GluA4 in complex with TARP-2, desensitized state, structure of TMD/LBD domains

2025-12-24 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2025-06-19 2025-09-24 2025-09-24 2025-12-24 Ministerio de Ciencia e Innovacion (MCIN) PID2019-106284GA-I00 Spain GluA4 in complex with TARP-2, desensitized state, structure of TMD/LBD domains Vega-Gutierrez C Herguedas B Gria4, Voltage-dependent calcium channel gamma-2, AMPA Receptor, GluA4-TARP2, Membrane protein, Desensitized state, TMD/LBD Vega-Gutierrez C Picanol-Parraga J Sanchez-Valls I Ribon-Fuster VDP Soto D Herguedas B GluA4 AMPA receptor gating mechanisms and modulation by auxiliary proteins. Nat.Struct.Mol.Biol. US 32 2416 2428 2025 40954371 doi:10.1038/s41594-025-01666-7 1545-9985 9rn4 FULLOVERLAP EMDB EMD-54080 associated EM volume

GluA4 in complex with TARP-2, Desensitized state, structure of TMD/LBD domain GluA4 in complex with TARP-2, Desensitized state, structure of TMD/LBD domain 0 1 2 Rattus novergicus 0.62 Isoform 2 of Glutamate receptor 4 Rattus norvegicus 0.09867193799999999 4 Homo sapiens LEVO GAFPSSVQIGGLFIRNTDQEYTAFRLAIFLHNTSPNASEAPFNLVPHVDNIETANSFAVTNAFCSQYSRGVFAIFGLYDK RSVHTLTSFCSALHISLITPSFPTEGESQFVLQLRPSLRGALLSLLDHYEWNCFVFLYDTDRGYSILQAIMEKAGQNGWH VSAICVENFNDVSYRQLLEELDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISLERFIHGGANVT GFQLVDFNTPMVTKLMDRWKKLDQREYPGSETPPKYTSALTYDGVLVMAETFRSLRRQKIDISRRGNAGDCLANPAAPWG QGIDMERTLKQVRIQGLTGNVQFDHYGRRVNYTMDVFELKSTGPRKVGYWNDMDKLVLIQDMPTLGNDTAAIENRTVVVT TIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTKIWNGMVGELVYGKAEIAIAP LTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEPED GKEGPSDQPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAED LAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKGKFAFLLESTMNEYIEQRKPC DTMKVGGNLDSKGYGVATPKGSSLRTPVNLAVLKLSEAGVLDKLKNKWWYDKGECGPKDSGSKDKTSALSLSNVAGVFYI LVGGLGLAMLVALIEFCYKSRAEAKRMKLTFSEATRNKARLSITGSVGENGRVLTPDCPKAVHTGTAIRQSSGLAVIASD LP P19493 Voltage-dependent calcium channel gamma-2 subunit Rattus norvegicus 0.035950801 4 Homo sapiens LEVO MGLFDRGVQMLLTIVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQI DHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISAN AGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAITRIPSYRYRYQRRSRSS SRSTEPSHSRDASPVGVKGFNTLPSTEISMYTLSRDPLKAATTPTATYNSDRDNSFLQVHNCIQKDSKDSLHANTANRRT TPV Q71RJ2 PALMITIC ACID Rattus norvegicus 0.00025642399999999994 4 PLM CALCIUM ION 4.0078e-05 1 CA (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 0.00035654 4 OLC singleParticle particle 3.1 8.0 150.0 NaCl sodium chloride 20.0 NH2C(CH2OH)3 Tris(hydroxymethyl)aminomethane 0.02 C56H92O25 Glyco-diosgenin (GDN) Quantifoil R1.2/1.3 GOLD 300 GLOW DISCHARGE 30 ETHANE 100 277.15 FEI VITROBOT MARK IV

The sample was incubated with L-Glutamate to capture the receptor in its desensitized state

TFS KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOCONTINUUM (6k x 4k) 12910 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION

An Ab-initio Reconstruction was generated in CryoSPARC 4.3.1

3.4 FSC 0.143 CUT-OFF cryoSPARC 4.3.1 39760 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_54080.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 329.52002 329.52002 329.52002 90.0 90.0 90.0 X Y Z -0.43934274 1.0266078 0.0054164235 0.037147257 0.8238 0.8238 0.8238 0.197 AUTHOR ::::EMDATABANK.org::::EMD-54080:::: 3TKD PDB experimental model RIGID BODY FIT

I performed fitting using Chimera for the TMD domain (previously modeled and individually deposited in the PDB) and PDB entry 3TKD was fitted into chains A-D. B-factors were reset, GluA4 residues were substituted, water molecules were removed. Subsequently, rigid-body refinement was performed using Phenix.

emd_54080_msk_1.map emd_54080_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 329.52002 329.52002 329.52002 90.0 90.0 90.0 X Y Z -0.7974385 1.4440286 0.0039599063 0.06745123 0.8238 0.8238 0.8238 AUTHOR ::::EMDATABANK.org::::EMD-54080:::: emd_54080_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 329.52002 329.52002 329.52002 90.0 90.0 90.0 X Y Z -0.7867217 1.4130484 0.0039944723 0.06739609 0.8238 0.8238 0.8238 AUTHOR ::::EMDATABANK.org::::EMD-54080::::