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- EMDB-24741: Cryo EM analysis reveals inherent flexibility of authentic murine... -

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Basic information

Entry
Database: EMDB / ID: EMD-24741
TitleCryo EM analysis reveals inherent flexibility of authentic murine papillomavirus capsids
Map dataRecombined Full Virus Capsid
Sample
  • Virus: Mouse papillomavirus 1
    • Protein or peptide: Major capsid protein L1
KeywordsMmuPV1 / papillomavirus / L1 / capsomer / subparticle / VIRUS
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 / Mouse papillomavirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHartmann SR / Hafenstein S
Funding support United States, 2 items
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, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ryj
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ryj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24741.png

Downloads & links

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Map

FileDownload / File: emd_24741.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRecombined Full Virus Capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 600 pix.
= 660. Å		1.1 Å/pix.
x 600 pix.
= 660. Å		1.1 Å/pix.
x 600 pix.
= 660. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-12.272377000000001 - 19.263096000000001
Average (Standard dev.)0.000000000003009 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 660.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z660.000660.000660.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-300-300
NX/NY/NZ600600600
MAP C/R/S321
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean-12.27219.2630.000

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Supplemental data

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Sample components

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Entire : Mouse papillomavirus 1

EntireName: Mouse papillomavirus 1
Components
  • Virus: Mouse papillomavirus 1
    • Protein or peptide: Major capsid protein L1

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Supramolecule #1: Mouse papillomavirus 1

SupramoleculeName: Mouse papillomavirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2171376 / Sci species name: Mouse papillomavirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus papillomavirus type 1
Molecular weightTheoretical: 57.623543 KDa
SequenceString: MAMWTPQTGK LYLPPTTPVA KVQSTDEYVY PTSLFCHAHT DRLLTVGHPF FSVIDNDKVT VPKVSGNQYR VFRLKFPDPN KFALPQKDF YDPEKERLVW RLRGLEIGRG GPLGIGTTGH PLFNKLGDTE NPNKYQQGSK DNRQNTSMDP KQTQLFIVGC E PPTGEHWD ...String:
MAMWTPQTGK LYLPPTTPVA KVQSTDEYVY PTSLFCHAHT DRLLTVGHPF FSVIDNDKVT VPKVSGNQYR VFRLKFPDPN KFALPQKDF YDPEKERLVW RLRGLEIGRG GPLGIGTTGH PLFNKLGDTE NPNKYQQGSK DNRQNTSMDP KQTQLFIVGC E PPTGEHWD VAKPCGALEK GDCPPIQLVN SVIEDGDMCD IGFGNMNFKE LQQDRSGVPL DIVSTRCKWP DFLKMTNEAY GD KMFFFGR REQVYARHFF TRNGSVGEPI PNSVSPSDFY YAPDSTQDQK TLAPSVYFGT PSGSLVSSDG QLFNRPFWLQ RAQ GNNNGV CWHNELFVTV VDNTRNTNFT ISQQTNTPNP DTYDSTNFKN YLRHVEQFEL SLIAQLCKVP LDPGVLAHIN TMNP TILEN WNLGFVPPPQ QSISDDYRYI TSSATRCPDQ NPPKEREDPY KGLIFWEVDL TERFSQDLDQ FALGRKFLYQ AGIRT AVTG RGVKRAASTT SASSRRVVKR KRGSK

UniProtKB: Major capsid protein L1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 1.0 X / Component - Name: PBS
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2859 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10181
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10181
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER

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