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- EMDB-30781: The cryo-EM structure of human papillomavirus type 58 pseudovirus -

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Basic information

Entry
Database: EMDB / ID: EMD-30781
TitleThe cryo-EM structure of human papillomavirus type 58 pseudovirus
Map dataThe Cryo-EM structure of human papillomavirus type pseudovirus
Sample
  • Virus: Human papillomavirus type 58
    • Protein or peptide: Major capsid protein L1
Keywordsparticles / VIRUS
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / 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: 4.11 Å
AuthorsHe MZ / Chi X
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 8, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dn5
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dn5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30781.png

Downloads & links

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Map

FileDownload / File: emd_30781.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe Cryo-EM structure of human papillomavirus type pseudovirus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 720 pix.
= 812.16 Å		1.13 Å/pix.
x 720 pix.
= 812.16 Å		1.13 Å/pix.
x 720 pix.
= 812.16 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: 4.5 / Movie #1: 4.5
Minimum - Maximum-20.607337999999999 - 31.447403000000001
Average (Standard dev.)-0.034202088 (±1.9131762)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 812.16003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z720720720
origin x/y/z0.0000.0000.000
length x/y/z812.160812.160812.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS720720720
D min/max/mean-20.60731.447-0.034

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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
    • Protein or peptide: Major capsid protein L1

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Supramolecule #1: Human papillomavirus type 58

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

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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 58
Molecular weightTheoretical: 59.103199 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLILCCTLA ILFCVADVNV FHIFLQMSVW RPSEATVYLP PVPVSKVVST DEYVSRTSIY YYAGSSRLLA VGNPYFSIKS PNNNKKVLV PKVSGLQYRV FRVRLPDPNK FGFPDTSFYN PDTQRLVWAC VGLEIGRGQP LGVGVSGHPY LNKFDDTETS N RYPAQPGS ...String:
MVLILCCTLA ILFCVADVNV FHIFLQMSVW RPSEATVYLP PVPVSKVVST DEYVSRTSIY YYAGSSRLLA VGNPYFSIKS PNNNKKVLV PKVSGLQYRV FRVRLPDPNK FGFPDTSFYN PDTQRLVWAC VGLEIGRGQP LGVGVSGHPY LNKFDDTETS N RYPAQPGS DNRECLSMDY KQTQLCLIGC KPPTGEHWGK GVACNNNAAA TDCPPLELFN SIIEDGDMVD TGFGCMDFGT LQ ANKSDVP IDICNSTCKY PDYLKMASEP YGDSLFFFLR REQMFVRHFF NRAGKLGEAV PDDLYIKGSG NTAVIQSSAF FPT PSGSIV TSESQLFNKP YWLQRAQGHN NGICWGNQLF VTVVDTTRST NMTLCTEVTK EGTYKNDNFK EYVRHVEEYD LQFV FQLCK ITLTAEIMTY IHTMDSNILE DWQFGLTPPP SASLQDTYRF VTSQAITCQK TAPPKEKEDP LNKYTFWEVN LKEKF SADL DQFPLGRKFL LQSGLKAKPR LKRSAPTTRA PSTKRKKVKK

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
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

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13458
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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