5Y9E

Crystal structure of HPV58 pentamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.042 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus.

Li, Z.Wang, D.Gu, Y.Song, S.He, M.Shi, J.Liu, X.Wei, S.Li, J.Yu, H.Zheng, Q.Yan, X.Baker, T.S.Zhang, J.McLellan, J.S.Li, S.Xia, N.

(2017) MBio 8: --

  • DOI: 10.1128/mBio.00787-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Persistent, high-risk human papillomavirus (HPV) infection is the primary cause of cervical cancer. Neutralizing antibodies elicited by L1-only virus-like particles (VLPs) can block HPV infection; however, the lack of high-resolution structures has l ...

    Persistent, high-risk human papillomavirus (HPV) infection is the primary cause of cervical cancer. Neutralizing antibodies elicited by L1-only virus-like particles (VLPs) can block HPV infection; however, the lack of high-resolution structures has limited our understanding of the mode of virus infection and the requirement for type specificity at the molecular level. Here, we describe two antibodies, A12A3 and 28F10, that specifically bind to and neutralize HPV58 and HPV59, respectively, through two distinct binding stoichiometries. We show that the epitopes of A12A3 are clustered in the DE loops of two adjacent HPV58 L1 monomers, whereas 28F10 recognizes the HPV59 FG loop of a single monomer. Via structure-based mutagenesis and analysis of antibody binding, we further identified the residues HPV58 D154, S168, and N170 and HPV59 M267, Q270, E273, Y276, K278, and R283, which play critical roles in virus infection. By substituting these strategic epitope residues into other HPV genotypes, we could then redirect the type-specific binding of the antibodies to these genotypes, thus highlighting the importance of these specific residues, HPV58 R161, S168, and N308 and HPV59 Q270, E273, and D281. Overall, our findings provide molecular insights into potential structural determinants of HPV required for infectivity and type specificity. IMPORTANCE High-risk human papillomaviruses (HPVs) are considered the major causative pathogens of cancers that affect epithelial mucosa, such as cervical cancer. However, because of the lack of high-resolution structural information on the sites of neutralization, we have yet to determine the precise mode of HPV infection and how different types of HPV cause infection. Our crystal structures in this study have uncovered discrete binding stoichiometries for two different antibodies. We show that one A12A3 Fab binds to the center of one HPV58 pentamer, whereas five 28F10 Fabs bind along the top fringe of one HPV59 pentamer. Furthermore, through targeted epitope analysis, we show that 6 to 7 discontinuous residues of the L1 major capsid protein of HPV are determinants, at least in part, for virus infection and type specificity. This knowledge will help us to unravel the process of HPV infection and can potentially be used to drive the development of therapeutics that target neutralization-sensitive sites.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA Jason.S.McLellan@dartmouth.edu shaowei@xmu.edu.cn nsxia@xmu.edu.cn.,Department of Chemistry and Biochemistry; Division of Biological Sciences, University of California, San Diego, San Diego, California, USA.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China.,National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China Jason.S.McLellan@dartmouth.edu shaowei@xmu.edu.cn nsxia@xmu.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major capsid protein L1
A, B, C, D, E
490Human papillomavirus type 58Mutation(s): 1 
Gene Names: L1
Find proteins for P26535 (Human papillomavirus type 58)
Go to UniProtKB:  P26535
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.042 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 187.213α = 90.00
b = 101.804β = 95.68
c = 136.195γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-08-24 
  • Released Date: 2017-10-25 
  • Deposition Author(s): Li, S.W., Li, Z.H.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670935
National Natural Science Foundation of ChinaChina81671645
National Natural Science Foundation of ChinaChina81571996
Natural Science Foundation of Fujian ProvinceChina2015YZ0002

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release