3J78 | pdb_00003j78

Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs)

ELECTRON MICROSCOPY

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
experimental model	PDB	3I9B
experimental model	PDB	3J3B

Sample
80S ribosome bound to mRNA containing Kozak sequence and to two tRNAs
Sample Components
80S ribosome
transfer RNA
messenger RNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK II
Cryogen Name	ETHANE
Sample Vitrification Details	Plunged into liquid ethane (FEI VITROBOT MARK II)

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	23163
Reported Resolution (Å)	6.3
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, 3I9B, 3I9B, 3I9B, 3J3B)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	cross-correlation
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--rigid body DETAILS--3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNAs and mRNA were modeled using individual tRNA ...	REFINEMENT PROTOCOL--rigid body DETAILS--3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNAs and mRNA were modeled using individual tRNAs and mRNA from the crystal structure (3I9B) of the classical-state 70S ribosome. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B.

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

Imaging Experiment	1
Date of Experiment	2013-01-02
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1159
Maximum Defocus (nm)	4844
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	133333
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