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Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
1DGI
pdb_00001dgi
10.2210/pdb1dgi/pdb
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Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
human poliovirus(serotype 1)complexed with three domain CD155
Specimen Preperation
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
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
Date of Experiment
1999-06-01
Temprature (Kelvin)
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
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
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