5FVM | pdb_00005fvm

Cryo electron microscopy of a complex of Tor and Lst8

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JSV

Sample
COMPLEX OF TOR1 WITH LST8

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- OTHER, METHOD- 11-13 S AT 4 DEG C,

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	28877
Reported Resolution (Å)	6.7
Resolution Method
Other Details	THE FAT AND KINASE DOMAINS (FATKIN) WERE FIT USING 4JSV FATKIN AS AN INITIAL MODEL. THE REMAINDER OF THE STRUCTURE WAS FIT WITH A POLY-ALANINE, AND AN ...	THE FAT AND KINASE DOMAINS (FATKIN) WERE FIT USING 4JSV FATKIN AS AN INITIAL MODEL. THE REMAINDER OF THE STRUCTURE WAS FIT WITH A POLY-ALANINE, AND AN APPROXIMATE SEQUENCE REGISTER WAS ESTABLISHED BASED ON THE PREDICED HELICAL ELEMENTS IN THE N-TERMINAL REGION AND THE HELICES VISIBLE IN THE EM DENSITY. THE ENTIRE MODEL IS POLY-ALANINE. THE TOPOLOGY OF THE MODEL WAS VERIFIED BY DETERMINING THE STRUCTURES OF VARINTS IN WHICH TENDEM RFPS WERE INSERTED INTO THE STRUCTURE. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3329. (DEPOSITION ID: 14248).
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (4JSV)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	METHOD--FLEXIBLE

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment	2015-05-16
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	2500
Maximum Defocus (nm)	3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	47000
Calibrated Magnification	105263
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 (GCTF)

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.