HEADER MEMBRANE PROTEIN 25-JAN-24 8Y2C TITLE CRYO-EM STRUCTURE OF HUMAN DOPAMINE TRANSPORTER IN APO STATE 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 APO STATE, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.ZHAO,Y.LI REVDAT 4 06-NOV-24 8Y2C 1 REMARK REVDAT 3 28-AUG-24 8Y2C 1 JRNL REVDAT 2 21-AUG-24 8Y2C 1 JRNL REVDAT 1 14-AUG-24 8Y2C 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 V. 632 686 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 39112701 JRNL DOI 10.1038/S41586-024-07796-0 REMARK 2 REMARK 2 RESOLUTION. 3.16 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) : 3.160 REMARK 3 NUMBER OF PARTICLES : 55436 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 8Y2C 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_1300044685. 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 APO STATE 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 LYS A 257 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: 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 OH TYR A 593 OD1 ASP A 605 2.16 REMARK 500 OD1 ASN A 82 OG SER A 357 2.18 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 TRP A 132 51.46 -92.36 REMARK 500 CYS A 135 86.63 -150.94 REMARK 500 TRP A 177 49.93 -91.82 REMARK 500 PRO A 187 7.04 -69.76 REMARK 500 LEU A 298 57.75 -95.25 REMARK 500 LEU A 441 58.27 -93.23 REMARK 500 ARG A 544 67.19 33.48 REMARK 500 ALA A 570 35.44 -98.67 REMARK 500 ASP A 600 34.60 -99.24 REMARK 500 ARG A 606 49.68 -85.13 REMARK 500 PHE A 612 50.63 -90.89 REMARK 500 LEU A 618 58.99 -92.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38850 RELATED DB: EMDB REMARK 900 STRUCTURE OF A PROTEINA DBREF 8Y2C A 66 620 UNP Q01959 SC6A3_HUMAN 66 620 SEQRES 1 A 555 LYS ILE ASP PHE LEU LEU SER VAL ILE GLY PHE ALA VAL SEQRES 2 A 555 ASP LEU ALA ASN VAL TRP ARG PHE PRO TYR LEU CYS TYR SEQRES 3 A 555 LYS ASN GLY GLY GLY ALA PHE LEU VAL PRO TYR LEU LEU SEQRES 4 A 555 PHE MET VAL ILE ALA GLY MET PRO LEU PHE TYR MET GLU SEQRES 5 A 555 LEU ALA LEU GLY GLN PHE ASN ARG GLU GLY ALA ALA GLY SEQRES 6 A 555 VAL TRP LYS ILE CYS PRO ILE LEU LYS GLY VAL GLY PHE SEQRES 7 A 555 THR VAL ILE LEU ILE SER LEU TYR VAL GLY PHE PHE TYR SEQRES 8 A 555 ASN VAL ILE ILE ALA TRP ALA LEU HIS TYR LEU PHE SER SEQRES 9 A 555 SER PHE THR THR GLU LEU PRO TRP ILE HIS CYS ASN ASN SEQRES 10 A 555 SER TRP ASN SER PRO ASN CYS SER ASP ALA HIS PRO GLY SEQRES 11 A 555 ASP SER SER GLY ASP SER SER GLY LEU ASN ASP THR PHE SEQRES 12 A 555 GLY THR THR PRO ALA ALA GLU TYR PHE GLU ARG GLY VAL SEQRES 13 A 555 LEU HIS LEU HIS GLN SER HIS GLY ILE ASP ASP LEU GLY SEQRES 14 A 555 PRO PRO ARG TRP GLN LEU THR ALA CYS LEU VAL LEU VAL SEQRES 15 A 555 ILE VAL LEU LEU TYR PHE SER LEU TRP LYS GLY VAL LYS SEQRES 16 A 555 THR SER GLY LYS VAL VAL TRP ILE THR ALA THR MET PRO SEQRES 17 A 555 TYR VAL VAL LEU THR ALA LEU LEU LEU ARG GLY VAL THR SEQRES 18 A 555 LEU PRO GLY ALA ILE ASP GLY ILE ARG ALA TYR LEU SER SEQRES 19 A 555 VAL ASP PHE TYR ARG LEU CYS GLU ALA SER VAL TRP ILE SEQRES 20 A 555 ASP ALA ALA THR GLN VAL CYS PHE SER LEU GLY VAL GLY SEQRES 21 A 555 PHE GLY VAL LEU ILE ALA PHE SER SER TYR ASN LYS PHE SEQRES 22 A 555 THR ASN ASN CYS TYR ARG ASP ALA ILE VAL THR THR SER SEQRES 23 A 555 ILE ASN SER LEU THR SER PHE SER SER GLY PHE VAL VAL SEQRES 24 A 555 PHE SER PHE LEU GLY TYR MET ALA GLN LYS HIS SER VAL SEQRES 25 A 555 PRO ILE GLY ASP VAL ALA LYS ASP GLY PRO GLY LEU ILE SEQRES 26 A 555 PHE ILE ILE TYR PRO GLU ALA ILE ALA THR LEU PRO LEU SEQRES 27 A 555 SER SER ALA TRP ALA VAL VAL PHE PHE ILE MET LEU LEU SEQRES 28 A 555 THR LEU GLY ILE ASP SER ALA MET GLY GLY MET GLU SER SEQRES 29 A 555 VAL ILE THR GLY LEU ILE ASP GLU PHE GLN LEU LEU HIS SEQRES 30 A 555 ARG HIS ARG GLU LEU PHE THR LEU PHE ILE VAL LEU ALA SEQRES 31 A 555 THR PHE LEU LEU SER LEU PHE CYS VAL THR ASN GLY GLY SEQRES 32 A 555 ILE TYR VAL PHE THR LEU LEU ASP HIS PHE ALA ALA GLY SEQRES 33 A 555 THR SER ILE LEU PHE GLY VAL LEU ILE GLU ALA ILE GLY SEQRES 34 A 555 VAL ALA TRP PHE TYR GLY VAL GLY GLN PHE SER ASP ASP SEQRES 35 A 555 ILE GLN GLN MET THR GLY GLN ARG PRO SER LEU TYR TRP SEQRES 36 A 555 ARG LEU CYS TRP LYS LEU VAL SER PRO CYS PHE LEU LEU SEQRES 37 A 555 PHE VAL VAL VAL VAL SER ILE VAL THR PHE ARG PRO PRO SEQRES 38 A 555 HIS TYR GLY ALA TYR ILE PHE PRO ASP TRP ALA ASN ALA SEQRES 39 A 555 LEU GLY TRP VAL ILE ALA THR SER SER MET ALA MET VAL SEQRES 40 A 555 PRO ILE TYR ALA ALA TYR LYS PHE CYS SER LEU PRO GLY SEQRES 41 A 555 SER PHE ARG GLU LYS LEU ALA TYR ALA ILE ALA PRO GLU SEQRES 42 A 555 LYS ASP ARG GLU LEU VAL ASP ARG GLY GLU VAL ARG GLN SEQRES 43 A 555 PHE THR LEU ARG HIS TRP LEU LYS VAL HET NAG A 701 14 HET NAG A 702 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 2 NAG 2(C8 H15 N O6) HELIX 1 AA1 LYS A 66 VAL A 78 1 13 HELIX 2 AA2 ASP A 79 TRP A 84 1 6 HELIX 3 AA3 TRP A 84 ASN A 93 1 10 HELIX 4 AA4 PHE A 98 GLY A 110 1 13 HELIX 5 AA5 GLY A 110 ARG A 125 1 16 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 TRP A 256 1 20 HELIX 10 AB1 TRP A 267 LEU A 287 1 21 HELIX 11 AB2 ALA A 290 ALA A 296 1 7 HELIX 12 AB3 ASP A 301 CYS A 306 1 6 HELIX 13 AB4 ALA A 308 GLY A 323 1 16 HELIX 14 AB5 GLY A 327 SER A 334 1 8 HELIX 15 AB6 CYS A 342 SER A 376 1 35 HELIX 16 AB7 LEU A 389 THR A 400 1 12 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 THR A 482 PHE A 498 1 17 HELIX 22 AC4 GLY A 500 THR A 512 1 13 HELIX 23 AC5 SER A 517 LEU A 526 1 10 HELIX 24 AC6 LEU A 526 THR A 542 1 17 HELIX 25 AC7 PRO A 554 ALA A 570 1 17 HELIX 26 AC8 MET A 571 LEU A 583 1 13 HELIX 27 AC9 SER A 586 ALA A 596 1 11 HELIX 28 AD1 PRO A 597 LYS A 599 5 3 HELIX 29 AD2 ASP A 600 ASP A 605 1 6 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 ND2 ASN A 181 C1 NAG A 701 1555 1555 1.44 LINK ND2 ASN A 188 C1 NAG A 702 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