HEADER TRANSPORT PROTEIN 18-AUG-24 9J72 TITLE CRYO-EM STRUCTURE OF URAT1 IN COMPLEX WITH URIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 22 MEMBER 12; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: URAT1,URATE ANION EXCHANGER 1,URATE:ANION ANTIPORTER COMPND 5 SLC22A12; 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: SLC22A12, URAT1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS PROTEIN STRUCTURE, STRUCTURAL PROTEIN, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.ZHAO,Z.YU REVDAT 1 13-AUG-25 9J72 0 JRNL AUTH Z.YU,T.HU,J.SU,J.ZHAO,R.LI,Q.MA,Q.CHEN,Q.BAI,Y.DONG,P.YUAN, JRNL AUTH 2 N.LI,X.C.ZHANG,Y.ZHAO JRNL TITL MOLECULAR MECHANISM OF DRUG INHIBITION OF URAT1. JRNL REF NAT COMMUN V. 16 6551 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40670375 JRNL DOI 10.1038/S41467-025-61226-X REMARK 2 REMARK 2 RESOLUTION. 3.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 3.470 REMARK 3 NUMBER OF PARTICLES : 165544 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9J72 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 21-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300050493. 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 : STRUCTURE OF URAT1 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : OTHER 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 THR A 58 REMARK 465 SER A 59 REMARK 465 GLN A 60 REMARK 465 ALA A 61 REMARK 465 SER A 62 REMARK 465 ILE A 63 REMARK 465 PRO A 64 REMARK 465 GLY A 65 REMARK 465 ASP A 66 REMARK 465 PHE A 67 REMARK 465 GLU A 100 REMARK 465 SER A 101 REMARK 465 ASN A 102 REMARK 465 THR A 103 REMARK 465 THR A 104 REMARK 465 ALA A 105 REMARK 465 THR A 106 REMARK 465 ASN A 107 REMARK 465 TRP A 108 REMARK 465 SER A 109 REMARK 465 ASP A 110 REMARK 465 GLN A 325 REMARK 465 GLU A 326 REMARK 465 GLU A 327 REMARK 465 PRO A 328 REMARK 465 ASN A 329 REMARK 465 GLY A 330 REMARK 465 ASN A 331 REMARK 465 GLN A 332 REMARK 465 ALA A 333 REMARK 465 GLY A 334 REMARK 465 ALA A 335 REMARK 465 ARG A 336 REMARK 465 LEU A 337 REMARK 465 GLY A 338 REMARK 465 THR A 339 REMARK 465 LEU A 340 REMARK 465 LEU A 341 REMARK 465 HIS A 342 REMARK 465 THR A 343 REMARK 465 PRO A 344 REMARK 465 GLY A 345 REMARK 465 LEU A 346 REMARK 465 GLU A 517 REMARK 465 THR A 518 REMARK 465 LYS A 519 REMARK 465 ASN A 520 REMARK 465 LEU A 521 REMARK 465 PRO A 522 REMARK 465 LEU A 523 REMARK 465 PRO A 524 REMARK 465 ASP A 525 REMARK 465 THR A 526 REMARK 465 ILE A 527 REMARK 465 GLN A 528 REMARK 465 ASP A 529 REMARK 465 ILE A 530 REMARK 465 GLN A 531 REMARK 465 LYS A 532 REMARK 465 GLN A 533 REMARK 465 SER A 534 REMARK 465 VAL A 535 REMARK 465 LYS A 536 REMARK 465 LYS A 537 REMARK 465 VAL A 538 REMARK 465 THR A 539 REMARK 465 HIS A 540 REMARK 465 ASP A 541 REMARK 465 ILE A 542 REMARK 465 ALA A 543 REMARK 465 GLY A 544 REMARK 465 GLY A 545 REMARK 465 SER A 546 REMARK 465 VAL A 547 REMARK 465 LEU A 548 REMARK 465 LYS A 549 REMARK 465 SER A 550 REMARK 465 ALA A 551 REMARK 465 ARG A 552 REMARK 465 LEU A 553 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 PHE A 241 CG CD1 CD2 CE1 CE2 CZ 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 ARG A 13 -116.95 58.07 REMARK 500 GLU A 38 44.58 -82.34 REMARK 500 ASN A 56 -172.21 59.72 REMARK 500 ASP A 82 54.06 -91.76 REMARK 500 CYS A 139 -119.73 63.29 REMARK 500 HIS A 165 50.72 -92.57 REMARK 500 ARG A 308 54.57 -93.22 REMARK 500 VAL A 317 -50.66 69.24 REMARK 500 SER A 457 -0.76 70.04 REMARK 500 PRO A 461 -5.49 -53.93 REMARK 500 THR A 462 60.41 61.34 REMARK 500 VAL A 463 -60.12 -102.61 REMARK 500 LEU A 482 31.49 -92.41 REMARK 500 PRO A 484 -15.70 -47.98 REMARK 500 TYR A 492 61.18 61.57 REMARK 500 LEU A 514 35.41 -97.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 477 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61191 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF URAT1 IN COMPLEX WITH URIC ACID DBREF 9J72 A 1 553 UNP Q3ZAV1 S22AC_RAT 1 553 SEQADV 9J72 SER A 35 UNP Q3ZAV1 ASN 35 CONFLICT SEQADV 9J72 PHE A 365 UNP Q3ZAV1 TYR 365 CONFLICT SEQRES 1 A 553 MET ALA PHE PRO GLU LEU LEU ASP ARG VAL GLY GLY ARG SEQRES 2 A 553 GLY ARG PHE GLN LEU LEU GLN ALA VAL ALA LEU VAL THR SEQRES 3 A 553 PRO ILE LEU TRP VAL THR THR GLN SER MET LEU GLU ASN SEQRES 4 A 553 PHE SER ALA ALA VAL PRO HIS HIS ARG CYS TRP VAL PRO SEQRES 5 A 553 LEU LEU ASP ASN SER THR SER GLN ALA SER ILE PRO GLY SEQRES 6 A 553 ASP PHE GLY ARG ASP VAL LEU LEU ALA VAL SER ILE PRO SEQRES 7 A 553 PRO GLY PRO ASP GLN ARG PRO HIS GLN CYS LEU ARG PHE SEQRES 8 A 553 ARG GLN PRO GLN TRP GLN LEU ILE GLU SER ASN THR THR SEQRES 9 A 553 ALA THR ASN TRP SER ASP ALA ASP THR GLU PRO CYS GLU SEQRES 10 A 553 ASP GLY TRP VAL TYR ASP HIS SER THR PHE ARG SER THR SEQRES 11 A 553 ILE VAL THR THR TRP ASP LEU VAL CYS ASP SER GLN ALA SEQRES 12 A 553 LEU ARG PRO MET ALA GLN SER ILE PHE LEU ALA GLY ILE SEQRES 13 A 553 LEU VAL GLY ALA ALA VAL CYS GLY HIS ALA SER ASP ARG SEQRES 14 A 553 PHE GLY ARG ARG ARG VAL LEU THR TRP SER TYR LEU LEU SEQRES 15 A 553 VAL SER VAL SER GLY THR ILE ALA ALA LEU MET PRO THR SEQRES 16 A 553 PHE PRO LEU TYR CYS LEU PHE ARG PHE LEU VAL ALA SER SEQRES 17 A 553 ALA VAL ALA GLY VAL MET MET ASN THR ALA SER LEU LEU SEQRES 18 A 553 MET GLU TRP THR SER ALA GLN ALA GLY PRO LEU MET MET SEQRES 19 A 553 THR LEU ASN ALA LEU GLY PHE SER PHE GLY GLN VAL LEU SEQRES 20 A 553 THR GLY SER VAL ALA TYR GLY VAL ARG SER TRP ARG MET SEQRES 21 A 553 LEU GLN LEU ALA VAL SER ALA PRO PHE PHE LEU PHE PHE SEQRES 22 A 553 VAL TYR SER TRP TRP LEU PRO GLU SER ALA ARG TRP LEU SEQRES 23 A 553 ILE THR VAL GLY ARG LEU ASP GLN SER LEU ARG GLU LEU SEQRES 24 A 553 GLN ARG VAL ALA ALA VAL ASN ARG ARG LYS ALA GLU ALA SEQRES 25 A 553 ASP THR LEU THR VAL GLU VAL LEU ARG SER ALA MET GLN SEQRES 26 A 553 GLU GLU PRO ASN GLY ASN GLN ALA GLY ALA ARG LEU GLY SEQRES 27 A 553 THR LEU LEU HIS THR PRO GLY LEU ARG LEU ARG THR PHE SEQRES 28 A 553 ILE SER MET LEU CYS TRP PHE ALA PHE GLY PHE THR PHE SEQRES 29 A 553 PHE GLY LEU ALA LEU ASP LEU GLN ALA LEU GLY SER ASN SEQRES 30 A 553 ILE PHE LEU LEU GLN ALA LEU ILE GLY ILE VAL ASP LEU SEQRES 31 A 553 PRO VAL LYS MET GLY SER LEU LEU LEU LEU SER ARG LEU SEQRES 32 A 553 GLY ARG ARG LEU CYS GLN ALA SER SER LEU VAL LEU PRO SEQRES 33 A 553 GLY LEU CYS ILE LEU ALA ASN ILE LEU VAL PRO ARG GLU SEQRES 34 A 553 MET GLY ILE LEU ARG SER SER LEU ALA VAL LEU GLY LEU SEQRES 35 A 553 GLY SER LEU GLY ALA ALA PHE THR CYS VAL THR ILE PHE SEQRES 36 A 553 SER SER GLU LEU PHE PRO THR VAL ILE ARG MET THR ALA SEQRES 37 A 553 VAL GLY LEU GLY GLN VAL ALA ALA ARG GLY GLY ALA MET SEQRES 38 A 553 LEU GLY PRO LEU VAL ARG LEU LEU GLY VAL TYR GLY SER SEQRES 39 A 553 TRP LEU PRO LEU LEU VAL TYR GLY VAL VAL PRO VAL LEU SEQRES 40 A 553 SER GLY LEU ALA ALA LEU LEU LEU PRO GLU THR LYS ASN SEQRES 41 A 553 LEU PRO LEU PRO ASP THR ILE GLN ASP ILE GLN LYS GLN SEQRES 42 A 553 SER VAL LYS LYS VAL THR HIS ASP ILE ALA GLY GLY SER SEQRES 43 A 553 VAL LEU LYS SER ALA ARG LEU HET URC A 601 12 HETNAM URC URIC ACID HETSYN URC 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE FORMUL 2 URC C5 H4 N4 O3 HELIX 1 AA1 ALA A 2 GLY A 11 1 10 HELIX 2 AA2 ARG A 15 LEU A 37 1 23 HELIX 3 AA3 ARG A 69 ILE A 77 1 9 HELIX 4 AA4 THR A 130 ASP A 136 1 7 HELIX 5 AA5 LEU A 144 HIS A 165 1 22 HELIX 6 AA6 ARG A 172 ALA A 191 1 20 HELIX 7 AA7 THR A 195 THR A 225 1 31 HELIX 8 AA8 GLN A 228 VAL A 255 1 28 HELIX 9 AA9 TRP A 258 SER A 276 1 19 HELIX 10 AB1 SER A 282 GLY A 290 1 9 HELIX 11 AB2 ARG A 291 ARG A 307 1 17 HELIX 12 AB3 GLU A 311 LEU A 315 5 5 HELIX 13 AB4 VAL A 317 MET A 324 1 8 HELIX 14 AB5 LEU A 348 ALA A 368 1 21 HELIX 15 AB6 ASP A 389 ARG A 402 1 14 HELIX 16 AB7 GLY A 404 VAL A 426 1 23 HELIX 17 AB8 MET A 430 ALA A 447 1 18 HELIX 18 AB9 ALA A 447 PHE A 455 1 9 HELIX 19 AC1 ARG A 465 ALA A 480 1 16 HELIX 20 AC2 MET A 481 GLY A 483 5 3 HELIX 21 AC3 LEU A 485 VAL A 491 5 7 HELIX 22 AC4 SER A 494 LEU A 513 1 20 SHEET 1 AA1 2 HIS A 47 CYS A 49 0 SHEET 2 AA1 2 TRP A 120 TYR A 122 -1 O VAL A 121 N ARG A 48 SHEET 1 AA2 2 ARG A 90 PHE A 91 0 SHEET 2 AA2 2 THR A 113 GLU A 114 -1 O GLU A 114 N ARG A 90 SSBOND 1 CYS A 49 CYS A 116 1555 1555 2.03 SSBOND 2 CYS A 88 CYS A 139 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 3625 PRO A 516 HETATM 3626 N1 URC A 601 115.431 107.151 112.635 1.00 91.10 N HETATM 3627 C2 URC A 601 114.825 108.196 113.323 1.00 91.10 C HETATM 3628 C6 URC A 601 115.991 107.288 111.362 1.00 91.10 C HETATM 3629 N3 URC A 601 114.741 109.488 112.733 1.00 91.10 N HETATM 3630 O11 URC A 601 114.361 107.979 114.428 1.00 91.10 O HETATM 3631 C4 URC A 601 115.279 109.687 111.476 1.00 91.10 C HETATM 3632 C5 URC A 601 115.866 108.638 110.838 1.00 91.10 C HETATM 3633 N9 URC A 601 115.326 110.877 110.678 1.00 91.10 N HETATM 3634 O13 URC A 601 116.494 106.295 110.870 1.00 91.10 O HETATM 3635 N7 URC A 601 116.321 109.103 109.599 1.00 91.10 N HETATM 3636 C8 URC A 601 116.005 110.451 109.478 1.00 91.10 C HETATM 3637 O24 URC A 601 116.271 111.137 108.517 1.00 91.10 O CONECT 376 746 CONECT 599 938 CONECT 746 376 CONECT 938 599 CONECT 3626 3627 3628 CONECT 3627 3626 3629 3630 CONECT 3628 3626 3632 3634 CONECT 3629 3627 3631 CONECT 3630 3627 CONECT 3631 3629 3632 3633 CONECT 3632 3628 3631 3635 CONECT 3633 3631 3636 CONECT 3634 3628 CONECT 3635 3632 3636 CONECT 3636 3633 3635 3637 CONECT 3637 3636 MASTER 240 0 1 22 4 0 0 6 3636 1 16 43 END