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- PDB-5j7v: Faustovirus major capsid protein -

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Basic information

Entry
Database: PDB / ID: 5j7v
TitleFaustovirus major capsid protein
Componentsmajor capsid protein
KeywordsVIRUS / double jelly-roll
Function / homologyGroup II dsDNA virus coat/capsid protein / Putative major capsid protein p72
Function and homology information
Biological speciesFaustovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15.5 Å
AuthorsKlose, T. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure of faustovirus, a large dsDNA virus.
Authors: Thomas Klose / Dorine G Reteno / Samia Benamar / Adam Hollerbach / Philippe Colson / Bernard La Scola / Michael G Rossmann /
Abstract: Many viruses protect their genome with a combination of a protein shell with or without a membrane layer. Here we describe the structure of faustovirus, the first DNA virus (to our knowledge) that ...Many viruses protect their genome with a combination of a protein shell with or without a membrane layer. Here we describe the structure of faustovirus, the first DNA virus (to our knowledge) that has been found to use two protein shells to encapsidate and protect its genome. The crystal structure of the major capsid protein, in combination with cryo-electron microscopy structures of two different maturation stages of the virus, shows that the outer virus shell is composed of a double jelly-roll protein that can be found in many double-stranded DNA viruses. The structure of the repeating hexameric unit of the inner shell is different from all other known capsid proteins. In addition to the unique architecture, the region of the genome that encodes the major capsid protein stretches over 17,000 bp and contains a large number of introns and exons. This complexity might help the virus to rapidly adapt to new environments or hosts.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2018Group: Experimental preparation / Category: em_vitrification / Item: _em_vitrification.details
Revision 1.5Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Apr 13, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.8May 15, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: major capsid protein
B: major capsid protein
C: major capsid protein


Theoretical massNumber of molelcules
Total (without water)215,3463
Polymers215,3463
Non-polymers00
Water00
1
A: major capsid protein
B: major capsid protein
C: major capsid protein
x 2760


Theoretical massNumber of molelcules
Total (without water)594,354,0578280
Polymers594,354,0578280
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2759
2
A: major capsid protein
B: major capsid protein
C: major capsid protein
x 46


  • icosahedral asymmetric unit
  • 9.91 MDa, 138 polymers
Theoretical massNumber of molelcules
Total (without water)9,905,901138
Polymers9,905,901138
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation45
3
A: major capsid protein
B: major capsid protein
C: major capsid protein
x 230


  • icosahedral pentamer
  • 49.5 MDa, 690 polymers
Theoretical massNumber of molelcules
Total (without water)49,529,505690
Polymers49,529,505690
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation229
4
A: major capsid protein
B: major capsid protein
C: major capsid protein
x 46


  • icosahedral asymmetric unit, std point frame
  • 9.91 MDa, 138 polymers
Theoretical massNumber of molelcules
Total (without water)9,905,901138
Polymers9,905,901138
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to point frame1
identity operation1_555x,y,z1
point symmetry operation45
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein major capsid protein


Mass: 71781.891 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Faustovirus / References: UniProt: A0A0H3TLP8*PLUS

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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: Faustovirus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Faustovirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Vermamoeba vermiformis / Strain: CDC 19
Virus shell
IDEntity assembly-IDNameDiameter (nm)Triangulation number (T number)
11outer capsid shell2600277
21inner capsid shell190016
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Details: Plunged into liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN22.1particle selectione2boxer.py was used to manually select particles.
2Leginon3.1image acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.10.2model fitting
9jsprinitial Euler assignment
10jsprfinal Euler assignment
12jspr3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 15.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9640 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model building

3D fitting-ID: 1 / Accession code: 5J7O / Initial refinement model-ID: 1 / PDB-ID: 5J7O

5j7o

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2B
3C

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