3J3P | pdb_00003j3p

Conformational Shift of a Major Poliovirus Antigen Confirmed by Immuno-Cryogenic Electron Microscopy: 135S Poliovirus and C3-Fab Complex

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FPT
experimental model	PDB	1XYR

Sample
Poliovirus 135S particle and C3 Fab complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details	Vitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	9810
Reported Resolution (Å)	9.1
Resolution Method	FSC 0.5 CUT-OFF
Other Details	Reconstruction computed from focal pairs. Pairs not summed for reconstruction calculation.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1FPT, 1FPT, 1FPT)	2 (1XYR)
Refinement Space	REAL	REAL
Refinement Protocol	RIGID BODY FIT	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--Rigid Body DETAILS--Atomic coordinates for C3 Fab (Nature Struct. Biol. 2, 232-243) (PDB entry 1FPT) were manually fitted using ...	REFINEMENT PROTOCOL--Rigid Body DETAILS--Atomic coordinates for C3 Fab (Nature Struct. Biol. 2, 232-243) (PDB entry 1FPT) were manually fitted using UCSF Chimera (Journal of Computational Chemistry 25, 1605-1612). A core-weighted, rigid-body fitting algorithm implemented in CHARRM (J Struct Biol 141, 63-76) was used to refine the fit.	REFINEMENT PROTOCOL--Rigid Body DETAILS--The coordinates of PDB entry 1XYR were placed into the 135S-C3 cryo-EM map. BC loop coordinates were manipul ...	REFINEMENT PROTOCOL--Rigid Body DETAILS--The coordinates of PDB entry 1XYR were placed into the 135S-C3 cryo-EM map. BC loop coordinates were manipulated to fit the cryo-EM data (see primary citation for details).

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	14

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI/PHILIPS CM200FEG
Minimum Defocus (nm)	1120
Maximum Defocus (nm)	1630
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	38000
Calibrated Magnification	38000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	CHARMM
RECONSTRUCTION	EM3DR	2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	CTF and decay correction of each particle

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.