HEADER TRANSPORT PROTEIN 24-SEP-25 9WX7 TITLE STRUCTURE OF THE L-PROLINE-FREE HUMAN PROLINE TRANSPORTER PURIFIED IN TITLE 2 DDM/CHS BUFFER COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM-DEPENDENT PROLINE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SOLUTE CARRIER FAMILY 6 MEMBER 7; 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: SLC6A7, PROT; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS HUMAN PROLINE TRANSPORTER PURIFIED, 12 TRANSMEMBRANE HELICES, KEYWDS 2 TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.X.WU,Y.ZHOU,N.Q.WANG,J.Q.WANG REVDAT 1 25-MAR-26 9WX7 0 JRNL AUTH Y.ZHOU,J.X.WU JRNL TITL STRUCTURAL INSIGHTS INTO TRANSPORT MECHANISM OF PROLINE JRNL TITL 2 TRANSPORTER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.57 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) : 2.570 REMARK 3 NUMBER OF PARTICLES : 226167 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 9WX7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 30-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300064066. 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 : PROT 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 : 7.50 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 POLARA 300 REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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) : 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 LYS A 2 REMARK 465 LYS A 3 REMARK 465 LEU A 4 REMARK 465 GLN A 5 REMARK 465 GLY A 6 REMARK 465 ALA A 7 REMARK 465 HIS A 8 REMARK 465 LEU A 9 REMARK 465 ARG A 10 REMARK 465 LYS A 11 REMARK 465 PRO A 12 REMARK 465 VAL A 13 REMARK 465 THR A 14 REMARK 465 PRO A 15 REMARK 465 ASP A 16 REMARK 465 LEU A 17 REMARK 465 LEU A 18 REMARK 465 MET A 19 REMARK 465 THR A 20 REMARK 465 PRO A 21 REMARK 465 SER A 22 REMARK 465 ASP A 23 REMARK 465 GLN A 24 REMARK 465 GLY A 25 REMARK 465 ASP A 26 REMARK 465 VAL A 27 REMARK 465 ASP A 28 REMARK 465 LEU A 29 REMARK 465 ASP A 30 REMARK 465 VAL A 31 REMARK 465 ASP A 32 REMARK 465 PHE A 33 REMARK 465 ALA A 34 REMARK 465 ALA A 35 REMARK 465 HIS A 36 REMARK 465 ARG A 37 REMARK 465 GLY A 38 REMARK 465 ASN A 39 REMARK 465 ARG A 170 REMARK 465 VAL A 171 REMARK 465 SER A 172 REMARK 465 LYS A 173 REMARK 465 ASP A 174 REMARK 465 GLY A 175 REMARK 465 ASN A 176 REMARK 465 GLY A 177 REMARK 465 ALA A 178 REMARK 465 LEU A 179 REMARK 465 PRO A 180 REMARK 465 LEU A 181 REMARK 465 ASN A 182 REMARK 465 LEU A 183 REMARK 465 THR A 594 REMARK 465 LEU A 595 REMARK 465 ALA A 596 REMARK 465 GLY A 597 REMARK 465 SER A 598 REMARK 465 GLN A 599 REMARK 465 SER A 600 REMARK 465 PRO A 601 REMARK 465 LYS A 602 REMARK 465 PRO A 603 REMARK 465 LEU A 604 REMARK 465 MET A 605 REMARK 465 VAL A 606 REMARK 465 HIS A 607 REMARK 465 MET A 608 REMARK 465 ARG A 609 REMARK 465 LYS A 610 REMARK 465 TYR A 611 REMARK 465 GLY A 612 REMARK 465 GLY A 613 REMARK 465 ILE A 614 REMARK 465 THR A 615 REMARK 465 SER A 616 REMARK 465 PHE A 617 REMARK 465 GLU A 618 REMARK 465 ASN A 619 REMARK 465 THR A 620 REMARK 465 ALA A 621 REMARK 465 ILE A 622 REMARK 465 GLU A 623 REMARK 465 VAL A 624 REMARK 465 ASP A 625 REMARK 465 ARG A 626 REMARK 465 GLU A 627 REMARK 465 ILE A 628 REMARK 465 ALA A 629 REMARK 465 GLU A 630 REMARK 465 GLU A 631 REMARK 465 GLU A 632 REMARK 465 GLU A 633 REMARK 465 SER A 634 REMARK 465 MET A 635 REMARK 465 MET A 636 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 CYS A 157 -150.30 -99.63 REMARK 500 PHE A 504 -56.72 -126.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 701 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 54 O REMARK 620 2 ASN A 59 OD1 87.5 REMARK 620 3 SER A 298 O 66.5 145.7 REMARK 620 4 SER A 298 OG 113.6 99.8 72.9 REMARK 620 5 ASN A 330 OD1 68.0 67.3 81.8 55.8 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66332 RELATED DB: EMDB REMARK 900 STRUCTURE OF THE SUBSTRATE-FREE HUMAN PROLINE TRANSPORTER PURIFIED REMARK 900 IN DDM/CHS BUFFER DBREF 9WX7 A 1 636 UNP Q99884 SC6A7_HUMAN 1 636 SEQRES 1 A 636 MET LYS LYS LEU GLN GLY ALA HIS LEU ARG LYS PRO VAL SEQRES 2 A 636 THR PRO ASP LEU LEU MET THR PRO SER ASP GLN GLY ASP SEQRES 3 A 636 VAL ASP LEU ASP VAL ASP PHE ALA ALA HIS ARG GLY ASN SEQRES 4 A 636 TRP THR GLY LYS LEU ASP PHE LEU LEU SER CYS ILE GLY SEQRES 5 A 636 TYR CYS VAL GLY LEU GLY ASN VAL TRP ARG PHE PRO TYR SEQRES 6 A 636 ARG ALA TYR THR ASN GLY GLY GLY ALA PHE LEU VAL PRO SEQRES 7 A 636 TYR PHE LEU MET LEU ALA ILE CYS GLY ILE PRO LEU PHE SEQRES 8 A 636 PHE LEU GLU LEU SER LEU GLY GLN PHE SER SER LEU GLY SEQRES 9 A 636 PRO LEU ALA VAL TRP LYS ILE SER PRO LEU PHE LYS GLY SEQRES 10 A 636 ALA GLY ALA ALA MET LEU LEU ILE VAL GLY LEU VAL ALA SEQRES 11 A 636 ILE TYR TYR ASN MET ILE ILE ALA TYR VAL LEU PHE TYR SEQRES 12 A 636 LEU PHE ALA SER LEU THR SER ASP LEU PRO TRP GLU HIS SEQRES 13 A 636 CYS GLY ASN TRP TRP ASN THR GLU LEU CYS LEU GLU HIS SEQRES 14 A 636 ARG VAL SER LYS ASP GLY ASN GLY ALA LEU PRO LEU ASN SEQRES 15 A 636 LEU THR CYS THR VAL SER PRO SER GLU GLU TYR TRP SER SEQRES 16 A 636 ARG TYR VAL LEU HIS ILE GLN GLY SER GLN GLY ILE GLY SEQRES 17 A 636 SER PRO GLY GLU ILE ARG TRP ASN LEU CYS LEU CYS LEU SEQRES 18 A 636 LEU LEU ALA TRP VAL ILE VAL PHE LEU CYS ILE LEU LYS SEQRES 19 A 636 GLY VAL LYS SER SER GLY LYS VAL VAL TYR PHE THR ALA SEQRES 20 A 636 THR PHE PRO TYR LEU ILE LEU LEU MET LEU LEU VAL ARG SEQRES 21 A 636 GLY VAL THR LEU PRO GLY ALA TRP LYS GLY ILE GLN PHE SEQRES 22 A 636 TYR LEU THR PRO GLN PHE HIS HIS LEU LEU SER SER LYS SEQRES 23 A 636 VAL TRP ILE GLU ALA ALA LEU GLN ILE PHE TYR SER LEU SEQRES 24 A 636 GLY VAL GLY PHE GLY GLY LEU LEU THR PHE ALA SER TYR SEQRES 25 A 636 ASN THR PHE HIS GLN ASN ILE TYR ARG ASP THR PHE ILE SEQRES 26 A 636 VAL THR LEU GLY ASN ALA ILE THR SER ILE LEU ALA GLY SEQRES 27 A 636 PHE ALA ILE PHE SER VAL LEU GLY TYR MET SER GLN GLU SEQRES 28 A 636 LEU GLY VAL PRO VAL ASP GLN VAL ALA LYS ALA GLY PRO SEQRES 29 A 636 GLY LEU ALA PHE VAL VAL TYR PRO GLN ALA MET THR MET SEQRES 30 A 636 LEU PRO LEU SER PRO PHE TRP SER PHE LEU PHE PHE PHE SEQRES 31 A 636 MET LEU LEU THR LEU GLY LEU ASP SER GLN PHE ALA PHE SEQRES 32 A 636 LEU GLU THR ILE VAL THR ALA VAL THR ASP GLU PHE PRO SEQRES 33 A 636 TYR TYR LEU ARG PRO LYS LYS ALA VAL PHE SER GLY LEU SEQRES 34 A 636 ILE CYS VAL ALA MET TYR LEU MET GLY LEU ILE LEU THR SEQRES 35 A 636 THR ASP GLY GLY MET TYR TRP LEU VAL LEU LEU ASP ASP SEQRES 36 A 636 TYR SER ALA SER PHE GLY LEU MET VAL VAL VAL ILE THR SEQRES 37 A 636 THR CYS LEU ALA VAL THR ARG VAL TYR GLY ILE GLN ARG SEQRES 38 A 636 PHE CYS ARG ASP ILE HIS MET MET LEU GLY PHE LYS PRO SEQRES 39 A 636 GLY LEU TYR PHE ARG ALA CYS TRP LEU PHE LEU SER PRO SEQRES 40 A 636 ALA THR LEU LEU ALA LEU MET VAL TYR SER ILE VAL LYS SEQRES 41 A 636 TYR GLN PRO SER GLU TYR GLY SER TYR ARG PHE PRO PRO SEQRES 42 A 636 TRP ALA GLU LEU LEU GLY ILE LEU MET GLY LEU LEU SER SEQRES 43 A 636 CYS LEU MET ILE PRO ALA GLY MET LEU VAL ALA VAL LEU SEQRES 44 A 636 ARG GLU GLU GLY SER LEU TRP GLU ARG LEU GLN GLN ALA SEQRES 45 A 636 SER ARG PRO ALA MET ASP TRP GLY PRO SER LEU GLU GLU SEQRES 46 A 636 ASN ARG THR GLY MET TYR VAL ALA THR LEU ALA GLY SER SEQRES 47 A 636 GLN SER PRO LYS PRO LEU MET VAL HIS MET ARG LYS TYR SEQRES 48 A 636 GLY GLY ILE THR SER PHE GLU ASN THR ALA ILE GLU VAL SEQRES 49 A 636 ASP ARG GLU ILE ALA GLU GLU GLU GLU SER MET MET HET NA A 701 1 HET CL A 702 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 NA NA 1+ FORMUL 3 CL CL 1- HELIX 1 AA1 TRP A 40 GLY A 52 1 13 HELIX 2 AA2 GLY A 56 VAL A 60 5 5 HELIX 3 AA3 TRP A 61 THR A 69 1 9 HELIX 4 AA4 GLY A 72 CYS A 86 1 15 HELIX 5 AA5 CYS A 86 SER A 102 1 17 HELIX 6 AA6 LEU A 106 ILE A 111 5 6 HELIX 7 AA7 SER A 112 LEU A 114 5 3 HELIX 8 AA8 PHE A 115 SER A 147 1 33 HELIX 9 AA9 LEU A 152 HIS A 156 5 5 HELIX 10 AB1 SER A 188 TYR A 197 1 10 HELIX 11 AB2 HIS A 200 SER A 204 5 5 HELIX 12 AB3 ARG A 214 LYS A 234 1 21 HELIX 13 AB4 ALA A 247 LEU A 264 1 18 HELIX 14 AB5 GLY A 266 THR A 276 1 11 HELIX 15 AB6 GLN A 278 LEU A 283 1 6 HELIX 16 AB7 SER A 284 GLY A 300 1 17 HELIX 17 AB8 GLY A 304 TYR A 312 1 9 HELIX 18 AB9 ASN A 318 GLY A 353 1 36 HELIX 19 AC1 GLY A 365 THR A 376 1 12 HELIX 20 AC2 LEU A 380 PHE A 415 1 36 HELIX 21 AC3 PHE A 415 ARG A 420 1 6 HELIX 22 AC4 LYS A 422 LEU A 439 1 18 HELIX 23 AC5 ILE A 440 THR A 443 5 4 HELIX 24 AC6 GLY A 445 SER A 457 1 13 HELIX 25 AC7 PHE A 460 ARG A 475 1 16 HELIX 26 AC8 GLY A 478 GLY A 491 1 14 HELIX 27 AC9 GLY A 495 PHE A 504 1 10 HELIX 28 AD1 PHE A 504 LYS A 520 1 17 HELIX 29 AD2 PRO A 532 GLU A 561 1 30 HELIX 30 AD3 SER A 564 ARG A 574 1 11 HELIX 31 AD4 THR A 588 VAL A 592 5 5 SHEET 1 AA1 2 GLU A 525 TYR A 526 0 SHEET 2 AA1 2 TYR A 529 ARG A 530 -1 O TYR A 529 N TYR A 526 SSBOND 1 CYS A 157 CYS A 166 1555 1555 2.03 LINK O CYS A 54 NA NA A 701 1555 1555 2.77 LINK OD1 ASN A 59 NA NA A 701 1555 1555 2.42 LINK O SER A 298 NA NA A 701 1555 1555 2.90 LINK OG SER A 298 NA NA A 701 1555 1555 2.35 LINK OD1 ASN A 330 NA NA A 701 1555 1555 3.00 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 117 4265 CONECT 149 4265 CONECT 924 1002 CONECT 1002 924 CONECT 1948 4265 CONECT 1950 4265 CONECT 2200 4265 CONECT 4265 117 149 1948 1950 CONECT 4265 2200 MASTER 234 0 2 31 2 0 0 6 4265 1 9 49 END