PDB Short entry for 8ET7 HEADER TRANSPORT PROTEIN 16-OCT-22 8ET7 TITLE CRYO-EM STRUCTURE OF THE ORGANIC CATION TRANSPORTER 1 IN COMPLEX WITH TITLE 2 DIPHENHYDRAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OCT1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS ORGANIC CATION, TRANSPORT, MEMBRANE PROTEIN, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.SUO,N.J.WRIGHT,S.-Y.LEE REVDAT 3 02-AUG-23 8ET7 1 JRNL REVDAT 2 12-JUL-23 8ET7 1 JRNL REVDAT 1 31-MAY-23 8ET7 0 JRNL AUTH Y.SUO,N.J.WRIGHT,H.GUTERRES,J.G.FEDOR,K.J.BUTAY,M.J.BORGNIA, JRNL AUTH 2 W.IM,S.Y.LEE JRNL TITL MOLECULAR BASIS OF POLYSPECIFIC DRUG AND XENOBIOTIC JRNL TITL 2 RECOGNITION BY OCT1 AND OCT2. JRNL REF NAT.STRUCT.MOL.BIOL. V. 30 1001 2023 JRNL REFN ESSN 1545-9985 JRNL PMID 37291422 JRNL DOI 10.1038/S41594-023-01017-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.SUO,N.J.WRIGHT,H.GUTERRES,J.G.FEDOR,K.J.BUTAY,M.J.BORGNIA, REMARK 1 AUTH 2 W.IM,S.Y.LEE REMARK 1 TITL MOLECULAR BASIS OF POLYSPECIFIC DRUG BINDING AND TRANSPORT REMARK 1 TITL 2 BY OCT1 AND OCT2. REMARK 1 REF BIORXIV 2023 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 36993738 REMARK 1 DOI 10.1101/2023.03.15.532610 REMARK 2 REMARK 2 RESOLUTION. 3.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, LATITUDE, GCTF, COOT, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 164.400 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) : 3.770 REMARK 3 NUMBER OF PARTICLES : 189193 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 8ET7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1000268244. 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 : OCT1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.00 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 : 7145 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) : 800.00 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) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 81000 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, B 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 LYS A 534 REMARK 465 ALA A 535 REMARK 465 LYS A 536 REMARK 465 PRO A 537 REMARK 465 LYS A 538 REMARK 465 GLU A 539 REMARK 465 ASN A 540 REMARK 465 THR A 541 REMARK 465 ILE A 542 REMARK 465 TYR A 543 REMARK 465 LEU A 544 REMARK 465 GLN A 545 REMARK 465 VAL A 546 REMARK 465 GLN A 547 REMARK 465 THR A 548 REMARK 465 SER A 549 REMARK 465 GLU A 550 REMARK 465 LEU A 551 REMARK 465 PRO A 552 REMARK 465 GLY A 553 REMARK 465 THR A 554 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 GLU A 57 CG CD OE1 OE2 REMARK 470 GLN A 60 CG CD OE1 NE2 REMARK 470 GLU A 82 CG CD OE1 OE2 REMARK 470 GLU A 92 CG CD OE1 OE2 REMARK 470 ASP A 94 CG OD1 OD2 REMARK 470 GLN A 97 CG CD OE1 NE2 REMARK 470 SER A 101 OG REMARK 470 LEU A 116 CG CD1 CD2 REMARK 470 ASP A 316 CG OD1 OD2 REMARK 470 MET A 319 CG SD CE REMARK 470 LYS A 323 CG CD CE NZ REMARK 470 GLU A 324 CG CD OE1 OE2 REMARK 470 ASP A 325 CG OD1 OD2 REMARK 470 THR A 327 OG1 CG2 REMARK 470 GLU A 328 CG CD OE1 OE2 REMARK 470 LYS A 329 CG CD CE NZ REMARK 470 THR A 371 OG1 CG2 REMARK 470 ILE A 421 CG1 CG2 CD1 REMARK 470 GLN A 425 CG CD OE1 NE2 REMARK 470 LEU A 427 CG CD1 CD2 REMARK 470 GLU A 489 CG CD OE1 OE2 REMARK 470 VAL A 490 CG1 CG2 REMARK 470 GLU A 529 CG CD OE1 OE2 REMARK 470 ARG A 533 CG CD NE CZ NH1 NH2 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 ALA A 83 13.22 -141.16 REMARK 500 SER A 101 144.39 71.51 REMARK 500 ALA A 111 17.40 59.66 REMARK 500 ASN A 112 149.21 -170.46 REMARK 500 GLN A 122 -168.53 -78.77 REMARK 500 VAL A 141 -63.74 -107.13 REMARK 500 SER A 321 -179.54 -172.39 REMARK 500 ASN A 530 30.75 -96.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-28587 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE ORGANIC CATION TRANSPORTER 1 IN COMPLEX REMARK 900 WITH DIPHENHYDRAMINE DBREF 8ET7 A 1 554 PDB 8ET7 8ET7 1 554 SEQRES 1 A 554 MET PRO THR VAL ASP ASP VAL LEU GLU GLN VAL GLY GLU SEQRES 2 A 554 PHE GLY TRP PHE GLN LYS GLN ALA PHE LEU THR LEU CYS SEQRES 3 A 554 LEU LEU SER ALA ALA PHE ALA PRO ILE TYR VAL GLY ILE SEQRES 4 A 554 VAL PHE LEU GLY PHE THR PRO ASP HIS ARG CYS ARG SER SEQRES 5 A 554 PRO GLY VAL ALA GLU LEU SER GLN ARG CYS GLY TRP SER SEQRES 6 A 554 LEU ALA GLU GLU LEU ASN TYR THR VAL PRO GLY LEU GLY SEQRES 7 A 554 ALA ALA GLY GLU ALA PHE PRO ARG GLN CYS ARG ARG TYR SEQRES 8 A 554 GLU VAL ASP TRP ASN GLN SER ALA LEU SER CYS VAL ASP SEQRES 9 A 554 PRO LEU ALA SER LEU ALA ALA ASN ARG SER HIS LEU PRO SEQRES 10 A 554 LEU GLY PRO CYS GLN HIS GLY TRP VAL TYR ASP THR PRO SEQRES 11 A 554 GLY SER SER ILE VAL THR GLU PHE ASN LEU VAL CYS ALA SEQRES 12 A 554 ASP SER TRP LYS VAL ASP LEU PHE GLN SER CYS VAL ASN SEQRES 13 A 554 VAL GLY PHE PHE LEU GLY SER LEU GLY VAL GLY TYR ILE SEQRES 14 A 554 ALA ASP ARG PHE GLY ARG LYS LEU CYS LEU LEU ALA THR SEQRES 15 A 554 THR LEU ILE SER ALA VAL SER GLY VAL LEU MET ALA VAL SEQRES 16 A 554 ALA PRO ASP TYR THR SER MET LEU LEU PHE ARG LEU LEU SEQRES 17 A 554 GLN GLY LEU VAL SER LYS GLY SER TRP MET SER GLY TYR SEQRES 18 A 554 THR LEU ILE THR GLU PHE VAL GLY SER GLY TYR ARG ARG SEQRES 19 A 554 THR VAL ALA ILE LEU TYR GLN MET ALA PHE THR VAL GLY SEQRES 20 A 554 LEU VAL LEU LEU SER GLY VAL ALA TYR ALA ILE PRO HIS SEQRES 21 A 554 TRP ARG TRP LEU GLN LEU ALA VAL SER LEU PRO THR PHE SEQRES 22 A 554 LEU PHE LEU LEU TYR TYR TRP CYS VAL PRO GLU SER PRO SEQRES 23 A 554 ARG TRP LEU LEU SER GLN LYS ARG ASN THR GLN ALA ILE SEQRES 24 A 554 LYS ILE MET ASP HIS ILE ALA GLN LYS ASN GLY LYS LEU SEQRES 25 A 554 PRO PRO ALA ASP LEU LYS MET LEU SER LEU LYS GLU ASP SEQRES 26 A 554 SER THR GLU LYS LEU SER PRO SER PHE ALA ASP LEU PHE SEQRES 27 A 554 ARG THR PRO GLN LEU ARG LYS HIS THR PHE ILE LEU MET SEQRES 28 A 554 TYR LEU TRP PHE THR SER SER VAL LEU TYR GLN GLY LEU SEQRES 29 A 554 ILE MET HIS MET GLY ALA THR GLY GLY ASN LEU TYR LEU SEQRES 30 A 554 ASP PHE PHE TYR SER ALA LEU VAL GLU PHE PRO ALA ALA SEQRES 31 A 554 PHE ILE ILE LEU VAL THR ILE ASP ARG VAL GLY ARG ILE SEQRES 32 A 554 TYR PRO LEU ALA VAL SER ASN LEU VAL ALA GLY ALA ALA SEQRES 33 A 554 CYS LEU ILE MET ILE PHE ILE SER GLN ASP LEU HIS TRP SEQRES 34 A 554 LEU ASN ILE THR VAL ALA CYS VAL GLY ARG MET GLY ILE SEQRES 35 A 554 THR ILE VAL PHE GLN MET VAL CYS LEU VAL ASN ALA GLU SEQRES 36 A 554 LEU TYR PRO THR PHE ILE ARG ASN LEU GLY VAL MET VAL SEQRES 37 A 554 CYS SER SER LEU CYS ASP LEU GLY GLY ILE ILE THR PRO SEQRES 38 A 554 PHE LEU VAL PHE ARG LEU MET GLU VAL TRP GLN GLY LEU SEQRES 39 A 554 PRO LEU ILE LEU PHE THR VAL VAL GLY LEU VAL ALA GLY SEQRES 40 A 554 GLY MET THR LEU LEU LEU PRO GLU THR LYS GLY VAL ALA SEQRES 41 A 554 LEU PRO GLU THR ILE GLU ASP ALA GLU ASN LEU GLY ARG SEQRES 42 A 554 LYS ALA LYS PRO LYS GLU ASN THR ILE TYR LEU GLN VAL SEQRES 43 A 554 GLN THR SER GLU LEU PRO GLY THR HET NAG B 1 26 HET NAG B 2 27 HET 2PM A 601 40 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM 2PM N-[2-(BENZHYDRYLOXY)ETHYL]-N,N-DIMETHYLAMINE 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 2PM DIPHENHYDRAMINE; ANTISTOMINUM; BENZHYDRAMINE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 2PM C17 H21 N O HELIX 1 AA1 THR A 3 GLY A 12 1 10 HELIX 2 AA2 GLY A 15 PHE A 32 1 18 HELIX 3 AA3 PHE A 32 GLY A 38 1 7 HELIX 4 AA4 SER A 52 CYS A 62 1 11 HELIX 5 AA5 SER A 65 VAL A 74 1 10 HELIX 6 AA6 ALA A 83 ARG A 89 1 7 HELIX 7 AA7 LEU A 106 ALA A 111 1 6 HELIX 8 AA8 SER A 133 ASN A 139 1 7 HELIX 9 AA9 SER A 145 VAL A 166 1 22 HELIX 10 AB1 VAL A 166 PHE A 173 1 8 HELIX 11 AB2 GLY A 174 ALA A 194 1 21 HELIX 12 AB3 ASP A 198 VAL A 228 1 31 HELIX 13 AB4 TYR A 232 ILE A 258 1 27 HELIX 14 AB5 HIS A 260 TYR A 278 1 19 HELIX 15 AB6 TYR A 279 CYS A 281 5 3 HELIX 16 AB7 SER A 285 GLN A 292 1 8 HELIX 17 AB8 ARG A 294 GLY A 310 1 17 HELIX 18 AB9 PRO A 314 LEU A 320 5 7 HELIX 19 AC1 PHE A 334 ARG A 339 5 6 HELIX 20 AC2 THR A 340 HIS A 367 1 28 HELIX 21 AC3 ASN A 374 VAL A 385 1 12 HELIX 22 AC4 VAL A 385 GLY A 401 1 17 HELIX 23 AC5 ILE A 403 ILE A 423 1 21 HELIX 24 AC6 HIS A 428 TYR A 457 1 30 HELIX 25 AC7 ILE A 461 TRP A 491 1 31 HELIX 26 AC8 GLY A 493 THR A 510 1 18 HELIX 27 AC9 LEU A 511 LEU A 513 5 3 HELIX 28 AD1 THR A 524 ASN A 530 1 7 SHEET 1 AA1 2 HIS A 48 ARG A 49 0 SHEET 2 AA1 2 VAL A 126 TYR A 127 -1 O VAL A 126 N ARG A 49 SSBOND 1 CYS A 50 CYS A 121 1555 1555 2.03 SSBOND 2 CYS A 62 CYS A 102 1555 1555 2.03 SSBOND 3 CYS A 88 CYS A 142 1555 1555 2.03 LINK ND2 ASN A 71 C1 NAG B 1 1555 1555 1.43 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 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