HEADER TRANSPORT PROTEIN 26-SEP-23 8WJH TITLE CRYO-EM STRUCTURE OF OAT4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 22 MEMBER 11; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ORGANIC ANION TRANSPORTER 4,OAT4,ORGANIC ANION:DICARBOXYLATE COMPND 5 EXCHANGER OAT4; COMPND 6 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: SLC22A11, OAT4; 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 8WJH 1 TITLE REMARK REVDAT 1 28-AUG-24 8WJH 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. 3.10 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 460072 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 8WJH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 27-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300041384. 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 OAT4 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 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 LYS A 306 REMARK 465 GLU A 307 REMARK 465 ALA A 308 REMARK 465 LYS A 309 REMARK 465 ASN A 310 REMARK 465 LEU A 311 REMARK 465 LYS A 328 REMARK 465 GLU A 329 REMARK 465 PRO A 330 REMARK 465 ARG A 331 REMARK 465 SER A 332 REMARK 465 VAL A 333 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 THR A 51 OG1 CG2 REMARK 470 MET A 53 CG SD CE REMARK 470 LEU A 54 CG CD1 CD2 REMARK 470 ASP A 55 CG OD1 OD2 REMARK 470 ASN A 56 CG OD1 ND2 REMARK 470 SER A 58 OG REMARK 470 VAL A 60 CG1 CG2 REMARK 470 SER A 61 OG REMARK 470 THR A 62 OG1 CG2 REMARK 470 ASN A 63 CG OD1 ND2 REMARK 470 MET A 64 CG SD CE REMARK 470 THR A 65 OG1 CG2 REMARK 470 PRO A 66 CG CD REMARK 470 LYS A 67 CG CD CE NZ REMARK 470 LEU A 69 CG CD1 CD2 REMARK 470 LEU A 70 CG CD1 CD2 REMARK 470 THR A 71 OG1 CG2 REMARK 470 ILE A 72 CG1 CG2 CD1 REMARK 470 SER A 73 OG 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 CYS A 28 CA - CB - SG ANGL. DEV. = 8.3 DEGREES REMARK 500 CYS A 136 CB - CA - C ANGL. DEV. = 13.3 DEGREES REMARK 500 LEU A 296 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 ASP A 385 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 LEU A 509 CA - CB - CG ANGL. DEV. = 14.1 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 THR A 62 -7.25 -56.64 REMARK 500 ALA A 102 -4.61 -57.20 REMARK 500 LEU A 134 46.83 -84.99 REMARK 500 CYS A 136 -51.82 70.98 REMARK 500 ARG A 253 -2.85 60.43 REMARK 500 LYS A 288 60.59 -114.31 REMARK 500 GLU A 314 -41.80 72.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37580 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF OAT4 DBREF 8WJH A 1 517 UNP Q9NSA0 S22AB_HUMAN 1 517 SEQRES 1 A 517 MET ALA PHE SER LYS LEU LEU GLU GLN ALA GLY GLY VAL SEQRES 2 A 517 GLY LEU PHE GLN THR LEU GLN VAL LEU THR PHE ILE LEU SEQRES 3 A 517 PRO CYS LEU MET ILE PRO SER GLN MET LEU LEU GLU ASN SEQRES 4 A 517 PHE SER ALA ALA ILE PRO GLY HIS ARG CYS TRP THR HIS SEQRES 5 A 517 MET LEU ASP ASN GLY SER ALA VAL SER THR ASN MET THR SEQRES 6 A 517 PRO LYS ALA LEU LEU THR ILE SER ILE PRO PRO GLY PRO SEQRES 7 A 517 ASN GLN GLY PRO HIS GLN CYS ARG ARG PHE ARG GLN PRO SEQRES 8 A 517 GLN TRP GLN LEU LEU ASP PRO ASN ALA THR ALA THR SER SEQRES 9 A 517 TRP SER GLU ALA ASP THR GLU PRO CYS VAL ASP GLY TRP SEQRES 10 A 517 VAL TYR ASP ARG SER VAL PHE THR SER THR ILE VAL ALA SEQRES 11 A 517 LYS TRP ASP LEU VAL CYS SER SER GLN GLY LEU LYS PRO SEQRES 12 A 517 LEU SER GLN SER ILE PHE MET SER GLY ILE LEU VAL GLY SEQRES 13 A 517 SER PHE ILE TRP GLY LEU LEU SER TYR ARG PHE GLY ARG SEQRES 14 A 517 LYS PRO MET LEU SER TRP CYS CYS LEU GLN LEU ALA VAL SEQRES 15 A 517 ALA GLY THR SER THR ILE PHE ALA PRO THR PHE VAL ILE SEQRES 16 A 517 TYR CYS GLY LEU ARG PHE VAL ALA ALA PHE GLY MET ALA SEQRES 17 A 517 GLY ILE PHE LEU SER SER LEU THR LEU MET VAL GLU TRP SEQRES 18 A 517 THR THR THR SER ARG ARG ALA VAL THR MET THR VAL VAL SEQRES 19 A 517 GLY CYS ALA PHE SER ALA GLY GLN ALA ALA LEU GLY GLY SEQRES 20 A 517 LEU ALA PHE ALA LEU ARG ASP TRP ARG THR LEU GLN LEU SEQRES 21 A 517 ALA ALA SER VAL PRO PHE PHE ALA ILE SER LEU ILE SER SEQRES 22 A 517 TRP TRP LEU PRO GLU SER ALA ARG TRP LEU ILE ILE LYS SEQRES 23 A 517 GLY LYS PRO ASP GLN ALA LEU GLN GLU LEU ARG LYS VAL SEQRES 24 A 517 ALA ARG ILE ASN GLY HIS LYS GLU ALA LYS ASN LEU THR SEQRES 25 A 517 ILE GLU VAL LEU MET SER SER VAL LYS GLU GLU VAL ALA SEQRES 26 A 517 SER ALA LYS GLU PRO ARG SER VAL LEU ASP LEU PHE CYS SEQRES 27 A 517 VAL PRO VAL LEU ARG TRP ARG SER CYS ALA MET LEU VAL SEQRES 28 A 517 VAL ASN PHE SER LEU LEU ILE SER TYR TYR GLY LEU VAL SEQRES 29 A 517 PHE ASP LEU GLN SER LEU GLY ARG ASP ILE PHE LEU LEU SEQRES 30 A 517 GLN ALA LEU PHE GLY ALA VAL ASP PHE LEU GLY ARG ALA SEQRES 31 A 517 THR THR ALA LEU LEU LEU SER PHE LEU GLY ARG ARG THR SEQRES 32 A 517 ILE GLN ALA GLY SER GLN ALA MET ALA GLY LEU ALA ILE SEQRES 33 A 517 LEU ALA ASN MET LEU VAL PRO GLN ASP LEU GLN THR LEU SEQRES 34 A 517 ARG VAL VAL PHE ALA VAL LEU GLY LYS GLY CYS PHE GLY SEQRES 35 A 517 ILE SER LEU THR CYS LEU THR ILE TYR LYS ALA GLU LEU SEQRES 36 A 517 PHE PRO THR PRO VAL ARG MET THR ALA ASP GLY ILE LEU SEQRES 37 A 517 HIS THR VAL GLY ARG LEU GLY ALA MET MET GLY PRO LEU SEQRES 38 A 517 ILE LEU MET SER ARG GLN ALA LEU PRO LEU LEU PRO PRO SEQRES 39 A 517 LEU LEU TYR GLY VAL ILE SER ILE ALA SER SER LEU VAL SEQRES 40 A 517 VAL LEU PHE PHE LEU PRO GLU THR GLN GLY HET CL A 601 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- HELIX 1 AA1 MET A 1 ALA A 10 1 10 HELIX 2 AA2 GLY A 14 LEU A 36 1 23 HELIX 3 AA3 LEU A 37 ALA A 42 1 6 HELIX 4 AA4 THR A 51 ASN A 56 1 6 HELIX 5 AA5 THR A 65 ILE A 74 1 10 HELIX 6 AA6 GLN A 92 LEU A 96 5 5 HELIX 7 AA7 SER A 106 ALA A 108 5 3 HELIX 8 AA8 THR A 127 ASP A 133 1 7 HELIX 9 AA9 GLY A 140 SER A 164 1 25 HELIX 10 AB1 GLY A 168 THR A 187 1 20 HELIX 11 AB2 ILE A 188 ALA A 190 5 3 HELIX 12 AB3 THR A 192 THR A 222 1 31 HELIX 13 AB4 THR A 223 ARG A 253 1 31 HELIX 14 AB5 ASP A 254 LEU A 276 1 23 HELIX 15 AB6 SER A 279 LYS A 286 1 8 HELIX 16 AB7 LYS A 288 ASN A 303 1 16 HELIX 17 AB8 GLU A 314 VAL A 320 1 7 HELIX 18 AB9 VAL A 320 ALA A 327 1 8 HELIX 19 AC1 ASP A 335 VAL A 339 1 5 HELIX 20 AC2 VAL A 339 ASP A 366 1 28 HELIX 21 AC3 ASP A 366 GLY A 371 1 6 HELIX 22 AC4 ASP A 373 LEU A 399 1 27 HELIX 23 AC5 GLY A 400 VAL A 422 1 23 HELIX 24 AC6 LEU A 426 PHE A 456 1 31 HELIX 25 AC7 PRO A 457 MET A 484 1 28 HELIX 26 AC8 SER A 485 ALA A 488 5 4 HELIX 27 AC9 LEU A 491 LEU A 512 1 22 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 2.04 SSBOND 2 CYS A 85 CYS A 136 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