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- PDB-7dnl: 2-fold subparticles refinement of human papillomavirus type 58 ps... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dnl | ||||||
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Title | 2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in complexed with the Fab fragment of A4B4 | ||||||
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![]() | IMMUNE SYSTEM/VIRAL PROTEIN / Immune complex / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.19 Å | ||||||
![]() | He, M.Z. / Chi, X. / Zha, Z.H. / Zheng, Q.B. / Gu, Y. / Li, S.W. / Xia, N.S. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 473.7 KB | Display | ![]() |
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PDB format | ![]() | 396.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30787MC ![]() 7dn5C ![]() 7dnhC ![]() 7dnkC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: Antibody | Mass: 24455.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 23084.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 59103.199 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
EM software | Name: cisTEM / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING ONLY |
Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94862 / Symmetry type: POINT |