HEADER TRANSPORT PROTEIN 07-AUG-25 9W8D TITLE HUMAN VMAT2 IN COMPLEX WITH MDMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTIC VESICULAR AMINE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SOLUTE CARRIER FAMILY 18 MEMBER 2,VESICULAR AMINE COMPND 5 TRANSPORTER 2,VAT2,VESICULAR MONOAMINE TRANSPORTER 2; 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: SLC18A2, SVMT, VMAT2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS TRANSPORTER C WITH 3, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.WU,D.H.JIANG REVDAT 1 07-OCT-26 9W8D 0 JRNL AUTH D.WU,D.H.JIANG JRNL TITL TRANSPORTER C WITH 3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, 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 : 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) : 2.890 REMARK 3 NUMBER OF PARTICLES : 281302 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 9W8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 14-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300062466. 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 VMAT2 IN COMPLEX WITH REMARK 245 MDMA 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 SER A 4 REMARK 465 GLU A 5 REMARK 465 LEU A 6 REMARK 465 ALA A 7 REMARK 465 LEU A 8 REMARK 465 VAL A 9 REMARK 465 ARG A 10 REMARK 465 TRP A 11 REMARK 465 LEU A 12 REMARK 465 GLN A 13 REMARK 465 GLU A 14 REMARK 465 SER A 15 REMARK 465 ARG A 16 REMARK 465 LYS A 55 REMARK 465 ASN A 56 REMARK 465 ALA A 57 REMARK 465 THR A 58 REMARK 465 GLU A 59 REMARK 465 ILE A 60 REMARK 465 GLN A 61 REMARK 465 THR A 62 REMARK 465 ALA A 63 REMARK 465 ARG A 64 REMARK 465 PRO A 65 REMARK 465 VAL A 66 REMARK 465 HIS A 67 REMARK 465 THR A 68 REMARK 465 ALA A 69 REMARK 465 SER A 70 REMARK 465 ILE A 71 REMARK 465 SER A 72 REMARK 465 ASP A 73 REMARK 465 SER A 74 REMARK 465 PHE A 75 REMARK 465 GLN A 76 REMARK 465 SER A 77 REMARK 465 ILE A 78 REMARK 465 PHE A 79 REMARK 465 SER A 80 REMARK 465 TYR A 81 REMARK 465 TYR A 82 REMARK 465 ASP A 83 REMARK 465 ASN A 84 REMARK 465 SER A 85 REMARK 465 THR A 86 REMARK 465 MET A 87 REMARK 465 VAL A 88 REMARK 465 THR A 89 REMARK 465 GLY A 90 REMARK 465 ASN A 91 REMARK 465 ALA A 92 REMARK 465 THR A 93 REMARK 465 ARG A 94 REMARK 465 ASP A 95 REMARK 465 LEU A 96 REMARK 465 THR A 97 REMARK 465 LEU A 98 REMARK 465 HIS A 99 REMARK 465 GLN A 100 REMARK 465 THR A 101 REMARK 465 ALA A 102 REMARK 465 THR A 103 REMARK 465 GLN A 104 REMARK 465 HIS A 105 REMARK 465 MET A 106 REMARK 465 VAL A 107 REMARK 465 THR A 108 REMARK 465 ASN A 109 REMARK 465 ALA A 110 REMARK 465 SER A 111 REMARK 465 ALA A 112 REMARK 465 VAL A 113 REMARK 465 PRO A 114 REMARK 465 SER A 115 REMARK 465 ASP A 116 REMARK 465 CYS A 117 REMARK 465 PRO A 118 REMARK 465 SER A 119 REMARK 465 GLU A 120 REMARK 465 ASP A 121 REMARK 465 LYS A 122 REMARK 465 ASP A 123 REMARK 465 LEU A 124 REMARK 465 LEU A 125 REMARK 465 ASN A 126 REMARK 465 GLU A 127 REMARK 465 ALA A 475 REMARK 465 LYS A 476 REMARK 465 GLU A 477 REMARK 465 GLU A 478 REMARK 465 LYS A 479 REMARK 465 MET A 480 REMARK 465 ALA A 481 REMARK 465 ILE A 482 REMARK 465 LEU A 483 REMARK 465 MET A 484 REMARK 465 ASP A 485 REMARK 465 HIS A 486 REMARK 465 ASN A 487 REMARK 465 CYS A 488 REMARK 465 PRO A 489 REMARK 465 ILE A 490 REMARK 465 LYS A 491 REMARK 465 THR A 492 REMARK 465 LYS A 493 REMARK 465 MET A 494 REMARK 465 TYR A 495 REMARK 465 THR A 496 REMARK 465 GLN A 497 REMARK 465 ASN A 498 REMARK 465 ASN A 499 REMARK 465 ILE A 500 REMARK 465 GLN A 501 REMARK 465 SER A 502 REMARK 465 TYR A 503 REMARK 465 PRO A 504 REMARK 465 ILE A 505 REMARK 465 GLY A 506 REMARK 465 GLU A 507 REMARK 465 ASP A 508 REMARK 465 GLU A 509 REMARK 465 GLU A 510 REMARK 465 SER A 511 REMARK 465 GLU A 512 REMARK 465 SER A 513 REMARK 465 ASP A 514 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 ARG A 17 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 49 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER A 50 OG REMARK 470 ILE A 51 CG1 CG2 CD1 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 HIS A 53 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 54 CG CD OE1 OE2 REMARK 470 SER A 273 OG REMARK 470 ARG A 274 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 MET A 355 CG SD CE 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 SER A 18 76.28 -100.30 REMARK 500 GLN A 271 73.56 44.35 REMARK 500 THR A 283 80.38 58.69 REMARK 500 PRO A 284 157.37 -46.51 REMARK 500 PRO A 376 6.41 -65.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-65744 RELATED DB: EMDB REMARK 900 TRANSPORTER C WITH 3 DBREF 9W8D A 1 514 UNP Q05940 VMAT2_HUMAN 1 514 SEQRES 1 A 514 MET ALA LEU SER GLU LEU ALA LEU VAL ARG TRP LEU GLN SEQRES 2 A 514 GLU SER ARG ARG SER ARG LYS LEU ILE LEU PHE ILE VAL SEQRES 3 A 514 PHE LEU ALA LEU LEU LEU ASP ASN MET LEU LEU THR VAL SEQRES 4 A 514 VAL VAL PRO ILE ILE PRO SER TYR LEU TYR SER ILE LYS SEQRES 5 A 514 HIS GLU LYS ASN ALA THR GLU ILE GLN THR ALA ARG PRO SEQRES 6 A 514 VAL HIS THR ALA SER ILE SER ASP SER PHE GLN SER ILE SEQRES 7 A 514 PHE SER TYR TYR ASP ASN SER THR MET VAL THR GLY ASN SEQRES 8 A 514 ALA THR ARG ASP LEU THR LEU HIS GLN THR ALA THR GLN SEQRES 9 A 514 HIS MET VAL THR ASN ALA SER ALA VAL PRO SER ASP CYS SEQRES 10 A 514 PRO SER GLU ASP LYS ASP LEU LEU ASN GLU ASN VAL GLN SEQRES 11 A 514 VAL GLY LEU LEU PHE ALA SER LYS ALA THR VAL GLN LEU SEQRES 12 A 514 ILE THR ASN PRO PHE ILE GLY LEU LEU THR ASN ARG ILE SEQRES 13 A 514 GLY TYR PRO ILE PRO ILE PHE ALA GLY PHE CYS ILE MET SEQRES 14 A 514 PHE VAL SER THR ILE MET PHE ALA PHE SER SER SER TYR SEQRES 15 A 514 ALA PHE LEU LEU ILE ALA ARG SER LEU GLN GLY ILE GLY SEQRES 16 A 514 SER SER CYS SER SER VAL ALA GLY MET GLY MET LEU ALA SEQRES 17 A 514 SER VAL TYR THR ASP ASP GLU GLU ARG GLY ASN VAL MET SEQRES 18 A 514 GLY ILE ALA LEU GLY GLY LEU ALA MET GLY VAL LEU VAL SEQRES 19 A 514 GLY PRO PRO PHE GLY SER VAL LEU TYR GLU PHE VAL GLY SEQRES 20 A 514 LYS THR ALA PRO PHE LEU VAL LEU ALA ALA LEU VAL LEU SEQRES 21 A 514 LEU ASP GLY ALA ILE GLN LEU PHE VAL LEU GLN PRO SER SEQRES 22 A 514 ARG VAL GLN PRO GLU SER GLN LYS GLY THR PRO LEU THR SEQRES 23 A 514 THR LEU LEU LYS ASP PRO TYR ILE LEU ILE ALA ALA GLY SEQRES 24 A 514 SER ILE CYS PHE ALA ASN MET GLY ILE ALA MET LEU GLU SEQRES 25 A 514 PRO ALA LEU PRO ILE TRP MET MET GLU THR MET CYS SER SEQRES 26 A 514 ARG LYS TRP GLN LEU GLY VAL ALA PHE LEU PRO ALA SER SEQRES 27 A 514 ILE SER TYR LEU ILE GLY THR ASN ILE PHE GLY ILE LEU SEQRES 28 A 514 ALA HIS LYS MET GLY ARG TRP LEU CYS ALA LEU LEU GLY SEQRES 29 A 514 MET ILE ILE VAL GLY VAL SER ILE LEU CYS ILE PRO PHE SEQRES 30 A 514 ALA LYS ASN ILE TYR GLY LEU ILE ALA PRO ASN PHE GLY SEQRES 31 A 514 VAL GLY PHE ALA ILE GLY MET VAL ASP SER SER MET MET SEQRES 32 A 514 PRO ILE MET GLY TYR LEU VAL ASP LEU ARG HIS VAL SER SEQRES 33 A 514 VAL TYR GLY SER VAL TYR ALA ILE ALA ASP VAL ALA PHE SEQRES 34 A 514 CYS MET GLY TYR ALA ILE GLY PRO SER ALA GLY GLY ALA SEQRES 35 A 514 ILE ALA LYS ALA ILE GLY PHE PRO TRP LEU MET THR ILE SEQRES 36 A 514 ILE GLY ILE ILE ASP ILE LEU PHE ALA PRO LEU CYS PHE SEQRES 37 A 514 PHE LEU ARG SER PRO PRO ALA LYS GLU GLU LYS MET ALA SEQRES 38 A 514 ILE LEU MET ASP HIS ASN CYS PRO ILE LYS THR LYS MET SEQRES 39 A 514 TYR THR GLN ASN ASN ILE GLN SER TYR PRO ILE GLY GLU SEQRES 40 A 514 ASP GLU GLU SER GLU SER ASP HET B41 A 601 14 HETNAM B41 (2S)-1-(1,3-BENZODIOXOL-5-YL)-N-METHYLPROPAN-2-AMINE HETSYN B41 3,4 METHYLENEDIOXY-N-METHYLAMPHETAMINE; MDMA; ECSTASY FORMUL 2 B41 C11 H15 N O2 HELIX 1 AA1 ARG A 19 GLU A 54 1 36 HELIX 2 AA2 VAL A 129 GLY A 157 1 29 HELIX 3 AA3 TYR A 158 SER A 179 1 22 HELIX 4 AA4 SER A 181 TYR A 211 1 31 HELIX 5 AA5 ASP A 213 VAL A 246 1 34 HELIX 6 AA6 THR A 249 LEU A 270 1 22 HELIX 7 AA7 PRO A 284 LEU A 289 1 6 HELIX 8 AA8 ASP A 291 GLU A 312 1 22 HELIX 9 AA9 ALA A 314 MET A 323 1 10 HELIX 10 AB1 ARG A 326 VAL A 332 1 7 HELIX 11 AB2 PHE A 334 GLY A 356 1 23 HELIX 12 AB3 GLY A 356 ILE A 375 1 20 HELIX 13 AB4 PRO A 376 ALA A 378 5 3 HELIX 14 AB5 ASN A 380 HIS A 414 1 35 HELIX 15 AB6 TYR A 418 ILE A 447 1 30 HELIX 16 AB7 GLY A 448 ALA A 464 1 17 HELIX 17 AB8 PRO A 465 ARG A 471 5 7 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 CONECT 2853 2862 2866 CONECT 2854 2864 2866 CONECT 2855 2856 2865 CONECT 2856 2855 2857 2858 CONECT 2857 2856 CONECT 2858 2856 2859 CONECT 2859 2858 2860 2861 CONECT 2860 2859 2862 CONECT 2861 2859 2863 CONECT 2862 2853 2860 2864 CONECT 2863 2861 2864 CONECT 2864 2854 2862 2863 CONECT 2865 2855 CONECT 2866 2853 2854 MASTER 276 0 1 17 0 0 0 6 2865 1 14 40 END