 80 %
Details: Blot for 4-6 seconds before plunging into liquid ethane (FEI VITROBOT MARK II).
Method: Blot for 4-6 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Aug 13, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Details: 130 frames, 0.1 seconds per frame, 100 e/A2, super resolution
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2Cootmodel fitting
3FREALIGN3D reconstruction
4IMAGIC3D reconstruction
5TIGRIS3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4000 / Nominal pixel size: 1.023 Å / Actual pixel size: 1.023 Å
Details: Final map is a 13-fold average of VP6 trimers from the asymmetric unit of the reconstruction of the whole capsid. Data at resolutions higher than 15A were not used for alignments.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: REFINEMENT PROTOCOL--flexible DETAILS--Model was refined by real space refinement using COOT and all restraints.
Atomic model buildingPDB-ID: 1QHD

1qhd


Pdb chain-ID: A / Accession code: 1QHD / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 4 105 3271

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