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