4UER | pdb_00004uer

40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U5B

Sample
LACHANCEA KLUYVERI 40S- EIF1- EIF1A-EIF3-EIF3J INITIATION COMPLEX

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 75, TEMPERATURE- 120, INSTRUMENT- HOMEMADE PLUNGER, METHOD- 5 SECONDS BLOTTING BEFORE PLUNGING., DETAILS ...	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 75, TEMPERATURE- 120, INSTRUMENT- HOMEMADE PLUNGER, METHOD- 5 SECONDS BLOTTING BEFORE PLUNGING., DETAILS- CARBON FLOATED ON THE SAMPLE PRIOR TO RECOVERY ONTO THE GRID AND FLASH -FREEZING.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	27354
Reported Resolution (Å)	6.47
Resolution Method
Other Details	THIS DEPOSITION DETAILS AN S. CEREVISIAE MODEL FOR THE CLOSELY RELATED L. KLUYVERI STRUCTURE. INITIAL PLACEMENT OF FOLDED DOMAINS WAS ACCORDING TO THE ...	THIS DEPOSITION DETAILS AN S. CEREVISIAE MODEL FOR THE CLOSELY RELATED L. KLUYVERI STRUCTURE. INITIAL PLACEMENT OF FOLDED DOMAINS WAS ACCORDING TO THE MASS-SPECTROMETRY MODEL IN DOMAINS WERE FITTED INTO CRYOEM DENSITY LOW-PASS FILTERED AT MEAN LOCAL RESOLUTION AS RIGID BODIES USING CALCULATED DENSITIES GENERATED AT THE SAME RESOLUTION. CORRELATION COEFFICIENT WAS USED AS THE TARGET FUNCTION IN CHIMERA. THE RRM DOMAIN OF EIF3B IS DEPOSITED AS CA TRACE ONLY TO INDICATE THAT ITS POSITION HAS LOWER ANGULAR CONFIDENCE BECAUSE THE DOMAIN IS EXTREMELY SMALL AND GENERATED NO DIRECT CROSS-LINKS TO THE 40S TO AID PLACEMENT. EIF3B HAS BEEN NUMBERED ACCORDING TO THE SECOND START CODON AS THIS IS THOUGHT TO BE THE PREDOMINANT FORM OF THE PROTEIN IN VIVO. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2845.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3U5B)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	METHOD--RIGID BODY

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment	2014-04-06
Temperature (Kelvin)	100
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	5000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	59000
Calibrated Magnification	100719
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	CTFFIND	3
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	RELION	1.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	BY IMAGE

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.