|Entry||Database: EMDB / ID: 6119|
|Title||Electron cryo-microscopy of human papillomavirus 16 and H16.V5 Fab fragments|
|Keywords||virus-Fab complex / neutralization antibody / maturation|
|Sample||Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs|
|Source||Human papillomavirus 16 / virus|
Mus musculus / mammal / House mouse /
|Map data||Reconstruction of mature human papillomavirus 16 capsid complexed with Fab fragments after 1 hr incubation|
|Method||single particle (icosahedral) reconstruction, at 14.7 Å resolution|
|Authors||Lee H / Brendle SA / Bywaters SM / Guan J / Ashley RE / Yoder JD / Makhov AM / Conway JF / Christensen ND / Hafenstein S|
|Citation||J. Virol., 2015, 89, 1428-1438|
J. Virol., 2015, 89, 1428-1438 Yorodumi Papers
|Date||Deposition: Sep 30, 2014 / Header (metadata) release: Oct 8, 2014 / Map release: Dec 3, 2014 / Last update: May 27, 2015|
Downloads & links
|File||emd_6119.map.gz (map file in CCP4 format, 117502 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.86 Å|
CCP4 map header:
-Entire Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs
|Entire||Name: Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs|
Number of components: 2
Oligomeric State: Three hundred H16.V5 Fabs bind to one HPV16 capsid
|Mass||Theoretical: 42 MDa|
-Component #1: virus, Human papillomavirus 16
|Virus||Name: Human papillomavirus 16 / Class: VIRION|
Details: The virus sample was incubated with excessive Fab fragments for 1 hr.
Enveloped: No / Empty: No / Isolate: OTHER
|Mass||Theoretical: 27 MDa|
|Species||Species: Human papillomavirus 16 / virus|
|Source (natural)||Host Species: Homo sapiens / human / / Host category: VERTEBRATES|
|Shell #1||Name of element: L1/L2 / Diameter: 600 Å / T number(triangulation number): 7|
-Component #2: protein, H16.V5 Fab
|Protein||Name: H16.V5 Fab / Oligomeric Details: monomer / Recombinant expression: No / Number of Copies: 300|
|Mass||Theoretical: 50 kDa|
|Source||Species: Mus musculus / mammal / House mouse /|
|Source (natural)||Cell: hybridoma|
|Sample solution||Specimen conc.: 1 mg/ml|
Buffer solution: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4
|Support film||glow-discharged holey carbon Quantifoil grids|
|Vitrification||Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 102 K / Humidity: 90 % / Method: Blot for 0.7 seconds before plunging.|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2100 / Date: Aug 13, 2014|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 40000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1190 - 5670 nm|
|Specimen Holder||Model: GATAN LIQUID NITROGEN / Temperature: 95 K|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Image acquisition||Number of digital images: 138|
|Processing||Method: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2075|
Details: The particles were selected using semi-automatic program e2boxer.py (EMAN2).
|3D reconstruction||Algorithm: Cross-common lines / Software: Auto3dem / CTF correction: Each particle|
Details: Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images using Robem. Defocus and astigmatism values to perform contrast transfer function (CTF) correction were assessed using Robem for the extracted particles. The icosahedrally averaged reconstructions were initiated using a random model generated with setup_rmc and reached 14 A resolution estimated at a Fourier Shell Correlation (FSC) of 0.5. For the last step of refinement, the final maps were CTF-corrected using a B factor of 200 A2.
Resolution: 14.7 Å / Resolution method: FSC 0.5, semi-independent
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi