2024-05-15 REL PDBe PDBe PDBe 2018-04-19 2018-05-23 2018-06-13 2024-05-15 European Commission MSCI 749732 Netherlands European Commission ERC 282083 Netherlands Garaeva AA Oostergetel GT neutral amino acid transporter, MEMBRANE PROTEIN Garaeva AA Oostergetel GT Gati C Guskov A Paulino C Slotboom DJ Nat. Struct. Mol. Biol. US 25 515 521 2018 29872227 doi:10.1038/s41594-018-0076-y 1545-9985 6gct FULLOVERLAP human ASCT2 SLC1A5 human ASCT2 SLC1A5 0 1

human ASCT2 SLC1A5

Homo sapiens 0.172 Neutral amino acid transporter B(0) Homo sapiens 0.056638902 3 Komagataella pastoris LEVO MVADPPRDSKGLAAAEPTANGGLALASIEDQGAAAGGYCGSRDQVRRCLRANLLVLLTVVAVVAGVALGLGVSGAGGALA LGPERLSAFVFPGELLLRLLRMIILPLVVCSLIGGAASLDPGALGRLGAWALLFFLVTTLLASALGVGLALALQPGAASA AINASVGAAGSAENAPSKEVLDSFLDLARNIFPSNLVSAAFRSYSTTYEERNITGTRVKVPVGQEVEGMNILGLVVFAIV FGVALRKLGPEGELLIRFFNSFNEATMVLVSWIMWYAPVGIMFLVAGKIVEMEDVGLLFARLGKYILCCLLGHAIHGLLV LPLIYFLFTRKNPYRFLWGIVTPLATAFGTSSSSATLPLMMKCVEENNGVAKHISRFILPIGATVNMDGAALFQCVAAVF IAQLSQQSLDFVKIITILVTATASSVGAAGIPAGGVLTLAIILEAVNLPVDHISLILAVDWLVDRSCTVLNVEGDALGAG LLQNYVDRTESRSTEPELIQVKSELPLDPLPVPTEEGNPLLKHYRGPAGDATVASEKESVM Q15758 GLUTAMINE 0.000146144 3 GLN singleParticle particle 2.5 7.0

20mM Tris-HCl pH 7.4 300mM NaCl 1mM L-glutamine 0.05% DDM 0.005% CHS

Quantifoil, UltrAuFoil, R1.2/1.3 GOLD 200 CARBON HOLEY GLOW DISCHARGE 20 ETHANE 100 278 FEI VITROBOT MARK II FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 100.0 2.7 0.0004 0.0004 0.0025 0.0025 49407.0 49407.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 90.0 GIF Quantum LS 0 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 1-60 9.0 0.87

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

1 3KBC C3 3.85 FSC 0.143 CUT-OFF RELION 2.1

A total of 6345 dose-fractionated cryo-EM images were recorded and subjected to motion-correction and dose-weighting of frames by MotionCor2. The CTF parameters were estimated on the movie frames by ctffind4.1. Bad images showing contamination, a defocus below or above 0.4 and -3um or a bad CTF estimation were discarded, resulting in 4863 images used for further analysis with the software package RELION2.1. About 3000 particles were picked manually to generate 2D references which where improved in several rounds of autopick. A low threshold was used during the final autopick step to ensure that no particles are missed yielding more than a million particles. Particles were extracted with a box size of 240 pixels, and initial classification steps were performed with three-fold binned data. False positives or bad particles were removed in first rounds of 2D classification, resulting in 628,015 particles that were further sorted in several rounds of 3D classification. A map generated from the GltPh structure (PDB ID 3KBC) was used as reference for the first round, and the best output class was used in subsequent jobs in an iterative way. The best 3D class, comprising 184,080 particles from 4859 images, was subjected to auto-refinement, yielding a map with a resolution of 4.26 A before masking and 3.91 A after masking. Particles were further polished in RELION version 2.1 and subjected to another round of 2D and 3D classification resulting in a final dataset of 133,437 particles. The final polished map had a resolution of 4.26 A before masking and 3.85 A after masking. The map was sharpened using an isotropic B-factor of -171 A2, for manual inspection a B-factor of -225 A2 was used. The approach of focused refinement, where the less-resolved detergent micelle was subtracted from the particle images, did not improve resolution. During 3D classification and auto-refinement jobs a C3-symmetry was imposed. To check for conformational heterogeneity of the data, where single protomers within the trimer might adopt a different conformation, 3D classifications with no symmetry imposed were performed at different stages of image processing. We further performed 3D classification on the individual protomers of a single transporter using symmetry expansion and signal subtraction. Both approaches showed no indication of the existence of a different conformation. Local resolution estimates were estimated by RELION. All resolutions were estimated using the 0.143 cut-off criterion with gold-standard Fourier shell correlation (FSC) between two independently refined half maps. During post-processing, the approach of high-resolution noise substitution was used to correct for convolution effects of real-space masking on the FSC curve.

184080 ANGULAR RECONSTITUTION RELION 2.1 ANGULAR RECONSTITUTION RELION 2.1 AB INITIO MODEL REAL emd_4386_msk_1.map emd_4386_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 242.87999 242.87999 242.87999 90.0 90.0 90.0 X Y Z -0.26623076 0.34781563 0.000035370238 0.01159874 1.012 1.012 1.012 AUTHOR ::::EMDATABANK.org::::EMD-4386:::: emd_4386_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 242.87999 242.87999 242.87999 90.0 90.0 90.0 X Y Z -0.013833319 0.031977843 0.000017005364 0.0019790407 1.012 1.012 1.012 AUTHOR ::::EMDATABANK.org::::EMD-4386:::: half-map 1 used for post processing step and FSC resolution calculation. emd_4386_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 242.87999 242.87999 242.87999 90.0 90.0 90.0 X Y Z -0.010015492 0.0320312 0.000016473592 0.001977871 1.012 1.012 1.012 AUTHOR ::::EMDATABANK.org::::EMD-4386:::: half-map 2 used for post processing step and FSC resolution calculation.