HEADER MEMBRANE PROTEIN 27-OCT-23 8WX1 TITLE CRYO-EM STRUCTURE OF MOUSE SLC15A3 (OUTWARD-FACING OPEN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 15 MEMBER 3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SLC15A3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 OTHER_DETAILS: FOR THIS STRUCTURE WE USED SPODOPTERA FRUGIPERDA SOURCE 10 CELLS-EXPRESSED PROTEINS FOR CRYO-EM ANALYSIS. THUS THE DATASET FOR SOURCE 11 THIS STRUCTURE WERE COLLECTED FROM BOTH HOMO SAPIENS CELLS-EXPRESSED SOURCE 12 AND SPODOPTERA FRUGIPERDA CELLS-EXPRESSED PROTEINS. KEYWDS TRANSPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.KASAI,Z.ZHANG,U.OHTO,T.SHIMIZU REVDAT 5 02-JUL-25 8WX1 1 REMARK REVDAT 4 25-JUN-25 8WX1 1 JRNL REVDAT 3 18-JUN-25 8WX1 1 JRNL REVDAT 2 13-NOV-24 8WX1 1 REMARK REVDAT 1 30-OCT-24 8WX1 0 JRNL AUTH Z.ZHANG,S.KASAI,K.SAKANIWA,A.FUJIMURA,U.OHTO,T.SHIMIZU JRNL TITL THE STRUCTURES OF THE PEPTIDE TRANSPORTERS SLC15A3 AND JRNL TITL 2 SLC15A4 REVEAL THE RECOGNITION MECHANISMS FOR SUBSTRATE AND JRNL TITL 3 TASL. JRNL REF STRUCTURE V. 33 330 2025 JRNL REFN ISSN 0969-2126 JRNL PMID 39719710 JRNL DOI 10.1016/J.STR.2024.11.019 REMARK 2 REMARK 2 RESOLUTION. 3.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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) : 3.640 REMARK 3 NUMBER OF PARTICLES : 285251 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 8WX1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300042178. 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 : MOUSE SLC15A3; MOUSE SLC15A3; REMARK 245 MOUSE SLC15A3 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 : 8.00 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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 : 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 PRO A 4 REMARK 465 ARG A 5 REMARK 465 ALA A 6 REMARK 465 GLU A 7 REMARK 465 GLU A 8 REMARK 465 GLN A 9 REMARK 465 PRO A 10 REMARK 465 SER A 11 REMARK 465 ARG A 12 REMARK 465 SER A 13 REMARK 465 GLY A 14 REMARK 465 GLU A 15 REMARK 465 ARG A 16 REMARK 465 GLN A 17 REMARK 465 PRO A 18 REMARK 465 LEU A 19 REMARK 465 VAL A 20 REMARK 465 ALA A 21 REMARK 465 ARG A 22 REMARK 465 GLY A 23 REMARK 465 PRO A 24 REMARK 465 LEU A 137 REMARK 465 PRO A 138 REMARK 465 LEU A 139 REMARK 465 GLU A 140 REMARK 465 PRO A 141 REMARK 465 ALA A 142 REMARK 465 CYS A 143 REMARK 465 PRO A 144 REMARK 465 SER A 145 REMARK 465 SER A 146 REMARK 465 SER A 147 REMARK 465 CYS A 148 REMARK 465 ARG A 277 REMARK 465 SER A 278 REMARK 465 SER A 279 REMARK 465 SER A 280 REMARK 465 ARG A 281 REMARK 465 ASP A 282 REMARK 465 SER A 283 REMARK 465 GLU A 284 REMARK 465 SER A 285 REMARK 465 ALA A 286 REMARK 465 HIS A 287 REMARK 465 LEU A 288 REMARK 465 LEU A 289 REMARK 465 PRO A 290 REMARK 465 ASP A 291 REMARK 465 GLN A 292 REMARK 465 ARG A 293 REMARK 465 SER A 294 REMARK 465 ASN A 295 REMARK 465 GLN A 296 REMARK 465 PRO A 297 REMARK 465 ILE A 354 REMARK 465 SER A 355 REMARK 465 LEU A 356 REMARK 465 LEU A 357 REMARK 465 LEU A 358 REMARK 465 ARG A 359 REMARK 465 SER A 360 REMARK 465 ASP A 361 REMARK 465 SER A 362 REMARK 465 PRO A 567 REMARK 465 ALA A 568 REMARK 465 SER A 569 REMARK 465 GLN A 570 REMARK 465 ARG A 571 REMARK 465 SER A 572 REMARK 465 SER A 573 REMARK 465 SER A 574 REMARK 465 ARG A 575 REMARK 465 VAL A 576 REMARK 465 ARG A 577 REMARK 465 GLY A 578 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 363 OG REMARK 470 ASN A 364 CG OD1 ND2 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 MET A 188 -159.02 -68.16 REMARK 500 ASP A 189 -30.00 -32.40 REMARK 500 THR A 350 -5.76 65.71 REMARK 500 ASN A 351 66.87 33.24 REMARK 500 ARG A 366 70.65 60.67 REMARK 500 GLU A 369 -7.71 70.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 188 ASP A 189 -147.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37897 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF MOUSE SLC15A3 (OUTWARD-FACING OPEN) DBREF 8WX1 A 1 578 UNP Q8BPX9 S15A3_MOUSE 1 578 SEQRES 1 A 578 MET SER ALA PRO ARG ALA GLU GLU GLN PRO SER ARG SER SEQRES 2 A 578 GLY GLU ARG GLN PRO LEU VAL ALA ARG GLY PRO ARG GLY SEQRES 3 A 578 PRO ARG ARG TRP ARG ARG THR ALA ALA ALA ALA VAL LEU SEQRES 4 A 578 LEU VAL GLN MET LEU GLU ARG ALA ALA PHE PHE GLY VAL SEQRES 5 A 578 THR SER ASN LEU VAL LEU TYR LEU ASN SER LEU ASN PHE SEQRES 6 A 578 ASN TRP ASP GLY GLN GLN ALA SER ARG ALA THR LEU LEU SEQRES 7 A 578 PHE LEU GLY ALA SER TYR LEU LEU ALA PRO VAL GLY GLY SEQRES 8 A 578 TRP LEU ALA ASP VAL TYR LEU GLY ARG PHE LEU THR ILE SEQRES 9 A 578 SER LEU SER LEU LEU LEU TYR LEU ALA ALA SER GLY LEU SEQRES 10 A 578 LEU LEU THR THR ILE THR ASN ASP GLY ARG ARG SER PHE SEQRES 11 A 578 CYS GLY GLU MET PRO GLU LEU PRO LEU GLU PRO ALA CYS SEQRES 12 A 578 PRO SER SER SER CYS GLN GLY SER TRP SER SER PRO TYR SEQRES 13 A 578 CYS ALA THR THR LEU TYR LEU VAL LEU LEU LEU LEU ALA SEQRES 14 A 578 LEU ALA ALA SER SER VAL ARG SER THR LEU THR SER PHE SEQRES 15 A 578 GLY ALA ASP GLN VAL MET ASP LEU GLY ARG ASP ALA THR SEQRES 16 A 578 ARG ARG PHE PHE ASN TRP PHE TYR TRP SER ILE ASN LEU SEQRES 17 A 578 GLY ALA ILE LEU SER LEU LEU VAL VAL ALA PHE ILE GLU SEQRES 18 A 578 GLN ASN ILE SER PHE LEU TRP GLY TYR SER ILE ILE VAL SEQRES 19 A 578 GLY LEU VAL GLY LEU ALA PHE PHE ILE PHE LEU PHE ALA SEQRES 20 A 578 THR PRO VAL PHE ILE THR LYS PRO PRO THR GLY SER GLN SEQRES 21 A 578 VAL SER SER MET LEU LYS LEU ALA PHE GLN ASN CYS CYS SEQRES 22 A 578 PRO CYS ARG ARG SER SER SER ARG ASP SER GLU SER ALA SEQRES 23 A 578 HIS LEU LEU PRO ASP GLN ARG SER ASN GLN PRO GLY PRO SEQRES 24 A 578 SER PRO GLN GLU ASP MET ALA ASN PHE GLN VAL LEU VAL SEQRES 25 A 578 LYS ILE LEU PRO VAL MET VAL THR LEU VAL PRO TYR TRP SEQRES 26 A 578 MET VAL TYR PHE GLN MET GLN SER THR TYR VAL LEU GLN SEQRES 27 A 578 GLY LEU HIS LEU HIS ILE PRO ASN ILE PHE ARG THR ASN SEQRES 28 A 578 PRO ASN ILE SER LEU LEU LEU ARG SER ASP SER SER ASN SEQRES 29 A 578 TYR ARG ILE PRO GLU ALA TRP LEU LEU LEU ALA ASN VAL SEQRES 30 A 578 ALA VAL ILE LEU ILE LEU ILE PRO VAL LYS ASP HIS LEU SEQRES 31 A 578 ILE ASP PRO LEU LEU LEU ARG CYS LYS LEU LEU PRO SER SEQRES 32 A 578 SER LEU GLN LYS MET ALA LEU GLY MET PHE PHE GLY PHE SEQRES 33 A 578 THR SER ILE ILE VAL ALA GLY VAL LEU GLU LYS GLU ARG SEQRES 34 A 578 LEU GLN TYR ILE ALA ALA ASN GLN THR VAL PRO GLN LEU SEQRES 35 A 578 ILE GLY LYS ASP LEU TYR TYR ALA ALA PRO LEU SER ILE SEQRES 36 A 578 TRP TRP GLN ILE PRO GLN TYR LEU LEU ILE GLY VAL SER SEQRES 37 A 578 GLU ILE PHE ALA SER ILE PRO GLY LEU GLU PHE ALA TYR SEQRES 38 A 578 SER GLU ALA PRO ARG SER MET GLN GLY ALA ILE MET GLY SEQRES 39 A 578 ILE PHE PHE CYS LEU SER GLY VAL GLY SER LEU LEU GLY SEQRES 40 A 578 SER GLY LEU VAL ALA LEU LEU SER PHE PRO GLY GLY TRP SEQRES 41 A 578 MET TYR CYS PRO LYS ASP PHE GLY ASN ILE ASN ASN CYS SEQRES 42 A 578 GLN MET ASP ARG TYR PHE PHE LEU LEU ALA GLY ILE GLU SEQRES 43 A 578 ALA VAL THR ALA VAL LEU PHE LEU TRP ILE ALA GLY ARG SEQRES 44 A 578 TYR GLU ARG THR ARG GLN ASP PRO ALA SER GLN ARG SER SEQRES 45 A 578 SER SER ARG VAL ARG GLY HELIX 1 AA1 ARG A 25 ASN A 61 1 37 HELIX 2 AA2 ASP A 68 TYR A 97 1 30 HELIX 3 AA3 GLY A 99 THR A 123 1 25 HELIX 4 AA4 THR A 123 CYS A 131 1 9 HELIX 5 AA5 CYS A 157 VAL A 187 1 31 HELIX 6 AA6 GLY A 191 ILE A 224 1 34 HELIX 7 AA7 SER A 225 ALA A 247 1 23 HELIX 8 AA8 GLN A 260 CYS A 273 1 14 HELIX 9 AA9 SER A 300 HIS A 341 1 42 HELIX 10 AB1 ALA A 370 LYS A 399 1 30 HELIX 11 AB2 SER A 403 ALA A 435 1 33 HELIX 12 AB3 SER A 454 TRP A 456 5 3 HELIX 13 AB4 TRP A 457 GLU A 483 1 27 HELIX 14 AB5 MET A 488 SER A 515 1 28 HELIX 15 AB6 MET A 535 ASP A 566 1 32 SHEET 1 AA1 2 VAL A 439 ILE A 443 0 SHEET 2 AA1 2 ASP A 446 ALA A 450 -1 O TYR A 448 N GLN A 441 SSBOND 1 CYS A 131 CYS A 157 1555 1555 2.03 SSBOND 2 CYS A 523 CYS A 533 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 TER 3927 ASP A 566 CONECT 834 941 CONECT 941 834 CONECT 3570 3647 CONECT 3647 3570 MASTER 228 0 0 15 2 0 0 6 3926 1 4 45 END