3J5Y | pdb_00003j5y

Structure of the mammalian ribosomal pre-termination complex associated with eRF1-eRF3-GDPNP

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3E1Y
experimental model	PDB	2KTU
experimental model	PDB	1R5B
experimental model	PDB	1R5O
experimental model	PDB	3VMF

Sample
eRF1-eRF3-GDPNP-bound mammalian ribosomal pre-termination complex
Sample Components
80S ribosome
eukaryotic release factor 1
eukaryotic release factor 3
Transfer-messenger RNA Leu
messenger RNA

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	48973
Reported Resolution (Å)	9.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details	(Single particle details: Images were classified and refined with RELION) (Single particle--Applied symmetry: C1)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	Refinement Space	Refinement Protocol	Refinement Target	Overall B Value	Fitting Procedure	Details
1 (3E1Y, 3E1Y)	REAL	RIGID BODY FIT	Cross correlation			REFINEMENT PROTOCOL--RIGID BODY DETAILS--Domains w ...	REFINEMENT PROTOCOL--RIGID BODY DETAILS--Domains were fitted as rigid bodies using Chimera. Individual domains were then refined manually using hinge points as points of flexibility.
2 (2KTU)	REAL	RIGID BODY FIT	Cross correlation			REFINEMENT PROTOCOL--RIGID BODY
3 (1R5B)	REAL	RIGID BODY FIT	Cross correlation			REFINEMENT PROTOCOL--RIGID BODY
4 (1R5O)	REAL	RIGID BODY FIT	Cross correlation			REFINEMENT PROTOCOL--RIGID BODY
5 (3VMF)	REAL	RIGID BODY FIT	Cross correlation			REFINEMENT PROTOCOL--RIGID BODY

Data Acquisition
Detector Type	TVIPS TEMCAM-F415 (4k x 4k)
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment	2010-01-01
Temperature (Kelvin)	81
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.1
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN HELIUM
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	RELION

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	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.