HEADER TRANSPORT PROTEIN 07-APR-23 8SDZ TITLE STRUCTURE OF RAT ORGANIC ANION TRANSPORTER 1 (OAT1) IN COMPLEX WITH TITLE 2 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,ROAT1,RENAL ORGANIC ANION COMPND 5 TRANSPORTER 1,RROAT1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: SLC22A6, OAT1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS ORGANIC ANION TRANSPORTER, OAT, SLC22, DRUG TRANSPORTER, PROBENECID, KEYWDS 2 TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.DOU,J.JIANG REVDAT 3 22-NOV-23 8SDZ 1 JRNL REVDAT 2 01-NOV-23 8SDZ 1 JRNL REVDAT 1 18-OCT-23 8SDZ 0 JRNL AUTH T.DOU,T.LIAN,S.SHU,Y.HE,J.JIANG JRNL TITL THE SUBSTRATE AND INHIBITOR BINDING MECHANISM OF JRNL TITL 2 POLYSPECIFIC TRANSPORTER OAT1 REVEALED BY HIGH-RESOLUTION JRNL TITL 3 CRYO-EM. JRNL REF NAT.STRUCT.MOL.BIOL. V. 30 1794 2023 JRNL REFN ESSN 1545-9985 JRNL PMID 37845412 JRNL DOI 10.1038/S41594-023-01123-3 REMARK 2 REMARK 2 RESOLUTION. 2.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, LEGINON, CTFFIND, PHENIX, REMARK 3 RELION, CRYOSPARC, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 2.860 REMARK 3 NUMBER OF PARTICLES : 73688 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 8SDZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273635. 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 : RAT OAT1/PROBENECID COMPLEX REMARK 245 SOLUBILIZED IN DETERGENT LMNG 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 : 4160 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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 58 REMARK 465 LYS A 59 REMARK 465 ASP A 60 REMARK 465 TRP A 86 REMARK 465 GLY A 87 REMARK 465 PRO A 88 REMARK 465 PRO A 89 REMARK 465 PHE A 90 REMARK 465 TYR 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 THR A 318 REMARK 465 LEU A 319 REMARK 465 SER A 320 REMARK 465 LYS A 321 REMARK 465 GLY A 322 REMARK 465 GLN A 323 REMARK 465 GLY A 525 REMARK 465 LYS A 526 REMARK 465 GLN A 527 REMARK 465 ASN A 528 REMARK 465 GLN A 529 REMARK 465 GLN A 530 REMARK 465 GLN A 531 REMARK 465 GLN A 532 REMARK 465 GLU A 533 REMARK 465 GLN A 534 REMARK 465 GLN A 535 REMARK 465 LYS A 536 REMARK 465 GLN A 537 REMARK 465 MET A 538 REMARK 465 MET A 539 REMARK 465 PRO A 540 REMARK 465 LEU A 541 REMARK 465 GLN A 542 REMARK 465 ALA A 543 REMARK 465 SER A 544 REMARK 465 THR A 545 REMARK 465 GLN A 546 REMARK 465 GLU A 547 REMARK 465 LYS A 548 REMARK 465 ASN A 549 REMARK 465 GLY A 550 REMARK 465 LEU A 551 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 VAL A 475 OG1 THR A 478 2.14 REMARK 500 OG SER A 33 O HOH A 701 2.19 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 -107.21 59.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-40355 RELATED DB: EMDB REMARK 900 STRUCTURE OF RAT ORGANIC ANION TRANSPORTER 1 (OAT1) IN COMPLEX WITH REMARK 900 PROBENECID DBREF 8SDZ A 1 551 UNP O35956 S22A6_RAT 1 551 SEQRES 1 A 551 MET ALA PHE ASN ASP LEU LEU LYS GLN VAL GLY GLY VAL SEQRES 2 A 551 GLY ARG PHE GLN LEU ILE GLN VAL THR MET VAL VAL ALA SEQRES 3 A 551 PRO LEU LEU LEU MET ALA SER HIS ASN THR LEU GLN ASN SEQRES 4 A 551 PHE THR ALA ALA ILE PRO PRO HIS HIS CYS ARG PRO PRO SEQRES 5 A 551 ALA ASN ALA ASN LEU SER LYS ASP GLY GLY LEU GLU ALA SEQRES 6 A 551 TRP LEU PRO LEU ASP LYS GLN GLY GLN PRO GLU SER CYS SEQRES 7 A 551 LEU ARG PHE THR SER PRO GLN TRP GLY PRO PRO PHE TYR SEQRES 8 A 551 ASN GLY THR GLU ALA ASN GLY THR ARG VAL THR GLU PRO SEQRES 9 A 551 CYS ILE ASP GLY TRP VAL TYR ASP ASN SER THR PHE PRO SEQRES 10 A 551 SER THR ILE VAL THR GLU TRP ASN LEU VAL CYS SER HIS SEQRES 11 A 551 ARG ALA PHE ARG GLN LEU ALA GLN SER LEU TYR MET VAL SEQRES 12 A 551 GLY VAL LEU LEU GLY ALA MET VAL PHE GLY TYR LEU ALA SEQRES 13 A 551 ASP ARG LEU GLY ARG ARG LYS VAL LEU ILE LEU ASN TYR SEQRES 14 A 551 LEU GLN THR ALA VAL SER GLY THR CYS ALA ALA TYR ALA SEQRES 15 A 551 PRO ASN TYR THR VAL TYR CYS VAL PHE ARG LEU LEU SER SEQRES 16 A 551 GLY MET SER LEU ALA SER ILE ALA ILE ASN CYS MET THR SEQRES 17 A 551 LEU ASN VAL GLU TRP MET PRO ILE HIS THR ARG ALA TYR SEQRES 18 A 551 VAL GLY THR LEU ILE GLY TYR VAL TYR SER LEU GLY GLN SEQRES 19 A 551 PHE LEU LEU ALA GLY ILE ALA TYR ALA VAL PRO HIS TRP SEQRES 20 A 551 ARG HIS LEU GLN LEU VAL VAL SER VAL PRO PHE PHE ILE SEQRES 21 A 551 ALA PHE ILE TYR SER TRP PHE PHE ILE GLU SER ALA ARG SEQRES 22 A 551 TRP TYR SER SER SER GLY ARG LEU ASP LEU THR LEU ARG SEQRES 23 A 551 ALA LEU GLN ARG VAL ALA ARG ILE ASN GLY LYS GLN GLU SEQRES 24 A 551 GLU GLY ALA LYS LEU SER ILE GLU VAL LEU ARG THR SER SEQRES 25 A 551 LEU GLN LYS GLU LEU THR LEU SER LYS GLY GLN ALA SER SEQRES 26 A 551 ALA MET GLU LEU LEU ARG CYS PRO THR LEU ARG HIS LEU SEQRES 27 A 551 PHE LEU CYS LEU SER MET LEU TRP PHE ALA THR SER PHE SEQRES 28 A 551 ALA TYR TYR GLY LEU VAL MET ASP LEU GLN GLY PHE GLY SEQRES 29 A 551 VAL SER MET TYR LEU ILE GLN VAL ILE PHE GLY ALA VAL SEQRES 30 A 551 ASP LEU PRO ALA LYS PHE VAL CYS PHE LEU VAL ILE ASN SEQRES 31 A 551 SER MET GLY ARG ARG PRO ALA GLN MET ALA SER LEU LEU SEQRES 32 A 551 LEU ALA GLY ILE CYS ILE LEU VAL ASN GLY ILE ILE PRO SEQRES 33 A 551 LYS SER HIS THR ILE ILE ARG THR SER LEU ALA VAL LEU SEQRES 34 A 551 GLY LYS GLY CYS LEU ALA SER SER PHE ASN CYS ILE PHE SEQRES 35 A 551 LEU TYR THR GLY GLU LEU TYR PRO THR VAL ILE ARG GLN SEQRES 36 A 551 THR GLY LEU GLY MET GLY SER THR MET ALA ARG VAL GLY SEQRES 37 A 551 SER ILE VAL SER PRO LEU VAL SER MET THR ALA GLU PHE SEQRES 38 A 551 TYR PRO SER MET PRO LEU PHE ILE PHE GLY ALA VAL PRO SEQRES 39 A 551 VAL VAL ALA SER ALA VAL THR ALA LEU LEU PRO GLU THR SEQRES 40 A 551 LEU GLY GLN PRO LEU PRO ASP THR VAL GLN ASP LEU LYS SEQRES 41 A 551 SER ARG SER ARG GLY LYS GLN ASN GLN GLN GLN GLN GLU SEQRES 42 A 551 GLN GLN LYS GLN MET MET PRO LEU GLN ALA SER THR GLN SEQRES 43 A 551 GLU LYS ASN GLY LEU HET RTO A 601 19 HETNAM RTO 4-(DIPROPYLSULFAMOYL)BENZOIC ACID FORMUL 2 RTO C13 H19 N O4 S FORMUL 3 HOH *22(H2 O) HELIX 1 AA1 ALA A 2 VAL A 10 1 9 HELIX 2 AA2 GLY A 14 ALA A 26 1 13 HELIX 3 AA3 PRO A 27 THR A 36 1 10 HELIX 4 AA4 LEU A 37 ALA A 42 1 6 HELIX 5 AA5 GLY A 62 TRP A 66 5 5 HELIX 6 AA6 THR A 119 ASN A 125 1 7 HELIX 7 AA7 VAL A 127 HIS A 130 5 4 HELIX 8 AA8 ARG A 131 GLY A 160 1 30 HELIX 9 AA9 GLY A 160 TYR A 181 1 22 HELIX 10 AB1 ASN A 184 TRP A 213 1 30 HELIX 11 AB2 MET A 214 HIS A 217 5 4 HELIX 12 AB3 THR A 218 VAL A 244 1 27 HELIX 13 AB4 HIS A 246 VAL A 254 1 9 HELIX 14 AB5 VAL A 256 SER A 265 1 10 HELIX 15 AB6 TRP A 266 PHE A 268 5 3 HELIX 16 AB7 SER A 271 SER A 278 1 8 HELIX 17 AB8 ARG A 280 GLY A 296 1 17 HELIX 18 AB9 LYS A 297 LEU A 304 1 8 HELIX 19 AC1 SER A 305 GLN A 314 1 10 HELIX 20 AC2 MET A 327 CYS A 332 1 6 HELIX 21 AC3 CYS A 332 GLY A 355 1 24 HELIX 22 AC4 SER A 366 VAL A 377 1 12 HELIX 23 AC5 VAL A 377 MET A 392 1 16 HELIX 24 AC6 GLY A 393 ILE A 415 1 23 HELIX 25 AC7 HIS A 419 TYR A 449 1 31 HELIX 26 AC8 ILE A 453 MET A 477 1 25 HELIX 27 AC9 THR A 478 PHE A 481 5 4 HELIX 28 AD1 SER A 484 ALA A 502 1 19 HELIX 29 AD2 THR A 515 ARG 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 VAL 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 SSBOND 2 CYS A 78 CYS A 128 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