CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY
ELECTRON MICROSCOPY
Sample
HUMAN RHINOVIRUS 16 COMPLEXED WITH INTERCELLULAR ADHESION MOLECULE-1
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification Details
HRV16 WAS INCUBATED WITH D1D2-ICAM-1 FOR 16 HOURS AT 34
DEGREES CELSIUS (307 KELVIN) USING A SIXTEEN-FOLD EXCESS
OF D1D2-ICAM-1 FOR EACH OF THE SI ...
HRV16 WAS INCUBATED WITH D1D2-ICAM-1 FOR 16 HOURS AT 34
DEGREES CELSIUS (307 KELVIN) USING A SIXTEEN-FOLD EXCESS
OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING
SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED
AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR
LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
WITH A GATAN 626 CRYOTRANSFER HOLDER
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
44
Reported Resolution (Å)
28
Resolution Method
OTHER
Other Details
THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS
DETERMINED TO BE AT LEAST 28 ANGSTROMS, AS MEASURED BY
RANDOMLY SPLITTING THE PARTICLES INTO ...
THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS
DETERMINED TO BE AT LEAST 28 ANGSTROMS, AS MEASURED BY
RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND
COMPARING STRUCTURE FACTORS OBTAINED FROM SEPARATE
RECONSTRUCTIONS (BAKER ET AL. 1991, BIOPHYS.J. 60,
1445-1456). THE EIGENVALUE SPECTRUM GAVE AN INDICATION
OF THE RANDOMNESS OF THE DATA THAT WAS INCLUDED IN THE
RECONSTRUCTION. THE COMPLETENESS OF THE DATA WAS VERIFIED
IN THAT ALL EIGENVALUES EXCEEDED 1.0.
Refinement Type
Symmetry Type
POINT
Point Symmetry
I
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
VECTOR R-FACTOR
Overall B Value
Fitting Procedure
Details
REFINEMENT PROTOCOL--RIGID BODY REFINEMENT DETAILS--THE CRYSTAL STRUCTURE OF
HRV16 WAS PLACED INTO THE CALIBRATED CRYO-EM DENSITY MAP BY ALIGNING THE ...
REFINEMENT PROTOCOL--RIGID BODY REFINEMENT 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.
