4V8M | pdb_00004v8m

High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome

ELECTRON MICROSCOPY

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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	3U5F
experimental model	PDB	3U5G
experimental model	PDB	3U5H
experimental model	PDB	3U5I
experimental model	PDB	4A18
experimental model	PDB	4A1E
experimental model	PDB	4A17
experimental model	PDB	4A19
experimental model	PDB	4A1A
experimental model	PDB	4A1B
experimental model	PDB	4A1C
experimental model	PDB	4A1D
experimental model	PDB	2XZM
experimental model	PDB	2XZN
experimental model	PDB	3IZR
experimental model	PDB	3IZ6
experimental model	PDB	3IZ7
experimental model	PDB	3IZ9

Sample
TRYPANOSOMA BRUCEI 80S RIBOSOME

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	LIQUID ETHAN

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	164000
Reported Resolution (Å)	5.57
Resolution Method
Other Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2239 (DEPOSITION ID: 11259). THE STRUCTURE OF THE 80S FROM YEAST (3U5B AND OTHERS) AS WELL AS THE STRUCTURE OF THE 60S FROM TETRAHYMENA THERMOPHILA (4A17 AND OTHERS) WERE USED AS STARTING MODEL FOR THE 60S SUBUNIT MODEL. THE 40S FROM TETRAHYMENA THERMOPHILA (2XZM AND 2XZN) AS WELL AS THE 80S FROM YEAST WERE USED AS STARTING MODEL FOR THE 40S SUBUNIT MODEL. THE 80S MODEL OF TRITICUM AESTIVUM (3IZR AND OTHERS) WAS USED TO FIT MISSING PROTEINS FORM THE TWO X-RAY STRUCTURES.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I, 4A18, 4A1E, 4A17, 4A19, 4A1A, 4A1B, 4A1C, 4A1D, 2XZM, 2XZN, 3IZR, 3IZ6, 3IZ7, 3IZ9)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--RIGID BODY

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment	2011-01-01
Temperature (Kelvin)	93.15
Microscope Model	FEI TECNAI F30
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	59000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	MICROGRAPHS SCANNED WITH NIKON SUPER COOLSCAN 9000ED

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

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	PHASE-FLIPPING