HEADER TRANSPORT PROTEIN 16-JUL-24 9IRW TITLE STRUCTURE OF HUMAN URAT1 BOUND WITH URATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 22 MEMBER 12; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ORGANIC ANION TRANSPORTER 4-LIKE PROTEIN,RENAL-SPECIFIC COMPND 5 TRANSPORTER,RST,URATE ANION EXCHANGER 1,URAT1,URATE:ANION ANTIPORTER COMPND 6 SLC22A12; COMPND 7 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: SLC22A12, OATL4, URAT1, UNQ6453/PRO34004; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SLC22, URATE, GOUT, BENZBROMARONE, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR W.J.GUO,M.WEI,L.CHEN REVDAT 1 15-JAN-25 9IRW 0 JRNL AUTH W.J.GUO,M.WEI,L.CHEN JRNL TITL STRUCTURE OF HUMAN URAT1 BOUND WITH URATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.260 REMARK 3 NUMBER OF PARTICLES : 310852 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9IRW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1300049476. 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 URATE TRANSPORTER 1 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 : 4381 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) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 7000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM 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 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 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLU A -1 REMARK 465 PHE A 0 REMARK 465 THR A 58 REMARK 465 ALA A 59 REMARK 465 GLN A 60 REMARK 465 ALA A 61 REMARK 465 SER A 62 REMARK 465 ILE A 63 REMARK 465 LEU A 64 REMARK 465 GLY A 65 REMARK 465 SER A 66 REMARK 465 LEU A 67 REMARK 465 GLY A 80 REMARK 465 PRO A 81 REMARK 465 ASN A 82 REMARK 465 GLN A 83 REMARK 465 ARG A 84 REMARK 465 PRO A 101 REMARK 465 ASN A 102 REMARK 465 ALA A 103 REMARK 465 THR A 104 REMARK 465 ALA A 105 REMARK 465 THR A 106 REMARK 465 SER A 107 REMARK 465 TRP A 108 REMARK 465 SER A 109 REMARK 465 GLU A 110 REMARK 465 ALA A 111 REMARK 465 GLU A 326 REMARK 465 GLU A 327 REMARK 465 LEU A 328 REMARK 465 SER A 329 REMARK 465 VAL A 330 REMARK 465 GLY A 331 REMARK 465 GLN A 332 REMARK 465 ALA A 333 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 LEU A 543 REMARK 465 GLY A 544 REMARK 465 ASN 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 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 GLN A 97 52.55 -91.18 REMARK 500 PRO A 115 171.96 -59.82 REMARK 500 CYS A 116 48.35 -80.72 REMARK 500 ARG A 124 34.71 -98.57 REMARK 500 CYS A 139 -7.75 67.91 REMARK 500 ASP A 140 -37.54 -131.99 REMARK 500 MET A 324 62.16 60.31 REMARK 500 LEU A 337 -5.23 67.64 REMARK 500 PRO A 427 6.35 -69.29 REMARK 500 MET A 430 23.67 46.02 REMARK 500 ALA A 432 21.87 -140.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60823 RELATED DB: EMDB REMARK 900 STRUCTURE OF HUMAN URAT1 BOUND WITH URATE DBREF 9IRW A 1 553 UNP Q96S37 S22AC_HUMAN 1 553 SEQADV 9IRW GLY A -3 UNP Q96S37 EXPRESSION TAG SEQADV 9IRW PRO A -2 UNP Q96S37 EXPRESSION TAG SEQADV 9IRW GLU A -1 UNP Q96S37 EXPRESSION TAG SEQADV 9IRW PHE A 0 UNP Q96S37 EXPRESSION TAG SEQADV 9IRW VAL A 162 UNP Q96S37 ALA 162 CONFLICT SEQADV 9IRW SER A 186 UNP Q96S37 MET 186 CONFLICT SEQADV 9IRW THR A 195 UNP Q96S37 ALA 195 CONFLICT SEQADV 9IRW SER A 226 UNP Q96S37 ALA 226 CONFLICT SEQADV 9IRW ALA A 264 UNP Q96S37 VAL 264 CONFLICT SEQADV 9IRW ARG A 294 UNP Q96S37 TRP 294 CONFLICT SEQADV 9IRW ARG A 300 UNP Q96S37 TRP 300 CONFLICT SEQADV 9IRW ARG A 309 UNP Q96S37 GLY 309 CONFLICT SEQADV 9IRW VAL A 330 UNP Q96S37 MET 330 CONFLICT SEQADV 9IRW ALA A 333 UNP Q96S37 PRO 333 CONFLICT SEQADV 9IRW THR A 343 UNP Q96S37 MET 343 CONFLICT SEQADV 9IRW LEU A 348 UNP Q96S37 PHE 348 CONFLICT SEQADV 9IRW VAL A 383 UNP Q96S37 MET 383 CONFLICT SEQADV 9IRW LEU A 384 UNP Q96S37 PHE 384 CONFLICT SEQADV 9IRW ARG A 402 UNP Q96S37 HIS 402 CONFLICT SEQRES 1 A 557 GLY PRO GLU PHE MET ALA PHE SER GLU LEU LEU ASP LEU SEQRES 2 A 557 VAL GLY GLY LEU GLY ARG PHE GLN VAL LEU GLN THR MET SEQRES 3 A 557 ALA LEU MET VAL SER ILE MET TRP LEU CYS THR GLN SER SEQRES 4 A 557 MET LEU GLU ASN PHE SER ALA ALA VAL PRO SER HIS ARG SEQRES 5 A 557 CYS TRP ALA PRO LEU LEU ASP ASN SER THR ALA GLN ALA SEQRES 6 A 557 SER ILE LEU GLY SER LEU SER PRO GLU ALA LEU LEU ALA SEQRES 7 A 557 ILE SER ILE PRO PRO GLY PRO ASN GLN ARG PRO HIS GLN SEQRES 8 A 557 CYS ARG ARG PHE ARG GLN PRO GLN TRP GLN LEU LEU ASP SEQRES 9 A 557 PRO ASN ALA THR ALA THR SER TRP SER GLU ALA ASP THR SEQRES 10 A 557 GLU PRO CYS VAL ASP GLY TRP VAL TYR ASP ARG SER ILE SEQRES 11 A 557 PHE THR SER THR ILE VAL ALA LYS TRP ASN LEU VAL CYS SEQRES 12 A 557 ASP SER HIS ALA LEU LYS PRO MET ALA GLN SER ILE TYR SEQRES 13 A 557 LEU ALA GLY ILE LEU VAL GLY ALA ALA VAL CYS GLY PRO SEQRES 14 A 557 ALA SER ASP ARG PHE GLY ARG ARG LEU VAL LEU THR TRP SEQRES 15 A 557 SER TYR LEU GLN MET ALA VAL SER GLY THR ALA ALA ALA SEQRES 16 A 557 PHE ALA PRO THR PHE PRO VAL TYR CYS LEU PHE ARG PHE SEQRES 17 A 557 LEU LEU ALA PHE ALA VAL ALA GLY VAL MET MET ASN THR SEQRES 18 A 557 GLY THR LEU LEU MET GLU TRP THR SER ALA ARG ALA ARG SEQRES 19 A 557 PRO LEU VAL MET THR LEU ASN SER LEU GLY PHE SER PHE SEQRES 20 A 557 GLY HIS GLY LEU THR ALA ALA VAL ALA TYR GLY VAL ARG SEQRES 21 A 557 ASP TRP THR LEU LEU GLN LEU ALA VAL SER VAL PRO PHE SEQRES 22 A 557 PHE LEU CYS PHE LEU TYR SER TRP TRP LEU ALA GLU SER SEQRES 23 A 557 ALA ARG TRP LEU LEU THR THR GLY ARG LEU ASP ARG GLY SEQRES 24 A 557 LEU GLN GLU LEU ARG ARG VAL ALA ALA ILE ASN GLY LYS SEQRES 25 A 557 ARG ALA VAL GLN ASP THR LEU THR PRO GLU VAL LEU LEU SEQRES 26 A 557 SER ALA MET ARG GLU GLU LEU SER VAL GLY GLN ALA PRO SEQRES 27 A 557 ALA SER LEU GLY THR LEU LEU ARG THR PRO GLY LEU ARG SEQRES 28 A 557 LEU ARG THR CYS ILE SER THR LEU CYS TRP PHE ALA PHE SEQRES 29 A 557 GLY PHE THR PHE PHE GLY LEU ALA LEU ASP LEU GLN ALA SEQRES 30 A 557 LEU GLY SER ASN ILE PHE LEU LEU GLN VAL LEU ILE GLY SEQRES 31 A 557 VAL VAL ASP ILE PRO ALA LYS MET GLY ALA LEU LEU LEU SEQRES 32 A 557 LEU SER ARG LEU GLY ARG ARG PRO THR LEU ALA ALA SER SEQRES 33 A 557 LEU LEU LEU ALA GLY LEU CYS ILE LEU ALA ASN THR LEU SEQRES 34 A 557 VAL PRO HIS GLU MET GLY ALA LEU ARG SER ALA LEU ALA SEQRES 35 A 557 VAL LEU GLY LEU GLY GLY VAL GLY ALA ALA PHE THR CYS SEQRES 36 A 557 ILE THR ILE TYR SER SER GLU LEU PHE PRO THR VAL LEU SEQRES 37 A 557 ARG MET THR ALA VAL GLY LEU GLY GLN MET ALA ALA ARG SEQRES 38 A 557 GLY GLY ALA ILE LEU GLY PRO LEU VAL ARG LEU LEU GLY SEQRES 39 A 557 VAL HIS GLY PRO TRP LEU PRO LEU LEU VAL TYR GLY THR SEQRES 40 A 557 VAL PRO VAL LEU SER GLY LEU ALA ALA LEU LEU LEU PRO SEQRES 41 A 557 GLU THR GLN SER LEU PRO LEU PRO ASP THR ILE GLN ASP SEQRES 42 A 557 VAL GLN ASN GLN ALA VAL LYS LYS ALA THR HIS GLY THR SEQRES 43 A 557 LEU GLY ASN SER VAL LEU LYS SER THR GLN PHE HET URC A 701 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 PHE A 3 VAL A 10 1 8 HELIX 2 AA2 GLY A 14 LEU A 37 1 24 HELIX 3 AA3 GLU A 38 PHE A 40 5 3 HELIX 4 AA4 ALA A 51 ASN A 56 1 6 HELIX 5 AA5 PRO A 69 ALA A 74 1 6 HELIX 6 AA6 THR A 130 ASN A 136 1 7 HELIX 7 AA7 LEU A 144 GLY A 171 1 28 HELIX 8 AA8 GLY A 171 ALA A 191 1 21 HELIX 9 AA9 THR A 195 GLU A 223 1 29 HELIX 10 AB1 SER A 226 ARG A 228 5 3 HELIX 11 AB2 ALA A 229 VAL A 255 1 27 HELIX 12 AB3 ASP A 257 SER A 276 1 20 HELIX 13 AB4 TRP A 277 LEU A 279 5 3 HELIX 14 AB5 SER A 282 THR A 289 1 8 HELIX 15 AB6 LEU A 292 ASN A 306 1 15 HELIX 16 AB7 ARG A 309 THR A 314 1 6 HELIX 17 AB8 THR A 316 ALA A 323 1 8 HELIX 18 AB9 ARG A 347 ALA A 368 1 22 HELIX 19 AC1 LEU A 369 GLN A 372 5 4 HELIX 20 AC2 ILE A 378 LEU A 403 1 26 HELIX 21 AC3 GLY A 404 THR A 424 1 21 HELIX 22 AC4 LEU A 433 LEU A 459 1 27 HELIX 23 AC5 LEU A 464 LEU A 488 1 25 HELIX 24 AC6 LEU A 489 VAL A 491 5 3 HELIX 25 AC7 TRP A 495 ALA A 512 1 18 HELIX 26 AC8 THR A 526 GLN A 533 1 8 SHEET 1 AA1 2 ARG A 89 PHE A 91 0 SHEET 2 AA1 2 THR A 113 PRO A 115 -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