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Yorodumi- EMDB-8147: Cryo-EM structure of Human Papillomavirus Type 59 L1 Virus-like P... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8147 | |||||||||
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Title | Cryo-EM structure of Human Papillomavirus Type 59 L1 Virus-like Particle | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | Capsid / T=7 icosahedral / Virus-like Particle / VIRUS | |||||||||
Function / homology | Function and homology information 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 | Human papillomavirus type 59 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
Authors | Li ZH / Yan XD | |||||||||
Funding support | China, United States, 2 items
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Citation | Journal: Structure / Year: 2016 Title: The C-Terminal Arm of the Human Papillomavirus Major Capsid Protein Is Immunogenic and Involved in Virus-Host Interaction. Authors: Zhihai Li / Xiaodong Yan / Hai Yu / Daning Wang / Shuo Song / Yunbing Li / Maozhou He / Qiyang Hong / Qingbing Zheng / Qinjian Zhao / Ying Gu / Jun Zhang / Mandy E W Janssen / Giovanni ...Authors: Zhihai Li / Xiaodong Yan / Hai Yu / Daning Wang / Shuo Song / Yunbing Li / Maozhou He / Qiyang Hong / Qingbing Zheng / Qinjian Zhao / Ying Gu / Jun Zhang / Mandy E W Janssen / Giovanni Cardone / Norman H Olson / Timothy S Baker / Shaowei Li / Ningshao Xia / Abstract: Cervical cancer is the second most prevalent malignant tumor among women worldwide. High-risk human papillomaviruses (HPVs) are believed to be the major causative pathogens of mucosal epithelial ...Cervical cancer is the second most prevalent malignant tumor among women worldwide. High-risk human papillomaviruses (HPVs) are believed to be the major causative pathogens of mucosal epithelial cancers including cervical cancer. The HPV capsid is made up of 360 copies of major (L1) and 72 copies of minor (L2) capsid proteins. To date, limited high-resolution structural information about the HPV capsid has hindered attempts to understand details concerning the mechanisms by which HPV assembles and infects cells. In this study, we have constructed a pseudo-atomic model of the HPV59 L1-only capsid and demonstrate that the C-terminal arm of L1 participates in virus-host interactions. Moreover, when conjugated to a scaffold protein, keyhole limpet hemocyanin (KLH), this arm is immunogenic in vivo. These results provide new insights that will help elucidate HPV biology, and hence pave a way for the design of next-generation HPV vaccines. | |||||||||
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_8147.map.gz | 742.5 MB | EMDB map data format | |
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Header (meta data) | emd-8147-v30.xml emd-8147.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_8147.png | 245.1 KB | ||
Filedesc metadata | emd-8147.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8147 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8147 | HTTPS FTP |
-Validation report
Summary document | emd_8147_validation.pdf.gz | 574.1 KB | Display | EMDB validaton report |
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Full document | emd_8147_full_validation.pdf.gz | 573.7 KB | Display | |
Data in XML | emd_8147_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_8147_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8147 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8147 | HTTPS FTP |
-Related structure data
Related structure data | 5jb1MC 5j6rC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8147.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 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 : Human papillomavirus type 59
Entire | Name: Human papillomavirus type 59 |
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Components |
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-Supramolecule #1: Human papillomavirus type 59
Supramolecule | Name: Human papillomavirus type 59 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 37115 / Sci species name: Human papillomavirus type 59 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 19.8 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 580.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Major capsid protein L1
Macromolecule | Name: Major capsid protein L1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Human papillomavirus type 59 |
Molecular weight | Theoretical: 55.978418 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKVYLPPPSV AKVVSTDEYV TRTSIFYHAG SSRLLTVGHP YFKVPKGGNG RQDVPKVSAY QYRVFRVKLP DPNKFGLPDN TVYDPNSQR LVWACVGVEI GRGQPLGVGL SGHPLYNKLD DTENSHVASA VDTKDTRDNV SVDYKQTQLC IIGCVPAIGE H WTKGTACK ...String: MKVYLPPPSV AKVVSTDEYV TRTSIFYHAG SSRLLTVGHP YFKVPKGGNG RQDVPKVSAY QYRVFRVKLP DPNKFGLPDN TVYDPNSQR LVWACVGVEI GRGQPLGVGL SGHPLYNKLD DTENSHVASA VDTKDTRDNV SVDYKQTQLC IIGCVPAIGE H WTKGTACK PTTVVQGDCP PLELINTPIE DGDMVDTGYG AMDFKLLQDN KSEVPLDICQ SICKYPDYLQ MSADAYGDSM FF CLRREQV FARHFWNRSG TMGDQLPESL YIKGTDIRAN PGSYLYSPSP SGSVVTSDSQ LFNKPYWLHK AQGLNNGICW HNQ LFLTVV DTTRSTNLSV CASTTSSIPN VYTPTSFKEY ARHVEEFDLQ FIFQLCKITL TTEVMSYIHN MNTTILEDWN FGVT PPPTA SLVDTYRFVQ SAAVTCQKDT APPVKQDPYD KLKFWPVDLK ERFSADLDQF PLGRKFLLQL GARPKPTIGP RKRAA PAPT STPSPKRVKR RKSSRK UniProtKB: Major capsid protein L1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | |||||||||||||||
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Buffer | pH: 7.3 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Software - Name: Auto3DEM (ver. 4.05) Details: The effective resolution was estimated based on the 0.5 criteria of FSC between the cryoEM structure and the final model derived from the density map. Number images used: 3100 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |
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Output model | PDB-5jb1: |