2024-02-14 REL RCSB RCSB RCSB 2022-05-12 2022-07-20 2022-07-20 2024-02-14 Not funded Sub-tomogram averaging of erythrocyte ankyrin-1 complex Vallese F Kim K Yen LY Johnston JD Noble AJ Cali T Clarke OB Membrane protein, ankyrin complex, TRANSPORT PROTEIN-STRUCTURAL PROTEIN complex Vallese F Kim K Yen LY Johnston JD Noble AJ Cali T Clarke OB Architecture of the human erythrocyte ankyrin-1 complex. Nat.Struct.Mol.Biol. US 29 706 718 2022 35835865 doi:10.1038/s41594-022-00792-w 1545-9985 EMD-26874 other EM volume EMD-26886 other EM volume EMD-26916 other EM volume EMD-26917 other EM volume EMD-26918 other EM volume EMD-26919 other EM volume EMD-26940 other EM volume EMD-26943 other EM volume EMD-26944 other EM volume EMD-26948 other EM volume EMD-26949 other EM volume EMD-26950 other EM volume EMD-26951 other EM volume EMD-26952 other EM volume EMD-26953 other EM volume EMD-26954 other EM volume EMD-26955 other EM volume EMD-26956 other EM volume EMD-26958 other EM volume EMD-26960 other EM volume EMD-26974 other EM volume EMD-26972 other EM volume EMD-26973 other EM volume EMD-26975 other EM volume EMD-26979 other EM volume EMD-26978 other EM volume EMD-26988 other EM volume EMD-26982 other EM volume 8csl FULLOVERLAP Sub-tomogram average of ankyrin-1 complexes from native erythrocyte vesicles Sub-tomogram average of ankyrin-1 complexes from native erythrocyte vesicles 0 1 2 3 4 5 6 7 Homo sapiens Ankyrin-1 Homo sapiens 0.206522625 1 LEVO MPYSVGFREADAATSFLRAARSGNLDKALDHLRNGVDINTCNQNGLNGLHLASKEGHVKMVVELLHKEIILETTTKKGNT ALHIAALAGQDEVVRELVNYGANVNAQSQKGFTPLYMAAQENHLEVVKFLLENGANQNVATEDGFTPLAVALQQGHENVV AHLINYGTKGKVRLPALHIAARNDDTRTAAVLLQNDPNPDVLSKTGFTPLHIAAHYENLNVAQLLLNRGASVNFTPQNGI TPLHIASRRGNVIMVRLLLDRGAQIETKTKDELTPLHCAARNGHVRISEILLDHGAPIQAKTKNGLSPIHMAAQGDHLDC VRLLLQYDAEIDDITLDHLTPLHVAAHCGHHRVAKVLLDKGAKPNSRALNGFTPLHIACKKNHVRVMELLLKTGASIDAV TESGLTPLHVASFMGHLPIVKNLLQRGASPNVSNVKVETPLHMAARAGHTEVAKYLLQNKAKVNAKAKDDQTPLHCAARI GHTNMVKLLLENNANPNLATTAGHTPLHIAAREGHVETVLALLEKEASQACMTKKGFTPLHVAAKYGKVRVAELLLERDA HPNAAGKNGLTPLHVAVHHNNLDIVKLLLPRGGSPHSPAWNGYTPLHIAAKQNQVEVARSLLQYGGSANAESVQGVTPLH LAAQEGHAEMVALLLSKQANGNLGNKSGLTPLHLVAQEGHVPVADVLIKHGVMVDATTRMGYTPLHVASHYGNIKLVKFL LQHQADVNAKTKLGYSPLHQAAQQGHTDIVTLLLKNGASPNEVSSDGTTPLAIAKRLGYISVTDVLKVVTDETSFVLVSD KHRMSFPETVDEILDVSEDEGEELISFKAERRDSRDVDEEKELLDFVPKLDQVVESPAIPRIPCAMPETVVIRSEEQEQA SKEYDEDSLIPSSPATETSDNISPVASPVHTGFLVSFMVDARGGSMRGSRHNGLRVVIPPRTCAAPTRITCRLVKPQKLS TPPPLAEEEGLASRIIALGPTGAQFLSPVIVEIPHFASHGRGDRELVVLRSENGSVWKEHRSRYGESYLDQILNGMDEEL GSLEELEKKRVCRIITTDFPLYFVIMSRLCQDYDTIGPEGGSLKSKLVPLVQATFPENAVTKRVKLALQAQPVPDELVTK LLGNQATFSPIVTVEPRRRKFHRPIGLRIPLPPSWTDNPRDSGEGDTTSLRLLCSVIGGTDQAQWEDITGTTKLVYANEC ANFTTNVSARFWLSDCPRTAEAVNFATLLYKELTAVPYMAKFVIFAKMNDPREGRLRCYCMTDDKVDKTLEQHENFVEVA RSRDIEVLEGMSLFAELSGNLVPVKKAAQQRSFHFQSFRENRLAMPVKVRDSSREPGGSLSFLRKAMKYEDTQHILCHLN ITMPPCAKGSGAEDRRRTPTPLALRYSILSESTPGSLSGTEQAEMKMAVISEHLGLSWAELARELQFSVEDINRIRVENP NSLLEQSVALLNLWVIREGQNANMENLYTALQSIDRGEIVNMLEGSGRQSRNLKPDRRHTDRDYSLSPSQMNGYSSLQDE LLSPASLGCALSSPLRADQYWNEVAVLDAIPLAATEHDTMLEMSDMQVWSAGLTPSLVTAEDSSLECSKAEDSDATGHEW KLEGALSEEPRGPELGSLELVEDDTVDSDATNGLIDLLEQEEGQRSEEKLPGSKRQDDATGAGQDSENEVSLVSGHQRGQ ARITHSPTVSQVTERSQDRLQDWDADGSIVSYLQDAAQGSWQEEVTQGPHSFQGTSTMTEGLEPGGSQEYEKVLVSVSEH TWTEQPEAESSQADRDRRQQGQEEQVQEAKNTFTQVVQGNEFQNIPGEQVTEEQFTDEQGNIVTKKIIRKVVRQIDLSSA DAAQEHEEVTVEGPLEDPSELEVDIDYFMKHSKDHTSTPNP P16157 Band 3 anion transport protein Homo sapiens 0.101883859 7 LEVO MEELQDDYEDMMEENLEQEEYEDPDIPESQMEEPAAHDTEATATDYHTTSHPGTHKVYVELQELVMDEKNQELRWMEAAR WVQLEENLGENGAWGRPHLSHLTFWSLLELRRVFTKGTVLLDLQETSLAGVANQLLDRFIFEDQIRPQDREELLRALLLK HSHAGELEALGGVKPAVLTRSGDPSQPLLPQHSSLETQLFCEQGDGGTEGHSPSGILEKIPPDSEATLVLVGRADFLEQP VLGFVRLQEAAELEAVELPVPIRFLFVLLGPEAPHIDYTQLGRAAATLMSERVFRIDAYMAQSRGELLHSLEGFLDCSLV LPPTDAPSEQALLSLVPVQRELLRRRYQSSPAKPDSSFYKGLDLNGGPDDPLQQTGQLFGGLVRDIRRRYPYYLSDITDA FSPQVLAAVIFIYFAALSPAITFGGLLGEKTRNQMGVSELLISTAVQGILFALLGAQPLLVVGFSGPLLVFEEAFFSFCE TNGLEYIVGRVWIGFWLILLVVLVVAFEGSFLVRFISRYTQEIFSFLISLIFIYETFSKLIKIFQDHPLQKTYNYNVLMV PKPQGPLPNTALLSLVLMAGTFFFAMMLRKFKNSSYFPGKLRRVIGDFGVPISILIMVLVDFFIQDTYTQKLSVPDGFKV SNSSARGWVIHPLGLRSEFPIWMMFASALPALLVFILIFLESQITTLIVSKPERKMVKGSGFHLDLLLVVGMGGVAALFG MPWLSATTVRSVTHANALTVMGKASTPGAAAQIQEVKEQRISGLLVAVLVGLSILMEPILSRIPLAVLFGIFLYMGVTSL SGIQLFDRILLLFKPPKYHPDVPYVKRVKTWRMHLFTGIQIICLAVLWVVKSTPASLALPFVLILTVPLRRVLLPLIFRN VELQCLDADDAKATFDEEEGRDEYDEVAMPV P02730 Blood group Rh(CE) polypeptide Homo sapiens 0.045598917999999995 1 LEVO MSSKYPRSVRRCLPLWALTLEAALILLFYFFTHYDASLEDQKGLVASYQVGQDLTVMAALGLGFLTSNFRRHSWSSVAFN LFMLALGVQWAILLDGFLSQFPPGKVVITLFSIRLATMSAMSVLISAGAVLGKVNLAQLVVMVLVEVTALGTLRMVISNI FNTDYHMNLRHFYVFAAYFGLTVAWCLPKPLPKGTEDNDQRATIPSLSAMLGALFLWMFWPSVNSPLLRSPIQRKNAMFN TYYALAVSVVTAISGSSLAHPQRKISMTYVHSAVLAGGVAVGTSCHLIPSPWLAMVLGLVAGLISIGGAKCLPVCCNRVL GIHHISVMHSIFSLLGLLGEITYIVLLVLHTVWNGNGMIGFQVLLSIGELSLAIVIALTSGLLTGLLLNLKIWKAPHVAK YFDDQVFWKFPHLAVGF P18577 Ammonium transporter Rh type A Homo sapiens 0.044229629 2 LEVO MRFTFPLMAIVLEIAMIVLFGLFVEYETDQTVLEQLNITKPTDMGIFFELYPLFQDVHVMIFVGFGFLMTFLKKYGFSSV GINLLVAALGLQWGTIVQGILQSQGQKFNIGIKNMINADFSAATVLISFGAVLGKTSPTQMLIMTILEIVFFAHNEYLVS EIFKASDIGASMTIHAFGAYFGLAVAGILYRSGLRKGHENEESAYYSDLFAMIGTLFLWMFWPSFNSAIAEPGDKQCRAI VNTYFSLAACVLTAFAFSSLVEHRGKLNMVHIQNATLAGGVAVGTCADMAIHPFGSMIIGSIAGMVSVLGYKFLTPLFTT KLRIHDTCGVHNLHGLPGVVGGLAGIVAVAMGASNTSMAMQAAALGSSIGTAVVGGLMTGLILKLPLWGQPSDQNCYDDS VYWKVPKTR Q02094 Protein 4.2 Homo sapiens 0.077096914 1 LEVO MGQALGIKSCDFQAARNNEEHHTKALSSRRLFVRRGQPFTIILYFRAPVRAFLPALKKVALTAQTGEQPSKINRTQATFP ISSLGDRKWWSAVVEERDAQSWTISVTTPADAVIGHYSLLLQVSGRKQLLLGQFTLLFNPWNREDAVFLKNEAQRMEYLL NQNGLIYLGTADCIQAESWDFGQFEGDVIDLSLRLLSKDKQVEKWSQPVHVARVLGALLHFLKEQRVLPTPQTQATQEGA LLNKRRGSVPILRQWLTGRGRPVYDGQAWVLAAVACTVLRCLGIPARVVTTFASAQGTGGRLLIDEYYNEEGLQNGEGQR GRIWIFQTSTECWMTRPALPQGYDGWQILHPSAPNGGGVLGSCDLVPVRAVKEGTLGLTPAVSDLFAAINASCVVWKCCE DGTLELTDSNTKYVGNNISTKGVGSDRCEDITQNYKYPEGSLQEKEVLERVEKEKMEREKDNGIRPPSLETASPLYLLLK APSSLPLRGDAQISVTLVNHSEQEKAVQLAIGVQAVHYNGVLAAKLWRKKLHLTLSANLEKIITIGLFFSNFERNPPENT FLRLTAMATHSESNLSCFAQEDIAICRPHLAIKMPEKAEQYQPLTASVSLQNSLDAPMEDCVISILGRGLIHRERSYRFR SVWPENTMCAKFQFTPTHVGLQRLTVEVDCNMFQNLTNYKSVTVVAPELSA P16452 Glycophorin-B Homo sapiens 0.009789674 1 LEVO MYGKIIFVLLLSEIVSISALSTTEVAMHTSTSSSVTKSYISSQTNGETGQLVHRFTVPAPVVIILIILCVMAGIIGTILL ISYSIRRLIKA P06028 Glycophorin-A Homo sapiens 0.016348433 6 LEVO MYGKIIFVLLLSEIVSISASSTTGVAMHTSTSSSVTKSYISSQTNDTHKRDTYAATPRAHEVSEISVRTVYPPEEETGER VQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKKSPSDVKPLPSPDTDVPLSSVEIENPETSDQ P02724 subtomogramAveraging particle 5 7.4
130 mM KCl, 10 mM HEPES, pH 7.4
 ETHANE
Ghost membranes (~100 mg) were pelleted (6,000 x g, 10 minutes), washed 5 times in 130 mM KCl, 10 mM HEPES, pH 7.4, and then homogenized with the same buffer. The sample was sonicated using microprobe (amplitude = 30, pulse on = 5 sec, rest time = 10 sec, total pulse on = 50 sec). Large fragments are removed by centrifugation (6,000 x g, 10 minutes) and the supernatant was extruded (Avanti Polar Lipid) 10 times using a 400 nm filter. After extrusion, vesicles were collected by ultra-centrifugation at 35,000 rpm for 30 minutes (S120-AT3, Sorvall). The pellet, which contains vesicles, was resuspended at a final concentration of 5 mg/mL. All steps were performed at room temperature to facilitate vesicle formation.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.01 3.0 5.0 NITROGEN 20 GATAN K3 (6k x 4k) 3.14 1 C1 25.0 FSC 0.143 CUT-OFF 1596 100 60029
Picked using crYOLO, trained using manual picks.
 MAXIMUM LIKELIHOOD
Initial models were generated in Relion4 using stochastic gradient descent, with 8 classes requested. The resulting initial map that most closely resembled the ankyrin-1 complex was low-pass filtered to 60 A and used for multiple rounds of 3D classification in Relion 4
 emd_26965.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 80 80 80 0 0 0 80 80 80 320.0 320.0 320.0 90.0 90.0 90.0 X Y Z -0.22319034 0.67583936 0.029798644 0.13568047 4.0 4.0 4.0 0.2 AUTHOR Main map (sub-tomogram average of ankyrin complex particles). 8CS9 PDB experimental model RIGID BODY FIT
Erythrocyte ankyrin-1 complex (Class1, 8CS9) was rigid fit as a single body to the map using fitmap in UCSF Chimera, after which waters, ligands and sidechains were removed from the model.
 emd_26965_msk_1.map emd_26965_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 80 80 80 0 0 0 80 80 80 320.0 320.0 320.0 90.0 90.0 90.0 X Y Z -0.7998497 1.2323573 0.029211873 0.17562187 4.0 4.0 4.0 AUTHOR Half map 1 emd_26965_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 80 80 80 0 0 0 80 80 80 320.0 320.0 320.0 90.0 90.0 90.0 X Y Z -0.83232224 1.1738893 0.030385414 0.17563508 4.0 4.0 4.0 AUTHOR Half map 2