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 3J46 | pdb_00003j46

Structure of the SecY protein translocation channel in action


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I2P 
experimental modelPDB 3J01 
experimental modelPDB 3I8G 
Sample
active ribosome-nascent chain-SecYEG complex
Sample Components
70S ribosome
SecYEG channel
NC100- nascent chain
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification DetailsBlot 1-2 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles53000
Reported Resolution (Å)10.1
Resolution MethodFSC 0.5 CUT-OFF
Other DetailsThe structure was solved twice: first with a model starting from a 25-Angstrom filtered E. coli ribosome map generated in house, and then a second ti ...The structure was solved twice: first with a model starting from a 25-Angstrom filtered E. coli ribosome map generated in house, and then a second time using a filtered ribosome model (EMD-5036). In each case, after convergence, maps from two EMAN2 refinements with different parameters were averaged after alignment in Chimera. Four maps in total were averaged to reduce the noise. Resolution method was FSC at 0.5 cut-off for a comparison between the full experimental 3D density map and a calculated map of the docked E. coli ribosome model (this map was calculated to 7 Angstrom resolution with EMAN).
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (2I2P)2 (3J01)3 (3I8G, 3I8G)
Refinement SpaceREALREALREAL
Refinement ProtocolFLEXIBLE FITFLEXIBLE FITFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--FLEXIBLEREFINEMENT PROTOCOL--FLEXIBLEREFINEMENT PROTOCOL--FLEXIBLE DETAILS--A- and P-site tRNAs from T. thermophilus ribosome structure. mRNA from this structure also used for some model ...REFINEMENT PROTOCOL--FLEXIBLE DETAILS--A- and P-site tRNAs from T. thermophilus ribosome structure. mRNA from this structure also used for some modeling steps.
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment2012-02-10
Temperature (Kelvin)94
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelOTHER
Nominal Magnification42000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)160
Imaging DetailsLow dose imaging: automated single particle data collection program from TVIPS was used.
EM Software
TaskSoftware PackageVersion
MODEL FITTINGMDFF
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONEMAN2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
per micrograph