HEADER MEMBRANE PROTEIN 14-NOV-24 9KL5 TITLE CRYO-EM STRUCUTURE OF HUMAN OAT1 IN COMPLEX WITH PROBENECID COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 22 MEMBER 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ORGANIC ANION TRANSPORTER 1,HOAT1,PAH TRANSPORTER,HPAHT, COMPND 5 RENAL ORGANIC ANION TRANSPORTER 1,HROAT1; 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: SLC22A6, OAT1, PAHT; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 GNTI-; SOURCE 9 EXPRESSION_SYSTEM_ATCC_NUMBER: CRL-3022; SOURCE 10 EXPRESSION_SYSTEM_ORGAN: KIDNEY; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PEG BACMAM KEYWDS MEMBRANE TRANSPORTER, ANTIPORTER, GOUT, DRUG-DRUG INTERACTION, DRUG KEYWDS 2 ELIMINATION, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.M.JEON,J.EUN,Y.KIM REVDAT 2 19-NOV-25 9KL5 1 JRNL REVDAT 1 05-NOV-25 9KL5 0 JRNL AUTH H.M.JEON,J.EUN,K.H.KIM,Y.KIM JRNL TITL CRYO-EM STRUCTURES OF HUMAN OAT1 REVEAL DRUG BINDING AND JRNL TITL 2 INHIBITION MECHANISMS. JRNL REF STRUCTURE V. 33 1856 2025 JRNL REFN ISSN 0969-2126 JRNL PMID 40845848 JRNL DOI 10.1016/J.STR.2025.07.019 REMARK 2 REMARK 2 RESOLUTION. 3.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, COOT, REMARK 3 CRYOSPARC, RELION, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8SDZ REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.330 REMARK 3 NUMBER OF PARTICLES : 97785 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 9KL5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053756. 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 OAT1 IN COMPLEX WITH REMARK 245 PROBENECID REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 15.00 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 : HUMAN OAT1 IN COMPLEX WITH REMARK 245 PROBENECID, ADOPTING INWARD-FACING CONFORMATION AND EMBEDDED IN REMARK 245 LMNG/CHS MICELLE. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 22975 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5200.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : 96000 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 ALA A 53 REMARK 465 ASP A 54 REMARK 465 ALA A 55 REMARK 465 ASN A 56 REMARK 465 LEU A 57 REMARK 465 SER A 58 REMARK 465 LYS A 59 REMARK 465 ASN A 60 REMARK 465 GLY A 61 REMARK 465 GLY A 62 REMARK 465 LEU A 63 REMARK 465 GLU A 64 REMARK 465 TRP A 86 REMARK 465 GLY A 87 REMARK 465 LEU A 88 REMARK 465 PRO A 89 REMARK 465 PHE A 90 REMARK 465 LEU A 91 REMARK 465 ASN A 92 REMARK 465 GLY A 93 REMARK 465 THR A 94 REMARK 465 GLU A 95 REMARK 465 ALA A 96 REMARK 465 ASN A 97 REMARK 465 GLY A 98 REMARK 465 THR A 99 REMARK 465 GLY A 100 REMARK 465 ALA A 101 REMARK 465 MET A 319 REMARK 465 GLY A 320 REMARK 465 LYS A 321 REMARK 465 GLY A 322 REMARK 465 GLN A 323 REMARK 465 ALA A 324 REMARK 465 GLN A 510 REMARK 465 PRO A 511 REMARK 465 LEU A 512 REMARK 465 PRO A 513 REMARK 465 ASP A 514 REMARK 465 THR A 515 REMARK 465 VAL A 516 REMARK 465 GLN A 517 REMARK 465 ASP A 518 REMARK 465 LEU A 519 REMARK 465 GLU A 520 REMARK 465 SER A 521 REMARK 465 ARG A 522 REMARK 465 TRP A 523 REMARK 465 ALA A 524 REMARK 465 PRO A 525 REMARK 465 THR A 526 REMARK 465 GLN A 527 REMARK 465 LYS A 528 REMARK 465 GLU A 529 REMARK 465 ALA A 530 REMARK 465 GLY A 531 REMARK 465 ILE A 532 REMARK 465 TYR A 533 REMARK 465 PRO A 534 REMARK 465 ARG A 535 REMARK 465 LYS A 536 REMARK 465 GLY A 537 REMARK 465 LYS A 538 REMARK 465 GLN A 539 REMARK 465 THR A 540 REMARK 465 ARG A 541 REMARK 465 GLN A 542 REMARK 465 GLN A 543 REMARK 465 GLN A 544 REMARK 465 GLU A 545 REMARK 465 HIS A 546 REMARK 465 GLN A 547 REMARK 465 LYS A 548 REMARK 465 TYR A 549 REMARK 465 MET A 550 REMARK 465 VAL A 551 REMARK 465 PRO A 552 REMARK 465 LEU A 553 REMARK 465 GLN A 554 REMARK 465 ALA A 555 REMARK 465 SER A 556 REMARK 465 ALA A 557 REMARK 465 GLN A 558 REMARK 465 GLU A 559 REMARK 465 LYS A 560 REMARK 465 ASN A 561 REMARK 465 GLY A 562 REMARK 465 LEU A 563 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62400 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCUTURE OF HUMAN OAT1 IN COMPLEX WITH PROBENECID DBREF 9KL5 A 1 563 UNP Q4U2R8 S22A6_HUMAN 1 563 SEQRES 1 A 563 MET ALA PHE ASN ASP LEU LEU GLN GLN VAL GLY GLY VAL SEQRES 2 A 563 GLY ARG PHE GLN GLN ILE GLN VAL THR LEU VAL VAL LEU SEQRES 3 A 563 PRO LEU LEU LEU MET ALA SER HIS ASN THR LEU GLN ASN SEQRES 4 A 563 PHE THR ALA ALA ILE PRO THR HIS HIS CYS ARG PRO PRO SEQRES 5 A 563 ALA ASP ALA ASN LEU SER LYS ASN GLY GLY LEU GLU VAL SEQRES 6 A 563 TRP LEU PRO ARG ASP ARG GLN GLY GLN PRO GLU SER CYS SEQRES 7 A 563 LEU ARG PHE THR SER PRO GLN TRP GLY LEU PRO PHE LEU SEQRES 8 A 563 ASN GLY THR GLU ALA ASN GLY THR GLY ALA THR GLU PRO SEQRES 9 A 563 CYS THR ASP GLY TRP ILE TYR ASP ASN SER THR PHE PRO SEQRES 10 A 563 SER THR ILE VAL THR GLU TRP ASP LEU VAL CYS SER HIS SEQRES 11 A 563 ARG ALA LEU ARG GLN LEU ALA GLN SER LEU TYR MET VAL SEQRES 12 A 563 GLY VAL LEU LEU GLY ALA MET VAL PHE GLY TYR LEU ALA SEQRES 13 A 563 ASP ARG LEU GLY ARG ARG LYS VAL LEU ILE LEU ASN TYR SEQRES 14 A 563 LEU GLN THR ALA VAL SER GLY THR CYS ALA ALA PHE ALA SEQRES 15 A 563 PRO ASN PHE PRO ILE TYR CYS ALA PHE ARG LEU LEU SER SEQRES 16 A 563 GLY MET ALA LEU ALA GLY ILE SER LEU ASN CYS MET THR SEQRES 17 A 563 LEU ASN VAL GLU TRP MET PRO ILE HIS THR ARG ALA CYS SEQRES 18 A 563 VAL GLY THR LEU ILE GLY TYR VAL TYR SER LEU GLY GLN SEQRES 19 A 563 PHE LEU LEU ALA GLY VAL ALA TYR ALA VAL PRO HIS TRP SEQRES 20 A 563 ARG HIS LEU GLN LEU LEU VAL SER ALA PRO PHE PHE ALA SEQRES 21 A 563 PHE PHE ILE TYR SER TRP PHE PHE ILE GLU SER ALA ARG SEQRES 22 A 563 TRP HIS SER SER SER GLY ARG LEU ASP LEU THR LEU ARG SEQRES 23 A 563 ALA LEU GLN ARG VAL ALA ARG ILE ASN GLY LYS ARG GLU SEQRES 24 A 563 GLU GLY ALA LYS LEU SER MET GLU VAL LEU ARG ALA SER SEQRES 25 A 563 LEU GLN LYS GLU LEU THR MET GLY LYS GLY GLN ALA SER SEQRES 26 A 563 ALA MET GLU LEU LEU ARG CYS PRO THR LEU ARG HIS LEU SEQRES 27 A 563 PHE LEU CYS LEU SER MET LEU TRP PHE ALA THR SER PHE SEQRES 28 A 563 ALA TYR TYR GLY LEU VAL MET ASP LEU GLN GLY PHE GLY SEQRES 29 A 563 VAL SER ILE TYR LEU ILE GLN VAL ILE PHE GLY ALA VAL SEQRES 30 A 563 ASP LEU PRO ALA LYS LEU VAL GLY PHE LEU VAL ILE ASN SEQRES 31 A 563 SER LEU GLY ARG ARG PRO ALA GLN MET ALA ALA LEU LEU SEQRES 32 A 563 LEU ALA GLY ILE CYS ILE LEU LEU ASN GLY VAL ILE PRO SEQRES 33 A 563 GLN ASP GLN SER ILE VAL ARG THR SER LEU ALA VAL LEU SEQRES 34 A 563 GLY LYS GLY CYS LEU ALA ALA SER PHE ASN CYS ILE PHE SEQRES 35 A 563 LEU TYR THR GLY GLU LEU TYR PRO THR MET ILE ARG GLN SEQRES 36 A 563 THR GLY MET GLY MET GLY SER THR MET ALA ARG VAL GLY SEQRES 37 A 563 SER ILE VAL SER PRO LEU VAL SER MET THR ALA GLU LEU SEQRES 38 A 563 TYR PRO SER MET PRO LEU PHE ILE TYR GLY ALA VAL PRO SEQRES 39 A 563 VAL ALA ALA SER ALA VAL THR VAL LEU LEU PRO GLU THR SEQRES 40 A 563 LEU GLY GLN PRO LEU PRO ASP THR VAL GLN ASP LEU GLU SEQRES 41 A 563 SER ARG TRP ALA PRO THR GLN LYS GLU ALA GLY ILE TYR SEQRES 42 A 563 PRO ARG LYS GLY LYS GLN THR ARG GLN GLN GLN GLU HIS SEQRES 43 A 563 GLN LYS TYR MET VAL PRO LEU GLN ALA SER ALA GLN GLU SEQRES 44 A 563 LYS ASN GLY LEU HET RTO A 601 19 HET CL A 602 1 HETNAM RTO 4-(DIPROPYLSULFAMOYL)BENZOIC ACID HETNAM CL CHLORIDE ION FORMUL 2 RTO C13 H19 N O4 S FORMUL 3 CL CL 1- HELIX 1 AA1 ALA A 2 GLY A 11 1 10 HELIX 2 AA2 GLY A 14 LEU A 26 1 13 HELIX 3 AA3 PRO A 27 LEU A 30 5 4 HELIX 4 AA4 MET A 31 THR A 36 1 6 HELIX 5 AA5 LEU A 37 ALA A 42 1 6 HELIX 6 AA6 THR A 119 ASP A 125 1 7 HELIX 7 AA7 HIS A 130 GLY A 160 1 31 HELIX 8 AA8 GLY A 160 ALA A 180 1 21 HELIX 9 AA9 ASN A 184 GLU A 212 1 29 HELIX 10 AB1 PRO A 215 HIS A 217 5 3 HELIX 11 AB2 THR A 218 VAL A 244 1 27 HELIX 12 AB3 HIS A 246 ALA A 256 1 11 HELIX 13 AB4 ALA A 256 TYR A 264 1 9 HELIX 14 AB5 SER A 265 PHE A 268 5 4 HELIX 15 AB6 SER A 271 SER A 278 1 8 HELIX 16 AB7 ARG A 280 GLY A 296 1 17 HELIX 17 AB8 LYS A 297 LYS A 303 1 7 HELIX 18 AB9 SER A 305 LEU A 313 1 9 HELIX 19 AC1 ALA A 326 CYS A 332 1 7 HELIX 20 AC2 CYS A 332 TYR A 354 1 23 HELIX 21 AC3 SER A 366 VAL A 377 1 12 HELIX 22 AC4 VAL A 377 LEU A 392 1 16 HELIX 23 AC5 ARG A 394 ILE A 415 1 22 HELIX 24 AC6 SER A 420 TYR A 449 1 30 HELIX 25 AC7 ILE A 453 MET A 477 1 25 HELIX 26 AC8 THR A 478 LEU A 481 5 4 HELIX 27 AC9 SER A 484 ALA A 499 1 16 HELIX 28 AD1 VAL A 500 LEU A 504 5 5 SHEET 1 AA1 2 HIS A 47 CYS A 49 0 SHEET 2 AA1 2 TRP A 109 TYR A 111 -1 O ILE A 110 N HIS A 48 SSBOND 1 CYS A 49 CYS A 105 1555 1555 2.03 SSBOND 2 CYS A 78 CYS A 128 1555 1555 2.02 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 3664 GLY A 509 HETATM 3665 C13 RTO A 601 128.591 125.874 132.835 1.00103.14 C HETATM 3666 C15 RTO A 601 130.629 126.460 133.958 1.00103.59 C HETATM 3667 C17 RTO A 601 129.678 124.156 134.328 1.00104.25 C HETATM 3668 C01 RTO A 601 130.000 134.244 132.110 1.00100.98 C HETATM 3669 C02 RTO A 601 128.981 133.108 132.044 1.00104.13 C HETATM 3670 C03 RTO A 601 129.207 132.059 133.135 1.00104.77 C HETATM 3671 C05 RTO A 601 127.335 130.379 133.319 1.00107.66 C HETATM 3672 C06 RTO A 601 126.170 130.842 132.444 1.00103.59 C HETATM 3673 C07 RTO A 601 124.837 130.812 133.188 1.00101.50 C HETATM 3674 C11 RTO A 601 129.548 128.054 132.527 1.00106.28 C HETATM 3675 C12 RTO A 601 128.549 127.131 132.254 1.00102.98 C HETATM 3676 C14 RTO A 601 129.630 125.540 133.688 1.00103.62 C HETATM 3677 C16 RTO A 601 130.589 127.718 133.377 1.00104.41 C HETATM 3678 N04 RTO A 601 128.606 130.793 132.740 1.00114.17 N HETATM 3679 O09 RTO A 601 130.846 130.205 131.515 1.00108.30 O HETATM 3680 O10 RTO A 601 128.962 129.649 130.403 1.00106.79 O HETATM 3681 O18 RTO A 601 128.633 123.650 134.813 1.00100.15 O HETATM 3682 O19 RTO A 601 130.763 123.524 134.373 1.00109.03 O HETATM 3683 S08 RTO A 601 129.496 129.705 131.763 1.00123.67 S HETATM 3684 CL CL A 602 126.373 133.274 129.274 1.00 30.00 CL CONECT 369 598 CONECT 510 785 CONECT 598 369 CONECT 785 510 CONECT 3665 3675 3676 CONECT 3666 3676 3677 CONECT 3667 3676 3681 3682 CONECT 3668 3669 CONECT 3669 3668 3670 CONECT 3670 3669 3678 CONECT 3671 3672 3678 CONECT 3672 3671 3673 CONECT 3673 3672 CONECT 3674 3675 3677 3683 CONECT 3675 3665 3674 CONECT 3676 3665 3666 3667 CONECT 3677 3666 3674 CONECT 3678 3670 3671 3683 CONECT 3679 3683 CONECT 3680 3683 CONECT 3681 3667 CONECT 3682 3667 CONECT 3683 3674 3678 3679 3680 MASTER 197 0 2 28 2 0 0 6 3683 1 23 44 END