HEADER TRANSPORT PROTEIN 16-OCT-22 8ET9 TITLE CRYO-EM STRUCTURE OF THE ORGANIC CATION TRANSPORTER 2 IN COMPLEX WITH TITLE 2 1-METHYL-4-PHENYLPYRIDINIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: OCT2; 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 CATION, TRANSPORT, MEMBRANE PROTEIN, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.SUO,N.J.WRIGHT,S.-Y.LEE REVDAT 3 02-AUG-23 8ET9 1 JRNL REVDAT 2 12-JUL-23 8ET9 1 JRNL REVDAT 1 31-MAY-23 8ET9 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. 3.61 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 : 141.900 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) : 3.610 REMARK 3 NUMBER OF PARTICLES : 73474 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 8ET9 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_1000268602. 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 : OCT2 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 : 8029 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 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 PRO A 2 REMARK 465 LEU A 318 REMARK 465 GLN A 319 REMARK 465 GLU A 320 REMARK 465 GLU A 321 REMARK 465 ARG A 322 REMARK 465 LYS A 323 REMARK 465 GLU A 324 REMARK 465 THR A 325 REMARK 465 GLU A 326 REMARK 465 VAL A 327 REMARK 465 GLY A 328 REMARK 465 ILE A 424 REMARK 465 PRO A 425 REMARK 465 ASP A 426 REMARK 465 GLY A 427 REMARK 465 PRO A 535 REMARK 465 ARG A 536 REMARK 465 LYS A 537 REMARK 465 ASN A 538 REMARK 465 LYS A 539 REMARK 465 GLU A 540 REMARK 465 LYS A 541 REMARK 465 MET A 542 REMARK 465 ILE A 543 REMARK 465 TYR A 544 REMARK 465 LEU A 545 REMARK 465 GLN A 546 REMARK 465 VAL A 547 REMARK 465 LEU A 548 REMARK 465 LEU A 549 REMARK 465 SER A 550 REMARK 465 ASP A 551 REMARK 465 ILE A 552 REMARK 465 PRO A 553 REMARK 465 ASP A 554 REMARK 465 ASN A 555 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 53 OG REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 LEU A 59 CG CD1 CD2 REMARK 470 SER A 60 OG REMARK 470 GLN A 61 CG CD OE1 NE2 REMARK 470 ARG A 62 CG CD NE CZ NH1 NH2 REMARK 470 SER A 66 OG REMARK 470 LEU A 67 CG CD1 CD2 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 GLU A 69 CG CD OE1 OE2 REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 LEU A 71 CG CD1 CD2 REMARK 470 VAL A 78 CG1 CG2 REMARK 470 SER A 80 OG REMARK 470 SER A 81 OG REMARK 470 GLU A 83 CG CD OE1 OE2 REMARK 470 SER A 85 OG REMARK 470 ARG A 91 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 92 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 VAL A 94 CG1 CG2 REMARK 470 ASP A 95 CG OD1 OD2 REMARK 470 ASN A 97 CG OD1 ND2 REMARK 470 GLN A 98 CG CD OE1 NE2 REMARK 470 THR A 99 OG1 CG2 REMARK 470 LEU A 101 CG CD1 CD2 REMARK 470 SER A 102 OG REMARK 470 THR A 104 OG1 CG2 REMARK 470 ASP A 105 CG OD1 OD2 REMARK 470 LEU A 107 CG CD1 CD2 REMARK 470 SER A 109 OG REMARK 470 LEU A 110 CG CD1 CD2 REMARK 470 ASN A 113 CG OD1 ND2 REMARK 470 ARG A 114 CG CD NE CZ NH1 NH2 REMARK 470 SER A 115 OG REMARK 470 HIS A 116 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 117 CG CD1 CD2 REMARK 470 LEU A 119 CG CD1 CD2 REMARK 470 GLN A 123 CG CD OE1 NE2 REMARK 470 ASP A 124 CG OD1 OD2 REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 LYS A 330 CG CD CE NZ REMARK 470 ARG A 340 CG CD NE CZ NH1 NH2 REMARK 470 MET A 369 CG SD CE REMARK 470 LEU A 428 CG CD1 CD2 REMARK 470 PHE A 429 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TRP A 430 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 430 CZ3 CH2 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 ILE A 491 CG1 CG2 CD1 REMARK 470 GLU A 494 CG CD OE1 OE2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 HIS A 533 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 534 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LEU A 43 HG SER A 134 1.59 REMARK 500 N PHE A 161 OD2 ASP A 475 2.06 REMARK 500 O LEU A 43 OG SER A 134 2.13 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 GLN A 98 -4.72 74.24 REMARK 500 ALA A 112 -4.74 74.36 REMARK 500 CYS A 143 -61.80 -95.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-28589 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE ORGANIC CATION TRANSPORTER 2 IN COMPLEX REMARK 900 WITH 1-METHYL-4-PHENYLPYRIDINIUM DBREF 8ET9 A 1 555 PDB 8ET9 8ET9 1 555 SEQRES 1 A 555 MET PRO THR THR PHE ASP ASP ILE LEU GLU HIS ILE GLY SEQRES 2 A 555 GLU PHE GLY ARG PHE GLN LYS GLN THR PHE PHE LEU LEU SEQRES 3 A 555 CYS LEU LEU SER ALA ALA PHE ALA PRO ILE TYR VAL GLY SEQRES 4 A 555 ILE VAL PHE LEU GLY PHE THR PRO ASP HIS ARG CYS ARG SEQRES 5 A 555 SER PRO GLY VAL ALA GLU LEU SER GLN ARG CYS GLY TRP SEQRES 6 A 555 SER LEU GLU GLU GLU LEU ASN TYR THR VAL PRO GLY VAL SEQRES 7 A 555 GLY SER SER GLY GLU ALA SER PRO SER GLN CYS ARG ARG SEQRES 8 A 555 TYR GLU VAL ASP TRP ASN GLN THR GLY LEU SER CYS THR SEQRES 9 A 555 ASP PRO LEU ALA SER LEU ALA ALA ASN ARG SER HIS LEU SEQRES 10 A 555 PRO LEU GLY PRO CYS GLN ASP GLY TRP VAL TYR ASP THR SEQRES 11 A 555 PRO GLY SER SER ILE VAL THR GLU PHE ASN LEU VAL CYS SEQRES 12 A 555 ALA ASP SER TRP MET LEU ASP LEU VAL GLN ALA ALA VAL SEQRES 13 A 555 ASN VAL GLY PHE PHE VAL GLY SER MET SER ILE GLY TYR SEQRES 14 A 555 ILE ALA ASP ARG PHE GLY ARG LYS LEU CYS LEU LEU VAL SEQRES 15 A 555 THR ILE LEU ILE ASN ALA ILE SER GLY VAL LEU MET ALA SEQRES 16 A 555 VAL ALA PRO ASN TYR THR TRP MET LEU ILE PHE ARG LEU SEQRES 17 A 555 ILE GLN GLY LEU VAL SER LYS GLY GLY TRP LEU ILE GLY SEQRES 18 A 555 TYR THR LEU PRO THR GLU PHE VAL GLY LEU GLU TYR ARG SEQRES 19 A 555 ARG THR VAL GLY ILE LEU TYR GLN MET ALA PHE SER VAL SEQRES 20 A 555 GLY LEU LEU VAL LEU ALA GLY VAL ALA TYR ALA ILE PRO SEQRES 21 A 555 HIS TRP ARG TRP LEU GLN LEU ALA VAL THR LEU PRO ASN SEQRES 22 A 555 PHE PHE PHE LEU LEU TYR TYR TRP CYS ILE PRO GLU SER SEQRES 23 A 555 PRO ARG TRP LEU ILE SER GLN ASN LYS ASN ALA LYS ALA SEQRES 24 A 555 MET LYS ILE ILE LYS HIS ILE ALA LYS LYS ASN GLY LYS SEQRES 25 A 555 LYS LEU PRO LYS SER LEU GLN GLU GLU ARG LYS GLU THR SEQRES 26 A 555 GLU VAL GLY GLU LYS LEU ASN PRO SER PHE LEU ASP LEU SEQRES 27 A 555 VAL ARG THR PRO GLN ILE ARG LYS HIS THR LEU ILE LEU SEQRES 28 A 555 MET TYR ASN TRP PHE THR SER SER VAL LEU TYR GLN GLY SEQRES 29 A 555 LEU ILE MET HIS MET GLY ILE ALA GLY GLY ASN ILE TYR SEQRES 30 A 555 LEU ASP PHE PHE TYR SER ALA LEU VAL GLU PHE PRO ALA SEQRES 31 A 555 ALA PHE ILE ILE ILE LEU THR ILE ASP ARG ILE GLY ARG SEQRES 32 A 555 ARG TYR PRO TRP ALA ALA ALA ASN MET VAL ALA GLY ALA SEQRES 33 A 555 ALA CYS LEU ILE THR ALA PHE ILE PRO ASP GLY LEU PHE SEQRES 34 A 555 TRP LEU LYS THR THR VAL ALA CYS LEU GLY ARG MET GLY SEQRES 35 A 555 ILE THR MET ALA PHE GLU MET VAL CYS PHE VAL ASN THR SEQRES 36 A 555 GLU LEU TYR PRO THR PHE ILE ARG ASN LEU GLY VAL LEU SEQRES 37 A 555 VAL CYS SER SER LEU CYS ASP ILE GLY GLY ILE ILE THR SEQRES 38 A 555 PRO PHE LEU VAL TYR ARG LEU ALA SER ILE TRP LEU GLU SEQRES 39 A 555 LEU PRO LEU VAL VAL PHE ALA VAL LEU GLY LEU ILE ALA SEQRES 40 A 555 GLY GLY LEU VAL LEU LEU LEU PRO GLU THR LYS GLY LYS SEQRES 41 A 555 PRO LEU PRO GLU THR ILE GLU ASP ALA GLU ASN PRO HIS SEQRES 42 A 555 ARG PRO ARG LYS ASN LYS GLU LYS MET ILE TYR LEU GLN SEQRES 43 A 555 VAL LEU LEU SER ASP ILE PRO ASP ASN HET WRF A 601 25 HETNAM WRF 1-METHYL-4-PHENYLPYRIDIN-1-IUM FORMUL 2 WRF C12 H12 N 1+ HELIX 1 AA1 THR A 4 GLY A 13 1 10 HELIX 2 AA2 GLY A 16 GLY A 39 1 24 HELIX 3 AA3 GLY A 39 GLY A 44 1 6 HELIX 4 AA4 SER A 53 CYS A 63 1 11 HELIX 5 AA5 SER A 66 THR A 74 1 9 HELIX 6 AA6 ALA A 84 ARG A 90 1 7 HELIX 7 AA7 SER A 134 ASN A 140 1 7 HELIX 8 AA8 ASP A 145 GLY A 175 1 31 HELIX 9 AA9 GLY A 175 ALA A 195 1 21 HELIX 10 AB1 ASN A 199 VAL A 229 1 31 HELIX 11 AB2 TYR A 233 ILE A 259 1 27 HELIX 12 AB3 HIS A 261 THR A 270 1 10 HELIX 13 AB4 THR A 270 TYR A 280 1 11 HELIX 14 AB5 TRP A 281 ILE A 283 5 3 HELIX 15 AB6 SER A 286 GLN A 293 1 8 HELIX 16 AB7 LYS A 295 GLY A 311 1 17 HELIX 17 AB8 LEU A 336 THR A 341 1 6 HELIX 18 AB9 THR A 341 HIS A 368 1 28 HELIX 19 AC1 ASN A 375 GLY A 402 1 28 HELIX 20 AC2 ARG A 403 PHE A 423 1 21 HELIX 21 AC3 PHE A 429 TYR A 458 1 30 HELIX 22 AC4 PRO A 459 TRP A 492 1 34 HELIX 23 AC5 GLU A 494 LEU A 512 1 19 HELIX 24 AC6 THR A 525 ASN A 531 1 7 SHEET 1 AA1 2 HIS A 49 CYS A 51 0 SHEET 2 AA1 2 TRP A 126 TYR A 128 -1 O VAL A 127 N ARG A 50 SSBOND 1 CYS A 51 CYS A 122 1555 1555 2.03 SSBOND 2 CYS A 63 CYS A 103 1555 1555 2.03 SSBOND 3 CYS A 89 CYS A 143 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