HEADER MEMBRANE PROTEIN 24-OCT-22 8EX6 TITLE HUMAN S1P TRANSPORTER SPNS2 IN AN INWARD-FACING OPEN CONFORMATION TITLE 2 (STATE 1*) 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_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS TRANSPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.AHMED,H.ZHAO,Y.DAI,C.H.LEE REVDAT 4 19-JUN-24 8EX6 1 REMARK REVDAT 3 28-JUN-23 8EX6 1 JRNL REVDAT 2 07-JUN-23 8EX6 1 JRNL REVDAT 1 31-MAY-23 8EX6 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. 3.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.540 REMARK 3 NUMBER OF PARTICLES : 555587 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 8EX6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1000269560. 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 : HUMAN S1P TRANSPORTER SPNS2 IN REMARK 245 AN INWARD-FACING OPEN REMARK 245 CONFORMATION (STATE 1*) 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 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) : 7500.00 REMARK 245 ILLUMINATION MODE : OTHER 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 246 O GLY A 333 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 394 31.12 -90.06 REMARK 500 ASN A 439 56.37 -95.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-28652 RELATED DB: EMDB REMARK 900 HUMAN S1P TRANSPORTER SPNS2 IN AN INWARD-FACING OPEN CONFORMATION REMARK 900 (STATE 1*) DBREF 8EX6 A 103 549 UNP Q8IVW8 SPNS2_HUMAN 103 549 SEQADV 8EX6 GLU A 99 UNP Q8IVW8 EXPRESSION TAG SEQADV 8EX6 LYS A 100 UNP Q8IVW8 EXPRESSION TAG SEQADV 8EX6 ARG A 101 UNP Q8IVW8 EXPRESSION TAG SEQADV 8EX6 LYS A 102 UNP Q8IVW8 EXPRESSION TAG SEQRES 1 A 451 GLU LYS ARG LYS ALA ALA ALA ALA ILE LEU SER LEU GLY SEQRES 2 A 451 ASN VAL LEU ASN TYR LEU ASP ARG TYR THR VAL ALA GLY SEQRES 3 A 451 VAL LEU LEU ASP ILE GLN GLN HIS PHE GLY VAL LYS ASP SEQRES 4 A 451 ARG GLY ALA GLY LEU LEU GLN SER VAL PHE ILE CYS SER SEQRES 5 A 451 PHE MET VAL ALA ALA PRO ILE PHE GLY TYR LEU GLY ASP SEQRES 6 A 451 ARG PHE ASN ARG LYS VAL ILE LEU SER CYS GLY ILE PHE SEQRES 7 A 451 PHE TRP SER ALA VAL THR PHE SER SER SER PHE ILE PRO SEQRES 8 A 451 GLN GLN TYR PHE TRP LEU LEU VAL LEU SER ARG GLY LEU SEQRES 9 A 451 VAL GLY ILE GLY GLU ALA SER TYR SER THR ILE ALA PRO SEQRES 10 A 451 THR ILE ILE GLY ASP LEU PHE THR LYS ASN THR ARG THR SEQRES 11 A 451 LEU MET LEU SER VAL PHE TYR PHE ALA ILE PRO LEU GLY SEQRES 12 A 451 SER GLY LEU GLY TYR ILE THR GLY SER SER VAL LYS GLN SEQRES 13 A 451 ALA ALA GLY ASP TRP HIS TRP ALA LEU ARG VAL SER PRO SEQRES 14 A 451 VAL LEU GLY MET ILE THR GLY THR LEU ILE LEU ILE LEU SEQRES 15 A 451 VAL PRO ALA THR LYS ARG GLY HIS ALA ASP GLN LEU GLY SEQRES 16 A 451 ASP GLN LEU LYS ALA ARG THR SER TRP LEU ARG ASP MET SEQRES 17 A 451 LYS ALA LEU ILE ARG ASN ARG SER TYR VAL PHE SER SER SEQRES 18 A 451 LEU ALA THR SER ALA VAL SER PHE ALA THR GLY ALA LEU SEQRES 19 A 451 GLY MET TRP ILE PRO LEU TYR LEU HIS ARG ALA GLN VAL SEQRES 20 A 451 VAL GLN LYS THR ALA GLU THR CYS ASN SER PRO PRO CYS SEQRES 21 A 451 GLY ALA LYS ASP SER LEU ILE PHE GLY ALA ILE THR CYS SEQRES 22 A 451 PHE THR GLY PHE LEU GLY VAL VAL THR GLY ALA GLY ALA SEQRES 23 A 451 THR ARG TRP CYS ARG LEU LYS THR GLN ARG ALA ASP PRO SEQRES 24 A 451 LEU VAL CYS ALA VAL GLY MET LEU GLY SER ALA ILE PHE SEQRES 25 A 451 ILE CYS LEU ILE PHE VAL ALA ALA LYS SER SER ILE VAL SEQRES 26 A 451 GLY ALA TYR ILE CYS ILE PHE VAL GLY GLU THR LEU LEU SEQRES 27 A 451 PHE SER ASN TRP ALA ILE THR ALA ASP ILE LEU MET TYR SEQRES 28 A 451 VAL VAL ILE PRO THR ARG ARG ALA THR ALA VAL ALA LEU SEQRES 29 A 451 GLN SER PHE THR SER HIS LEU LEU GLY ASP ALA GLY SER SEQRES 30 A 451 PRO TYR LEU ILE GLY PHE ILE SER ASP LEU ILE ARG GLN SEQRES 31 A 451 SER THR LYS ASP SER PRO LEU TRP GLU PHE LEU SER LEU SEQRES 32 A 451 GLY TYR ALA LEU MET LEU CYS PRO PHE VAL VAL VAL LEU SEQRES 33 A 451 GLY GLY MET PHE PHE LEU ALA THR ALA LEU PHE PHE VAL SEQRES 34 A 451 SER ASP ARG ALA ARG ALA GLU GLN GLN VAL ASN GLN LEU SEQRES 35 A 451 ALA MET PRO PRO ALA SER VAL LYS VAL HET S1P A 601 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 GLU A 99 VAL A 125 1 27 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 ARG A 167 SER A 186 1 20 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 ASP A 258 ARG A 264 5 7 HELIX 8 AA8 VAL A 265 VAL A 281 1 17 HELIX 9 AA9 TRP A 302 ASN A 312 1 11 HELIX 10 AB1 ASN A 312 LYS A 348 1 37 HELIX 11 AB2 LYS A 361 LEU A 390 1 30 HELIX 12 AB3 ARG A 394 SER A 421 1 28 HELIX 13 AB4 SER A 421 PHE A 437 1 17 HELIX 14 AB5 TRP A 440 VAL A 451 1 12 HELIX 15 AB6 ILE A 452 THR A 454 5 3 HELIX 16 AB7 ARG A 455 GLY A 471 1 17 HELIX 17 AB8 GLY A 474 THR A 490 1 17 HELIX 18 AB9 SER A 493 MET A 506 1 14 HELIX 19 AC1 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