HEADER MEMBRANE PROTEIN 15-JUN-23 8T6B TITLE HUMAN VMAT2 IN COMPLEX WITH SEROTONIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTIC VESICULAR AMINE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MONOAMINE TRANSPORTER,SOLUTE CARRIER FAMILY 18 MEMBER 2, COMPND 5 VESICULAR AMINE TRANSPORTER 2,VAT2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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 MEMBRANE PROTEIN, TRANSPORTER EXPDTA ELECTRON MICROSCOPY AUTHOR S.PIDATHALA,Y.DAI,C.H.LEE REVDAT 3 13-DEC-23 8T6B 1 JRNL REVDAT 2 15-NOV-23 8T6B 1 JRNL REVDAT 1 01-NOV-23 8T6B 0 JRNL AUTH S.PIDATHALA,S.LIAO,Y.DAI,X.LI,C.LONG,C.L.CHANG,Z.ZHANG, JRNL AUTH 2 C.H.LEE JRNL TITL MECHANISMS OF NEUROTRANSMITTER TRANSPORT AND DRUG INHIBITION JRNL TITL 2 IN HUMAN VMAT2. JRNL REF NATURE V. 623 1086 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 37914936 JRNL DOI 10.1038/S41586-023-06727-9 REMARK 2 REMARK 2 RESOLUTION. 3.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 3.720 REMARK 3 NUMBER OF PARTICLES : 120545 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 8T6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000275330. 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 SEROTONIN 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 : 7.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 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) : 6450.00 REMARK 245 ILLUMINATION MODE : OTHER 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 GLU A 54 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 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 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 ILE A 43 -63.50 -90.08 REMARK 500 THR A 212 -103.60 60.44 REMARK 500 GLN A 266 10.45 -68.43 REMARK 500 THR A 322 32.77 -97.34 REMARK 500 TRP A 328 11.29 54.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41068 RELATED DB: EMDB REMARK 900 HUMAN VMAT2 IN COMPLEX WITH SEROTONIN DBREF 8T6B A 19 514 UNP Q05940 VMAT2_HUMAN 19 514 SEQADV 8T6B SER A 418 UNP Q05940 TYR 418 ENGINEERED MUTATION SEQRES 1 A 496 ARG LYS LEU ILE LEU PHE ILE VAL PHE LEU ALA LEU LEU SEQRES 2 A 496 LEU ASP ASN MET LEU LEU THR VAL VAL VAL PRO ILE ILE SEQRES 3 A 496 PRO SER TYR LEU TYR SER ILE LYS HIS GLU LYS ASN ALA SEQRES 4 A 496 THR GLU ILE GLN THR ALA ARG PRO VAL HIS THR ALA SER SEQRES 5 A 496 ILE SER ASP SER PHE GLN SER ILE PHE SER TYR TYR ASP SEQRES 6 A 496 ASN SER THR MET VAL THR GLY ASN ALA THR ARG ASP LEU SEQRES 7 A 496 THR LEU HIS GLN THR ALA THR GLN HIS MET VAL THR ASN SEQRES 8 A 496 ALA SER ALA VAL PRO SER ASP CYS PRO SER GLU ASP LYS SEQRES 9 A 496 ASP LEU LEU ASN GLU ASN VAL GLN VAL GLY LEU LEU PHE SEQRES 10 A 496 ALA SER LYS ALA THR VAL GLN LEU ILE THR ASN PRO PHE SEQRES 11 A 496 ILE GLY LEU LEU THR ASN ARG ILE GLY TYR PRO ILE PRO SEQRES 12 A 496 ILE PHE ALA GLY PHE CYS ILE MET PHE VAL SER THR ILE SEQRES 13 A 496 MET PHE ALA PHE SER SER SER TYR ALA PHE LEU LEU ILE SEQRES 14 A 496 ALA ARG SER LEU GLN GLY ILE GLY SER SER CYS SER SER SEQRES 15 A 496 VAL ALA GLY MET GLY MET LEU ALA SER VAL TYR THR ASP SEQRES 16 A 496 ASP GLU GLU ARG GLY ASN VAL MET GLY ILE ALA LEU GLY SEQRES 17 A 496 GLY LEU ALA MET GLY VAL LEU VAL GLY PRO PRO PHE GLY SEQRES 18 A 496 SER VAL LEU TYR GLU PHE VAL GLY LYS THR ALA PRO PHE SEQRES 19 A 496 LEU VAL LEU ALA ALA LEU VAL LEU LEU ASP GLY ALA ILE SEQRES 20 A 496 GLN LEU PHE VAL LEU GLN PRO SER ARG VAL GLN PRO GLU SEQRES 21 A 496 SER GLN LYS GLY THR PRO LEU THR THR LEU LEU LYS ASP SEQRES 22 A 496 PRO TYR ILE LEU ILE ALA ALA GLY SER ILE CYS PHE ALA SEQRES 23 A 496 ASN MET GLY ILE ALA MET LEU GLU PRO ALA LEU PRO ILE SEQRES 24 A 496 TRP MET MET GLU THR MET CYS SER ARG LYS TRP GLN LEU SEQRES 25 A 496 GLY VAL ALA PHE LEU PRO ALA SER ILE SER TYR LEU ILE SEQRES 26 A 496 GLY THR ASN ILE PHE GLY ILE LEU ALA HIS LYS MET GLY SEQRES 27 A 496 ARG TRP LEU CYS ALA LEU LEU GLY MET ILE ILE VAL GLY SEQRES 28 A 496 VAL SER ILE LEU CYS ILE PRO PHE ALA LYS ASN ILE TYR SEQRES 29 A 496 GLY LEU ILE ALA PRO ASN PHE GLY VAL GLY PHE ALA ILE SEQRES 30 A 496 GLY MET VAL ASP SER SER MET MET PRO ILE MET GLY TYR SEQRES 31 A 496 LEU VAL ASP LEU ARG HIS VAL SER VAL SER GLY SER VAL SEQRES 32 A 496 TYR ALA ILE ALA ASP VAL ALA PHE CYS MET GLY TYR ALA SEQRES 33 A 496 ILE GLY PRO SER ALA GLY GLY ALA ILE ALA LYS ALA ILE SEQRES 34 A 496 GLY PHE PRO TRP LEU MET THR ILE ILE GLY ILE ILE ASP SEQRES 35 A 496 ILE LEU PHE ALA PRO LEU CYS PHE PHE LEU ARG SER PRO SEQRES 36 A 496 PRO ALA LYS GLU GLU LYS MET ALA ILE LEU MET ASP HIS SEQRES 37 A 496 ASN CYS PRO ILE LYS THR LYS MET TYR THR GLN ASN ASN SEQRES 38 A 496 ILE GLN SER TYR PRO ILE GLY GLU ASP GLU GLU SER GLU SEQRES 39 A 496 SER ASP HET SRO A 601 13 HETNAM SRO SEROTONIN HETSYN SRO 3-(2-AMINOETHYL)-1H-INDOL-5-OL FORMUL 2 SRO C10 H12 N2 O HELIX 1 AA1 LYS A 20 MET A 35 1 16 HELIX 2 AA2 MET A 35 LYS A 52 1 18 HELIX 3 AA3 GLU A 127 GLY A 157 1 31 HELIX 4 AA4 TYR A 158 SER A 179 1 22 HELIX 5 AA5 TYR A 182 THR A 212 1 31 HELIX 6 AA6 ASP A 213 MET A 221 1 9 HELIX 7 AA7 GLY A 222 GLY A 247 1 26 HELIX 8 AA8 LYS A 248 GLN A 266 1 19 HELIX 9 AA9 LEU A 267 VAL A 269 5 3 HELIX 10 AB1 PRO A 284 LEU A 289 1 6 HELIX 11 AB2 ASP A 291 THR A 322 1 32 HELIX 12 AB3 GLY A 331 ALA A 333 5 3 HELIX 13 AB4 PHE A 334 ALA A 352 1 19 HELIX 14 AB5 HIS A 353 MET A 355 5 3 HELIX 15 AB6 GLY A 356 ILE A 372 1 17 HELIX 16 AB7 ASN A 380 GLY A 383 5 4 HELIX 17 AB8 LEU A 384 MET A 403 1 20 HELIX 18 AB9 PRO A 404 HIS A 414 1 11 HELIX 19 AC1 VAL A 417 ILE A 447 1 31 HELIX 20 AC2 GLY A 448 ALA A 464 1 17 HELIX 21 AC3 PRO A 465 SER A 472 5 8 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