Crystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosaccharides

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Structural basis of oligosaccharide receptor recognition by human papillomavirus.

Dasgupta, J.Bienkowska-Haba, M.Ortega, M.E.Patel, H.D.Bodevin, S.Spillmann, D.Bishop, B.Sapp, M.Chen, X.S.

(2011) J Biol Chem 286: 2617-2624

  • DOI: https://doi.org/10.1074/jbc.M110.160184
  • Primary Citation of Related Structures:  
    5W1O, 5W1X

  • PubMed Abstract: 

    High risk human papillomavirus types 16 (HPV16) and 18 (HPV18) can cause cervical cancer. Efficient infection by HPV16 and HPV18 pseudovirions requires interactions of particles with cell-surface receptor heparan sulfate oligosaccharide. To understand the virus-receptor interactions for HPV infection, we determined the crystal structures of HPV16 and HPV18 capsids bound to the oligosaccharide receptor fragment using oligomeric heparin. The HPV-heparin structures revealed multiple binding sites for the highly negatively charged oligosaccharide fragment on the capsid surface, which is different from previously reported virus-receptor interactions in which a single type of binding pocket is present for a particular receptor. We performed structure-guided mutagenesis to generate mutant viruses, and cell binding and infectivity assays demonstrated the functional role of viral residues involved in heparin binding. These results provide a basis for understanding virus-heparan sulfate receptor interactions critical for HPV infection and for the potential development of inhibitors against HPV infection.

  • Organizational Affiliation

    Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein L1
A, B, C, D, E
427Human papillomavirusMutation(s): 0 
Gene Names: L1
Find proteins for Q81007 (Human papillomavirus)
Explore Q81007 
Go to UniProtKB:  Q81007
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81007
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose
F, H, I, J, K
F, H, I, J, K, L, M, N, O, P
Glycosylation Resources
GlyTouCan:  G75183WV
GlyCosmos:  G75183WV
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose
Glycosylation Resources
GlyTouCan:  G29325GF
GlyCosmos:  G29325GF
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.62α = 90
b = 101.252β = 90.63
c = 128.182γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary