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- PDB-3j7m: Virus model of brome mosaic virus (first half data set) -

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Basic information

Entry
Database: PDB / ID: 3j7m
TitleVirus model of brome mosaic virus (first half data set)
ComponentsCapsid protein
KeywordsVIRUS / capsid protein / BMV / beta barrel
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell endoplasmic reticulum / viral nucleocapsid / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Satellite virus coat domain / Bromovirus coat protein / Bromovirus coat protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBrome mosaic virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang, Z. / Hryc, C. / Bammes, B. / Afonine, P.V. / Jakana, J. / Chen, D.H. / Liu, X. / Baker, M.L. / Kao, C. / Ludtke, S.J. ...Wang, Z. / Hryc, C. / Bammes, B. / Afonine, P.V. / Jakana, J. / Chen, D.H. / Liu, X. / Baker, M.L. / Kao, C. / Ludtke, S.J. / Schmid, M.F. / Adams, P.D. / Chiu, W.
CitationJournal: Nat Commun / Year: 2014
Title: An atomic model of brome mosaic virus using direct electron detection and real-space optimization.
Authors: Zhao Wang / Corey F Hryc / Benjamin Bammes / Pavel V Afonine / Joanita Jakana / Dong-Hua Chen / Xiangan Liu / Matthew L Baker / Cheng Kao / Steven J Ludtke / Michael F Schmid / Paul D Adams / Wah Chiu /
Abstract: Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains ...Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.
History
DepositionJul 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2May 18, 2016Group: Derived calculations
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
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 complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-6000
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)61,2353
Polymers61,2353
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,674,075180
Polymers3,674,075180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 5


  • icosahedral pentamer
  • 306 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)306,17315
Polymers306,17315
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 367 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)367,40718
Polymers367,40718
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


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

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Components

#1: Protein Capsid protein / CP / Coat protein


Mass: 20411.525 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Brome mosaic virus / References: UniProt: P03602

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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: Brome mosaic virus / Type: VIRUS
Details of virusEmpty: NO / Enveloped: NO / Host category: PLANTAE(HIGHER PLANTS) / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Triticum aestivum
Buffer solutionpH: 5.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV).

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Jan 10, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER
Image recordingFilm or detector model: DIRECT ELECTRON DE-12 (4k x 3k)

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Processing

EM software
IDNameCategory
1EMAN3D reconstruction
2MPSA3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Single Particle / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30000 / Nominal pixel size: 0.93 Å / Actual pixel size: 0.99 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 0 0 3618

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