HEADER TRANSPORT PROTEIN 08-SEP-24 9DK9 TITLE STRUCTURE OF URAT1 WITH NO EXTERNAL LIGAND ADDED COMPND MOL_ID: 1; COMPND 2 MOLECULE: URAT1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS MEMBRANE PROTEIN, MEMBRANE TRANSPORTER, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.SUO,J.G.FEDOR,S.-Y.LEE REVDAT 1 18-JUN-25 9DK9 0 JRNL AUTH Y.SUO,J.G.FEDOR,H.ZHANG,K.TSOLOVA,X.SHI,K.SHARMA,S.KUMARI, JRNL AUTH 2 M.BORGNIA,P.ZHAN,W.IM,S.Y.LEE JRNL TITL MOLECULAR BASIS OF THE URATE TRANSPORTER URAT1 INHIBITION BY JRNL TITL 2 GOUT DRUGS. JRNL REF NAT COMMUN V. 16 5178 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40467597 JRNL DOI 10.1038/S41467-025-60480-3 REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, LATITUDE, CRYOSPARC, COOT, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8ET6 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 200.000 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) : 2.680 REMARK 3 NUMBER OF PARTICLES : 527705 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 9DK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1000288059. 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 : URAT1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 10.00 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 : 18880 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 : 2.70 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 : 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLN A 519 REMARK 465 SER A 520 REMARK 465 LEU A 521 REMARK 465 PRO A 522 REMARK 465 ALA 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 VAL A 530 REMARK 465 GLN A 531 REMARK 465 ASN A 532 REMARK 465 GLN A 533 REMARK 465 ALA A 534 REMARK 465 VAL A 535 REMARK 465 LYS A 536 REMARK 465 LYS A 537 REMARK 465 ALA A 538 REMARK 465 THR A 539 REMARK 465 HIS A 540 REMARK 465 GLY A 541 REMARK 465 THR A 542 REMARK 465 GLY A 543 REMARK 465 ASN A 544 REMARK 465 PRO 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 THR A 551 REMARK 465 GLN A 552 REMARK 465 PHE A 553 REMARK 465 SER A 554 REMARK 465 ASN A 555 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 LEU A 31 CG CD1 CD2 REMARK 470 SER A 57 OG REMARK 470 THR A 58 OG1 CG2 REMARK 470 GLN A 60 CG CD OE1 NE2 REMARK 470 SER A 62 OG REMARK 470 VAL A 63 CG1 CG2 REMARK 470 PRO A 64 CG CD REMARK 470 LEU A 67 CG CD1 CD2 REMARK 470 LEU A 98 CG CD1 CD2 REMARK 470 LEU A 99 CG CD1 CD2 REMARK 470 ASP A 100 CG OD1 OD2 REMARK 470 PRO A 101 CG CD REMARK 470 ASN A 102 CG OD1 ND2 REMARK 470 THR A 104 OG1 CG2 REMARK 470 THR A 106 OG1 CG2 REMARK 470 ASN A 107 CG OD1 ND2 REMARK 470 TRP A 108 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 108 CZ3 CH2 REMARK 470 SER A 109 OG REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 THR A 113 OG1 CG2 REMARK 470 LEU A 321 CG CD1 CD2 REMARK 470 LEU A 328 CG CD1 CD2 REMARK 470 VAL A 330 CG1 CG2 REMARK 470 SER A 336 OG REMARK 470 LEU A 464 CG CD1 CD2 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 139 -110.66 57.74 REMARK 500 ASP A 370 58.00 -96.63 REMARK 500 PRO A 461 171.90 -59.74 REMARK 500 ALA A 512 4.04 -69.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-46948 RELATED DB: EMDB REMARK 900 STRUCTURE OF URAT1 WITH NO EXTERNAL LIGAND ADDED DBREF 9DK9 A 1 555 PDB 9DK9 9DK9 1 555 SEQRES 1 A 555 MET ALA PHE SER GLU LEU LEU ASP GLN VAL GLY GLY LEU SEQRES 2 A 555 GLY ARG PHE GLN VAL LEU GLN THR VAL ALA LEU VAL VAL SEQRES 3 A 555 PRO ILE MET TRP LEU CYS THR GLN SER MET LEU GLU ASN SEQRES 4 A 555 PHE SER ALA ALA VAL PRO SER HIS ARG CYS TRP VAL PRO SEQRES 5 A 555 LEU LEU ASP ASN SER THR ALA GLN ALA SER VAL PRO GLY SEQRES 6 A 555 ALA LEU GLY PRO GLU ALA LEU LEU ALA VAL SER ILE PRO SEQRES 7 A 555 PRO GLY PRO ASN GLN GLY PRO HIS GLN CYS ARG ARG PHE SEQRES 8 A 555 ARG GLN PRO GLN TRP GLN LEU LEU ASP PRO ASN ALA THR SEQRES 9 A 555 ALA THR ASN TRP SER GLU ALA ALA THR GLU PRO CYS VAL SEQRES 10 A 555 ASP GLY TRP VAL TYR ASP ARG SER THR PHE THR SER THR SEQRES 11 A 555 ILE VAL ALA LYS TRP ASP LEU VAL CYS ASP SER GLN ALA SEQRES 12 A 555 LEU LYS PRO MET ALA GLN SER ILE TYR LEU ALA GLY ILE SEQRES 13 A 555 LEU VAL GLY ALA ALA VAL CYS GLY PRO ALA SER ASP ARG SEQRES 14 A 555 PHE GLY ARG ARG LEU VAL LEU THR TRP SER TYR LEU GLN SEQRES 15 A 555 MET ALA VAL SER GLY THR ALA ALA ALA PHE ALA PRO THR SEQRES 16 A 555 PHE PRO VAL TYR CYS LEU PHE ARG PHE LEU VAL ALA PHE SEQRES 17 A 555 ALA VAL ALA GLY VAL MET MET ASN THR GLY THR LEU VAL SEQRES 18 A 555 MET GLU TRP THR SER ALA GLN ALA ARG PRO LEU VAL MET SEQRES 19 A 555 THR LEU ASN SER LEU GLY PHE SER PHE GLY HIS VAL LEU SEQRES 20 A 555 MET ALA ALA VAL ALA TYR GLY VAL ARG ASP TRP ALA LEU SEQRES 21 A 555 LEU GLN LEU VAL VAL SER VAL PRO PHE PHE LEU CYS PHE SEQRES 22 A 555 VAL TYR SER CYS TRP LEU ALA GLU SER ALA ARG TRP LEU SEQRES 23 A 555 LEU ILE THR GLY ARG LEU ASP ARG GLY LEU ARG GLU LEU SEQRES 24 A 555 GLN ARG VAL ALA ALA ILE ASN GLY LYS ARG ALA VAL GLY SEQRES 25 A 555 ASP THR LEU THR PRO GLN VAL LEU LEU SER ALA MET GLN SEQRES 26 A 555 GLU GLU LEU SER VAL GLY GLN ALA PRO ALA SER LEU GLY SEQRES 27 A 555 THR LEU LEU ARG THR PRO GLY LEU ARG LEU ARG THR CYS SEQRES 28 A 555 ILE SER THR LEU CYS TRP PHE ALA PHE GLY PHE THR PHE SEQRES 29 A 555 PHE GLY LEU ALA LEU ASP LEU GLN ALA LEU GLY SER ASN SEQRES 30 A 555 ILE PHE LEU LEU GLN VAL LEU ILE GLY VAL VAL ASP ILE SEQRES 31 A 555 PRO ALA LYS ILE GLY THR LEU LEU LEU LEU SER ARG LEU SEQRES 32 A 555 GLY ARG ARG PRO THR GLN ALA ALA SER LEU VAL LEU ALA SEQRES 33 A 555 GLY LEU CYS ILE LEU ALA ASN THR LEU VAL PRO HIS GLU SEQRES 34 A 555 MET GLY ALA LEU ARG SER ALA LEU ALA VAL LEU GLY LEU SEQRES 35 A 555 GLY GLY LEU GLY ALA ALA PHE THR CYS ILE THR ILE TYR SEQRES 36 A 555 SER GLY GLU LEU PHE PRO THR VAL LEU ARG MET THR ALA SEQRES 37 A 555 VAL GLY LEU GLY GLN MET ALA ALA ARG GLY GLY ALA ILE SEQRES 38 A 555 LEU GLY PRO LEU VAL ARG LEU LEU GLY VAL HIS GLY PRO SEQRES 39 A 555 TRP LEU PRO LEU LEU VAL TYR GLY THR VAL PRO VAL LEU SEQRES 40 A 555 SER GLY LEU ALA ALA LEU LEU LEU PRO GLU THR GLN SER SEQRES 41 A 555 LEU PRO ALA PRO ASP THR ILE GLN ASP VAL GLN ASN GLN SEQRES 42 A 555 ALA VAL LYS LYS ALA THR HIS GLY THR GLY ASN PRO SER SEQRES 43 A 555 VAL LEU LYS SER THR GLN PHE SER ASN HELIX 1 AA1 PHE A 3 GLY A 11 1 9 HELIX 2 AA2 GLY A 14 LEU A 37 1 24 HELIX 3 AA3 LEU A 37 ALA A 42 1 6 HELIX 4 AA4 VAL A 51 ASN A 56 1 6 HELIX 5 AA5 ASN A 56 VAL A 63 1 8 HELIX 6 AA6 GLY A 68 VAL A 75 1 8 HELIX 7 AA7 GLN A 95 ASP A 100 5 6 HELIX 8 AA8 SER A 109 ALA A 111 5 3 HELIX 9 AA9 THR A 130 ASP A 136 1 7 HELIX 10 AB1 VAL A 138 GLN A 142 5 5 HELIX 11 AB2 ALA A 143 ASP A 168 1 26 HELIX 12 AB3 ARG A 172 ALA A 191 1 20 HELIX 13 AB4 THR A 195 THR A 225 1 31 HELIX 14 AB5 SER A 226 GLN A 228 5 3 HELIX 15 AB6 ALA A 229 TYR A 253 1 25 HELIX 16 AB7 ALA A 259 VAL A 267 1 9 HELIX 17 AB8 VAL A 267 SER A 276 1 10 HELIX 18 AB9 SER A 282 THR A 289 1 8 HELIX 19 AC1 LEU A 292 GLY A 307 1 16 HELIX 20 AC2 LYS A 308 LEU A 315 1 8 HELIX 21 AC3 THR A 316 MET A 324 1 9 HELIX 22 AC4 MET A 324 VAL A 330 1 7 HELIX 23 AC5 SER A 336 LEU A 340 5 5 HELIX 24 AC6 THR A 343 GLY A 345 5 3 HELIX 25 AC7 LEU A 346 ASP A 370 1 25 HELIX 26 AC8 ASP A 370 GLY A 375 1 6 HELIX 27 AC9 ASN A 377 LEU A 403 1 27 HELIX 28 AD1 GLY A 404 VAL A 426 1 23 HELIX 29 AD2 MET A 430 PHE A 460 1 31 HELIX 30 AD3 LEU A 464 VAL A 486 1 23 HELIX 31 AD4 ARG A 487 HIS A 492 5 6 HELIX 32 AD5 PRO A 494 ALA A 512 1 19 SHEET 1 AA1 2 ARG A 48 CYS A 49 0 SHEET 2 AA1 2 TRP A 120 VAL A 121 -1 O VAL A 121 N ARG A 48 SHEET 1 AA2 2 PRO A 79 GLY A 80 0 SHEET 2 AA2 2 GLY A 84 PRO A 85 -1 O GLY A 84 N GLY A 80 SHEET 1 AA3 2 ARG A 90 PHE A 91 0 SHEET 2 AA3 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 7661 THR A 518 CONECT 720 1551 CONECT 1208 1915 CONECT 1551 720 CONECT 1915 1208 MASTER 198 0 0 32 6 0 0 6 3816 1 4 43 END