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- EMDB-0816: CryoEM structure of HPV6 PsV subparticle -

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Basic information

Entry
Database: EMDB / ID: EMD-0816
TitleCryoEM structure of HPV6 PsV subparticle
Map dataPsV6-subparticle
Sample
  • Virus: Human papillomavirus type 6
    • Protein or peptide: Major capsid protein L1
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 / Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus type 6
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 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 25, 2019-
Map releaseDec 25, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l31
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6l31
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0816.png

Downloads & links

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Map

FileDownload / File: emd_0816.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPsV6-subparticle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 420 pix.
= 470.4 Å		1.12 Å/pix.
x 420 pix.
= 470.4 Å		1.12 Å/pix.
x 420 pix.
= 470.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3 / Movie #1: 3
Minimum - Maximum-8.978474 - 12.593203
Average (Standard dev.)0.0047269636 (±1.1049566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 470.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z470.400470.400470.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-8.97812.5930.005

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Supplemental data

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Sample components

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Entire : Human papillomavirus type 6

EntireName: Human papillomavirus type 6
Components
  • Virus: Human papillomavirus type 6
    • Protein or peptide: Major capsid protein L1

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Supramolecule #1: Human papillomavirus type 6

SupramoleculeName: Human papillomavirus type 6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 31552 / Sci species name: Human papillomavirus type 6 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SUBSPECIES / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Escherichia coli (E. coli)

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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: Human papillomavirus type 6
Molecular weightTheoretical: 49.754789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ATDAYVTRTN IFYHASSSRL LAVGHPYFSI KRANKTVVPK VSGYQYRVFK VVLPDPNKFA LPDSSLFDPT TQRLVWACTG LEVGRGQPL GVGVSGHPFL NKYDDVENSG SGGNPGQDNR VNVGMDYKQT QLCMVGCAPP LGEHWGKGKQ CTNTPVQAGD C PPLELITS ...String:
ATDAYVTRTN IFYHASSSRL LAVGHPYFSI KRANKTVVPK VSGYQYRVFK VVLPDPNKFA LPDSSLFDPT TQRLVWACTG LEVGRGQPL GVGVSGHPFL NKYDDVENSG SGGNPGQDNR VNVGMDYKQT QLCMVGCAPP LGEHWGKGKQ CTNTPVQAGD C PPLELITS VIQDGDMVDT GFGAMNFADL QTNKSDVPID ICGTTCKYPD YLQMAADPYG DRLFFFLRKE QMFARHFFNR AG EVGEPVP DTLIIKGSGN RTSVGSSIYV NTPSGSLVSS EAQLFNKPYW LQKAQGHNNG ICWGNQLFVT VVDTTRSTNM TLC ASVTTS STYTNSDYKE YMRHVEEYDL QFIFQLCSIT LSAEVMAYIH TMNPSVLEDW NFGLSPPPNG TLEDTYRYVQ SQAI TCQKP TPEKEKPDPY KNLSFWEVNL KEKFSSELDQ YPLGRKFLLQ SG

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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 III (4k x 4k) / Average electron dose: 30.0 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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 173490
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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