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 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)
TypeSourceAccession CodeDetails
experimental modelPDB 3E1Y 
experimental modelPDB 2KTU 
experimental modelPDB 1R5B 
experimental modelPDB 1R5O 
experimental modelPDB 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 StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsplunged into liquid ethane (FEI VITROBOT MARK IV)
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles48973
Reported Resolution (Å)9.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details(Single particle details: Images were classified and refined with RELION) (Single particle--Applied symmetry: C1)
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
IdRefinement SpaceRefinement ProtocolRefinement TargetOverall B ValueFitting ProcedureDetails
1 (3E1Y, 3E1Y)REALRIGID BODY FITCross correlationREFINEMENT 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)REALRIGID BODY FITCross correlationREFINEMENT PROTOCOL--RIGID BODY
3 (1R5B)REALRIGID BODY FITCross correlationREFINEMENT PROTOCOL--RIGID BODY
4 (1R5O)REALRIGID BODY FITCross correlationREFINEMENT PROTOCOL--RIGID BODY
5 (3VMF)REALRIGID BODY FITCross correlationREFINEMENT PROTOCOL--RIGID BODY
Data Acquisition
Detector TypeTVIPS TEMCAM-F415 (4k x 4k)
Electron Dose (electrons/Å**2)25
Imaging Experiment1
Date of Experiment2010-01-01
Temperature (Kelvin)81
Microscope ModelFEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.1
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN HELIUM
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONRELION
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
Each Particle