3J6Y | pdb_00003j6y

S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U5B
experimental model	PDB	3U5C
experimental model	PDB	3U5D
experimental model	PDB	3U5E

Sample
ribosome-IRES complex
Sample Components
80S Ribosome
Internal Ribosome Entry Site

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK II
Cryogen Name	ETHANE
Sample Vitrification Details	Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	51373
Reported Resolution (Å)	6.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details	(Single particle--Applied symmetry: C1)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3U5B, 3U5C, 3U5D, 3U5E)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Cross-correlation
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--rigid body DETAILS--(1) TSV IRES was modeled with iFoldRNA and ModeRNA programs and then fitted into the cryo-EM map in Chimera. (2) The 80S-IRES complex was refined against the map, using stereochemically restrained real-space refinement in RSRef.

Data Acquisition
Detector Type	FEI FALCON I (4k x 4k)
Electron Dose (electrons/Å**2)	30

Imaging Experiment	1
Date of Experiment	2012-12-26
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1150
Maximum Defocus (nm)	6530
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	0.01
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	133333
Calibrated Magnification	132138
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	CTFFIND	3
MODEL FITTING	CNS
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN	2
RECONSTRUCTION	FREALIGN
RECONSTRUCTION	IMAGIC
RECONSTRUCTION	RSAMPLE

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	CTFFIND3, FREALIGN per micrograph