|Entry||Database: EMDB / ID: 5557|
|Title||Structure of the EV71 strain 1095 procapsid|
|Map data||Reconstruction of EV71 strain 1095 procapsid|
|Sample||EV71 strain 1095 procapsid:|
|Keywords||picornavirus / enterovirus 71 / hand foot and mouth disease / cryo-EM / single particle reconstruction|
|Source||Human enterovirus 71|
|Method||single particle reconstruction / cryo EM / 8.78 Å resolution|
|Authors||Cifuente JO / Lee H / Yoder JD / Shingler KL / Carnegie MS / Yoder JL / Ashley RE / Makhov AM / Conway JF / Hafenstein S|
|Citation||Journal: J. Virol. / Year: 2013|
Title: Structures of the procapsid and mature virion of enterovirus 71 strain 1095.
Authors: Javier O Cifuente / Hyunwook Lee / Joshua D Yoder / Kristin L Shingler / Michael S Carnegie / Jennifer L Yoder / Robert E Ashley / Alexander M Makhov / James F Conway / Susan Hafenstein
|Date||Deposition: Dec 21, 2012 / Header (metadata) release: Jul 3, 2013 / Map release: Jul 17, 2013 / Last update: Jul 17, 2013|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5557.map.gz (map file in CCP4 format, 161805 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.2545 Å|
CCP4 map header:
-Entire EV71 strain 1095 procapsid
|Entire||Name: EV71 strain 1095 procapsid / Number of components: 1|
-Component #1: virus, Human enterovirus 71
|Virus||Name: Human enterovirus 71 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN|
|Mass||Theoretical: 8 MDa|
|Species||Species: Human enterovirus 71|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: 10mM Tris-HCl, 200mM NaCl, 50mM MgCl2 / pH: 7.4|
|Vitrification||Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 120 K|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Aug 15, 2011|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 50400 X (calibrated)|
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 790 - 3910 nm / Energy filter: FEI
|Specimen Holder||Model: GATAN LIQUID NITROGEN / Temperature: K ( 83 - K)|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 20 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns|
|Processing||Method: single particle reconstruction / Number of projections: 8805|
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 better than 10 A resolution estimated at a Fourier Shell Correlation, FSC=0.5. For the last step of refinement, the final maps were CTF corrected using a B factor of 300 A2.
Applied symmetry: I (icosahedral)
|3D reconstruction||Algorithm: Cross-common lines / Euler angles: AUTO3DEM / Software: Auto3dem, EMAN2 / CTF correction: Each particle / Resolution: 8.78 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Software: VEDA / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: RECIPROCAL / Details: Protocol: Rigid body|
Input PDB model: 3VBU
Chain ID: A, B, C
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