2024-11-13 REL RCSB RCSB RCSB 2018-09-29 2018-10-24 2018-11-28 2024-11-13 National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) R01NS038631 United States National Institutes of Health/National Institute of Mental Health (NIH/NIMH) 1F32MH115595 United States Diheteromeric NMDA receptor GluN1/GluN2A in the '1-Knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1 Jalali-Yazdi F Chowdhury S Ligand-gated Ion Channel, NMDA Receptor, ionotropic Glutamate Receptors, membrane protein, TRANSPORT PROTEIN Jalali-Yazdi F Chowdhury S Yoshioka C Gouaux E Mechanisms for Zinc and Proton Inhibition of the GluN1/GluN2A NMDA Receptor. Cell 175 1520 1532.e15 2018 30500536 doi:10.1016/j.cell.2018.10.043 1097-4172 EMD-9148 other EM volume EMD-9149 other EM volume EMD-9150 other EM volume EMD-9151 other EM volume EMD-9152 other EM volume EMD-9153 other EM volume EMD-9154 other EM volume EMD-9155 other EM volume EMD-9156 other EM volume EMD-9157 other EM volume EMD-9158 other EM volume EMD-9159 other EM volume EMD-9160 other EM volume EMD-9161 other EM volume EMD-9162 other EM volume EMD-9163 other EM volume EMD-9164 other EM volume EMD-9165 other EM volume 6mm9 FULLOVERLAP Diheteromeric NMDA receptor GluN1/GluN2A in the '1-Knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1 Diheteromeric NMDA receptor GluN1/GluN2A in the '1-Knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1 0 1 2
Sample was heterologously expressed in TSA-201 cells, detergent solubilized, and affinity purified
Rattus norvegicus 0.5 Glutamate receptor ionotropic, NMDA 1 Rattus norvegicus 0.094189781 2 Homo sapiens LEVO MSTMHLLTFALLFSCSFARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCE DLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNW NHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEARELEARVIILSASEDDAATVYRAAAMLNM TGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPL FKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKI VTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVA DGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQS TLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFA MIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQA VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS RSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYK P35439 Glutamate receptor ionotropic, NMDA 2A Rattus norvegicus 0.093740352 2 Homo sapiens LEVO MGRLGYWTLLVLPALLVWRDPAQNAAAEKGPPALNIAVLLGHSHDVTERELRNLWGPEQATGLPLDVNVVALLMNRTDPK SLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLK IMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLIL SEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASC YGQAEKPETPLHTLHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHAVWPRYKSFSDCE PDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLV TNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFLEPFSASVWVM MFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVI FLASYTANLAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSL KTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGIC HNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIW Q00959 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 34 NAG singleParticle particle 4.0 6.1 150.0 NaCl Sodium Chloride 20.0 C6H13NO4S MES 1.0 C56H92O29 Digitonin 1.0 ZnCl2 Zinc Chloride Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 291 FEI VITROBOT MARK IV
Sample was blotted for 3 seconds at blot force 1..
This sample was monodisperse
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 GATAN K2 BASE (4k x 4k) 1 2163 22.0 52.0 1
Cleaned -up particles were used in CryoSPARC for de novo model generation.
 1 C1 FOURIER SPACE 5.97 FSC 0.143 CUT-OFF cisTEM
After additional rounds of refinement/further classification, the final particle set for each class was exported to cisTEM (Grant et al., 2018). Further refinement in cisTEM was carried out by masking out the micelle, while keeping the TMD of the receptors for alignment. The area outside of the mask was filtered to 20 A and down-weighted for alignment. For a more accurate and conservative resolution estimate, the cisTEM-generated half-maps were used in RELION to generate the Fourier Shell Coefficient (FSC) curve, and the resolution was calculated at FSC = 0.143 (Scheres and Chen, 2012).
94934 RANDOM ASSIGNMENT RELION MAXIMUM LIKELIHOOD RELION RELION emd_9147.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 328.32 328.32 328.32 90.0 90.0 90.0 X Y Z -12.195869 21.940761999999999 -0.00000000000535 1.0 1.71 1.71 1.71 3.9 AUTHOR GluN1/GluN2A diheteromeric NMDAR, at pH 6.1, in 1 micromolar zinc, in the 1-knuckle conformation 4PE5 A 25-830 PDB experimental model 5TQ0 B 34-388 PDB experimental model 5I57 A 3-288 PDB experimental model 5UOW B 25-832 PDB experimental model RIGID BODY FIT emd_9147_msk_1.map emd_9147_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 330.24 330.24 330.24 90.0 90.0 90.0 X Y Z -4.10861 10.696913 0.04422609 0.5306559 1.7199999 1.7199999 1.7199999 EMDB half-map for resolution estimation emd_9147_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 330.24 330.24 330.24 90.0 90.0 90.0 X Y Z -4.629491 10.162159000000001 0.042312406 0.5284708 1.7199999 1.7199999 1.7199999 EMDB half-map for resolution estimation