HEADER TRANSPORT PROTEIN 09-DEC-25 9ZLV TITLE HUMAN MFSD2B BOUND TO S1P IN OUTWARD-FACING CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOSINE-1-PHOSPHATE TRANSPORTER MFSD2B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAJOR FACILITATOR SUPERFAMILY DOMAIN-CONTAINING PROTEIN 2B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MFSD2B; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS TRANSPORTER, LIPID, OUTWARD FACING, SUBSTRATE BOUND, TRANSPORT KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.AHMED,Y.DAI,C.H.LEE REVDAT 1 21-OCT-26 9ZLV 0 JRNL AUTH S.AHMED,M.HUANG,Y.DAI,X.YANG,J.DONG,X.YU,C.H.LEE,L.N.NGUYEN JRNL TITL STRUCTURE AND MECHANISM OF HUMAN SPHINGOSINE-1-PHOSPHATE JRNL TITL 2 TRANSPORTER MFSD2B. JRNL REF NAT COMMUN V. 17 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 42717192 JRNL DOI 10.1038/S41467-026-76690-2 REMARK 2 REMARK 2 RESOLUTION. 3.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.030 REMARK 3 NUMBER OF PARTICLES : 146629 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9ZLV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000303032. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SPHINGOSINE-1-PHOSPHATE REMARK 245 TRANSPORTER MFSD2B REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1100.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2100.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 216 REMARK 465 THR A 217 REMARK 465 PRO A 218 REMARK 465 GLY A 219 REMARK 465 ASP A 258 REMARK 465 PRO A 259 REMARK 465 SER A 260 REMARK 465 ALA A 261 REMARK 465 PRO A 262 REMARK 465 ALA A 263 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-74413 RELATED DB: EMDB REMARK 900 HUMAN MFSD2B BOUND TO S1P IN OUTWARD-FACING CONFORMATION DBREF1 9ZLV A 41 478 UNP A0A2I3JL00_HUMAN DBREF2 9ZLV A A0A2I3JL00 41 478 SEQADV 9ZLV ARG A 36 UNP A0A2I3JL0 EXPRESSION TAG SEQADV 9ZLV LYS A 37 UNP A0A2I3JL0 EXPRESSION TAG SEQADV 9ZLV ALA A 38 UNP A0A2I3JL0 EXPRESSION TAG SEQADV 9ZLV GLU A 39 UNP A0A2I3JL0 EXPRESSION TAG SEQADV 9ZLV GLU A 40 UNP A0A2I3JL0 EXPRESSION TAG SEQRES 1 A 443 ARG LYS ALA GLU GLU PHE CYS THR LYS VAL CYS TYR GLY SEQRES 2 A 443 ILE GLY GLY VAL PRO ASN GLN ILE ALA SER SER ALA THR SEQRES 3 A 443 ALA PHE TYR LEU GLN LEU PHE LEU LEU ASP ILE ALA GLN SEQRES 4 A 443 ILE PRO ALA ALA GLN VAL SER LEU VAL LEU PHE GLY GLY SEQRES 5 A 443 LYS VAL SER GLY ALA ALA ALA ASP PRO VAL ALA GLY PHE SEQRES 6 A 443 PHE ILE ASN ARG SER GLN ARG THR GLY SER GLY ARG LEU SEQRES 7 A 443 MET PRO TRP VAL LEU GLY CYS THR PRO PHE ILE ALA LEU SEQRES 8 A 443 ALA TYR PHE PHE LEU TRP PHE LEU PRO PRO PHE THR SER SEQRES 9 A 443 LEU ARG GLY LEU TRP TYR THR THR PHE TYR CYS LEU PHE SEQRES 10 A 443 GLN ALA LEU ALA THR PHE PHE GLN VAL PRO TYR THR ALA SEQRES 11 A 443 LEU THR MET LEU LEU THR PRO CYS PRO ARG GLU ARG ASP SEQRES 12 A 443 SER ALA THR ALA TYR ARG MET THR VAL GLU MET ALA GLY SEQRES 13 A 443 THR LEU MET GLY ALA THR VAL HIS GLY LEU ILE VAL SER SEQRES 14 A 443 GLY ALA HIS ARG PRO HIS ARG CYS GLU ALA THR ALA THR SEQRES 15 A 443 PRO GLY PRO VAL THR VAL SER PRO ASN ALA ALA HIS LEU SEQRES 16 A 443 TYR CYS ILE ALA ALA ALA VAL VAL VAL VAL THR TYR PRO SEQRES 17 A 443 VAL CYS ILE SER LEU LEU CYS LEU GLY VAL LYS GLU ARG SEQRES 18 A 443 PRO ASP PRO SER ALA PRO ALA SER GLY PRO GLY LEU SER SEQRES 19 A 443 PHE LEU ALA GLY LEU SER LEU THR THR ARG HIS PRO PRO SEQRES 20 A 443 TYR LEU LYS LEU VAL ILE SER PHE LEU PHE ILE SER ALA SEQRES 21 A 443 ALA VAL GLN VAL GLU GLN SER TYR LEU VAL LEU PHE CYS SEQRES 22 A 443 THR HIS ALA SER GLN LEU HIS ASP HIS VAL GLN GLY LEU SEQRES 23 A 443 VAL LEU THR VAL LEU VAL SER ALA VAL LEU SER THR PRO SEQRES 24 A 443 LEU TRP GLU TRP VAL LEU GLN ARG PHE GLY LYS LYS THR SEQRES 25 A 443 SER ALA PHE GLY ILE PHE ALA MET VAL PRO PHE ALA ILE SEQRES 26 A 443 LEU LEU ALA ALA VAL PRO THR ALA PRO VAL ALA TYR VAL SEQRES 27 A 443 VAL ALA PHE VAL SER GLY VAL SER ILE ALA VAL SER LEU SEQRES 28 A 443 LEU LEU PRO TRP SER MET LEU PRO ASP VAL VAL ASP ASP SEQRES 29 A 443 PHE GLN LEU GLN HIS ARG HIS GLY PRO GLY LEU GLU THR SEQRES 30 A 443 ILE PHE TYR SER SER TYR VAL PHE PHE THR LYS LEU SER SEQRES 31 A 443 GLY ALA CYS ALA LEU GLY ILE SER THR LEU SER LEU GLU SEQRES 32 A 443 PHE SER GLY TYR LYS ALA GLY VAL CYS LYS GLN ALA GLU SEQRES 33 A 443 GLU VAL VAL VAL THR LEU LYS VAL LEU ILE GLY ALA VAL SEQRES 34 A 443 PRO THR CYS MET ILE LEU ALA GLY LEU CYS ILE LEU MET SEQRES 35 A 443 VAL HET S1P A 501 25 HETNAM S1P (2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YL HETNAM 2 S1P DIHYDROGEN PHOSPHATE HETSYN S1P SPHINGOSINE 1-PHOSPHATE FORMUL 2 S1P C18 H38 N O5 P HELIX 1 AA1 LYS A 37 GLY A 51 1 15 HELIX 2 AA2 GLY A 51 ILE A 72 1 22 HELIX 3 AA3 PRO A 76 GLY A 109 1 34 HELIX 4 AA4 LEU A 113 TRP A 132 1 20 HELIX 5 AA5 LEU A 140 THR A 171 1 32 HELIX 6 AA6 CYS A 173 SER A 204 1 32 HELIX 7 AA7 ASN A 226 VAL A 253 1 28 HELIX 8 AA8 SER A 269 ARG A 279 1 11 HELIX 9 AA9 HIS A 280 ALA A 311 1 32 HELIX 10 AB1 HIS A 317 GLY A 344 1 28 HELIX 11 AB2 LYS A 345 SER A 348 5 4 HELIX 12 AB3 ALA A 349 ALA A 354 1 6 HELIX 13 AB4 ALA A 354 VAL A 365 1 12 HELIX 14 AB5 THR A 367 LEU A 402 1 36 HELIX 15 AB6 GLY A 409 GLY A 441 1 33 HELIX 16 AB7 ALA A 450 ILE A 461 1 12 HELIX 17 AB8 GLY A 462 VAL A 478 1 17 SSBOND 1 CYS A 212 CYS A 447 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 CONECT 1367 3066 CONECT 3066 1367 CONECT 3291 3292 3293 CONECT 3292 3291 3312 CONECT 3293 3291 3294 3295 CONECT 3294 3293 CONECT 3295 3293 3296 3297 CONECT 3296 3295 CONECT 3297 3295 3298 CONECT 3298 3297 3299 CONECT 3299 3298 3300 CONECT 3300 3299 3301 CONECT 3301 3300 3302 CONECT 3302 3301 3303 CONECT 3303 3302 3304 CONECT 3304 3303 3305 CONECT 3305 3304 3306 CONECT 3306 3305 3307 CONECT 3307 3306 3308 CONECT 3308 3307 3309 CONECT 3309 3308 3310 CONECT 3310 3309 3311 CONECT 3311 3310 CONECT 3312 3292 3313 3314 3315 CONECT 3313 3312 CONECT 3314 3312 CONECT 3315 3312 MASTER 115 0 1 17 0 0 0 6 3314 1 27 35 END