2025-02-19 REL PDBe PDBe PDBe 2023-10-17 2025-02-19 2025-02-19 2025-02-19 Innovative Medicines Initiative 777372 Switzerland Wellcome Trust 106169/Z/14/Z United Kingdom Structure of human SPNS2 in LMNG Li HZ Pike ACW McKinley G Mukhopadhyay SMM Moreau C Scacioc A Abrusci P Borkowska O Chalk R Stefanic S Burgess-Brown N Duerr KL Sauer DB SLC TRANSPORTER, MEMBRANE PROTEIN, S1P, EXPORTER, LIPID TRANSPORT Li HZ Pike ACW Chang YN Prakaash D Gelova Z Stanka J Moreau C Scott HC Wunder F Wolf G Scacioc A McKinley G Batoulis H Mukhopadhyay S Garofoli A Pinto-Fernandez A Kessler BM Burgess-Brown NA Stefanic S Wiedmer T Durr KL Puetter V Ehrmann A Khalid S Ingles-Prieto A Superti-Furga G Sauer DB Transport and inhibition of the sphingosine-1-phosphate exporter SPNS2. Nat Commun UK 16 721 721 2025 39820269 doi:10.1038/s41467-025-55942-7 2041-1723 8qv5 FULLOVERLAP Complex of SPNS2 with nanobody D12 Complex of SPNS2 with nanobody D12 0 1 2 Homo sapiens 0.07453 Sphingosine-1-phosphate transporter SPNS2 Homo sapiens 0.058962211 1 Homo sapiens LEVO MMCLECASAAAGGAEEEEADAERRRRRRGAQRGAGGSGCCGARGAGGAGVSAAGDEVQTLSGSVRRAPTGPPGTPGTPGC AATAKGPGAQQPKPASLGRGRGAAAAILSLGNVLNYLDRYTVAGVLLDIQQHFGVKDRGAGLLQSVFICSFMVAAPIFGY LGDRFNRKVILSCGIFFWSAVTFSSSFIPQQYFWLLVLSRGLVGIGEASYSTIAPTIIGDLFTKNTRTLMLSVFYFAIPL GSGLGYITGSSVKQAAGDWHWALRVSPVLGMITGTLILILVPATKRGHADQLGDQLKARTSWLRDMKALIRNRSYVFSSL ATSAVSFATGALGMWIPLYLHRAQVVQKTAETCNSPPCGAKDSLIFGAITCFTGFLGVVTGAGATRWCRLKTQRADPLVC AVGMLGSAIFICLIFVAAKSSIVGAYICIFVGETLLFSNWAITADILMYVVIPTRRATAVALQSFTSHLLGDAGSPYLIG FISDLIRQSTKDSPLWEFLSLGYALMLCPFVVVLGGMFFLATALFFVSDRARAEQQVNQLAMPPASVKVAENLYFQ Q8IVW8 Nanobody D12 Vicugna pacos 0.015674475 1 Escherichia coli LEVO QVQLVESGGGLVQAGGSLRLSCAASGRLLSWYDMAWFRQAPGKEREFVAAVTSTGAGTHYVDSVKGRFTISRVNAKNTMY LQMNSLKPEDTAVYYCAAANTRLTALSLRTTTGSWAYWGKGTPVTVSSADYKDDDDKHHHHHH singleParticle particle 6 7.5 20.0 HEPES 150.0 Sodium chloride 0.002 Lauryl Maltose Neopentyl Glyco (LMNG)
20mM HEPES pH 7.5, 150mM NaCl, 0.002% LMNG
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV
SEC purified
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 1.0 2.4 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
eBIC Krios II
GATAN K3 (6k x 4k) 1 8680 2.0 20.71
eBIC Diamond Krios II
 1 3376229
cryoSPARC Ab initio
 C1 FOURIER SPACE 3.69 FSC 0.143 CUT-OFF cryoSPARC 3.3.1 308935 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 2 cryoSPARC 3.3.1
Mulitple rounds of ab-intio (two classes) followed by heterogeneous refinement to converge on final set of particles
 emd_18667.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 212.736 212.736 212.736 90.0 90.0 90.0 X Y Z -0.67923427 0.98010975 0.000008471919 0.023934484 0.831 0.831 0.831 0.18 AUTHOR cryoSPARC autosharpened map from masked local refinement using for model refinement AlphaFold in silico model OTHER REAL emd_18667_msk_1.map emd_18667_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 212.736 212.736 212.736 90.0 90.0 90.0 X Y Z -0.13832656 0.27918944 0.000008471918 0.0114834905 0.831 0.831 0.831 AUTHOR Unsharpened fullmap from local refinement emd_18667_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 212.736 212.736 212.736 90.0 90.0 90.0 X Y Z -0.16892785 0.30468476 0.00057758426 0.017086942 0.831 0.831 0.831 AUTHOR Final half-map 1 emd_18667_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 212.736 212.736 212.736 90.0 90.0 90.0 X Y Z -0.18599449 0.3204929 0.0005636014 0.017240243 0.831 0.831 0.831 AUTHOR Final half-map 2