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- EMDB-5990: Electron cryo-microscopy of quasi-human papillomavirus 16 complex... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5990 | |||||||||
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Title | Electron cryo-microscopy of quasi-human papillomavirus 16 complexed with Fab H16.1A | |||||||||
![]() | Reconstruction of quasi-HPV16-Fab1A complex | |||||||||
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![]() | neutralization / quasi-human papillomavirus 16 / H16.1A | |||||||||
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 | unidentified (others) / ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.0 Å | |||||||||
![]() | Guan J / Brendle S / Bywaters S / Lee H / Ashley RE / Conway JF / Makhov AM / Christensen N / Hafenstein S | |||||||||
![]() | ![]() Title: Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization. Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Hyunwook Lee / Robert E Ashley / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein / ![]() Abstract: Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals ...Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope. Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays. | |||||||||
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 | ![]() | 465.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10 KB 10 KB | Display Display | ![]() |
Images | ![]() | 365.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 330.8 KB | Display | ![]() |
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Full document | ![]() | 330.4 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j8zMC ![]() 6121C ![]() 6184C ![]() 3j8vC ![]() 3j8wC 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 quasi-HPV16-Fab1A complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 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 : Quasi-HPV16 complex with Fab H16.1A
Entire | Name: Quasi-HPV16 complex with Fab H16.1A |
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Components |
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-Supramolecule #1000: Quasi-HPV16 complex with Fab H16.1A
Supramolecule | Name: Quasi-HPV16 complex with Fab H16.1A / type: sample / ID: 1000 Oligomeric state: Three hundred H16.1A Fabs bind to one HPV16 capsid Number unique components: 2 |
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-Supramolecule #1: Human papillomavirus 16
Supramolecule | Name: Human papillomavirus 16 / type: virus / ID: 1 / Details: Isolated by gradient centrifugation. / NCBI-ID: 337041 / Sci species name: Human papillomavirus 16 / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 27.8 MDa |
Virus shell | Shell ID: 1 / Name: L1 L2 / Diameter: 720 Å / T number (triangulation number): 7 |
-Macromolecule #1: H16.1A Fab
Macromolecule | Name: H16.1A Fab / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: unidentified (others) |
-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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Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Jan 9, 2013 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 50 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 50000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: auto3dem |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: auto3dem / Number images used: 2300 |