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Basic information

Entry
Database: PDB / ID: 7ryj
TitleCryo EM analysis reveals inherent flexibility of authentic murine papillomavirus capsids
ComponentsMajor capsid protein L1
KeywordsVIRUS / MmuPV1 / papillomavirus / L1 / capsomer / subparticle
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein L1
Similarity search - Component
Biological speciesMus musculus papillomavirus type 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHartmann, S.R. / Hafenstein, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10 OD026822-01 United States
National Institutes of Health/Office of the DirectorAl134910-01A1 United States
CitationJournal: Viruses / Year: 2021
Title: Cryo EM Analysis Reveals Inherent Flexibility of Authentic Murine Papillomavirus Capsids.
Authors: Samantha R Hartmann / Daniel J Goetschius / Jiafen Hu / Joshua J Graff / Carol M Bator / Neil D Christensen / Susan L Hafenstein /
Abstract: Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. However, studies have been hampered due to restricted tropism that makes production and ...Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. However, studies have been hampered due to restricted tropism that makes production and purification of high titer virus problematic. This issue has been overcome by developing alternative HPV production methods such as virus-like particles (VLPs), which are devoid of a native viral genome. Structural studies have been limited in resolution due to the heterogeneity, fragility, and stability of the VLP capsids. The mouse papillomavirus (MmuPV1) presented here has provided the opportunity to study a native papillomavirus in the context of a common laboratory animal. Using cryo EM to solve the structure of MmuPV1, we achieved 3.3 Å resolution with a local symmetry refinement method that defined smaller, symmetry related subparticles. The resulting high-resolution structure allowed us to build the MmuPV1 asymmetric unit for the first time and identify putative L2 density. We also used our program ISECC to quantify capsid flexibility, which revealed that capsomers move as rigid bodies connected by flexible linkers. The MmuPV1 flexibility was comparable to that of a HPV VLP previously characterized. The resulting MmuPV1 structure is a promising step forward in the study of papillomavirus and will provide a framework for continuing biochemical, genetic, and biophysical research for papillomaviruses.
History
DepositionAug 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond / pdbx_struct_oper_list
Item: _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-24741
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  • Superimposition on EM map
  • EMDB-24741
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Downloads & links

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Assembly

Deposited unit
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)345,7416
Polymers345,7416
Non-polymers00
Water00
1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1
x 60


Theoretical massNumber of molelcules
Total (without water)20,744,475360
Polymers20,744,475360
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: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1
x 5


  • icosahedral pentamer
  • 1.73 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,728,70630
Polymers1,728,70630
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1
x 6


  • icosahedral 23 hexamer
  • 2.07 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)2,074,44836
Polymers2,074,44836
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major capsid protein L1


Mass: 57623.543 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus papillomavirus type 1 / References: UniProt: A0A2D3I4N0

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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: Mouse papillomavirus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mouse papillomavirus 1
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Mus musculus
Buffer solutionpH: 7.4
Buffer componentConc.: 1 X / Name: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2859

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC2.8.3particle selectionTemplate picker from manual picks
4cryoSPARC2.8.3CTF correctionCTFFIND4
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10181
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10181 / Symmetry type: POINT

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