3J46 | pdb_00003j46

Structure of the SecY protein translocation channel in action

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I2P
experimental model	PDB	3J01
experimental model	PDB	3I8G

Sample
active ribosome-nascent chain-SecYEG complex
Sample Components
70S ribosome
SecYEG channel
NC100- nascent chain

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	Blot 1-2 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	53000
Reported Resolution (Å)	10.1
Resolution Method	FSC 0.5 CUT-OFF
Other Details	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 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 Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (2I2P)	2 (3J01)	3 (3I8G, 3I8G)
Refinement Space	REAL	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	FLEXIBLE FIT	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--FLEXIBLE	REFINEMENT PROTOCOL--FLEXIBLE	REFINEMENT 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 Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment	2012-02-10
Temperature (Kelvin)	94
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	42000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	160
Imaging Details	Low dose imaging: automated single particle data collection program from TVIPS was used.

EM Software
Task	Software Package	Version
MODEL FITTING	MDFF
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN	2

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

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.