REL PDBe PDBe PDBe 2005-04-08 2005-04-08 2006-01-16 2013-03-13 Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses. Mukhopadhyay S Zhang W Gabler S Chipman PR Strauss EG Strauss JH Baker TS Kuhn RJ Rossmann MG Mukhopadhyay S Zhang W Gabler S Chipman PR Strauss EG Strauss JH Baker TS Kuhn RJ Rossmann MG Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses. STRUCTURE 14 63 73 2006 16407066 doi:10.1016/j.str.2005.07.025 1z8y FULLOVERLAP Sindbis TE12 E2-N318Q Sindbis TE12 E2-N318Q
Sample is a single deglycosylated virus. For mutagenesis and purification, please see Pletnev et al. (2001) Cell. Virus contains 3 proteins (E1, E2, capsid), a lipid bilyer, and a positive-strand RNA genome.
1 Sindbis virus
deglycosylated virus
Sindbis virus Homo sapiens INVERTEBRATES 52 glycoprotein 710 4 lipid bilayer 480 4 capsid 410 4 VIRION STRAIN true false Sindbis strain TE12 singleParticle particle 6 7.4
20 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA
 NEGATIVE
no staining
holey carbon 400 mesh copper grid
 ETHANE HOMEMADE PLUNGER
Vitrification instrument: Purdue manufactured, gravity driven device. Vitrification carried out in hood.
Vitrified immediately after blotting. standard methods FEI/PHILIPS CM200T FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.0 1.1 2.58 38000.0 39220.0 GATAN LIQUID NITROGEN 87 100 objective lens astigmatism was corrected at 100,000 times magnification
Low dose
2000-06-21 KODAK SO-163 FILM ZEISS SCAI 7 27 18
optical density range is 0.33-1.35
1.0 8. Side entry liquid nitrogen-cooled cryo specimen holder 0 0
The particles were selected interactively at the computer terminal.
CTF correction of each particle.
 I OTHER 9.0 FSC 0.5 CUT-OFF Purdue Suite
resolution determined by splitting data set into two groups.
7085
Euler angles (theta, phi, omega) are defined as three successive rotations in a right hand coordinate system. First, the viewer is rotated counterclockwise around the z-axis (angle 'phi') and then rotated counterclockwise around the new y-axis (angle 'theta') and rotate clockwise around the new z-axis (angle 'omega').
 3 emd_1121.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 441 441 441 -220 -220 -220 441 441 441 787.18 787.18 787.18 90 90 90 Y X Z -297.649999999999977 402.470000000000027 7.03224 65.091200000000001 1.78499 1.78499 1.78499 138.0 center of virus is where z=0
::::EMDATABANK.org::::EMD-1121::::
 1I9W RIGID BODY FIT EMFIT
Protocol: Rigid body. each protein in the asymmetric unit was fitting individually.
sumf REAL 1XYK RIGID BODY FIT EMFIT
Protocol: Rigid body. each protein in the asymmetric unit was fitting individually.
sumf REAL