STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY
ELECTRON MICROSCOPY
Sample
SPIROPLASMA VIRUS
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
Reported Resolution (Å)
27
Resolution Method
OTHER
Other Details
CA TRACING OF A MODEL OF THE CAPSID PROTEIN VP1 OF SPV4
BASED ON THE CRYSTAL STRUCTURAL COORDINATES OF THE
MAJOR CAPSID PROTEIN F OF PHIX174 (RESIDUES ...
CA TRACING OF A MODEL OF THE CAPSID PROTEIN VP1 OF SPV4
BASED ON THE CRYSTAL STRUCTURAL COORDINATES OF THE
MAJOR CAPSID PROTEIN F OF PHIX174 (RESIDUES 1001 - 1427).
A 71 AMINO ACID PORTION OF VP1 WAS MODELLED (GLY 226 - THR
297) AS AN INSERTION LOOP BETWEEN RESIDUES THR 1187 AND
THR 1188 OF THE F CAPSID PROTEIN OF PHIX174.
THE COORDINATES ARE IN THE P, Q, R FRAME IN ANGSTROM UNITS
AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS
CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q AND R ALONG
MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON.
RESIDUES 1001 - 1187 AND 1187 - 1426 ARE THE CA COORDINATES
OF THE F CAPSID PROTEIN OF PHIX174. INSERTED BETWEEN
RESIDUES 1187 AND 1188 IS A MODELLED CA TRACING OF A 71
AMINO ACID INSERTION LOOP OF SPV4 (RESIDUES 226 - 297) OF
THE VP1 CAPSID PROTEIN, BASED ON THE CRYO-EM RECONSTRUCTION
ENVELOPE AND STRUCTURAL ALIGNMENT AND SECONDARY STRUCTURE
PREDICTION.
THE RESOLUTION OF THE FINAL
RECONSTRUCTED DENSITY MAP WAS DETERMINED TO BE AT LEAST
27 ANGSTROMS AS MEASURED BY STRUCTURE FACTOR COMPARISONS
(BAKER ET AL. 1991, BIOPHYS. J. 60,1445-1456) AND FOURIER
RING CORRELATION MEASUREMENTS (CONWAY ET AL. 1996, J.
STRUC. BIOL. 116, 200-208)
Refinement Type
Symmetry Type
POINT
Point Symmetry
I
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
DETAILS--THE CRYSTAL STRUCTURE OF HRV16 WAS PLACED INTO THE CALIBRATED CRYO-EM
DENSITY MAP BY ALIGNING THE ICOSAHEDRAL SYMMETRY AXES. APPROPRIATELY
...
DETAILS--THE CRYSTAL STRUCTURE OF HRV16 WAS PLACED INTO THE CALIBRATED CRYO-EM
DENSITY MAP BY ALIGNING THE ICOSAHEDRAL SYMMETRY AXES. APPROPRIATELY
GLYCOSYLATED MODELS OF D1D2-ICAM-1 WITH VARIOUS INTERDOMAIN ANGLES (AS SEEN IN
DIFFERENT CRYSTAL STRUCTURES OF D1D2-ICAM-1), WERE FIRST MANUALLY FITTED INTO
THE CRYO-EM DENSITY CORRESPONDING TO THE ICAM-1 FRAGMENT, AND SUBSEQUENTLY
REFINED AS RIGID BODIES IN RECIPROCAL SPACE. OBSERVED STRUCTURE FACTORS WERE
OBTAINED BY INVERSE FOURIER TRANSFORM OF CRYO-EM DIFFERENCE MAPS CALCULATED BY-
1) SUBSTRACTION OF THE HRV16 AND RNA CONTRIBUTION FROM THE CRYO-EM
RECONSTRUCTED DENSITY OF THE COMPLEXES; 2) REDUCTION OF THE DIFFERENCE MAPS TO
AN ICOSAHEDRAL ASYMMETRIC UNIT. THE COORDINATES ARE IN THE P, Q, R FRAME IN
ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS
CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY PERPENDICULAR
TWO-FOLD AXES OF THE ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE
OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL COMPLEX PARTICLE
USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS. RESIDUES NOT VISIBLE IN THE
ORIGINAL CRYSTAL STRUCTURES ARE NOT INCLUDED IN THE CRYO-EM STRUCTURE MODEL.
FOR EXAMPLE, HRV16 RESIDUES 2001-2009, 4008-4022 AND 4045-4068 ARE NOT VISIBLE
IN THE CRYSTAL STRUCTURE (PDB ENTRY 1AYM) AND THEREFORE ARE NOT INCLUDED IN THE
COORDINATES BELOW.
