1D3I

CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 14 (HRV14) 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 14 COMPLEXED WITH INTERCELLULAR ADHESION MOLECULE-1

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification Details	HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY ...	HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-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	36
Reported Resolution (Å)	26
Resolution Method	OTHER
Other Details	THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 26 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO ...	THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 26 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 HRV14 WAS PLACED INTO THE CALIBRATED CRYO-EM DENSITY MAP BY ALIGNING THE ...	REFINEMENT PROTOCOL--RIGID BODY REFINEMENT DETAILS--THE CRYSTAL STRUCTURE OF HRV14 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 HRV14 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, HRV14 RESIDUES 1001-1016, 2001-2007 AND 4001-4028 ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE (PDB ENTRY 4RHV) AND THEREFORE ARE NOT INCLUDED IN THE COORDINATES BELOW.

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment	1993-06-01
Temperature (Kelvin)	120
Microscope Model	FEI/PHILIPS EM420
Minimum Defocus (nm)
Maximum Defocus (nm)	1250
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	49000
Calibrated Magnification
Source
Acceleration Voltage (kV)	80
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	PURDUE PROGRAMS
RECONSTRUCTION	PURDUE PROGRAMS

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.