HEADER TRANSPORT PROTEIN 17-JUL-25 9PMD TITLE HUMAN OCTN2 IN AN INWARD-FACING CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORGANIC CATION/CARNITINE TRANSPORTER 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIGH-AFFINITY SODIUM-DEPENDENT CARNITINE COTRANSPORTER, COMPND 5 SOLUTE CARRIER FAMILY 22 MEMBER 5; 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: SLC22A5, OCTN2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK-293F; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS-BASED VECTOR (BACMAM) KEYWDS TRANSPORTER, CARNITINE TRANSPORTER, ORGANIC CATION TRANSPORTER, SLC22 KEYWDS 2 FAMILY, SODIUM-DEPENDENT TRANSPORT, MEMBRANE PROTEIN, SOLUTE KEYWDS 3 CARRIER, METABOLIC TRANSPORT, FATTY ACID OXIDATION, OCTN2, SLC22A5, KEYWDS 4 TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.S.DAVIES,Y.Z.ZENG,A.G.STEWART REVDAT 2 10-DEC-25 9PMD 1 JRNL REVDAT 1 03-DEC-25 9PMD 0 JRNL AUTH J.S.DAVIES,Y.C.ZENG,C.BRIOT,S.H.J.BROWN,R.M.RYAN,A.G.STEWART JRNL TITL STRUCTURAL BASIS OF SODIUM ION-DEPENDENT CARNITINE TRANSPORT JRNL TITL 2 BY OCTN2. JRNL REF NAT COMMUN 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41318751 JRNL DOI 10.1038/S41467-025-66867-6 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, ISOLDE, COOT, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC 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 : FLEXIBLE FIT 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) : 2.990 REMARK 3 NUMBER OF PARTICLES : 94746 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9PMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000298113. 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 : NOVEL ORGANIC CATION TRANSPORT REMARK 245 2 (OCTN2;SLC22A5) IN AN INWARD- REMARK 245 FACING CONFORMATION REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : PELCO EASYGLOW 15 MA 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 K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 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) : 8100.00 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 GLY A 529 REMARK 465 MET A 530 REMARK 465 LYS A 531 REMARK 465 HIS A 532 REMARK 465 ARG A 533 REMARK 465 LYS A 534 REMARK 465 THR A 535 REMARK 465 PRO A 536 REMARK 465 SER A 537 REMARK 465 HIS A 538 REMARK 465 THR A 539 REMARK 465 ARG A 540 REMARK 465 MET A 541 REMARK 465 LEU A 542 REMARK 465 LYS A 543 REMARK 465 ASP A 544 REMARK 465 GLY A 545 REMARK 465 GLN A 546 REMARK 465 GLU A 547 REMARK 465 ARG A 548 REMARK 465 PRO A 549 REMARK 465 THR A 550 REMARK 465 ILE A 551 REMARK 465 LEU A 552 REMARK 465 LYS A 553 REMARK 465 SER A 554 REMARK 465 THR A 555 REMARK 465 ALA A 556 REMARK 465 PHE A 557 REMARK 465 GLY A 558 REMARK 465 ALA A 559 REMARK 465 ALA A 560 REMARK 465 PHE A 561 REMARK 465 GLU A 562 REMARK 465 SER A 563 REMARK 465 ARG A 564 REMARK 465 LEU A 565 REMARK 465 GLU A 566 REMARK 465 VAL A 567 REMARK 465 LEU A 568 REMARK 465 PHE A 569 REMARK 465 GLN A 570 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 OD1 ASP A 165 HH12 ARG A 169 1.58 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 CYS A 81 13.59 -141.06 REMARK 500 CYS A 136 -110.21 53.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 28 O REMARK 620 2 ASN A 32 OD1 104.7 REMARK 620 3 ASN A 210 OD1 174.5 72.0 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9PDQ RELATED DB: PDB REMARK 900 CONTAINS THE SAME PROTEIN IN THE OCCLUDED CONFORMATION REMARK 900 RELATED ID: 9PFB RELATED DB: PDB REMARK 900 CONTAINS THE SAME PROTEIN IN THE DRUG BOUND CONFORMATION REMARK 900 RELATED ID: EMD-71735 RELATED DB: EMDB REMARK 900 HUMAN OCTN2 IN AN INWARD-FACING CONFORMATION DBREF 9PMD A 1 557 UNP O76082 S22A5_HUMAN 1 557 SEQADV 9PMD GLY A 558 UNP O76082 EXPRESSION TAG SEQADV 9PMD ALA A 559 UNP O76082 EXPRESSION TAG SEQADV 9PMD ALA A 560 UNP O76082 EXPRESSION TAG SEQADV 9PMD PHE A 561 UNP O76082 EXPRESSION TAG SEQADV 9PMD GLU A 562 UNP O76082 EXPRESSION TAG SEQADV 9PMD SER A 563 UNP O76082 EXPRESSION TAG SEQADV 9PMD ARG A 564 UNP O76082 EXPRESSION TAG SEQADV 9PMD LEU A 565 UNP O76082 EXPRESSION TAG SEQADV 9PMD GLU A 566 UNP O76082 EXPRESSION TAG SEQADV 9PMD VAL A 567 UNP O76082 EXPRESSION TAG SEQADV 9PMD LEU A 568 UNP O76082 EXPRESSION TAG SEQADV 9PMD PHE A 569 UNP O76082 EXPRESSION TAG SEQADV 9PMD GLN A 570 UNP O76082 EXPRESSION TAG SEQRES 1 A 570 MET ARG ASP TYR ASP GLU VAL THR ALA PHE LEU GLY GLU SEQRES 2 A 570 TRP GLY PRO PHE GLN ARG LEU ILE PHE PHE LEU LEU SER SEQRES 3 A 570 ALA SER ILE ILE PRO ASN GLY PHE THR GLY LEU SER SER SEQRES 4 A 570 VAL PHE LEU ILE ALA THR PRO GLU HIS ARG CYS ARG VAL SEQRES 5 A 570 PRO ASP ALA ALA ASN LEU SER SER ALA TRP ARG ASN HIS SEQRES 6 A 570 THR VAL PRO LEU ARG LEU ARG ASP GLY ARG GLU VAL PRO SEQRES 7 A 570 HIS SER CYS ARG ARG TYR ARG LEU ALA THR ILE ALA ASN SEQRES 8 A 570 PHE SER ALA LEU GLY LEU GLU PRO GLY ARG ASP VAL ASP SEQRES 9 A 570 LEU GLY GLN LEU GLU GLN GLU SER CYS LEU ASP GLY TRP SEQRES 10 A 570 GLU PHE SER GLN ASP VAL TYR LEU SER THR ILE VAL THR SEQRES 11 A 570 GLU TRP ASN LEU VAL CYS GLU ASP ASP TRP LYS ALA PRO SEQRES 12 A 570 LEU THR ILE SER LEU PHE PHE VAL GLY VAL LEU LEU GLY SEQRES 13 A 570 SER PHE ILE SER GLY GLN LEU SER ASP ARG PHE GLY ARG SEQRES 14 A 570 LYS ASN VAL LEU PHE VAL THR MET GLY MET GLN THR GLY SEQRES 15 A 570 PHE SER PHE LEU GLN ILE PHE SER LYS ASN PHE GLU MET SEQRES 16 A 570 PHE VAL VAL LEU PHE VAL LEU VAL GLY MET GLY GLN ILE SEQRES 17 A 570 SER ASN TYR VAL ALA ALA PHE VAL LEU GLY THR GLU ILE SEQRES 18 A 570 LEU GLY LYS SER VAL ARG ILE ILE PHE SER THR LEU GLY SEQRES 19 A 570 VAL CYS ILE PHE TYR ALA PHE GLY TYR MET VAL LEU PRO SEQRES 20 A 570 LEU PHE ALA TYR PHE ILE ARG ASP TRP ARG MET LEU LEU SEQRES 21 A 570 VAL ALA LEU THR MET PRO GLY VAL LEU CYS VAL ALA LEU SEQRES 22 A 570 TRP TRP PHE ILE PRO GLU SER PRO ARG TRP LEU ILE SER SEQRES 23 A 570 GLN GLY ARG PHE GLU GLU ALA GLU VAL ILE ILE ARG LYS SEQRES 24 A 570 ALA ALA LYS ALA ASN GLY ILE VAL VAL PRO SER THR ILE SEQRES 25 A 570 PHE ASP PRO SER GLU LEU GLN ASP LEU SER SER LYS LYS SEQRES 26 A 570 GLN GLN SER HIS ASN ILE LEU ASP LEU LEU ARG THR TRP SEQRES 27 A 570 ASN ILE ARG MET VAL THR ILE MET SER ILE MET LEU TRP SEQRES 28 A 570 MET THR ILE SER VAL GLY TYR PHE GLY LEU SER LEU ASP SEQRES 29 A 570 THR PRO ASN LEU HIS GLY ASP ILE PHE VAL ASN CYS PHE SEQRES 30 A 570 LEU SER ALA MET VAL GLU VAL PRO ALA TYR VAL LEU ALA SEQRES 31 A 570 TRP LEU LEU LEU GLN TYR LEU PRO ARG ARG TYR SER MET SEQRES 32 A 570 ALA THR ALA LEU PHE LEU GLY GLY SER VAL LEU LEU PHE SEQRES 33 A 570 MET GLN LEU VAL PRO PRO ASP LEU TYR TYR LEU ALA THR SEQRES 34 A 570 VAL LEU VAL MET VAL GLY LYS PHE GLY VAL THR ALA ALA SEQRES 35 A 570 PHE SER MET VAL TYR VAL TYR THR ALA GLU LEU TYR PRO SEQRES 36 A 570 THR VAL VAL ARG ASN MET GLY VAL GLY VAL SER SER THR SEQRES 37 A 570 ALA SER ARG LEU GLY SER ILE LEU SER PRO TYR PHE VAL SEQRES 38 A 570 TYR LEU GLY ALA TYR ASP ARG PHE LEU PRO TYR ILE LEU SEQRES 39 A 570 MET GLY SER LEU THR ILE LEU THR ALA ILE LEU THR LEU SEQRES 40 A 570 PHE LEU PRO GLU SER PHE GLY THR PRO LEU PRO ASP THR SEQRES 41 A 570 ILE ASP GLN MET LEU ARG VAL LYS GLY MET LYS HIS ARG SEQRES 42 A 570 LYS THR PRO SER HIS THR ARG MET LEU LYS ASP GLY GLN SEQRES 43 A 570 GLU ARG PRO THR ILE LEU LYS SER THR ALA PHE GLY ALA SEQRES 44 A 570 ALA PHE GLU SER ARG LEU GLU VAL LEU PHE GLN HET NA A 601 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *2(H2 O) HELIX 1 AA1 ASP A 3 THR A 8 1 6 HELIX 2 AA2 ALA A 9 GLY A 12 5 4 HELIX 3 AA3 GLY A 15 SER A 28 1 14 HELIX 4 AA4 ILE A 29 LEU A 37 1 9 HELIX 5 AA5 SER A 38 ILE A 43 1 6 HELIX 6 AA6 SER A 59 ASN A 64 1 6 HELIX 7 AA7 ARG A 85 LEU A 95 1 11 HELIX 8 AA8 THR A 127 ASN A 133 1 7 HELIX 9 AA9 VAL A 135 ASP A 139 5 5 HELIX 10 AB1 TRP A 140 GLY A 168 1 29 HELIX 11 AB2 GLY A 168 GLN A 187 1 20 HELIX 12 AB3 ILE A 188 SER A 190 5 3 HELIX 13 AB4 ASN A 192 LEU A 222 1 31 HELIX 14 AB5 SER A 225 LEU A 233 1 9 HELIX 15 AB6 LEU A 233 ILE A 253 1 21 HELIX 16 AB7 ASP A 255 CYS A 270 1 16 HELIX 17 AB8 VAL A 271 PHE A 276 5 6 HELIX 18 AB9 SER A 280 GLN A 287 1 8 HELIX 19 AC1 ARG A 289 GLY A 305 1 17 HELIX 20 AC2 SER A 316 ASP A 320 5 5 HELIX 21 AC3 ASN A 330 LEU A 335 5 6 HELIX 22 AC4 THR A 337 ASP A 364 1 28 HELIX 23 AC5 THR A 365 LEU A 368 5 4 HELIX 24 AC6 ASP A 371 VAL A 382 1 12 HELIX 25 AC7 VAL A 382 LEU A 397 1 16 HELIX 26 AC8 PRO A 398 PHE A 416 1 19 HELIX 27 AC9 MET A 417 VAL A 420 5 4 HELIX 28 AD1 PRO A 421 LEU A 424 5 4 HELIX 29 AD2 TYR A 425 TYR A 454 1 30 HELIX 30 AD3 PRO A 455 VAL A 457 5 3 HELIX 31 AD4 VAL A 458 LEU A 483 1 26 HELIX 32 AD5 GLY A 484 TYR A 486 5 3 HELIX 33 AD6 PHE A 489 LEU A 507 1 19 HELIX 34 AD7 THR A 520 MET A 524 5 5 SHEET 1 AA1 2 LEU A 69 ARG A 72 0 SHEET 2 AA1 2 ARG A 75 PRO A 78 -1 O ARG A 75 N ARG A 72 SHEET 1 AA2 2 ARG A 83 TYR A 84 0 SHEET 2 AA2 2 GLN A 110 GLU A 111 -1 O GLU A 111 N ARG A 83 SSBOND 1 CYS A 50 CYS A 113 1555 1555 2.03 SSBOND 2 CYS A 81 CYS A 136 1555 1555 2.03 LINK O SER A 28 NA NA A 601 1555 1555 2.23 LINK OD1 ASN A 32 NA NA A 601 1555 1555 2.29 LINK OD1 ASN A 210 NA NA A 601 1555 1555 2.78 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 8433 LYS A 528 HETATM 8434 NA NA A 601 137.780 135.673 122.370 1.00 99.44 NA HETATM 8435 O HOH A 701 126.649 128.849 122.833 1.00116.25 O HETATM 8436 O HOH A 702 131.149 133.197 118.679 1.00 98.60 O CONECT 451 8434 CONECT 517 8434 CONECT 787 1768 CONECT 1273 2133 CONECT 1768 787 CONECT 2133 1273 CONECT 3306 8434 CONECT 8434 451 517 3306 MASTER 196 0 1 34 4 0 0 6 4193 1 8 44 END