HEADER MEMBRANE PROTEIN 13-NOV-24 9KKK TITLE CRYO-EM STRUCTURE OF HUMAN SLC22A6 (OAT1) IN THE APO-STATE 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: HEK293S GNTI-; SOURCE 9 EXPRESSION_SYSTEM_ATCC_NUMBER: CRL-3022; SOURCE 10 EXPRESSION_SYSTEM_ORGAN: KIDNEY KEYWDS ANTIPORTER, ORGANIC ANION, DRUG-DRUG INTERACTION. NEPHROTOXICITY, KEYWDS 2 MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.M.JEON,J.EUN,Y.KIM REVDAT 2 19-NOV-25 9KKK 1 JRNL REVDAT 1 05-NOV-25 9KKK 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. 3.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, COOT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8SDU 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) : 3.850 REMARK 3 NUMBER OF PARTICLES : 255646 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 9KKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1300053747. 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 ORGANIC ANION TRANSPORTER REMARK 245 1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 9.00 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 LMNG/GDN/CHS REMARK 245 MICELLE, ADOPTING INWARD-FACING CONFORMATION. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 25948 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS TALOS 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : 100000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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 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 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 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 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 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 71 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 72 CG CD OE1 NE2 REMARK 470 THR A 115 OG1 CG2 REMARK 470 ARG A 286 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 303 CG CD CE NZ REMARK 470 LEU A 309 CG CD1 CD2 REMARK 470 LYS A 315 CG CD CE NZ REMARK 470 LEU A 329 CG CD1 CD2 REMARK 470 ARG A 331 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 481 CG CD1 CD2 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 O ARG A 80 OG1 THR A 102 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 CYS A 128 -98.92 58.43 REMARK 500 THR A 218 76.42 -100.34 REMARK 500 ASP A 359 32.74 -143.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62390 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN OAT1 IN APO-STATE DBREF 9KKK 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 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 ALA A 42 1 16 HELIX 4 AA4 THR A 119 ASP A 125 1 7 HELIX 5 AA5 VAL A 127 ARG A 131 5 5 HELIX 6 AA6 ALA A 132 GLY A 160 1 29 HELIX 7 AA7 ARG A 161 ALA A 180 1 20 HELIX 8 AA8 ASN A 184 MET A 214 1 31 HELIX 9 AA9 ARG A 219 VAL A 244 1 26 HELIX 10 AB1 HIS A 246 ALA A 256 1 11 HELIX 11 AB2 ALA A 256 SER A 265 1 10 HELIX 12 AB3 SER A 271 SER A 278 1 8 HELIX 13 AB4 LEU A 281 GLY A 296 1 16 HELIX 14 AB5 GLU A 299 LYS A 303 5 5 HELIX 15 AB6 SER A 305 LEU A 313 1 9 HELIX 16 AB7 ALA A 326 ARG A 331 1 6 HELIX 17 AB8 LEU A 335 VAL A 357 1 23 HELIX 18 AB9 LEU A 360 GLY A 364 5 5 HELIX 19 AC1 SER A 366 LEU A 392 1 27 HELIX 20 AC2 GLY A 393 ILE A 415 1 23 HELIX 21 AC3 GLN A 419 TYR A 449 1 31 HELIX 22 AC4 ILE A 453 THR A 478 1 26 HELIX 23 AC5 SER A 484 ALA A 499 1 16 HELIX 24 AC6 VAL A 500 LEU A 504 5 5 HELIX 25 AC7 THR A 515 ALA A 524 1 10 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 SHEET 1 AA2 2 ARG A 80 PHE A 81 0 SHEET 2 AA2 2 THR A 102 GLU A 103 -1 O GLU A 103 N ARG A 80 SSBOND 1 CYS A 49 CYS A 105 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 3762 ALA A 524 CONECT 363 604 CONECT 604 363 MASTER 225 0 0 25 4 0 0 6 3761 1 2 44 END