HEADER TRANSPORT PROTEIN 02-AUG-24 9J04 TITLE CRYO-EM STRUCTURE OF HOAT1 IN COMPLEX WITH CIDOFOVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 22 MEMBER 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ORGANIC ANION TRANSPORTER 1,HOAT1,PAH TRANSPORTER,HPAHT, COMPND 5 RENAL ORGANIC ANION TRANSPORTER 1,HROAT1; 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: SLC22A6, OAT1, PAHT; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS TRANSPORTER, ORGANIC ANION, UPTAKE, RENAL PATHOPHYSIOLOGY, TRANSPORT KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.X.YANG,Y.B.LUO,X.N.WU REVDAT 1 13-AUG-25 9J04 0 JRNL AUTH X.N.WU,Y.B.LUO,S.J.FENG JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF TWO DIFFERENT DRUGS BY JRNL TITL 2 HUMAN OAT1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.15 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) : 3.150 REMARK 3 NUMBER OF PARTICLES : 129163 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 9J04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 06-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300050089. 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 HOAT1 IN REMARK 245 COMPLEX WITH CIDOFOVIR 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 876.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2790.00 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) : 5700.00 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 MET A 1 REMARK 465 ASN A 56 REMARK 465 LEU A 57 REMARK 465 SER A 58 REMARK 465 LYS A 59 REMARK 465 ASN A 60 REMARK 465 GLY A 61 REMARK 465 GLY A 62 REMARK 465 LEU A 63 REMARK 465 GLN A 85 REMARK 465 TRP A 86 REMARK 465 GLY A 87 REMARK 465 LEU A 88 REMARK 465 PRO A 89 REMARK 465 PHE A 90 REMARK 465 LEU A 91 REMARK 465 ASN A 92 REMARK 465 GLY A 93 REMARK 465 THR A 94 REMARK 465 GLU A 95 REMARK 465 ALA A 96 REMARK 465 ASN A 97 REMARK 465 GLY A 98 REMARK 465 THR A 99 REMARK 465 GLY A 100 REMARK 465 ALA A 101 REMARK 465 LEU A 317 REMARK 465 THR A 318 REMARK 465 MET A 319 REMARK 465 GLY A 320 REMARK 465 LYS A 321 REMARK 465 GLY A 322 REMARK 465 GLN A 323 REMARK 465 ARG A 522 REMARK 465 TRP A 523 REMARK 465 ALA A 524 REMARK 465 PRO A 525 REMARK 465 THR A 526 REMARK 465 GLN A 527 REMARK 465 LYS A 528 REMARK 465 GLU A 529 REMARK 465 ALA A 530 REMARK 465 GLY A 531 REMARK 465 ILE A 532 REMARK 465 TYR A 533 REMARK 465 PRO A 534 REMARK 465 ARG A 535 REMARK 465 LYS A 536 REMARK 465 GLY A 537 REMARK 465 LYS A 538 REMARK 465 GLN A 539 REMARK 465 THR A 540 REMARK 465 ARG A 541 REMARK 465 GLN A 542 REMARK 465 GLN A 543 REMARK 465 GLN A 544 REMARK 465 GLU A 545 REMARK 465 HIS A 546 REMARK 465 GLN A 547 REMARK 465 LYS A 548 REMARK 465 TYR A 549 REMARK 465 MET A 550 REMARK 465 VAL A 551 REMARK 465 PRO A 552 REMARK 465 LEU A 553 REMARK 465 GLN A 554 REMARK 465 ALA A 555 REMARK 465 SER A 556 REMARK 465 ALA A 557 REMARK 465 GLN A 558 REMARK 465 GLU A 559 REMARK 465 LYS A 560 REMARK 465 ASN A 561 REMARK 465 GLY A 562 REMARK 465 LEU A 563 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 36 57.92 -95.56 REMARK 500 GLN A 38 46.81 -78.50 REMARK 500 ASN A 39 -31.37 -131.25 REMARK 500 ARG A 80 20.50 -142.84 REMARK 500 PHE A 81 72.61 58.27 REMARK 500 ASP A 107 22.71 -140.44 REMARK 500 CYS A 128 -8.48 64.17 REMARK 500 PRO A 215 -178.29 -68.19 REMARK 500 VAL A 414 -52.10 -124.22 REMARK 500 PRO A 450 -175.34 -68.36 REMARK 500 SER A 498 1.39 -69.78 REMARK 500 THR A 501 2.33 -67.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61048 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HOAT1 IN COMPLEX WITH CIDOFOVIR DBREF 9J04 A 1 563 UNP Q4U2R8 S22A6_HUMAN 1 563 SEQRES 1 A 563 MET ALA PHE ASN ASP LEU LEU GLN GLN VAL GLY GLY VAL SEQRES 2 A 563 GLY ARG PHE GLN GLN ILE GLN VAL THR LEU VAL VAL LEU SEQRES 3 A 563 PRO LEU LEU LEU MET ALA SER HIS ASN THR LEU GLN ASN SEQRES 4 A 563 PHE THR ALA ALA ILE PRO THR HIS HIS CYS ARG PRO PRO SEQRES 5 A 563 ALA ASP ALA ASN LEU SER LYS ASN GLY GLY LEU GLU VAL SEQRES 6 A 563 TRP LEU PRO ARG ASP ARG GLN GLY GLN PRO GLU SER CYS SEQRES 7 A 563 LEU ARG PHE THR SER PRO GLN TRP GLY LEU PRO PHE LEU SEQRES 8 A 563 ASN GLY THR GLU ALA ASN GLY THR GLY ALA THR GLU PRO SEQRES 9 A 563 CYS THR ASP GLY TRP ILE TYR ASP ASN SER THR PHE PRO SEQRES 10 A 563 SER THR ILE VAL THR GLU TRP ASP LEU VAL CYS SER HIS SEQRES 11 A 563 ARG ALA LEU ARG GLN LEU ALA GLN SER LEU TYR MET VAL SEQRES 12 A 563 GLY VAL LEU LEU GLY ALA MET VAL PHE GLY TYR LEU ALA SEQRES 13 A 563 ASP ARG LEU GLY ARG ARG LYS VAL LEU ILE LEU ASN TYR SEQRES 14 A 563 LEU GLN THR ALA VAL SER GLY THR CYS ALA ALA PHE ALA SEQRES 15 A 563 PRO ASN PHE PRO ILE TYR CYS ALA PHE ARG LEU LEU SER SEQRES 16 A 563 GLY MET ALA LEU ALA GLY ILE SER LEU ASN CYS MET THR SEQRES 17 A 563 LEU ASN VAL GLU TRP MET PRO ILE HIS THR ARG ALA CYS SEQRES 18 A 563 VAL GLY THR LEU ILE GLY TYR VAL TYR SER LEU GLY GLN SEQRES 19 A 563 PHE LEU LEU ALA GLY VAL ALA TYR ALA VAL PRO HIS TRP SEQRES 20 A 563 ARG HIS LEU GLN LEU LEU VAL SER ALA PRO PHE PHE ALA SEQRES 21 A 563 PHE PHE ILE TYR SER TRP PHE PHE ILE GLU SER ALA ARG SEQRES 22 A 563 TRP HIS SER SER SER GLY ARG LEU ASP LEU THR LEU ARG SEQRES 23 A 563 ALA LEU GLN ARG VAL ALA ARG ILE ASN GLY LYS ARG GLU SEQRES 24 A 563 GLU GLY ALA LYS LEU SER MET GLU VAL LEU ARG ALA SER SEQRES 25 A 563 LEU GLN LYS GLU LEU THR MET GLY LYS GLY GLN ALA SER SEQRES 26 A 563 ALA MET GLU LEU LEU ARG CYS PRO THR LEU ARG HIS LEU SEQRES 27 A 563 PHE LEU CYS LEU SER MET LEU TRP PHE ALA THR SER PHE SEQRES 28 A 563 ALA TYR TYR GLY LEU VAL MET ASP LEU GLN GLY PHE GLY SEQRES 29 A 563 VAL SER ILE TYR LEU ILE GLN VAL ILE PHE GLY ALA VAL SEQRES 30 A 563 ASP LEU PRO ALA LYS LEU VAL GLY PHE LEU VAL ILE ASN SEQRES 31 A 563 SER LEU GLY ARG ARG PRO ALA GLN MET ALA ALA LEU LEU SEQRES 32 A 563 LEU ALA GLY ILE CYS ILE LEU LEU ASN GLY VAL ILE PRO SEQRES 33 A 563 GLN ASP GLN SER ILE VAL ARG THR SER LEU ALA VAL LEU SEQRES 34 A 563 GLY LYS GLY CYS LEU ALA ALA SER PHE ASN CYS ILE PHE SEQRES 35 A 563 LEU TYR THR GLY GLU LEU TYR PRO THR MET ILE ARG GLN SEQRES 36 A 563 THR GLY MET GLY MET GLY SER THR MET ALA ARG VAL GLY SEQRES 37 A 563 SER ILE VAL SER PRO LEU VAL SER MET THR ALA GLU LEU SEQRES 38 A 563 TYR PRO SER MET PRO LEU PHE ILE TYR GLY ALA VAL PRO SEQRES 39 A 563 VAL ALA ALA SER ALA VAL THR VAL LEU LEU PRO GLU THR SEQRES 40 A 563 LEU GLY GLN PRO LEU PRO ASP THR VAL GLN ASP LEU GLU SEQRES 41 A 563 SER ARG TRP ALA PRO THR GLN LYS GLU ALA GLY ILE TYR SEQRES 42 A 563 PRO ARG LYS GLY LYS GLN THR ARG GLN GLN GLN GLU HIS SEQRES 43 A 563 GLN LYS TYR MET VAL PRO LEU GLN ALA SER ALA GLN GLU SEQRES 44 A 563 LYS ASN GLY LEU HET L8P A 601 18 HETNAM L8P ({[(2S)-1-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-3- HETNAM 2 L8P HYDROXYPROPAN-2-YL]OXY}METHYL)PHOSPHONIC ACID HETSYN L8P CIDOFOVIR FORMUL 2 L8P C8 H14 N3 O6 P HELIX 1 AA1 ALA A 2 GLY A 11 1 10 HELIX 2 AA2 GLY A 14 LEU A 26 1 13 HELIX 3 AA3 PRO A 27 LEU A 29 5 3 HELIX 4 AA4 LEU A 30 THR A 36 1 7 HELIX 5 AA5 THR A 119 ASP A 125 1 7 HELIX 6 AA6 ARG A 131 LEU A 155 1 25 HELIX 7 AA7 GLY A 160 SER A 175 1 16 HELIX 8 AA8 ASN A 184 VAL A 211 1 28 HELIX 9 AA9 VAL A 229 SER A 231 5 3 HELIX 10 AB1 LEU A 232 VAL A 244 1 13 HELIX 11 AB2 HIS A 246 ALA A 256 1 11 HELIX 12 AB3 PRO A 257 TYR A 264 1 8 HELIX 13 AB4 SER A 271 GLY A 279 1 9 HELIX 14 AB5 ARG A 280 GLY A 296 1 17 HELIX 15 AB6 LYS A 297 LEU A 304 1 8 HELIX 16 AB7 SER A 305 LEU A 313 1 9 HELIX 17 AB8 CYS A 332 VAL A 357 1 26 HELIX 18 AB9 SER A 366 GLY A 375 1 10 HELIX 19 AC1 LEU A 379 VAL A 384 1 6 HELIX 20 AC2 VAL A 384 ILE A 389 1 6 HELIX 21 AC3 ARG A 394 LEU A 411 1 18 HELIX 22 AC4 ASN A 412 VAL A 414 5 3 HELIX 23 AC5 THR A 424 TYR A 449 1 26 HELIX 24 AC6 ILE A 453 MET A 464 1 12 HELIX 25 AC7 ARG A 466 SER A 476 1 11 HELIX 26 AC8 MET A 477 LEU A 481 5 5 HELIX 27 AC9 SER A 484 SER A 498 1 15 HELIX 28 AD1 VAL A 500 LEU A 504 5 5 SHEET 1 AA1 2 HIS A 47 CYS A 49 0 SHEET 2 AA1 2 TRP A 109 TYR A 111 -1 O ILE A 110 N HIS A 48 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 3765 SER A 521 HETATM 3766 P L8P A 601 105.899 116.654 102.079 1.00105.55 P HETATM 3767 N1 L8P A 601 106.894 111.705 101.421 1.00105.55 N HETATM 3768 C2 L8P A 601 106.924 110.278 101.841 1.00105.55 C HETATM 3769 O2 L8P A 601 107.962 109.725 101.980 1.00105.55 O HETATM 3770 N3 L8P A 601 105.655 109.546 102.088 1.00105.55 N HETATM 3771 C4 L8P A 601 104.382 110.215 101.920 1.00105.55 C HETATM 3772 N4 L8P A 601 103.144 109.497 102.162 1.00105.55 N HETATM 3773 C5 L8P A 601 104.342 111.641 101.499 1.00105.55 C HETATM 3774 C6 L8P A 601 105.614 112.376 101.249 1.00105.55 C HETATM 3775 C1' L8P A 601 108.139 112.412 101.177 1.00105.55 C HETATM 3776 C2' L8P A 601 108.320 113.574 102.148 1.00105.55 C HETATM 3777 C3' L8P A 601 109.767 114.053 102.219 1.00105.55 C HETATM 3778 O3' L8P A 601 110.149 114.496 100.947 1.00105.55 O HETATM 3779 C4' L8P A 601 107.391 115.680 102.613 1.00105.55 C HETATM 3780 O4' L8P A 601 107.548 114.644 101.687 1.00105.55 O HETATM 3781 OP1 L8P A 601 104.779 116.439 103.067 1.00105.55 O HETATM 3782 OP2 L8P A 601 105.453 116.181 100.718 1.00105.55 O HETATM 3783 O6 L8P A 601 106.249 118.121 102.017 1.00105.55 O CONECT 3766 3779 3781 3782 3783 CONECT 3767 3768 3774 3775 CONECT 3768 3767 3769 3770 CONECT 3769 3768 CONECT 3770 3768 3771 CONECT 3771 3770 3772 3773 CONECT 3772 3771 CONECT 3773 3771 3774 CONECT 3774 3767 3773 CONECT 3775 3767 3776 CONECT 3776 3775 3777 3780 CONECT 3777 3776 3778 CONECT 3778 3777 CONECT 3779 3766 3780 CONECT 3780 3776 3779 CONECT 3781 3766 CONECT 3782 3766 CONECT 3783 3766 MASTER 209 0 1 28 2 0 0 6 3782 1 18 44 END