HEADER TRANSPORT PROTEIN 21-JUN-23 8JT9 TITLE HUMAN VMAT2 COMPLEX WITH KETANSERIN 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 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 TRANSPORTER1, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.H.JIANG,D.WU REVDAT 3 21-FEB-24 8JT9 1 JRNL REVDAT 2 24-JAN-24 8JT9 1 JRNL REVDAT 1 29-NOV-23 8JT9 0 JRNL AUTH D.WU,Q.CHEN,Z.YU,B.HUANG,J.ZHAO,Y.WANG,J.SU,F.ZHOU,R.YAN, JRNL AUTH 2 N.LI,Y.ZHAO,D.JIANG JRNL TITL TRANSPORT AND INHIBITION MECHANISMS OF HUMAN VMAT2. JRNL REF NATURE V. 626 427 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38081299 JRNL DOI 10.1038/S41586-023-06926-4 REMARK 2 REMARK 2 RESOLUTION. 2.97 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) : 2.970 REMARK 3 NUMBER OF PARTICLES : 504617 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 8JT9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038810. 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 : TRANSPORTER1 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 : 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 : 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) : 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 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 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 ILE A 44 CG1 CG2 CD1 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 VAL A 246 -65.55 -105.72 REMARK 500 VAL A 269 -61.75 -95.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36637 RELATED DB: EMDB REMARK 900 TRANSPORTER1 DBREF 8JT9 A 18 474 UNP Q05940 VMAT2_HUMAN 18 474 SEQRES 1 A 457 SER ARG LYS LEU ILE LEU PHE ILE VAL PHE LEU ALA LEU SEQRES 2 A 457 LEU LEU ASP ASN MET LEU LEU THR VAL VAL VAL PRO ILE SEQRES 3 A 457 ILE PRO SER TYR LEU TYR SER ILE LYS HIS GLU LYS ASN SEQRES 4 A 457 ALA THR GLU ILE GLN THR ALA ARG PRO VAL HIS THR ALA SEQRES 5 A 457 SER ILE SER ASP SER PHE GLN SER ILE PHE SER TYR TYR SEQRES 6 A 457 ASP ASN SER THR MET VAL THR GLY ASN ALA THR ARG ASP SEQRES 7 A 457 LEU THR LEU HIS GLN THR ALA THR GLN HIS MET VAL THR SEQRES 8 A 457 ASN ALA SER ALA VAL PRO SER ASP CYS PRO SER GLU ASP SEQRES 9 A 457 LYS ASP LEU LEU ASN GLU ASN VAL GLN VAL GLY LEU LEU SEQRES 10 A 457 PHE ALA SER LYS ALA THR VAL GLN LEU ILE THR ASN PRO SEQRES 11 A 457 PHE ILE GLY LEU LEU THR ASN ARG ILE GLY TYR PRO ILE SEQRES 12 A 457 PRO ILE PHE ALA GLY PHE CYS ILE MET PHE VAL SER THR SEQRES 13 A 457 ILE MET PHE ALA PHE SER SER SER TYR ALA PHE LEU LEU SEQRES 14 A 457 ILE ALA ARG SER LEU GLN GLY ILE GLY SER SER CYS SER SEQRES 15 A 457 SER VAL ALA GLY MET GLY MET LEU ALA SER VAL TYR THR SEQRES 16 A 457 ASP ASP GLU GLU ARG GLY ASN VAL MET GLY ILE ALA LEU SEQRES 17 A 457 GLY GLY LEU ALA MET GLY VAL LEU VAL GLY PRO PRO PHE SEQRES 18 A 457 GLY SER VAL LEU TYR GLU PHE VAL GLY LYS THR ALA PRO SEQRES 19 A 457 PHE LEU VAL LEU ALA ALA LEU VAL LEU LEU ASP GLY ALA SEQRES 20 A 457 ILE GLN LEU PHE VAL LEU GLN PRO SER ARG VAL GLN PRO SEQRES 21 A 457 GLU SER GLN LYS GLY THR PRO LEU THR THR LEU LEU LYS SEQRES 22 A 457 ASP PRO TYR ILE LEU ILE ALA ALA GLY SER ILE CYS PHE SEQRES 23 A 457 ALA ASN MET GLY ILE ALA MET LEU GLU PRO ALA LEU PRO SEQRES 24 A 457 ILE TRP MET MET GLU THR MET CYS SER ARG LYS TRP GLN SEQRES 25 A 457 LEU GLY VAL ALA PHE LEU PRO ALA SER ILE SER TYR LEU SEQRES 26 A 457 ILE GLY THR ASN ILE PHE GLY ILE LEU ALA HIS LYS MET SEQRES 27 A 457 GLY ARG TRP LEU CYS ALA LEU LEU GLY MET ILE ILE VAL SEQRES 28 A 457 GLY VAL SER ILE LEU CYS ILE PRO PHE ALA LYS ASN ILE SEQRES 29 A 457 TYR GLY LEU ILE ALA PRO ASN PHE GLY VAL GLY PHE ALA SEQRES 30 A 457 ILE GLY MET VAL ASP SER SER MET MET PRO ILE MET GLY SEQRES 31 A 457 TYR LEU VAL ASP LEU ARG HIS VAL SER VAL TYR GLY SER SEQRES 32 A 457 VAL TYR ALA ILE ALA ASP VAL ALA PHE CYS MET GLY TYR SEQRES 33 A 457 ALA ILE GLY PRO SER ALA GLY GLY ALA ILE ALA LYS ALA SEQRES 34 A 457 ILE GLY PHE PRO TRP LEU MET THR ILE ILE GLY ILE ILE SEQRES 35 A 457 ASP ILE LEU PHE ALA PRO LEU CYS PHE PHE LEU ARG SER SEQRES 36 A 457 PRO PRO HET UYX A 501 29 HETNAM UYX 3-[2-[4-(4-FLUOROPHENYL)CARBONYLPIPERIDIN-1-YL]ETHYL]- HETNAM 2 UYX 1~{H}-QUINAZOLINE-2,4-DIONE FORMUL 2 UYX C22 H22 F N3 O3 HELIX 1 AA1 ARG A 19 VAL A 40 1 22 HELIX 2 AA2 ILE A 43 GLU A 54 1 12 HELIX 3 AA3 VAL A 129 GLY A 157 1 29 HELIX 4 AA4 TYR A 158 SER A 179 1 22 HELIX 5 AA5 TYR A 182 TYR A 211 1 30 HELIX 6 AA6 ASP A 213 VAL A 246 1 34 HELIX 7 AA7 THR A 249 LEU A 270 1 22 HELIX 8 AA8 PRO A 284 LEU A 289 1 6 HELIX 9 AA9 ASP A 291 MET A 323 1 33 HELIX 10 AB1 ARG A 326 PHE A 334 1 9 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