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- EMDB-72538: Human papillomavirus purified from lysosomes -

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Basic information

Entry
Database: EMDB / ID: EMD-72538
TitleHuman papillomavirus purified from lysosomes
Map data
Sample
  • Virus: Human papillomavirus 16
KeywordsPathogen / multivalent complex / icosahedral symmetry / VIRUS
Biological speciesHuman papillomavirus 16
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsSutanto R / Rana J / Mosalaganti S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM150019 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD030275 United States
CitationJournal: bioRxiv / Year: 2025
Title: cryo-ET redefines HPV disassembly and transport paradigms.
Authors: Renaldo Sutanto / Jaimin Rana / Billy Tsai / Shyamal Mosalaganti /
Abstract: Human papillomavirus (HPV) causes 4.5% of all human cancers, although a complete cellular basis of infection remains unclear. The mechanisms of virus disassembly and transport are particularly ...Human papillomavirus (HPV) causes 4.5% of all human cancers, although a complete cellular basis of infection remains unclear. The mechanisms of virus disassembly and transport are particularly enigmatic. Here, we use cryo-electron tomography (cryo-ET) to provide direct visualization of high-risk HPV16 during its infection cycle. We demonstrate that, when HPV reaches the lysosome, it remains intact and infection competent, contrary to the prevailing view of viral inactivation within lysosomes. We challenge the current model of HPV trafficking, which predicts progressive disassembly of the L1 capsid during retrograde transport, by showing that HPV remains intact when it reaches the Golgi to the nucleus for infection. Finally, we provide snapshots of the HPV containing transport vesicles budding from the Golgi lumen in a COPI coat-dependent fashion and show that HPV is connected to the overlying membrane by proteinaceous structural bridges, possibly formed by the L2 capsid, to guide virus trafficking. Our results redefine the dominant models of HPV entry, revealing the virus capsid's resilience to disassembly during retrograde trafficking, a coat-dependent budding mechanism for transport, and demonstrate that the lysosome serves as a reservoir for infectious HPV.
History
DepositionSep 6, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72538.png

Downloads & links

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Map

FileDownload / File: emd_72538.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 800 pix.
= 1098.4 Å		1.37 Å/pix.
x 800 pix.
= 1098.4 Å		1.37 Å/pix.
x 800 pix.
= 1098.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.373 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.45869583 - 1.0658439
Average (Standard dev.)-0.00033084443 (±0.053416763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1098.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72538_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72538_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human papillomavirus 16

EntireName: Human papillomavirus 16
Components
  • Virus: Human papillomavirus 16

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Supramolecule #1: Human papillomavirus 16

SupramoleculeName: Human papillomavirus 16 / type: virus / ID: 1 / Parent: 0
Details: Recombinantly expressed in HeLa cells and purified from lyso-IP sorted lysosomes
NCBI-ID: 333760 / Sci species name: Human papillomavirus 16 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20 MDa
Virus shellShell ID: 1 / Diameter: 550.0 Å

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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: 4.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: CONTINUOUS / Support film - #0 - Film thickness: 2 / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 9895 / Average exposure time: 3.9 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 33158
Details: Template-picking and blob picking were used parallel
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 8561
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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