HEADER MEMBRANE PROTEIN 25-JAN-24 8Y2D TITLE CRYO-EM STRUCTURE OF HUMAN DOPAMINE TRANSPORTER IN COMPLEX WITH TITLE 2 DOPAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM-DEPENDENT DOPAMINE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DA TRANSPORTER,DAT,SOLUTE CARRIER FAMILY 6 MEMBER 3; COMPND 5 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: SLC6A3, DAT1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS HUMAN DOPAMINE TRANSPORTER IN COMPLEX WITH DOPAMINE, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.ZHAO,Y.LI REVDAT 2 21-AUG-24 8Y2D 1 JRNL REVDAT 1 14-AUG-24 8Y2D 0 JRNL AUTH Y.LI,X.WANG,Y.MENG,T.HU,J.ZHAO,R.LI,Q.BAI,P.YUAN,J.HAN, JRNL AUTH 2 K.HAO,Y.WEI,Y.QIU,N.LI,Y.ZHAO JRNL TITL DOPAMINE REUPTAKE AND INHIBITORY MECHANISMS IN HUMAN JRNL TITL 2 DOPAMINE TRANSPORTER. JRNL REF NATURE 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 39112701 JRNL DOI 10.1038/S41586-024-07796-0 REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.800 REMARK 3 NUMBER OF PARTICLES : 213969 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 8Y2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 31-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044686. 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 : HUMAN DOPAMINE TRANSPORTER IN REMARK 245 COMPLEX WITH DOPAMINE 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 : 7.50 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 6000.00 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 ALA A 192 REMARK 465 HIS A 193 REMARK 465 PRO A 194 REMARK 465 GLY A 195 REMARK 465 ASP A 196 REMARK 465 SER A 197 REMARK 465 SER A 198 REMARK 465 GLY A 199 REMARK 465 ASP A 200 REMARK 465 SER A 201 REMARK 465 SER A 202 REMARK 465 GLY A 203 REMARK 465 LEU A 204 REMARK 465 ASN A 205 REMARK 465 ASP A 206 REMARK 465 THR A 207 REMARK 465 PHE A 208 REMARK 465 GLY A 258 REMARK 465 VAL A 259 REMARK 465 LYS A 260 REMARK 465 THR A 261 REMARK 465 SER A 262 REMARK 465 GLY A 263 REMARK 465 LYS A 264 REMARK 465 VAL A 265 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 LEU A 138 53.05 -95.77 REMARK 500 PRO A 187 -3.22 -59.62 REMARK 500 LEU A 298 33.90 -97.35 REMARK 500 PRO A 387 45.99 -83.08 REMARK 500 ALA A 397 45.03 -94.74 REMARK 500 GLN A 439 54.41 -91.56 REMARK 500 LEU A 441 50.35 -94.66 REMARK 500 HIS A 444 53.14 -92.00 REMARK 500 ARG A 544 75.86 53.10 REMARK 500 LYS A 599 -14.39 -142.98 REMARK 500 ASP A 600 33.82 -99.29 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 703 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 75 O REMARK 620 2 VAL A 78 O 82.2 REMARK 620 3 LEU A 418 O 172.5 94.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 702 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 77 O REMARK 620 2 ASP A 79 OD1 80.8 REMARK 620 3 ASN A 82 OD1 115.4 84.7 REMARK 620 4 SER A 321 O 79.2 105.9 163.5 REMARK 620 5 ASN A 353 OD1 83.1 154.4 84.3 90.4 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38851 RELATED DB: EMDB REMARK 900 STRUCTURE OF A PROTEINA DBREF 8Y2D A 68 620 UNP Q01959 SC6A3_HUMAN 68 620 SEQRES 1 A 553 ASP PHE LEU LEU SER VAL ILE GLY PHE ALA VAL ASP LEU SEQRES 2 A 553 ALA ASN VAL TRP ARG PHE PRO TYR LEU CYS TYR LYS ASN SEQRES 3 A 553 GLY GLY GLY ALA PHE LEU VAL PRO TYR LEU LEU PHE MET SEQRES 4 A 553 VAL ILE ALA GLY MET PRO LEU PHE TYR MET GLU LEU ALA SEQRES 5 A 553 LEU GLY GLN PHE ASN ARG GLU GLY ALA ALA GLY VAL TRP SEQRES 6 A 553 LYS ILE CYS PRO ILE LEU LYS GLY VAL GLY PHE THR VAL SEQRES 7 A 553 ILE LEU ILE SER LEU TYR VAL GLY PHE PHE TYR ASN VAL SEQRES 8 A 553 ILE ILE ALA TRP ALA LEU HIS TYR LEU PHE SER SER PHE SEQRES 9 A 553 THR THR GLU LEU PRO TRP ILE HIS CYS ASN ASN SER TRP SEQRES 10 A 553 ASN SER PRO ASN CYS SER ASP ALA HIS PRO GLY ASP SER SEQRES 11 A 553 SER GLY ASP SER SER GLY LEU ASN ASP THR PHE GLY THR SEQRES 12 A 553 THR PRO ALA ALA GLU TYR PHE GLU ARG GLY VAL LEU HIS SEQRES 13 A 553 LEU HIS GLN SER HIS GLY ILE ASP ASP LEU GLY PRO PRO SEQRES 14 A 553 ARG TRP GLN LEU THR ALA CYS LEU VAL LEU VAL ILE VAL SEQRES 15 A 553 LEU LEU TYR PHE SER LEU TRP LYS GLY VAL LYS THR SER SEQRES 16 A 553 GLY LYS VAL VAL TRP ILE THR ALA THR MET PRO TYR VAL SEQRES 17 A 553 VAL LEU THR ALA LEU LEU LEU ARG GLY VAL THR LEU PRO SEQRES 18 A 553 GLY ALA ILE ASP GLY ILE ARG ALA TYR LEU SER VAL ASP SEQRES 19 A 553 PHE TYR ARG LEU CYS GLU ALA SER VAL TRP ILE ASP ALA SEQRES 20 A 553 ALA THR GLN VAL CYS PHE SER LEU GLY VAL GLY PHE GLY SEQRES 21 A 553 VAL LEU ILE ALA PHE SER SER TYR ASN LYS PHE THR ASN SEQRES 22 A 553 ASN CYS TYR ARG ASP ALA ILE VAL THR THR SER ILE ASN SEQRES 23 A 553 SER LEU THR SER PHE SER SER GLY PHE VAL VAL PHE SER SEQRES 24 A 553 PHE LEU GLY TYR MET ALA GLN LYS HIS SER VAL PRO ILE SEQRES 25 A 553 GLY ASP VAL ALA LYS ASP GLY PRO GLY LEU ILE PHE ILE SEQRES 26 A 553 ILE TYR PRO GLU ALA ILE ALA THR LEU PRO LEU SER SER SEQRES 27 A 553 ALA TRP ALA VAL VAL PHE PHE ILE MET LEU LEU THR LEU SEQRES 28 A 553 GLY ILE ASP SER ALA MET GLY GLY MET GLU SER VAL ILE SEQRES 29 A 553 THR GLY LEU ILE ASP GLU PHE GLN LEU LEU HIS ARG HIS SEQRES 30 A 553 ARG GLU LEU PHE THR LEU PHE ILE VAL LEU ALA THR PHE SEQRES 31 A 553 LEU LEU SER LEU PHE CYS VAL THR ASN GLY GLY ILE TYR SEQRES 32 A 553 VAL PHE THR LEU LEU ASP HIS PHE ALA ALA GLY THR SER SEQRES 33 A 553 ILE LEU PHE GLY VAL LEU ILE GLU ALA ILE GLY VAL ALA SEQRES 34 A 553 TRP PHE TYR GLY VAL GLY GLN PHE SER ASP ASP ILE GLN SEQRES 35 A 553 GLN MET THR GLY GLN ARG PRO SER LEU TYR TRP ARG LEU SEQRES 36 A 553 CYS TRP LYS LEU VAL SER PRO CYS PHE LEU LEU PHE VAL SEQRES 37 A 553 VAL VAL VAL SER ILE VAL THR PHE ARG PRO PRO HIS TYR SEQRES 38 A 553 GLY ALA TYR ILE PHE PRO ASP TRP ALA ASN ALA LEU GLY SEQRES 39 A 553 TRP VAL ILE ALA THR SER SER MET ALA MET VAL PRO ILE SEQRES 40 A 553 TYR ALA ALA TYR LYS PHE CYS SER LEU PRO GLY SER PHE SEQRES 41 A 553 ARG GLU LYS LEU ALA TYR ALA ILE ALA PRO GLU LYS ASP SEQRES 42 A 553 ARG GLU LEU VAL ASP ARG GLY GLU VAL ARG GLN PHE THR SEQRES 43 A 553 LEU ARG HIS TRP LEU LYS VAL HET LDP A 701 11 HET NA A 702 1 HET NA A 703 1 HET CL A 704 1 HETNAM LDP L-DOPAMINE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN LDP DOPAMINE FORMUL 2 LDP C8 H11 N O2 FORMUL 3 NA 2(NA 1+) FORMUL 5 CL CL 1- FORMUL 6 HOH *4(H2 O) HELIX 1 AA1 ASP A 68 VAL A 78 1 11 HELIX 2 AA2 ASP A 79 TRP A 84 1 6 HELIX 3 AA3 ARG A 85 ASN A 93 1 9 HELIX 4 AA4 PHE A 98 ARG A 125 1 28 HELIX 5 AA5 ALA A 129 ILE A 134 5 6 HELIX 6 AA6 GLY A 140 SER A 170 1 31 HELIX 7 AA7 THR A 211 GLY A 220 1 10 HELIX 8 AA8 HIS A 223 SER A 227 5 5 HELIX 9 AA9 ARG A 237 LEU A 255 1 19 HELIX 10 AB1 TRP A 267 LEU A 287 1 21 HELIX 11 AB2 GLY A 289 LEU A 298 1 10 HELIX 12 AB3 SER A 309 GLY A 323 1 15 HELIX 13 AB4 GLY A 327 SER A 334 1 8 HELIX 14 AB5 ASN A 341 HIS A 375 1 35 HELIX 15 AB6 PRO A 378 VAL A 382 5 5 HELIX 16 AB7 GLY A 388 ALA A 397 1 10 HELIX 17 AB8 LEU A 403 PHE A 438 1 36 HELIX 18 AB9 HIS A 444 LEU A 461 1 18 HELIX 19 AC1 PHE A 462 THR A 465 5 4 HELIX 20 AC2 GLY A 467 ALA A 479 1 13 HELIX 21 AC3 ALA A 480 PHE A 498 1 19 HELIX 22 AC4 GLY A 500 THR A 512 1 13 HELIX 23 AC5 SER A 517 THR A 542 1 26 HELIX 24 AC6 PRO A 554 ALA A 570 1 17 HELIX 25 AC7 ALA A 570 LEU A 583 1 14 HELIX 26 AC8 SER A 586 ALA A 596 1 11 HELIX 27 AC9 ASP A 600 ARG A 606 1 7 HELIX 28 AD1 VAL A 609 THR A 613 5 5 SHEET 1 AA1 2 HIS A 547 TYR A 548 0 SHEET 2 AA1 2 TYR A 551 ILE A 552 -1 O TYR A 551 N TYR A 548 SSBOND 1 CYS A 180 CYS A 189 1555 1555 2.03 LINK O GLY A 75 NA NA A 703 1555 1555 2.36 LINK O ALA A 77 NA NA A 702 1555 1555 2.29 LINK O VAL A 78 NA NA A 703 1555 1555 2.24 LINK OD1 ASP A 79 NA NA A 702 1555 1555 2.39 LINK OD1 ASN A 82 NA NA A 702 1555 1555 2.28 LINK O SER A 321 NA NA A 702 1555 1555 2.52 LINK OD1 ASN A 353 NA NA A 702 1555 1555 2.91 LINK O LEU A 418 NA NA A 703 1555 1555 2.73 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