|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 / ハツカネズミ, はつかねずみ /
|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 / ハツカネズミ, はつかねずみ /|
|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
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