EMD-4386

Single-particle
3.85 Å
EMD-4386 Deposition: 19/04/2018
Map released: 13/06/2018
Last modified: 15/05/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-4386

cryo-EM structure of the human neutral amino acid transporter ASCT2

EMD-4386

Single-particle
3.85 Å
EMD-4386 Deposition: 19/04/2018
Map released: 13/06/2018
Last modified: 15/05/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 2.5 mg/mL
Buffer
pH: 7.0
Details: 20mM Tris-HCl pH 7.4 300mM NaCl 1mM L-glutamine 0.05% DDM 0.005% CHS
Grid
Mesh: 200
Model: Quantifoil, UltrAuFoil, R1.2/1.3
Material: GOLD
Pretreatment
Type: GLOW DISCHARGE
Time: 20 s
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 278 K
Instrument: FEI VITROBOT MARK II
Microscopy [1]
Microscope: FEI TALOS ARCTICA
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
C2 aperture diameter: 100.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 0.0004 µm - 0.0025 µm
Calibrated defocus: 0.0004 µm - 0.0025 µm
Nominal magnification: 49407.0
Calibrated magnification: 49407.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Temperature
Minimum: 70.0 K
Maximum: 90.0 K
Specialist optics
Energy filter
Name: GIF Quantum LS
Lower energy threshold: 0 eV
Upper energy threshold: 20 eV
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Frames per image: 1-60
Average exposure time: 9.0 s
Average electron dose per image: 0.87 e/Å2
Details: Freshly purified protein was concentrated using Vivaspin concentrating devices with a molecular weight cutoff of 100kDa to 2-2.5 mg ml-1. 2.8 ul were applied on holey-carbon cryo-EM grids (Quantifoil Au R1.2-1.3, 200 and 300 mesh), which were prior glow-discharged at 5 mA for 20 s. Grids were blotted for 3-5 s in a Vitrobot (Mark 3, Thermo Fisher) at 20C temperature and 100% humidity, subsequently plunge-frozen in liquid ethane and stored in liquid nitrogen. Cryo-EM data were collected on a 200 keV Talos Arctica microscope (Thermo Fisher) using a post-column energy filter (Gatan) in zero-loss mode, using a 20 eV slit, a 100 um objective aperture, in an automated fashion using EPU software (Thermo Fisher) on a K2 summit detector (Gatan) in counting mode. Cryo-EM images were acquired at a pixel size of 1.012A (calibrated magnification of 49,407x), a defocus range from -0.4 to 2.5 um, an exposure time of 9 sec and a sub-frame exposure time of 150 ms (60 frames), and a total electron dose on the specimen level of about 52 electrons per A2. Best regions on the grid were screened with a self-written script to calculate the ice thickness and data quality was monitored on the fly using the software FOCUS
Image processing [1]
Final reconstruction
Resolution: 3.85 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 184080
Applied Symmetry
Point group: C3
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: PDB ENTRY
PDB model: 3KBC
Initial angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
RELION 2.1 -
Final angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
RELION 2.1 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 240 240 240
Dimensions (Å) 242.87999 242.87999 242.87999
Voxel size (Å) 1.012 1.012 1.012
Contour list
Primary Level Source
True 0.036 AUTHOR