HEADER TRANSPORT PROTEIN 26-SEP-23 8WJQ TITLE CRYO-EM STRUCTURE OF URAT1(R477S)-URATE COMPLEX 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,URAT1-URATE; 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, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.W.QIAN,J.J.HE REVDAT 2 04-SEP-24 8WJQ 1 TITLE COMPND REMARK REVDAT 1 28-AUG-24 8WJQ 0 JRNL AUTH J.HE,G.LIU,F.KONG,Q.TAN,Z.WANG,M.YANG,Y.HE,X.JIA,C.YAN, JRNL AUTH 2 C.WANG,H.QIAN JRNL TITL STRUCTURAL BASIS FOR THE TRANSPORT AND SUBSTRATE SELECTION JRNL TITL 2 OF HUMAN URATE TRANSPORTER 1. JRNL REF CELL REP V. 43 14628 2024 JRNL REFN ESSN 2211-1247 JRNL PMID 39146184 JRNL DOI 10.1016/J.CELREP.2024.114628 REMARK 2 REMARK 2 RESOLUTION. 3.80 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 392817 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 8WJQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 28-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300041397. 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 : CRYO-EM STRUCTURE OF REMARK 245 URAT1(R477S)-URATE COMPLEX 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 : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1700.00 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) : 5000.00 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 PHE A 3 REMARK 465 MET A 330 REMARK 465 GLY A 331 REMARK 465 GLN A 332 REMARK 465 PRO A 333 REMARK 465 PRO A 334 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 SER A 4 OG REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 LEU A 6 CG CD1 CD2 REMARK 470 LEU A 7 CG CD1 CD2 REMARK 470 ASP A 8 CG OD1 OD2 REMARK 470 LEU A 9 CG CD1 CD2 REMARK 470 VAL A 10 CG1 CG2 REMARK 470 GLN A 83 CG CD OE1 NE2 REMARK 470 ARG A 84 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 146 CG PRO A 146 CD -0.268 REMARK 500 PRO A 194 CG PRO A 194 CD -0.222 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 92 CG - CD - NE ANGL. DEV. = 14.3 DEGREES REMARK 500 GLU A 114 CA - CB - CG ANGL. DEV. = 15.6 DEGREES REMARK 500 ASP A 123 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 PRO A 146 CA - N - CD ANGL. DEV. = -19.2 DEGREES REMARK 500 PRO A 146 N - CD - CG ANGL. DEV. = -12.8 DEGREES REMARK 500 PRO A 194 C - N - CD ANGL. DEV. = -15.9 DEGREES REMARK 500 PRO A 194 CA - N - CD ANGL. DEV. = -17.7 DEGREES REMARK 500 PRO A 194 N - CD - CG ANGL. DEV. = -10.3 DEGREES REMARK 500 PRO A 407 CA - N - CD ANGL. DEV. = -9.0 DEGREES 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 LEU A 13 43.39 -141.61 REMARK 500 ALA A 42 22.26 81.28 REMARK 500 ASN A 82 30.47 74.55 REMARK 500 GLN A 83 11.54 59.87 REMARK 500 ARG A 92 -30.60 72.97 REMARK 500 SER A 107 30.35 -78.30 REMARK 500 LEU A 137 46.95 -89.00 REMARK 500 CYS A 139 -109.97 58.96 REMARK 500 LYS A 308 43.27 -101.90 REMARK 500 LEU A 315 80.06 58.59 REMARK 500 ASP A 370 -36.73 -36.30 REMARK 500 THR A 518 -158.80 -116.94 REMARK 500 GLN A 519 -2.86 75.16 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 291 0.07 SIDE CHAIN REMARK 500 ARG A 487 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37589 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF URAT1(R477S)-URATE COMPLEX DBREF 8WJQ A 1 538 UNP Q96S37 S22AC_HUMAN 1 538 SEQADV 8WJQ SER A 477 UNP Q96S37 ARG 477 CONFLICT SEQRES 1 A 538 MET ALA PHE SER GLU LEU LEU ASP LEU VAL GLY GLY LEU SEQRES 2 A 538 GLY ARG PHE GLN VAL LEU GLN THR MET ALA LEU MET VAL SEQRES 3 A 538 SER ILE MET TRP LEU CYS THR GLN SER MET LEU GLU ASN SEQRES 4 A 538 PHE SER ALA ALA VAL PRO SER HIS ARG CYS TRP ALA PRO SEQRES 5 A 538 LEU LEU ASP ASN SER THR ALA GLN ALA SER ILE LEU GLY SEQRES 6 A 538 SER LEU SER PRO GLU ALA LEU LEU ALA ILE SER ILE PRO SEQRES 7 A 538 PRO GLY PRO ASN GLN ARG PRO HIS GLN CYS ARG ARG PHE SEQRES 8 A 538 ARG GLN PRO GLN TRP GLN LEU LEU ASP PRO ASN ALA THR SEQRES 9 A 538 ALA THR SER TRP SER GLU ALA ASP THR GLU PRO CYS VAL SEQRES 10 A 538 ASP GLY TRP VAL TYR ASP ARG SER ILE PHE THR SER THR SEQRES 11 A 538 ILE VAL ALA LYS TRP ASN LEU VAL CYS ASP SER HIS ALA SEQRES 12 A 538 LEU LYS PRO MET ALA GLN SER ILE TYR LEU ALA GLY ILE SEQRES 13 A 538 LEU VAL GLY ALA ALA ALA CYS GLY PRO ALA SER ASP ARG SEQRES 14 A 538 PHE GLY ARG ARG LEU VAL LEU THR TRP SER TYR LEU GLN SEQRES 15 A 538 MET ALA VAL MET GLY THR ALA ALA ALA PHE ALA PRO ALA SEQRES 16 A 538 PHE PRO VAL TYR CYS LEU PHE ARG PHE LEU LEU ALA PHE SEQRES 17 A 538 ALA VAL ALA GLY VAL MET MET ASN THR GLY THR LEU LEU SEQRES 18 A 538 MET GLU TRP THR ALA ALA ARG ALA ARG PRO LEU VAL MET SEQRES 19 A 538 THR LEU ASN SER LEU GLY PHE SER PHE GLY HIS GLY LEU SEQRES 20 A 538 THR ALA ALA VAL ALA TYR GLY VAL ARG ASP TRP THR LEU SEQRES 21 A 538 LEU GLN LEU VAL VAL SER VAL PRO PHE PHE LEU CYS PHE SEQRES 22 A 538 LEU TYR SER TRP TRP LEU ALA GLU SER ALA ARG TRP LEU SEQRES 23 A 538 LEU THR THR GLY ARG LEU ASP TRP GLY LEU GLN GLU LEU SEQRES 24 A 538 TRP ARG VAL ALA ALA ILE ASN GLY LYS GLY ALA VAL GLN SEQRES 25 A 538 ASP THR LEU THR PRO GLU VAL LEU LEU SER ALA MET ARG SEQRES 26 A 538 GLU GLU LEU SER MET GLY GLN PRO PRO ALA SER LEU GLY SEQRES 27 A 538 THR LEU LEU ARG MET PRO GLY LEU ARG PHE ARG THR CYS SEQRES 28 A 538 ILE SER THR LEU CYS TRP PHE ALA PHE GLY PHE THR PHE SEQRES 29 A 538 PHE GLY LEU ALA LEU ASP LEU GLN ALA LEU GLY SER ASN SEQRES 30 A 538 ILE PHE LEU LEU GLN MET PHE ILE GLY VAL VAL ASP ILE SEQRES 31 A 538 PRO ALA LYS MET GLY ALA LEU LEU LEU LEU SER HIS LEU SEQRES 32 A 538 GLY ARG ARG PRO THR LEU ALA ALA SER LEU LEU LEU ALA SEQRES 33 A 538 GLY LEU CYS ILE LEU ALA ASN THR LEU VAL PRO HIS GLU SEQRES 34 A 538 MET GLY ALA LEU ARG SER ALA LEU ALA VAL LEU GLY LEU SEQRES 35 A 538 GLY GLY VAL GLY ALA ALA PHE THR CYS ILE THR ILE TYR SEQRES 36 A 538 SER SER GLU LEU PHE PRO THR VAL LEU ARG MET THR ALA SEQRES 37 A 538 VAL GLY LEU GLY GLN MET ALA ALA SER GLY GLY ALA ILE SEQRES 38 A 538 LEU GLY PRO LEU VAL ARG LEU LEU GLY VAL HIS GLY PRO SEQRES 39 A 538 TRP LEU PRO LEU LEU VAL TYR GLY THR VAL PRO VAL LEU SEQRES 40 A 538 SER GLY LEU ALA ALA LEU LEU LEU PRO GLU THR GLN SER SEQRES 41 A 538 LEU PRO LEU PRO ASP THR ILE GLN ASP VAL GLN ASN GLN SEQRES 42 A 538 ALA VAL LYS LYS ALA 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 SER A 4 GLY A 11 1 8 HELIX 2 AA2 GLY A 14 SER A 41 1 28 HELIX 3 AA3 ASN A 56 SER A 62 1 7 HELIX 4 AA4 SER A 68 ILE A 77 1 10 HELIX 5 AA5 GLY A 80 ARG A 84 5 5 HELIX 6 AA6 GLN A 95 ASP A 100 5 6 HELIX 7 AA7 SER A 109 THR A 113 5 5 HELIX 8 AA8 THR A 130 ASN A 136 1 7 HELIX 9 AA9 VAL A 138 HIS A 142 5 5 HELIX 10 AB1 ALA A 143 GLY A 171 1 29 HELIX 11 AB2 GLY A 171 PHE A 192 1 22 HELIX 12 AB3 ALA A 195 THR A 225 1 31 HELIX 13 AB4 ALA A 229 VAL A 255 1 27 HELIX 14 AB5 ASP A 257 TRP A 277 1 21 HELIX 15 AB6 SER A 282 THR A 289 1 8 HELIX 16 AB7 ARG A 291 ASN A 306 1 16 HELIX 17 AB8 LYS A 308 THR A 314 1 7 HELIX 18 AB9 THR A 316 SER A 329 1 14 HELIX 19 AC1 SER A 336 MET A 343 1 8 HELIX 20 AC2 MET A 343 ALA A 368 1 26 HELIX 21 AC3 LEU A 369 GLY A 375 5 7 HELIX 22 AC4 ASN A 377 LEU A 403 1 27 HELIX 23 AC5 GLY A 404 VAL A 426 1 23 HELIX 24 AC6 MET A 430 PHE A 460 1 31 HELIX 25 AC7 PRO A 461 GLY A 490 1 30 HELIX 26 AC8 PRO A 494 LEU A 513 1 20 HELIX 27 AC9 THR A 526 ALA A 538 1 13 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 89 ARG A 90 0 SHEET 2 AA2 2 GLU A 114 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 2.04 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