1DGI | pdb_00001dgi

Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155

ELECTRON MICROSCOPY

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	ELECTRON MICROSCOPY RECONSTRUCTION	7.5		WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION

Sample
human poliovirus(serotype 1)complexed with three domain CD155

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification Details	POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP 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	1156
Reported Resolution (Å)	22
Resolution Method	OTHER
Other Details	THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 22 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	REAL
Refinement Protocol	OTHER
Refinement Target	VISUAL AGREEMENT
Overall B Value
Fitting Procedure
Details	METHOD--MANUAL REFINEMENT PROTOCOL--MANUAL ADJUSTMENT DETAILS--THE CRYSTAL STRUCTURE OF POLIOVIRUS WAS PLACED INTO THE CALIBRATED CRYO-EM DENSITY MAP BY ALIGNING THE ICOSAHEDRAL SYMMETRY AXES. APPROPRIATELY GLYCOSYLATED MODELS OF CD155 WITH VARIOUS INTERDOMAIN ANGLES WERE MANUALLY FITTED INTO THE DIFFERENCE DENSITY CALCULAT BY SUBSTRACTING POLIOVIRUS NATIVE RECONSTRUCTION FROM THE COMPLEX RECONSTRUCTION. 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. CD155 MODEL BUILDING (D1-D2-D3)-- ATOMIC MODEL OF D1 WAS BUILT BASED ON MYELIN PROTEIN ZERO(1NEU). ATOMIC MODEL OF D2 WAS BUILT FROM A FAB FRAGMENT(1CIC).ATOMIC MODEL OF D3 WAS BUILT FROM AN INSECT IMMUNE PROTEIN(1BIH).THE ELBOW ANGLE BETWEEN D1 AND D2 WAS DETERMINED BY LEAST-SQUARE-FITTING THESE TWO DOMAINS THE CRYSTAL STRUCTURE OF CD2(1HNF).

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

Imaging Experiment	1
Date of Experiment	1999-06-01
Temperature (Kelvin)	120
Microscope Model	FEI/PHILIPS CM200FEG
Minimum Defocus (nm)	1300
Maximum Defocus (nm)	2100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	38000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	80
Imaging Details

EM Software
Task	Software Package	Version
RECONSTRUCTION	PURDUE PROGRAMS