7Y1Q
5.0 angstrom cryo-EM structure of transmembrane regions of mouse Basigin/MCT1 in complex with antibody 6E7F1
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6LZ0 |
Sample |
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Ternary complex of transmembrane regions of Basigin with monocarboxylate transporter 1 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | blot for 3.5-4.5 s before plunging |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 129990 |
Reported Resolution (Å) | 5.03 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (6LZ0, 6LZ0) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | BACKBONE TRACE | ||||
Refinement Target | Correlation coefficient | ||||
Overall B Value | 53.6 | ||||
Fitting Procedure | |||||
Details | The transmembrane regions of human MCT1 and Basigin-2 were first generated, with side chain of each residue truncated into beta carbon atom. The the m ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 1.56 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 2500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | DIFFRACTION |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | v3.3.2 |
IMAGE ACQUISITION | SerialEM | SerialEM Version 3.8.0 beta |
CTF CORRECTION | cryoSPARC | v3.3.2 |
MODEL FITTING | cryoSPARC | 2.15 |
MODEL REFINEMENT | PHENIX | 1.19.2 |
INITIAL EULER ASSIGNMENT | cryoSPARC | v3.3.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | v3.3.2 |
CLASSIFICATION | cryoSPARC | v3.3.2 |
RECONSTRUCTION | cryoSPARC | v3.3.2 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | Movies CTF amplitude correction was performed by patch CTF. | 1610675 | Minimum particle diameter (A) 120 Maximum particle diameter (A) 140 Lowpass filter to apply (A) 10 Circular blob |