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Yorodumi- EMDB-20218: CryoEM structure of human papillomavirus 16 pseudovirus in comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20218 | |||||||||
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Title | CryoEM structure of human papillomavirus 16 pseudovirus in complex human alpha-defensin 5 (HD5) | |||||||||
Map data | CryoEM structure of human papillomavirus 16 pseudovirus in complex with human alpha-defensin 5 (HD5) | |||||||||
Sample |
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Biological species | Homo sapiens (human) / Human papillomavirus type 16 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Gulati NM / Wiens ME / Smith JG / Stewart PL | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Pathog Immun / Year: 2019 Title: α-Defensin HD5 Stabilizes Capsid/Core Interactions. Authors: Neetu M Gulati / Masaru Miyagi / Mayim E Wiens / Jason G Smith / Phoebe L Stewart / Abstract: BACKGROUND: (HPV) is linked to nearly all cases of cervical cancer. Despite available vaccines, a deeper understanding of the immune response to HPV is needed. Human α-defensin 5 (HD5), an innate ...BACKGROUND: (HPV) is linked to nearly all cases of cervical cancer. Despite available vaccines, a deeper understanding of the immune response to HPV is needed. Human α-defensin 5 (HD5), an innate immune effector peptide, blocks infection of multiple sero-types of HPV, including high-risk HPV16. While a common mechanism of α-defensin anti-viral activity against nonenveloped viruses such as HPV has emerged, there is limited understanding of how α-defensins bind to viral capsids to block infection. METHODS: We have used cryo-electron microscopy (cryoEM), mass spectrometry (MS) crosslinking and differential lysine modification studies, and molecular dynamics (MD) simulations to probe the ...METHODS: We have used cryo-electron microscopy (cryoEM), mass spectrometry (MS) crosslinking and differential lysine modification studies, and molecular dynamics (MD) simulations to probe the interaction of HPV16 pseudovirions (PsVs) with HD5. RESULTS: CryoEM single particle reconstruction did not reveal HD5 density on the capsid surface. Rather, increased density was observed under the capsid shell in the presence of HD5. MS studies ...RESULTS: CryoEM single particle reconstruction did not reveal HD5 density on the capsid surface. Rather, increased density was observed under the capsid shell in the presence of HD5. MS studies indicate that HD5 binds near the L1 and L2 capsid proteins and specifically near the C-terminal region of L1. MD simulations indicate that favorable electrostatic interactions can be formed between HD5 and the L1 C-terminal tail. CONCLUSIONS: A model is presented for how HD5 affects HPV16 structure and cell entry. In this model, HD5 binds to disordered regions of L1 and L2 protruding from the icosahedrally ordered capsid. HD5 ...CONCLUSIONS: A model is presented for how HD5 affects HPV16 structure and cell entry. In this model, HD5 binds to disordered regions of L1 and L2 protruding from the icosahedrally ordered capsid. HD5 acts to cement interactions between L1 and L2 and leads to a closer association of the L2/genome core with the L1 capsid. This model provides a structural rationale for our prior observation that HD5 interferes with the separation of L1 from the L2/genome complex during cell entry. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20218.map.gz | 765.6 MB | EMDB map data format | |
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Header (meta data) | emd-20218-v30.xml emd-20218.xml | 9 KB 9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20218_fsc.xml | 29.4 KB | Display | FSC data file |
Images | emd_20218.png | 279.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20218 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20218 | HTTPS FTP |
-Validation report
Summary document | emd_20218_validation.pdf.gz | 390.5 KB | Display | EMDB validaton report |
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Full document | emd_20218_full_validation.pdf.gz | 390.1 KB | Display | |
Data in XML | emd_20218_validation.xml.gz | 19.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20218 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20218 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20218.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM structure of human papillomavirus 16 pseudovirus in complex with human alpha-defensin 5 (HD5) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of human papillomavirus type 16 pseudovirus with human al...
Entire | Name: Complex of human papillomavirus type 16 pseudovirus with human alpha-defensin 5 (HD5) |
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Components |
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-Supramolecule #1: Complex of human papillomavirus type 16 pseudovirus with human al...
Supramolecule | Name: Complex of human papillomavirus type 16 pseudovirus with human alpha-defensin 5 (HD5) type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #3: alpha-defensin 5 (HD5)
Supramolecule | Name: alpha-defensin 5 (HD5) / type: complex / ID: 3 / Parent: 1 Details: Synthesized linear HD5 peptide (CPC Scientific, Sunnyvale, CA) was subjected to thiol-disulfide reshuffling and purified to homogeneity by reverse-phase high-pressure liquid chromatography |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: Human papillomavirus type 16
Supramolecule | Name: Human papillomavirus type 16 / type: virus / ID: 2 / Parent: 1 / NCBI-ID: 333760 / Sci species name: Human papillomavirus type 16 / Sci species strain: pseudovirus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host system | Organism: Homo sapiens (human) / Recombinant cell: 293TT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |