HEADER IMMUNE SYSTEM 21-FEB-23 8G92 TITLE STRUCTURE OF INHIBITOR 16D-BOUND SPNS2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOSINE-1-PHOSPHATE TRANSPORTER SPNS2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN SPINSTER HOMOLOG 2; 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: SPNS2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 GNTI- KEYWDS SPNS2, SPHINGOSINE-1-PHOSPHATE, MAJOR FACILITATOR SUPERFAMILY, KEYWDS 2 TRANSPORTER, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR H.CHEN,X.LI REVDAT 2 13-DEC-23 8G92 1 JRNL REVDAT 1 24-MAY-23 8G92 0 JRNL AUTH H.CHEN,S.AHMED,H.ZHAO,N.ELGHOBASHI-MEINHARDT,Y.DAI,J.H.KIM, JRNL AUTH 2 J.G.MCDONALD,X.LI,C.H.LEE JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO SPNS2-MEDIATED JRNL TITL 2 TRANSPORT OF SPHINGOSINE-1-PHOSPHATE. JRNL REF CELL V. 186 2644 2023 JRNL REFN ISSN 1097-4172 JRNL PMID 37224812 JRNL DOI 10.1016/J.CELL.2023.04.028 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, PHENIX 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 214617 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8G92 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000271406. 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 : SPNS2 IN COMPLEX WITH INHIBITOR REMARK 245 16D REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 10.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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 GLU A 92 REMARK 465 LYS A 93 REMARK 465 ARG A 94 REMARK 465 LYS A 95 REMARK 465 ALA A 96 REMARK 465 GLU A 97 REMARK 465 GLU A 98 REMARK 465 ARG A 286 REMARK 465 GLY A 287 REMARK 465 HIS A 288 REMARK 465 ALA A 289 REMARK 465 ASP A 290 REMARK 465 GLN A 291 REMARK 465 LEU A 292 REMARK 465 GLY A 293 REMARK 465 ASP A 294 REMARK 465 GLN A 295 REMARK 465 LEU A 296 REMARK 465 LYS A 297 REMARK 465 ALA A 298 REMARK 465 ARG A 299 REMARK 465 THR A 300 REMARK 465 THR A 349 REMARK 465 ALA A 350 REMARK 465 GLU A 351 REMARK 465 THR A 352 REMARK 465 CYS A 353 REMARK 465 ASN A 354 REMARK 465 SER A 355 REMARK 465 PRO A 356 REMARK 465 PRO A 357 REMARK 465 CYS A 358 REMARK 465 GLY A 359 REMARK 465 LEU A 540 REMARK 465 ALA A 541 REMARK 465 MET A 542 REMARK 465 PRO A 543 REMARK 465 PRO A 544 REMARK 465 ALA A 545 REMARK 465 SER A 546 REMARK 465 VAL A 547 REMARK 465 LYS A 548 REMARK 465 VAL A 549 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 347 32.70 -92.20 REMARK 500 ARG A 394 36.62 -94.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29860 RELATED DB: EMDB REMARK 900 STRUCTURE OF INHIBITOR 16D-BOUND SPNS2 DBREF 8G92 A 103 549 UNP Q8IVW8 SPNS2_HUMAN 103 549 SEQADV 8G92 GLU A 92 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 LYS A 93 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 ARG A 94 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 LYS A 95 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 ALA A 96 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 GLU A 97 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 GLU A 98 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 GLU A 99 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 LYS A 100 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 ARG A 101 UNP Q8IVW8 EXPRESSION TAG SEQADV 8G92 LYS A 102 UNP Q8IVW8 EXPRESSION TAG SEQRES 1 A 458 GLU LYS ARG LYS ALA GLU GLU GLU LYS ARG LYS ALA ALA SEQRES 2 A 458 ALA ALA ILE LEU SER LEU GLY ASN VAL LEU ASN TYR LEU SEQRES 3 A 458 ASP ARG TYR THR VAL ALA GLY VAL LEU LEU ASP ILE GLN SEQRES 4 A 458 GLN HIS PHE GLY VAL LYS ASP ARG GLY ALA GLY LEU LEU SEQRES 5 A 458 GLN SER VAL PHE ILE CYS SER PHE MET VAL ALA ALA PRO SEQRES 6 A 458 ILE PHE GLY TYR LEU GLY ASP ARG PHE ASN ARG LYS VAL SEQRES 7 A 458 ILE LEU SER CYS GLY ILE PHE PHE TRP SER ALA VAL THR SEQRES 8 A 458 PHE SER SER SER PHE ILE PRO GLN GLN TYR PHE TRP LEU SEQRES 9 A 458 LEU VAL LEU SER ARG GLY LEU VAL GLY ILE GLY GLU ALA SEQRES 10 A 458 SER TYR SER THR ILE ALA PRO THR ILE ILE GLY ASP LEU SEQRES 11 A 458 PHE THR LYS ASN THR ARG THR LEU MET LEU SER VAL PHE SEQRES 12 A 458 TYR PHE ALA ILE PRO LEU GLY SER GLY LEU GLY TYR ILE SEQRES 13 A 458 THR GLY SER SER VAL LYS GLN ALA ALA GLY ASP TRP HIS SEQRES 14 A 458 TRP ALA LEU ARG VAL SER PRO VAL LEU GLY MET ILE THR SEQRES 15 A 458 GLY THR LEU ILE LEU ILE LEU VAL PRO ALA THR LYS ARG SEQRES 16 A 458 GLY HIS ALA ASP GLN LEU GLY ASP GLN LEU LYS ALA ARG SEQRES 17 A 458 THR SER TRP LEU ARG ASP MET LYS ALA LEU ILE ARG ASN SEQRES 18 A 458 ARG SER TYR VAL PHE SER SER LEU ALA THR SER ALA VAL SEQRES 19 A 458 SER PHE ALA THR GLY ALA LEU GLY MET TRP ILE PRO LEU SEQRES 20 A 458 TYR LEU HIS ARG ALA GLN VAL VAL GLN LYS THR ALA GLU SEQRES 21 A 458 THR CYS ASN SER PRO PRO CYS GLY ALA LYS ASP SER LEU SEQRES 22 A 458 ILE PHE GLY ALA ILE THR CYS PHE THR GLY PHE LEU GLY SEQRES 23 A 458 VAL VAL THR GLY ALA GLY ALA THR ARG TRP CYS ARG LEU SEQRES 24 A 458 LYS THR GLN ARG ALA ASP PRO LEU VAL CYS ALA VAL GLY SEQRES 25 A 458 MET LEU GLY SER ALA ILE PHE ILE CYS LEU ILE PHE VAL SEQRES 26 A 458 ALA ALA LYS SER SER ILE VAL GLY ALA TYR ILE CYS ILE SEQRES 27 A 458 PHE VAL GLY GLU THR LEU LEU PHE SER ASN TRP ALA ILE SEQRES 28 A 458 THR ALA ASP ILE LEU MET TYR VAL VAL ILE PRO THR ARG SEQRES 29 A 458 ARG ALA THR ALA VAL ALA LEU GLN SER PHE THR SER HIS SEQRES 30 A 458 LEU LEU GLY ASP ALA GLY SER PRO TYR LEU ILE GLY PHE SEQRES 31 A 458 ILE SER ASP LEU ILE ARG GLN SER THR LYS ASP SER PRO SEQRES 32 A 458 LEU TRP GLU PHE LEU SER LEU GLY TYR ALA LEU MET LEU SEQRES 33 A 458 CYS PRO PHE VAL VAL VAL LEU GLY GLY MET PHE PHE LEU SEQRES 34 A 458 ALA THR ALA LEU PHE PHE VAL SER ASP ARG ALA ARG ALA SEQRES 35 A 458 GLU GLN GLN VAL ASN GLN LEU ALA MET PRO PRO ALA SER SEQRES 36 A 458 VAL LYS VAL HET YUX A 601 25 HETNAM YUX 3-[3-(4-DECYLPHENYL)-1,2,4-OXADIAZOL-5-YL]PROPAN-1- HETNAM 2 YUX AMINE FORMUL 2 YUX C21 H33 N3 O HELIX 1 AA1 LYS A 100 VAL A 125 1 26 HELIX 2 AA2 VAL A 125 GLY A 134 1 10 HELIX 3 AA3 LYS A 136 PHE A 165 1 30 HELIX 4 AA4 ASN A 166 SER A 186 1 21 HELIX 5 AA5 PHE A 193 PHE A 222 1 30 HELIX 6 AA6 THR A 223 GLY A 257 1 35 HELIX 7 AA7 TRP A 259 VAL A 265 1 7 HELIX 8 AA8 SER A 266 LEU A 280 1 15 HELIX 9 AA9 TRP A 302 ASN A 312 1 11 HELIX 10 AB1 ARG A 313 GLN A 347 1 35 HELIX 11 AB2 LYS A 361 ARG A 389 1 29 HELIX 12 AB3 ARG A 394 LYS A 419 1 26 HELIX 13 AB4 SER A 421 ILE A 442 1 22 HELIX 14 AB5 ILE A 442 VAL A 451 1 10 HELIX 15 AB6 ARG A 455 LEU A 470 1 16 HELIX 16 AB7 GLY A 474 SER A 489 1 16 HELIX 17 AB8 SER A 493 MET A 506 1 14 HELIX 18 AB9 MET A 506 GLN A 539 1 34 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