HEADER MEMBRANE PROTEIN 13-MAR-24 9B1N TITLE PYRAZINOATE BOUND HUMAN URAT1 IN THE INWARD-FACING STATE (SITE2) 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 SLC TRANSPORTER, SLC22A FAMILY, URIC ACID, INWARD FACING, MEMBRANE KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.DAI,C.H.LEE REVDAT 1 18-SEP-24 9B1N 0 JRNL AUTH Y.DAI,C.H.LEE JRNL TITL TRANSPORT MECHANISM AND STRUCTURAL PHARMACOLOGY OF HUMAN JRNL TITL 2 URATE TRANSPORTER URAT1. JRNL REF CELL RES. 2024 JRNL REFN ISSN 1001-0602 JRNL PMID 39245778 JRNL DOI 10.1038/S41422-024-01023-1 REMARK 2 REMARK 2 RESOLUTION. 3.10 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 49989 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 9B1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1000282442. 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 : PYRAZINOATE BOUND HUMAN URAT1 REMARK 245 IN THE INWARD-FACING STATE REMARK 245 (SITE2). 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 : 6.50 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 : FEI TITAN 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) : 6890.00 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 PRO A 518 REMARK 465 LEU A 519 REMARK 465 PRO A 520 REMARK 465 ASP A 521 REMARK 465 THR A 522 REMARK 465 ILE A 523 REMARK 465 GLN A 524 REMARK 465 ASP A 525 REMARK 465 VAL A 526 REMARK 465 GLN A 527 REMARK 465 ASN A 528 REMARK 465 GLN A 529 REMARK 465 ALA A 530 REMARK 465 VAL A 531 REMARK 465 LYS A 532 REMARK 465 LYS A 533 REMARK 465 ALA A 534 REMARK 465 THR A 535 REMARK 465 HIS A 536 REMARK 465 GLY A 537 REMARK 465 THR A 538 REMARK 465 LEU A 539 REMARK 465 GLY A 540 REMARK 465 ASN A 541 REMARK 465 SER A 542 REMARK 465 VAL A 543 REMARK 465 LEU A 544 REMARK 465 LYS A 545 REMARK 465 SER A 546 REMARK 465 THR A 547 REMARK 465 GLN A 548 REMARK 465 PHE A 549 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 136 -122.04 57.41 REMARK 500 ALA A 364 0.21 -67.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-44085 RELATED DB: EMDB REMARK 900 PYRAZINOATE BOUND HUMAN URAT1 IN THE INWARD-FACING STATE (SITE2). DBREF 9B1N A 3 549 UNP Q96S37 S22AC_HUMAN 3 553 SEQADV 9B1N VAL A 60 UNP Q96S37 GLN 60 CONFLICT SEQADV 9B1N SER A 61 UNP Q96S37 ALA 61 CONFLICT SEQADV 9B1N THR A 62 UNP Q96S37 SER 62 CONFLICT SEQADV 9B1N A UNP Q96S37 ILE 63 DELETION SEQADV 9B1N A UNP Q96S37 LEU 64 DELETION SEQADV 9B1N A UNP Q96S37 GLY 65 DELETION SEQADV 9B1N PRO A 277 UNP Q96S37 ALA 280 CONFLICT SEQADV 9B1N ILE A 284 UNP Q96S37 LEU 287 CONFLICT SEQADV 9B1N ILE A 285 UNP Q96S37 THR 288 CONFLICT SEQADV 9B1N LYS A 286 UNP Q96S37 THR 289 CONFLICT SEQADV 9B1N LYS A 288 UNP Q96S37 ARG 291 CONFLICT SEQADV 9B1N PRO A 289 UNP Q96S37 LEU 292 CONFLICT SEQADV 9B1N GLN A 291 UNP Q96S37 TRP 294 CONFLICT SEQADV 9B1N ALA A 292 UNP Q96S37 GLY 295 CONFLICT SEQADV 9B1N ARG A 297 UNP Q96S37 TRP 300 CONFLICT SEQADV 9B1N LYS A 298 UNP Q96S37 ARG 301 CONFLICT SEQADV 9B1N ARG A 301 UNP Q96S37 ALA 304 CONFLICT SEQADV 9B1N HIS A 305 UNP Q96S37 LYS 308 CONFLICT SEQADV 9B1N LYS A 306 UNP Q96S37 GLY 309 CONFLICT SEQADV 9B1N GLU A 307 UNP Q96S37 ALA 310 CONFLICT SEQADV 9B1N ALA A 308 UNP Q96S37 VAL 311 CONFLICT SEQADV 9B1N LYS A 309 UNP Q96S37 GLN 312 CONFLICT SEQADV 9B1N ASN A 310 UNP Q96S37 ASP 313 CONFLICT SEQADV 9B1N A UNP Q96S37 THR 314 DELETION SEQADV 9B1N ILE A 313 UNP Q96S37 PRO 317 CONFLICT SEQADV 9B1N MET A 317 UNP Q96S37 LEU 321 CONFLICT SEQADV 9B1N SER A 319 UNP Q96S37 ALA 323 CONFLICT SEQADV 9B1N VAL A 320 UNP Q96S37 MET 324 CONFLICT SEQADV 9B1N LYS A 321 UNP Q96S37 ARG 325 CONFLICT SEQADV 9B1N VAL A 324 UNP Q96S37 LEU 328 CONFLICT SEQADV 9B1N ALA A 325 UNP Q96S37 SER 329 CONFLICT SEQADV 9B1N SER A 326 UNP Q96S37 MET 330 CONFLICT SEQADV 9B1N ALA A 327 UNP Q96S37 GLY 331 CONFLICT SEQADV 9B1N LYS A 328 UNP Q96S37 GLN 332 CONFLICT SEQADV 9B1N GLU A 329 UNP Q96S37 PRO 333 CONFLICT SEQADV 9B1N ARG A 331 UNP Q96S37 ALA 335 CONFLICT SEQADV 9B1N VAL A 333 UNP Q96S37 LEU 337 CONFLICT SEQADV 9B1N LEU A 334 UNP Q96S37 GLY 338 CONFLICT SEQADV 9B1N ASP A 335 UNP Q96S37 THR 339 CONFLICT SEQADV 9B1N PHE A 337 UNP Q96S37 LEU 341 CONFLICT SEQADV 9B1N CYS A 338 UNP Q96S37 ARG 342 CONFLICT SEQADV 9B1N VAL A 339 UNP Q96S37 MET 343 CONFLICT SEQRES 1 A 547 PHE SER GLU LEU LEU ASP LEU VAL GLY GLY LEU GLY ARG SEQRES 2 A 547 PHE GLN VAL LEU GLN THR MET ALA LEU MET VAL SER ILE SEQRES 3 A 547 MET TRP LEU CYS THR GLN SER MET LEU GLU ASN PHE SER SEQRES 4 A 547 ALA ALA VAL PRO SER HIS ARG CYS TRP ALA PRO LEU LEU SEQRES 5 A 547 ASP ASN SER THR ALA VAL SER THR SER LEU SER PRO GLU SEQRES 6 A 547 ALA LEU LEU ALA ILE SER ILE PRO PRO GLY PRO ASN GLN SEQRES 7 A 547 ARG PRO HIS GLN CYS ARG ARG PHE ARG GLN PRO GLN TRP SEQRES 8 A 547 GLN LEU LEU ASP PRO ASN ALA THR ALA THR SER TRP SER SEQRES 9 A 547 GLU ALA ASP THR GLU PRO CYS VAL ASP GLY TRP VAL TYR SEQRES 10 A 547 ASP ARG SER ILE PHE THR SER THR ILE VAL ALA LYS TRP SEQRES 11 A 547 ASN LEU VAL CYS ASP SER HIS ALA LEU LYS PRO MET ALA SEQRES 12 A 547 GLN SER ILE TYR LEU ALA GLY ILE LEU VAL GLY ALA ALA SEQRES 13 A 547 ALA CYS GLY PRO ALA SER ASP ARG PHE GLY ARG ARG LEU SEQRES 14 A 547 VAL LEU THR TRP SER TYR LEU GLN MET ALA VAL MET GLY SEQRES 15 A 547 THR ALA ALA ALA PHE ALA PRO ALA PHE PRO VAL TYR CYS SEQRES 16 A 547 LEU PHE ARG PHE LEU LEU ALA PHE ALA VAL ALA GLY VAL SEQRES 17 A 547 MET MET ASN THR GLY THR LEU LEU MET GLU TRP THR ALA SEQRES 18 A 547 ALA ARG ALA ARG PRO LEU VAL MET THR LEU ASN SER LEU SEQRES 19 A 547 GLY PHE SER PHE GLY HIS GLY LEU THR ALA ALA VAL ALA SEQRES 20 A 547 TYR GLY VAL ARG ASP TRP THR LEU LEU GLN LEU VAL VAL SEQRES 21 A 547 SER VAL PRO PHE PHE LEU CYS PHE LEU TYR SER TRP TRP SEQRES 22 A 547 LEU PRO GLU SER ALA ARG TRP LEU ILE ILE LYS GLY LYS SEQRES 23 A 547 PRO ASP GLN ALA LEU GLN GLU LEU ARG LYS VAL ALA ARG SEQRES 24 A 547 ILE ASN GLY HIS LYS GLU ALA LYS ASN LEU THR ILE GLU SEQRES 25 A 547 VAL LEU MET SER SER VAL LYS GLU GLU VAL ALA SER ALA SEQRES 26 A 547 LYS GLU PRO ARG SER VAL LEU ASP LEU PHE CYS VAL PRO SEQRES 27 A 547 GLY LEU ARG PHE ARG THR CYS ILE SER THR LEU CYS TRP SEQRES 28 A 547 PHE ALA PHE GLY PHE THR PHE PHE GLY LEU ALA LEU ASP SEQRES 29 A 547 LEU GLN ALA LEU GLY SER ASN ILE PHE LEU LEU GLN MET SEQRES 30 A 547 PHE ILE GLY VAL VAL ASP ILE PRO ALA LYS MET GLY ALA SEQRES 31 A 547 LEU LEU LEU LEU SER HIS LEU GLY ARG ARG PRO THR LEU SEQRES 32 A 547 ALA ALA SER LEU LEU LEU ALA GLY LEU CYS ILE LEU ALA SEQRES 33 A 547 ASN THR LEU VAL PRO HIS GLU MET GLY ALA LEU ARG SER SEQRES 34 A 547 ALA LEU ALA VAL LEU GLY LEU GLY GLY VAL GLY ALA ALA SEQRES 35 A 547 PHE THR CYS ILE THR ILE TYR SER SER GLU LEU PHE PRO SEQRES 36 A 547 THR VAL LEU ARG MET THR ALA VAL GLY LEU GLY GLN MET SEQRES 37 A 547 ALA ALA ARG GLY GLY ALA ILE LEU GLY PRO LEU VAL ARG SEQRES 38 A 547 LEU LEU GLY VAL HIS GLY PRO TRP LEU PRO LEU LEU VAL SEQRES 39 A 547 TYR GLY THR VAL PRO VAL LEU SER GLY LEU ALA ALA LEU SEQRES 40 A 547 LEU LEU PRO GLU THR GLN SER LEU PRO LEU PRO ASP THR SEQRES 41 A 547 ILE GLN ASP VAL GLN ASN GLN ALA VAL LYS LYS ALA THR SEQRES 42 A 547 HIS GLY THR LEU GLY ASN SER VAL LEU LYS SER THR GLN SEQRES 43 A 547 PHE HET NAG A 601 14 HET VGL A 602 9 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM VGL PYRAZINE-2-CARBOXYLIC ACID HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN VGL PYRAZINOIC ACID FORMUL 2 NAG C8 H15 N O6 FORMUL 3 VGL C5 H4 N2 O2 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 GLU A 38 PHE A 40 5 3 HELIX 4 AA4 ALA A 51 ASN A 56 1 6 HELIX 5 AA5 SER A 65 ILE A 74 1 10 HELIX 6 AA6 GLN A 92 ASP A 97 5 6 HELIX 7 AA7 THR A 101 TRP A 105 5 5 HELIX 8 AA8 SER A 106 ALA A 108 5 3 HELIX 9 AA9 THR A 127 ASN A 133 1 7 HELIX 10 AB1 VAL A 135 HIS A 139 5 5 HELIX 11 AB2 ALA A 140 GLY A 168 1 29 HELIX 12 AB3 GLY A 168 PHE A 189 1 22 HELIX 13 AB4 ALA A 192 GLU A 220 1 29 HELIX 14 AB5 ALA A 223 ARG A 225 5 3 HELIX 15 AB6 ALA A 226 VAL A 252 1 27 HELIX 16 AB7 ASP A 254 VAL A 264 1 11 HELIX 17 AB8 VAL A 264 SER A 273 1 10 HELIX 18 AB9 SER A 279 LYS A 286 1 8 HELIX 19 AC1 LYS A 288 GLY A 304 1 17 HELIX 20 AC2 HIS A 305 LEU A 311 5 7 HELIX 21 AC3 THR A 312 VAL A 320 1 9 HELIX 22 AC4 VAL A 320 ALA A 325 1 6 HELIX 23 AC5 SER A 326 GLU A 329 5 4 HELIX 24 AC6 VAL A 333 VAL A 339 1 7 HELIX 25 AC7 GLY A 341 ALA A 364 1 24 HELIX 26 AC8 ASP A 366 LEU A 370 5 5 HELIX 27 AC9 ASN A 373 VAL A 384 1 12 HELIX 28 AD1 VAL A 384 LEU A 399 1 16 HELIX 29 AD2 GLY A 400 VAL A 422 1 23 HELIX 30 AD3 MET A 426 SER A 453 1 28 HELIX 31 AD4 LEU A 460 VAL A 482 1 23 HELIX 32 AD5 ARG A 483 GLY A 489 5 7 HELIX 33 AD6 PRO A 490 LEU A 509 1 20 SHEET 1 AA1 2 HIS A 47 CYS A 49 0 SHEET 2 AA1 2 TRP A 117 TYR A 119 -1 O VAL A 118 N ARG A 48 SHEET 1 AA2 2 ARG A 86 PHE A 88 0 SHEET 2 AA2 2 THR A 110 PRO A 112 -1 O GLU A 111 N ARG A 87 SSBOND 1 CYS A 49 CYS A 113 1555 1555 2.03 SSBOND 2 CYS A 85 CYS A 136 1555 1555 2.03 LINK ND2 ASN A 56 C1 NAG A 601 1555 1555 1.45 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