2025-05-14 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2024-09-18 2025-05-14 2025-05-14 2025-05-14 Wellcome Trust 102161/Z/13/Z United Kingdom Medical Research Council (MRC, United Kingdom) MR/Y012623/1 United Kingdom Human adult muscle nAChR in resting state in nanodisc with alpha-bungarotoxin Li A Pike ACW Chi G Webster R Maxwell S Liu W Beeson D Sauer DB Dong YY Ligand-gated ion channel, nicotinic receptor, pLGIC, cys-loop receptor, MEMBRANE PROTEIN Li A Pike ACW Webster R Maxwell S Liu WW Chi G Palace J Beeson D Sauer DB Dong YY Structures of the human adult muscle-type nicotinic receptor in resting and desensitized states. Cell Rep US 44 115581 115581 2025 40252219 doi:10.1016/j.celrep.2025.115581 2211-1247 Liebschner D Afonine PV Baker ML Bunkoczi G Chen VB Croll TI Hintze B Hung LW Jain S McCoy AJ Moriarty NW Oeffner RD Poon BK Prisant MG Read RJ Richardson JS Richardson DC Sammito MD Sobolev OV Stockwell DH Terwilliger TC Urzhumtsev AG Videau LL Williams CJ Adams PD Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Acta Crystallogr., Sect. D: Biol. Crystallogr. DK 75 861 877 2019 31588918 doi:10.1107/S2059798319011471 0907-4449 0766 ABCRE6 9gu1 FULLOVERLAP Human adult muscle nAChR in resting state in nanodisc with alpha-bungarotoxin Human adult muscle nAChR in resting state in nanodisc with alpha-bungarotoxin 0 1 2 3 4 5 6 7
nAChR in complex with alpha-bungarotoxin and Fab35 in MSP2N2-POPC nanodisc
Homo sapiens 0.402 Acetylcholine receptor subunit alpha Homo sapiens 0.04974764499999999 2 Homo sapiens LEVO SEHETRLVAKLFKDYSSVVRPVEDHRQVVEVTVGLQLIQLINVDEVNQIVTTNVRLKQQWVDYNLKWNPDDYGGVKKIHI PSEKIWRPDLVLYNNADGDFAIVKFTKVLLQYTGHITWTPPAIFKSYCEIIVTHFPFDEQNCSMKLGTWTYDGSVVAINP ESDQPDLSNFMESGEWVIKESRGWKHSVTYSCCPDTPYLDITYHFVMQRLPLYFIVNVIIPCLLFSFLTGLVFYLPTDSG EKMTLSISVLLSLTVFLLVIVELIPSTSSAVPLIGKYMLFTMVFVIASIIITVIVINTHHRSPSTHVMPNWVRKVFIDTI PNIMFFSTMKRPSREKQDKKIFTEDIDISDISGKPGPPPMGFHSPLIKHPEVKSAIEGIKYIAETMKSDQESNNAAAEWK YVAMVMDHILLGVFMLVCIIGTLAVFAGRLIELNQQG P02708 Acetylcholine receptor subunit beta Homo sapiens 0.054596477 1 Homo sapiens LEVO SEAEGRLREKLFSGYDSSVRPAREVGDRVRVSVGLILAQLISLNEKDEEMSTKVYLDLEWTDYRLSWDPAEHDGIDSLRI TAESVWLPDVVLLNNNDGNFDVALDISVVVSSDGSVRWQPPGIYRSSCSIQVTYFPFDWQNCTMVFSSYSYDSSEVSLQT GLGPDGQGHQEIHIHEGTFIENGQWEIIHKPSRLIQPPGDPRGGREGQRQEVIFYLIIRRKPLFYLVNVIAPCILITLLA IFVFYLPPDAGEKMGLSIFALLTLTVFLLLLADKVPETSLSVPIIIKYLMFTMVLVTFSVILSVVVLNLHHRSPHTHQMP LWVRQIFIHKLPLYLRLKRPKPERDLMPEPPHCSSPGSGWGRGTDEYFIRKPPSDFLFPKPNRFQPELSAPDLRRFIDGP NRAVALLPELREVVSSISYIARQLQEQEDHDALKEDWQFVAMVVDRLFLWTFIIFTSVGTLVIFLDATYHLPPPDPFP P11230 Fab35 light chain Rattus norvegicus 0.023392982 2 Rattus norvegicus LEVO DIVITQSPSLLSASVGDRVTLTCKGSQNIDNYLAWYQQKLGEAPKLLIYKTNSLQTGIPSRFSGSGSGTDYTLTISSLHS EDLATYYCYQYINGYTFGTGTKLELKRADAAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLD SVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC Acetylcholine receptor subunit delta Homo sapiens 0.05691535899999999 1 Homo sapiens LEVO LNEEERLIRHLFQEKGYNKELRPVAHKEESVDVALALTLSNLISLKEVEETLTTNVWIEHGWTDNRLKWNAEEFGNISVL RLPPDMVWLPEIVLENNNDGSFQISYSCNVLVYHYGFVYWLPPAIFRSSCPISVTYFPFDWQNCSLKFSSLKYTAKEITL SLKQDAKENRTYPVEWIIIDPEGFTENGEWEIVHRPARVNVDPRAPLDSPSRQDITFYLIIRRKPLFYIINILVPCVLIS FMVNLVFYLPADSGEKTSVAISVLLAQSVFLLLISKRLPATSMAIPLIGKFLLFGMVLVTMVVVICVIVLNIHFRTPSTH VLSEGVKKLFLETLPELLHMSRPAEDGPSPGALVRRSSSLGYISKAEEYFLLKSRSDLMFEKQSERHGLARRLTTARRPP ASSEQAQQELFNELKPAVDGANFIVNHMRDQNNYNEEKDSWNRVARTVDRLCLFVVTPVMVVGTAWIFLQGVYNQPPPQP FPGDPYSYNVQDKRFI Q07001 Acetylcholine receptor subunit epsilon,Green fluorescent protein Homo sapiens 0.08060375 1 Homo sapiens LEVO KNEELRLYHHLFNNYDPGSRPVREPEDTVTISLKVTLTNLISLNEKEETLTTSVWIGIDWQDYRLNYSKDDFGGIETLRV PSELVWLPEIVLENNIDGQFGVAYDANVLVYEGGSVTWLPPAIYRSVCAVEVTYFPFDWQNCSLIFRSQTYNAEEVEFTF AVDNDGKTINKIDIDTEAYTENGEWAIDFCPGVIRRHHGGATDGPGETDVIYSLIIRRKPLFYVINIIVPCVLISGLVLL AYFLPAQAGGQKCTVSINVLLAQTVFLFLIAQKIPETSLSVPLLGRFLIFVMVVATLIVMNCVIVLNVSQRTPTTHAMSP RLRHVLLELLPRLLGSPPPPEAPRAPPVATMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICT TGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGID FKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSK DPNEKRDHMVLLEFVTAAGITLGMDELYKAPRAASPPRRASSVGLLLRAEELILKKPRSELVFEGQRHRQGTWTAAFCQS LGAAAPEVRCCVDAVNFVAESTRDQEATGEEVSDWVRMGNALDNICFWAALVLFSVGSSLIFLGAYFNRVPDLPYAPCIQ P Q04844 P42212 Q04844 Fab35 heavy chain Rattus norvegicus 0.023879758 2 Rattus norvegicus LEVO EVQLQESGPGLVQPSETLSLTCTVSGFSLTSYSVSWLRQPSGKGPEWMGRMWDDGGTVYNSGLKSRLSISRDTSKNQVFL KMNSLQTDDTGTYYCTRDERIRAINWFAYWGQGTLVTVSSAETTAPSVYPLAPGTALKSNSMVTLGCLVKGYFPEPVTVT WNSGALSSGVHTFPAVLQSGLYTLTSSVTVPSSTWPSQTVTCNVAHPGQQHQRWTRKLC Alpha-bungarotoxin Bungarus multicinctus 0.008005281 2 LEVO IVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG P60615 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 1 NAG COPPER (II) ION 6.354599999999999e-05 1 CU water 1.8015e-05 299 HOH singleParticle particle 4 7.5 20.0 C8H18N2O4S HEPES 150.0 NaCl sodium chloride
20 mM HEPES pH 7.5, 150 mM NaCl
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 277.15 FEI VITROBOT MARK IV
2.5 uL of sample was frozen; blot time 4.5 s, blot force -10.
This sample was monodisperse
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.2 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20
objective aperture 100 um
GATAN K3 BIOQUANTUM (6k x 4k) 4092 5760 1 30556 2.8 45.0 1 15454340
Extracted by topaz picking
 cryoSPARC 4.4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION
ab-initio model from cryoSPARC
 1 C1 FOURIER SPACE 2.48 FSC 0.143 CUT-OFF cryoSPARC 4.4.1
non-uniform refinement
319381 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 10 58889.0 RELION 5.0.0
Class3D without alignment (10 classes, t=20) with a mask covering the extracellular domain of nAChR
 emd_51569.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 486 486 486 0 0 0 486 486 486 404.35202 404.35202 404.35202 90.0 90.0 90.0 X Y Z -0.85746217 1.6217532 0.00009913326 0.025335414 0.832 0.832 0.832 0.14 AUTHOR cryosparc map for final model refinement, sharpened with a b-factor of -25 P02708 AlphaFold in silico model P11230 AlphaFold in silico model Q07001 AlphaFold in silico model Q04844 AlphaFold in silico model FLEXIBLE FIT
Initial fitting of alphafold models using chimeraX followed by manual rebuilding in COOT and final refinement in ISOLDE and PHENIX
REAL emd_51569_msk_2.map emd_51569_msk_1.map emd_51569_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 486 486 486 0 0 0 486 486 486 404.35202 404.35202 404.35202 90.0 90.0 90.0 X Y Z -0.504566 1.23273 -0.00016913592 0.020243866 0.832 0.832 0.832 AUTHOR unsharpened map from cryoSPARC non-uniform refinement emd_51569_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 486 486 486 0 0 0 486 486 486 404.35202 404.35202 404.35202 90.0 90.0 90.0 X Y Z -0.6181247 1.422238 0.00045863484 0.050791275 0.832 0.832 0.832 AUTHOR half map A from cryoSPARC non-uniform refinement emd_51569_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 486 486 486 0 0 0 486 486 486 404.35202 404.35202 404.35202 90.0 90.0 90.0 X Y Z -0.6395606 1.3842801 0.00046203236 0.050294913 0.832 0.832 0.832 AUTHOR half map A from cryoSPARC non-uniform refinement