HEADER TRANSPORT PROTEIN 22-MAY-25 9V3X TITLE SLC36A1 BOUND TO D-SERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTON-COUPLED AMINO ACID TRANSPORTER 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTON/AMINO ACID TRANSPORTER 1,HPAT1,SOLUTE CARRIER FAMILY COMPND 5 36 MEMBER 1; COMPND 6 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: SLC36A1, PAT1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS LYSOSOMAL MEMBRANE PROTEIN SER, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.S.ZHANG REVDAT 1 29-JUL-26 9V3X 0 JRNL AUTH J.YIN,S.ZHANG,C.LIU,M.XIE,Y.GAO,M.CHEN,Y.WANG,M.CHEN,H.FAN, JRNL AUTH 2 Z.YANG,H.LI,L.LIANG,B.ZHOU,X.CHEN,M.YANG JRNL TITL SUBSTRATE RECOGNITION AND TRANSPORT MECHANISM OF THE HUMAN JRNL TITL 2 PROTON-COUPLED AMINO-ACID TRANSPORTER 1 (SLC36A1). JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 42414312 JRNL DOI 10.1038/S41467-026-75306-Z REMARK 2 REMARK 2 RESOLUTION. 3.40 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 345000 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 9V3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059722. 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 : LYSOSOMAL MEMBRANE PROTEIN WITH REMARK 245 SER 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 : 7.20 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) : 1200.00 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) : 5000.00 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 MET A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 GLN A 4 REMARK 465 ARG A 5 REMARK 465 LEU A 6 REMARK 465 ARG A 7 REMARK 465 ASN A 8 REMARK 465 GLU A 9 REMARK 465 ASP A 10 REMARK 465 TYR A 11 REMARK 465 HIS A 12 REMARK 465 ASP A 13 REMARK 465 TYR A 14 REMARK 465 SER A 15 REMARK 465 SER A 16 REMARK 465 THR A 17 REMARK 465 ASP A 18 REMARK 465 VAL A 19 REMARK 465 SER A 20 REMARK 465 PRO A 21 REMARK 465 GLU A 22 REMARK 465 GLU A 23 REMARK 465 SER A 24 REMARK 465 PRO A 25 REMARK 465 SER A 26 REMARK 465 GLU A 27 REMARK 465 GLY A 28 REMARK 465 LEU A 29 REMARK 465 ASN A 30 REMARK 465 ASN A 31 REMARK 465 LEU A 32 REMARK 465 SER A 33 REMARK 465 SER A 34 REMARK 465 PRO A 35 REMARK 465 GLY A 36 REMARK 465 SER A 37 REMARK 465 TYR A 38 REMARK 465 GLN A 39 REMARK 465 ARG A 40 REMARK 465 PHE A 41 REMARK 465 PRO A 466 REMARK 465 ILE A 467 REMARK 465 PHE A 468 REMARK 465 ILE A 469 REMARK 465 ASN A 470 REMARK 465 SER A 471 REMARK 465 THR A 472 REMARK 465 CYS A 473 REMARK 465 ALA A 474 REMARK 465 PHE A 475 REMARK 465 ILE A 476 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 43 53.20 39.22 REMARK 500 ASN A 110 121.53 -39.26 REMARK 500 CYS A 129 15.08 -142.65 REMARK 500 LEU A 132 0.38 -63.19 REMARK 500 LEU A 324 43.28 -87.64 REMARK 500 ARG A 365 58.26 -97.62 REMARK 500 HIS A 369 48.86 -85.84 REMARK 500 CYS A 370 24.62 -140.38 REMARK 500 THR A 423 -160.40 -79.01 REMARK 500 PHE A 424 120.94 -35.18 REMARK 500 SER A 430 143.51 -38.09 REMARK 500 PRO A 431 -8.65 -54.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64759 RELATED DB: EMDB REMARK 900 SLC36A1 BOUND TO D-SERINE DBREF 9V3X A 1 476 UNP Q7Z2H8 S36A1_HUMAN 1 476 SEQRES 1 A 476 MET SER THR GLN ARG LEU ARG ASN GLU ASP TYR HIS ASP SEQRES 2 A 476 TYR SER SER THR ASP VAL SER PRO GLU GLU SER PRO SER SEQRES 3 A 476 GLU GLY LEU ASN ASN LEU SER SER PRO GLY SER TYR GLN SEQRES 4 A 476 ARG PHE GLY GLN SER ASN SER THR THR TRP PHE GLN THR SEQRES 5 A 476 LEU ILE HIS LEU LEU LYS GLY ASN ILE GLY THR GLY LEU SEQRES 6 A 476 LEU GLY LEU PRO LEU ALA VAL LYS ASN ALA GLY ILE VAL SEQRES 7 A 476 MET GLY PRO ILE SER LEU LEU ILE ILE GLY ILE VAL ALA SEQRES 8 A 476 VAL HIS CYS MET GLY ILE LEU VAL LYS CYS ALA HIS HIS SEQRES 9 A 476 PHE CYS ARG ARG LEU ASN LYS SER PHE VAL ASP TYR GLY SEQRES 10 A 476 ASP THR VAL MET TYR GLY LEU GLU SER SER PRO CYS SER SEQRES 11 A 476 TRP LEU ARG ASN HIS ALA HIS TRP GLY ARG ARG VAL VAL SEQRES 12 A 476 ASP PHE PHE LEU ILE VAL THR GLN LEU GLY PHE CYS CYS SEQRES 13 A 476 VAL TYR PHE VAL PHE LEU ALA ASP ASN PHE LYS GLN VAL SEQRES 14 A 476 ILE GLU ALA ALA ASN GLY THR THR ASN ASN CYS HIS ASN SEQRES 15 A 476 ASN GLU THR VAL ILE LEU THR PRO THR MET ASP SER ARG SEQRES 16 A 476 LEU TYR MET LEU SER PHE LEU PRO PHE LEU VAL LEU LEU SEQRES 17 A 476 VAL PHE ILE ARG ASN LEU ARG ALA LEU SER ILE PHE SER SEQRES 18 A 476 LEU LEU ALA ASN ILE THR MET LEU VAL SER LEU VAL MET SEQRES 19 A 476 ILE TYR GLN PHE ILE VAL GLN ARG ILE PRO ASP PRO SER SEQRES 20 A 476 HIS LEU PRO LEU VAL ALA PRO TRP LYS THR TYR PRO LEU SEQRES 21 A 476 PHE PHE GLY THR ALA ILE PHE SER PHE GLU GLY ILE GLY SEQRES 22 A 476 MET VAL LEU PRO LEU GLU ASN LYS MET LYS ASP PRO ARG SEQRES 23 A 476 LYS PHE PRO LEU ILE LEU TYR LEU GLY MET VAL ILE VAL SEQRES 24 A 476 THR ILE LEU TYR ILE SER LEU GLY CYS LEU GLY TYR LEU SEQRES 25 A 476 GLN PHE GLY ALA ASN ILE GLN GLY SER ILE THR LEU ASN SEQRES 26 A 476 LEU PRO ASN CYS TRP LEU TYR GLN SER VAL LYS LEU LEU SEQRES 27 A 476 TYR SER ILE GLY ILE PHE PHE THR TYR ALA LEU GLN PHE SEQRES 28 A 476 TYR VAL PRO ALA GLU ILE ILE ILE PRO PHE PHE VAL SER SEQRES 29 A 476 ARG ALA PRO GLU HIS CYS GLU LEU VAL VAL ASP LEU PHE SEQRES 30 A 476 VAL ARG THR VAL LEU VAL CYS LEU THR CYS ILE LEU ALA SEQRES 31 A 476 ILE LEU ILE PRO ARG LEU ASP LEU VAL ILE SER LEU VAL SEQRES 32 A 476 GLY SER VAL SER SER SER ALA LEU ALA LEU ILE ILE PRO SEQRES 33 A 476 PRO LEU LEU GLU VAL THR THR PHE TYR SER GLU GLY MET SEQRES 34 A 476 SER PRO LEU THR ILE PHE LYS ASP ALA LEU ILE SER ILE SEQRES 35 A 476 LEU GLY PHE VAL GLY PHE VAL VAL GLY THR TYR GLU ALA SEQRES 36 A 476 LEU TYR GLU LEU ILE GLN PRO SER ASN ALA PRO ILE PHE SEQRES 37 A 476 ILE ASN SER THR CYS ALA PHE ILE HET NAG A 501 14 HET DSN A 502 7 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM DSN D-SERINE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 DSN C3 H7 N O3 HELIX 1 AA1 THR A 48 LEU A 53 1 6 HELIX 2 AA2 LEU A 53 LYS A 58 1 6 HELIX 3 AA3 GLY A 62 GLY A 67 1 6 HELIX 4 AA4 GLY A 67 GLY A 76 1 10 HELIX 5 AA5 VAL A 78 LEU A 109 1 32 HELIX 6 AA6 ASP A 115 SER A 126 1 12 HELIX 7 AA7 TRP A 131 HIS A 137 5 7 HELIX 8 AA8 TRP A 138 GLN A 168 1 31 HELIX 9 AA9 ASP A 193 MET A 198 1 6 HELIX 10 AB1 PHE A 201 PHE A 210 1 10 HELIX 11 AB2 ASN A 213 VAL A 240 1 28 HELIX 12 AB3 THR A 257 PHE A 261 5 5 HELIX 13 AB4 VAL A 275 ASN A 280 1 6 HELIX 14 AB5 ASP A 284 ARG A 286 5 3 HELIX 15 AB6 LYS A 287 PHE A 314 1 28 HELIX 16 AB7 GLY A 315 ILE A 318 5 4 HELIX 17 AB8 SER A 321 LEU A 326 5 6 HELIX 18 AB9 CYS A 329 ARG A 365 1 37 HELIX 19 AC1 VAL A 373 ILE A 393 1 21 HELIX 20 AC2 ARG A 395 SER A 407 1 13 HELIX 21 AC3 SER A 407 ILE A 414 1 8 HELIX 22 AC4 ILE A 414 THR A 423 1 10 HELIX 23 AC5 SER A 430 GLY A 444 1 15 HELIX 24 AC6 TYR A 453 GLN A 461 1 9 SSBOND 1 CYS A 180 CYS A 329 1555 1555 2.03 LINK ND2 ASN A 174 C1 NAG A 501 1555 1555 1.44 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1035 3328 CONECT 1075 2262 CONECT 2262 1075 CONECT 3328 1035 3329 3339 CONECT 3329 3328 3330 3336 CONECT 3330 3329 3331 3337 CONECT 3331 3330 3332 3338 CONECT 3332 3331 3333 3339 CONECT 3333 3332 3340 CONECT 3334 3335 3336 3341 CONECT 3335 3334 CONECT 3336 3329 3334 CONECT 3337 3330 CONECT 3338 3331 CONECT 3339 3328 3332 CONECT 3340 3333 CONECT 3341 3334 CONECT 3342 3343 CONECT 3343 3342 3344 3347 CONECT 3344 3343 3345 3346 CONECT 3345 3344 CONECT 3346 3344 CONECT 3347 3343 3348 CONECT 3348 3347 MASTER 187 0 2 24 0 0 0 6 3347 1 24 37 END