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- EMDB-0818: Cryo-EM structure of HPV6 PsV in complex with the Fab fragment of... -

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Basic information

Entry
Database: EMDB / ID: EMD-0818
TitleCryo-EM structure of HPV6 PsV in complex with the Fab fragment of antibody 5D3
Map data
Sample
  • Complex: HPV6 PsV in complex with the Fab fragment of antibody 5D3
Biological speciesHuman papillomavirus type 6
Methodsingle particle reconstruction / cryo EM / Resolution: 16.55 Å
AuthorsLi SW / Liu XL / Gu Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670935 China
National Natural Science Foundation of China31730029 China
CitationJournal: Emerg Microbes Infect / Year: 2019
Title: Neutralization sites of human papillomavirus-6 relate to virus attachment and entry phase in viral infection.
Authors: Xinlin Liu / Jie Chen / Zhiping Wang / Daning Wang / Maozhou He / Ciying Qian / Shuo Song / Xin Chi / Zhibo Kong / Qingbing Zheng / Yingbin Wang / Hai Yu / Qinjian Zhao / Jun Zhang / Shaowei ...Authors: Xinlin Liu / Jie Chen / Zhiping Wang / Daning Wang / Maozhou He / Ciying Qian / Shuo Song / Xin Chi / Zhibo Kong / Qingbing Zheng / Yingbin Wang / Hai Yu / Qinjian Zhao / Jun Zhang / Shaowei Li / Ying Gu / Ningshao Xia /
Abstract: Human papillomavirus type 6 (HPV6) is the major etiologic agent of genital warts and recurrent respiratory papillomatosis. Although the commercial HPV vaccines cover HPV6, the neutralization sites ...Human papillomavirus type 6 (HPV6) is the major etiologic agent of genital warts and recurrent respiratory papillomatosis. Although the commercial HPV vaccines cover HPV6, the neutralization sites and mode for HPV6 are poorly understood. Here, we identify the HPV6 neutralization sites and discriminate the inhibition of virus attachment and entry by three potent neutralizing antibodies (nAbs), 5D3, 17D5, and 15F7. Mutagenesis assays showed that these nAbs predominantly target surface loops BC, DE, and FG of HPV6 L1. Cryo-EM structures of the HPV6 pseudovirus (PsV) and its immune complexes revealed three distinct binding modalities - full-occupation-bound to capsid, top-center-bound-, and top-rim-bound to pentamers - and illustrated a structural atlas for three classes of antibody-bound footprints that are located at center-distal ring, center, and center-proximal ring of pentamer surface for 5D3, 17D5, and 15F7, respectively. Two modes of neutralization were identified: mAb 5D3 and 17D5 block HPV PsV from attaching to the extracellular matrix (ECM) and the cell surface, whereas 15F7 allows PsV attachment but prohibits PsV from entering the cell. These findings highlight three neutralization sites of HPV6 L1 and outline two antibody-mediated neutralization mechanisms against HPV6, which will be relevant for HPV virology and antiviral inhibitor design. HighlightsMajor neutralization sites of HPV6 were mapped on the pseudovirus cryo-EM structuremAb 15F7 binds HPV6 capsid with a novel top-rim binding modality and confers a post-attachment neutralizationmAb 17D5 binds capsid in top-centre manner but unexpectedly prevents virus from attachment to cell surface.
History
DepositionOct 7, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 11, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 44.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 44.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0818.png

Downloads & links

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Map

FileDownload / File: emd_0818.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 769 pix.
= 867.432 Å		1.13 Å/pix.
x 769 pix.
= 867.432 Å		1.13 Å/pix.
x 769 pix.
= 867.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 44.2 / Movie #1: 44.2
Minimum - Maximum-156.26447 - 168.42258
Average (Standard dev.)0.44160235 (±23.103115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-384-384-384
Dimensions769769769
Spacing769769769
CellA=B=C: 867.432 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z769769769
origin x/y/z0.0000.0000.000
length x/y/z867.432867.432867.432
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS-384-384-384
NC/NR/NS769769769
D min/max/mean-156.264168.4230.442

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Supplemental data

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Sample components

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Entire : HPV6 PsV in complex with the Fab fragment of antibody 5D3

EntireName: HPV6 PsV in complex with the Fab fragment of antibody 5D3
Components
  • Complex: HPV6 PsV in complex with the Fab fragment of antibody 5D3

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Supramolecule #1: HPV6 PsV in complex with the Fab fragment of antibody 5D3

SupramoleculeName: HPV6 PsV in complex with the Fab fragment of antibody 5D3
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human papillomavirus type 6
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1367
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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