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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6619 | |||||||||
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Title | Electron cryo-microscopy of Human Papillomavirus | |||||||||
![]() | Reconstruction of HPV16 complex with Heparin | |||||||||
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![]() | DED high resolution map / L1 plus L2 / quasivirus / Heparin | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
![]() | Guan J / Bywaters SM / Brendle SA / Ashley RE / Makhov AM / Conway JF / Christensen ND / Hafenstein S | |||||||||
![]() | ![]() Title: Cryoelectron Microscopy Maps of Human Papillomavirus 16 Reveal L2 Densities and Heparin Binding Site. Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Robert E Ashley / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein / ![]() Abstract: Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. The current commercial vaccines are genotype specific and provide little therapeutic benefit to ...Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Host entry mechanisms represent an excellent target for alternative therapeutics, but HPV receptor use, the details of cell attachment, and host entry are inadequately understood. Here we present near-atomic resolution structures of the HPV16 capsid and HPV16 in complex with heparin, both determined from cryoelectron micrographs collected with direct electron detection technology. The structures clarify details of capsid architecture for the first time, including variation in L1 major capsid protein conformation and putative location of L2 minor protein. Heparin binds specifically around the capsid icosahedral vertices and may recapitulate the earliest stage of infection, providing a framework for continuing biochemical, genetic, and biophysical studies. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.6 KB 9.6 KB | Display Display | ![]() |
Images | ![]() ![]() | 89.1 KB 4.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5keqMC ![]() 6620C ![]() 5kepC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of HPV16 complex with Heparin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.147 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Human papillomavirus bound to heparin
Entire | Name: Human papillomavirus bound to heparin |
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Components |
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-Supramolecule #1000: Human papillomavirus bound to heparin
Supramolecule | Name: Human papillomavirus bound to heparin / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Human papillomavirus 16
Supramolecule | Name: Human papillomavirus 16 / type: virus / ID: 1 / Name.synonym: HPV16 / NCBI-ID: 337041 / Sci species name: Human papillomavirus 16 / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: HPV16 / Sci species serotype: HPV16 |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: L1 plus L2 / Diameter: 580 Å / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.2 mg/mL |
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Buffer | pH: 7.4 / Details: 1 M NaCl, 200 mM Tris |
Grid | Details: glow-discharged holey carbon support grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 102 K / Instrument: GATAN CRYOPLUNGE 3 |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Jan 20, 2015 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 6175 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 93000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Details | The particles were selected using semi-automatic program e2boxer.py. |
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CTF correction | Details: ctffind for whole image |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: OTHER / Software - Name: auto3dem / Number images used: 51422 |
Final two d classification | Number classes: 10 |
-Atomic model buiding 1
Initial model | PDB ID: ![]() 3oae |
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Refinement | Space: REAL |
Output model | ![]() PDB-5keq: |