2024-10-23 REL PDBe PDBe PDBe 2021-12-12 2022-02-23 2022-02-23 2024-10-23 Medical Research Council (MRC, United Kingdom) MC_U105174197 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/N002113/1 United Kingdom Spanish Ministry of Science, Innovation, and Universities PID2019-106284GA-I00 United Kingdom Desensitized state of GluA1/2 AMPA receptor in complex with TARP-gamma 8 (TMD-LBD) Herguedas B Kohegyi B Dohrke JN Watson JF Zhang D Ho H Shaikh S Lape R Krieger JM Greger IH glutamate, AMPA receptor, TARPs, MEMBRANE PROTEIN Herguedas B Kohegyi BK Dohrke JN Watson JF Zhang D Ho H Shaikh SA Lape R Krieger JM Greger IH Mechanisms underlying TARP modulation of the GluA1/2-gamma 8 AMPA receptor. Nat Commun UK 13 734 734 2022 35136046 doi:10.1038/s41467-022-28404-7 2041-1723 EMD-4572 other EM volume
EMD-4572 corresponds to the cryo-EM map ofsame complex in resting state
 EMD-13969 other EM volume
EMD-13969 corresponds to the same complex in active state
 7qhh FULLOVERLAP Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8 Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8 0 1 2 3
GluA2 and TARP8 are expressed as a tandem construct
Rattus norvegicus 0.490 Isoform Flip of Glutamate receptor 1 Rattus norvegicus 0.10266192999999998 2 Homo sapiens LEVO MPYIFAFFCTGFLGAVVGADYKDDDDKNFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTY RFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLRPELQEALISIIDHYKWQTFVYIYDAD RGLSVLQRVLDTAAEKNWQVTAVNILTTTEEGYRMLFQDLEKKKERLVVVDCESERLNAILGQIVKLEKNGIGYHYILAN LGFMDIDLNKFKESGANVTGFQLVNYTDTIPARIMQQWRTSDSRDHTRVDWKRPKYTSALTYDGVKVMAEAFQSLRRQRI DISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDDKFVPAA TDAQAGGDNSSVQNRTYIVTTILEDPYVMLKKNANQFEGNDRYEGYCVELAAEIAKHVGYSYRLEIVSDGKYGARDPDTK AWNGMVGELVYGRADVAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSV VLFLVSRFSPYEWHSEEFEEGRDQTTSDQSNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTA NLAAFLTVERMVSPIESAEDLAKQTEIAYGTLEAGSTKEFFRRSKIAVFEKMWTYMKSAEPSVFVRTTEEGMIRVRKSKG KYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSALRGPVNLAVLKLSEQGVLDKLKSKWWYDKGECGSKDS GSKDKTSALSLSNVAGVFYILIGGLGLAMLVALIEFCYKSRSESKRMKGFCLIPQQSINEAIRTSTLPRNSGAGASGGGG SGENGRVVSQDFPKSMQSIPCMSHSSGMPLGATGL P19490 Isoform Flip of Glutamate receptor 2 Rattus norvegicus 0.09624705499999998 2 Homo sapiens LEVO MQKIMHISVLLSPVLWGLIFGVSSNSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQ FSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLST LQAVLDSAAEKKWQVTAINVGNINNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANL GFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIE ISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPRKIGYWSEVDKMVVTLT ELPSGNDTSGLENKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKI WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVV LFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMRQGCDISPRSLSGRIVGGVWWFFTLIIISSYTAN LAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGK YAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVLDKLKNKWWYDKGECGAKDSG SKEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAKRMKVAKNPQNINPSSS P19491 Voltage-dependent calcium channel gamma-8 subunit Rattus norvegicus 0.043576004 2 Homo sapiens LEVO GESLKRWNEERGLWCEKGVQVLLTTIGAFAAFGLMTIAISTDYWLYTRALICNTTNLTAGDDGPPHRGGSGSSEKKDPGG LTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSAEYLLRVVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILG AGILFVAAGLSNIIGVIVYISANAGEPGPKRDEEKKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIERSREAHCQSRSD LLKAGGGAGGSGGSGPSAILRLPSYRFRYRRRSRSSSRGSSEASPSRDASPGGPGGPGFASTDISMYTLSRDPSKGSVAA GLASAGGGGGGAGVGAYGGAAGAAGGGGTGSERDRGSSAGFLTLHNAFPKEAASGVTVTVTGPPAAPAPAPPAPAAPAPG TLSKEAAASNTNTLNRKLEVLFQ Q8VHW5 GLUTAMIC ACID 0.000147129 4 GLU PALMITOLEIC ACID 0.00025440799999999997 10 PAM (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 0.00035654 2 OLC (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate 0.00032848700000000003 2 79N singleParticle particle 2.5 8.0
25 mM TRIS 150 mM NaCl 0.02 % GDN 87 uM CTZ 100 mM L-Glu
 Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK IV
3-4 second blots.
Sample was incubated with 87 uM CTZ for 30 minutes and 100 mM L-Glutamate was added before grid preparation
 FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 0.34 2.2 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 1 9664 4.0 51.0 1 Initial model was obtained in Relion C2 FOURIER SPACE 3.6 FSC 0.143 CUT-OFF RELION 3.1 105918 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_13972.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 339.19998 339.19998 339.19998 90.0 90.0 90.0 X Y Z -0.10115809 0.17380503 -0.000024065106 0.0027186105 1.06 1.06 1.06 0.0124 AUTHOR PostProcessed map of the GluA1/2/TARP-gamma8 in the desentitised state obtained in relion 6QKC PDB experimental model 3TKD PDB experimental model RIGID BODY FIT
First, rigid body fit was performed in Chimera using the coordinates of the TMD of 6QKC and the coordinates of the LBD in PDB code 3TKD. Manual model building was performed with Coot and Refinement was performed with Refmac. The TMD and LBD maps obtained independently aided model building but were not used for refinement.
REAL emd_13972_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 339.19998 339.19998 339.19998 90.0 90.0 90.0 X Y Z -0.0019398357 0.002646641 0.00000008331912 0.000034437304 1.06 1.06 1.06 AUTHOR Composite map generated from focused refinement of TMD and LBD regions. This map was used for manual model building emd_13972_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 339.19998 339.19998 339.19998 90.0 90.0 90.0 X Y Z -0.029144073 0.059920795 0.000086849315 0.0019514904 1.06 1.06 1.06 AUTHOR Half map obtained in 3D refinement emd_13972_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 339.19998 339.19998 339.19998 90.0 90.0 90.0 X Y Z -0.027516853 0.058142364 -0.0001349795 0.001943342 1.06 1.06 1.06 AUTHOR Half map obtained in 3D refinement