2024-11-20 REL PDBe PDBe PDBe 2023-05-16 2024-06-12 2024-06-12 2024-11-20 UK Research and Innovation (UKRI) BB/V018051/1 United Kingdom Structure of human SIT1:ACE2 complex (open PD conformation) bound to L-pipecolate Li HZ Pike ACW Chi G Hansen JS Lee SG Rodstrom KEJ Bushell SR Speedman D Evans A Wang D He D Shrestha L Nasrallah C Chalk R Moreira T MacLean EM Marsden B Bountra C Burgess-Brown NA Dafforn TR Carpenter EP Sauer DB amino acid transporter, proline, SLC6A20, ACE2, MEMBRANE PROTEIN Li HZ Pike ACW Lotsaris I Chi G Hansen JS Lee SC Rodstrom KEJ Bushell SR Speedman D Evans A Wang D He D Shrestha L Nasrallah C Burgess-Brown NA Vandenberg RJ Dafforn TR Carpenter EP Sauer DB Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2. Nat Commun UK 15 5503 5503 2024 38951531 doi:10.1038/s41467-024-48921-x 2041-1723 8p30 FULLOVERLAP SIT1:ACE2 complex SIT1:ACE2 complex 0 1 2 Homo sapiens 0.34 Processed angiotensin-converting enzyme 2 Homo sapiens 0.09342557 2 Homo sapiens LEVO MSSSSWLLLSLVAVTAADYKDDDDKSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFL KEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMA NSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEI KPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEK FFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLR NGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQW MKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQK LFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSIKVRISLKSALGDKAY EWNDNEMYLFRSSVAYAMRQYFLKVKNQMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRIND AFRLNDNSLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENPYASIDISKGENNP GFQNTDDVQTSF Q9BYF1 Sodium- and chloride-dependent transporter XTRP3 Homo sapiens 0.071376258 2 Homo sapiens LEVO MEKARPLWANSLQFVFACISYAVGLGNVWRFPYLCQMYGGGSFLVPYIIMLIVEGMPLLYLELAVGQRMRQGSIGAWRTI SPYLSGVGVASVVVSFFLSMYYNVINAWAFWYLFHSFQDPLPWSVCPLNGNHTGYDEECEKASSTQYFWYRKTLNISPSL QENGGVQWEPALCLLLAWLVVYLCILRGTESTGKVVYFTASLPYCVLIIYLIRGLTLHGATNGLMYMFTPKIEQLANPKA WINAATQIFFSLGLGFGSLIAFASYNEPSNNCQKHAIIVSLINSFTSIFASIVTFSIYGFKATFNYENCLKKVSLLLTNT FDLEDGFLTASNLEQVKGYLASAYPSKYSEMFPQIKNCSLESELDTAVQGTGLAFIVYTEAIKNMEVSQLWSVLYFFMLL MLGIGSMLGNTAAILTPLTDSKIISSHLPKEAISGLVCLVNCAIGMVFTMEAGNYWFDIFNDYAATLSLLLIVLVETIAV CYVYGLRRFESDLKAMTGRAVSWYWKVMWAGVSPLLIVSLFVFYLSDYILTGTLKYQAWDASQGQLVTKDYPAYALAVIG LLVASSTMCIPLAALGTFVQRRLKRGDADPVAAENLYFQSHHHHHHHHHHGSAWSHPQFEKGGGSGGGSGGSAWSHPQFE K Q9NP91 ZINC ION 6.5409e-05 2 ZN 2-acetamido-2-deoxy-alpha-D-glucopyranose 0.000221208 2 NDG 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 12 NAG (2S)-piperidine-2-carboxylic acid 0.000129157 2 YCP CHLORIDE ION 3.5453e-05 2 CL singleParticle particle 4 7.5 25.0 Tris 150.0 sodium chloride 0.02 glyco-diosgenin (GDN) 10.0 pipecolic acid Quantifoil R1.2/1.3 GOLD 200 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV
grid blotted for 4sec after a 20sec wait time.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.2 2.4 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) COUNTING 1-50 1 13194 1.77 50.0
Images were collected in super-resolution mode EPU bin2
 1 808912
particles from template and TOPAZ trained picking after initial 2D classification to remove junk
Ab initio
 C2 FOURIER SPACE 3.29 FSC 0.143 CUT-OFF cryoSPARC 3.3.1 206023 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1
Masked local refinement
 emd_17381.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 319.104 319.104 319.104 90.0 90.0 90.0 X Y Z -0.61603093 1.1443121 0.0019167946 0.028598262 1.2465 1.2465 1.2465 0.135 AUTHOR cryoSPARC NU refinement map sharpened with bfactor of -75 used for model refinement 6M18 PDB experimental model OTHER
Initial model fitting was peformed in Chimera and model building in COOT
REAL 116.0 emd_17381_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 319.104 319.104 319.104 90.0 90.0 90.0 X Y Z -0.22090463 0.59356654 0.0023541895 0.022909384 1.2465 1.2465 1.2465 AUTHOR Unsharpened NU refinement full map emd_17381_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 319.104 319.104 319.104 90.0 90.0 90.0 X Y Z -0.2656373 0.6786715 0.0017711598 0.026112923 1.2465 1.2465 1.2465 AUTHOR half map1 emd_17381_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 319.104 319.104 319.104 90.0 90.0 90.0 X Y Z -0.23764887 0.64532715 0.0017633014 0.026116878 1.2465 1.2465 1.2465 AUTHOR half map2