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- EMDB-30769: 3-fold sub-particles refinement of human papillomavirus type 58 p... -

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Basic information

Entry
Database: EMDB / ID: EMD-30769
Title3-fold sub-particles refinement of human papillomavirus type 58 pseudovirus
Map data3-fold subparticles refinement of human papillomavirus type 58 pseudo virus
Sample
  • Virus: Human papillomavirus type 58
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 speciesHuman papillomavirus type 58
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsHe MZ / Chi X / Zha ZH / Zheng QB / Gu Y / Li SW / Xia NS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1705283 China
CitationJournal: J Virol / Year: 2021
Title: Structural basis for the shared neutralization mechanism of three classes of human papillomavirus type 58 antibodies with disparate modes of binding.
Authors: Maozhou He / Xin Chi / Zhenghui Zha / Yunbing Li / Jie Chen / Yang Huang / Shiwen Huang / Miao Yu / Zhiping Wang / Shuo Song / Xinlin Liu / Shuangping Wei / Zekai Li / Tingting Li / Yingbin ...Authors: Maozhou He / Xin Chi / Zhenghui Zha / Yunbing Li / Jie Chen / Yang Huang / Shiwen Huang / Miao Yu / Zhiping Wang / Shuo Song / Xinlin Liu / Shuangping Wei / Zekai Li / Tingting Li / Yingbin Wang / Hai Yu / Qinjian Zhao / Jun Zhang / Qingbing Zheng / Ying Gu / Shaowei Li / Ningshao Xia /
Abstract: Human papillomavirus type 58 (HPV58) is associated with cervical cancer and poses a significant health burden worldwide. Although the commercial 9-valent HPV vaccine covers HPV58, the structural and ...Human papillomavirus type 58 (HPV58) is associated with cervical cancer and poses a significant health burden worldwide. Although the commercial 9-valent HPV vaccine covers HPV58, the structural and molecular-level neutralization sites of the HPV58 complete virion are not fully understood. Here, we report the high-resolution (∼3.5 Å) structure of the complete HPV58 pseudovirus (PsV58) using cryo-electron microscopy (cryo-EM). Three representative neutralizing monoclonal antibodies (nAbs 5G9, 2H3 and A4B4) were selected through clustering from a nAb panel against HPV58. Bypassing the steric hindrance and symmetry-mismatch in the HPV Fab-capsid immune-complex, we present three different neutralizing epitopes in the PsV58, and show that, despite differences in binding, these nAbs share a common neutralization mechanism. These results offer insight into HPV58 genotype specificity and broaden our understanding of HPV58 neutralization sites for antiviral research. Cervical cancer primarily results from persistent infection with high-risk types of human papillomavirus (HPV). HPV type 58 (HPV58) is an important causative agent, especially within Asia. Despite this, we still have limited data pertaining to the structural and neutralizing epitopes of HPV58, and this encumbers our in-depth understanding of the virus mode of infection. Here, we show that representative nAbs (5G9, 10B11, 2H3, 5H2 and A4B4) from three different groups share a common neutralization mechanism that appears to prohibit the virus from associating with the extracellular matrix and cell surface. Furthermore, we identify that the nAbs engage via three different binding patterns: top-center binding (5G9 and 10B11), top-fringe binding (2H3 and 5H2), and fringe binding (A4B4). Our work shows that, despite differences in the pattern in binding, nAbs against HPV58 share a common neutralization mechanism. These results provide new insight into the understanding of HPV58 infection.
History
DepositionDec 6, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30769.png

Downloads & links

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Map

FileDownload / File: emd_30769.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3-fold subparticles refinement of human papillomavirus type 58 pseudo virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 420 pix.
= 473.76 Å		1.13 Å/pix.
x 420 pix.
= 473.76 Å		1.13 Å/pix.
x 420 pix.
= 473.76 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: 4.7 / Movie #1: 4.7
Minimum - Maximum-17.70483 - 27.270735
Average (Standard dev.)-0.00012150718 (±1.428657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 473.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z473.760473.760473.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-17.70527.271-0.000

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Supplemental data

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Sample components

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Entire : Human papillomavirus type 58

EntireName: Human papillomavirus type 58
Components
  • Virus: Human papillomavirus type 58

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Supramolecule #1: Human papillomavirus type 58

SupramoleculeName: Human papillomavirus type 58 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10598 / Sci species name: Human papillomavirus type 58 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 269160
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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