HEADER TRANSPORT PROTEIN 31-DEC-23 8XO9 TITLE VMAT2 COMPLEX WITH NORADRENALINE IN CYTOSOL-FACING STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTIC VESICULAR AMINE TRANSPORTER,SYNAPTIC VESICULAR COMPND 3 AMINE TRANSPORTER,TRANSPORTER A; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: MONOAMINE TRANSPORTER,SOLUTE CARRIER FAMILY 18 MEMBER 2, COMPND 6 VESICULAR AMINE TRANSPORTER 2,VAT2; COMPND 7 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 TRANSPORTERA, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.H.JIANG,D.WU REVDAT 2 24-JUL-24 8XO9 1 COMPND REMARK ATOM REVDAT 1 08-MAY-24 8XO9 0 JRNL AUTH D.H.JIANG,D.WU JRNL TITL VMAT2 COMPLEX WITH NORADRENALINE IN CYTOSOL-FACING STATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 176326 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 8XO9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300043834. 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 : COMPLEX WITH NE 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 : 6.50 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 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 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 GLN A 475 REMARK 465 VAL A 476 REMARK 465 GLN A 477 REMARK 465 LEU A 478 REMARK 465 VAL A 479 REMARK 465 GLU A 480 REMARK 465 SER A 481 REMARK 465 GLY A 482 REMARK 465 GLY A 483 REMARK 465 ALA A 484 REMARK 465 LEU A 485 REMARK 465 VAL A 486 REMARK 465 GLN A 487 REMARK 465 PRO A 488 REMARK 465 GLY A 489 REMARK 465 GLY A 490 REMARK 465 SER A 491 REMARK 465 LEU A 492 REMARK 465 ARG A 493 REMARK 465 LEU A 494 REMARK 465 SER A 495 REMARK 465 CYS A 496 REMARK 465 ALA A 497 REMARK 465 ALA A 498 REMARK 465 SER A 499 REMARK 465 GLY A 500 REMARK 465 PHE A 501 REMARK 465 PRO A 502 REMARK 465 VAL A 503 REMARK 465 ASN A 504 REMARK 465 ARG A 505 REMARK 465 TYR A 506 REMARK 465 SER A 507 REMARK 465 MET A 508 REMARK 465 ARG A 509 REMARK 465 TRP A 510 REMARK 465 TYR A 511 REMARK 465 ARG A 512 REMARK 465 GLN A 513 REMARK 465 ALA A 514 REMARK 465 PRO A 515 REMARK 465 GLY A 516 REMARK 465 LYS A 517 REMARK 465 GLU A 518 REMARK 465 ARG A 519 REMARK 465 GLU A 520 REMARK 465 TRP A 521 REMARK 465 VAL A 522 REMARK 465 ALA A 523 REMARK 465 GLY A 524 REMARK 465 MET A 525 REMARK 465 SER A 526 REMARK 465 SER A 527 REMARK 465 ALA A 528 REMARK 465 GLY A 529 REMARK 465 ASP A 530 REMARK 465 ARG A 531 REMARK 465 SER A 532 REMARK 465 SER A 533 REMARK 465 TYR A 534 REMARK 465 GLU A 535 REMARK 465 ASP A 536 REMARK 465 SER A 537 REMARK 465 VAL A 538 REMARK 465 LYS A 539 REMARK 465 GLY A 540 REMARK 465 ARG A 541 REMARK 465 PHE A 542 REMARK 465 THR A 543 REMARK 465 ILE A 544 REMARK 465 SER A 545 REMARK 465 ARG A 546 REMARK 465 ASP A 547 REMARK 465 ASP A 548 REMARK 465 ALA A 549 REMARK 465 ARG A 550 REMARK 465 ASN A 551 REMARK 465 THR A 552 REMARK 465 VAL A 553 REMARK 465 TYR A 554 REMARK 465 LEU A 555 REMARK 465 GLN A 556 REMARK 465 MET A 557 REMARK 465 ASN A 558 REMARK 465 SER A 559 REMARK 465 LEU A 560 REMARK 465 LYS A 561 REMARK 465 PRO A 562 REMARK 465 GLU A 563 REMARK 465 ASP A 564 REMARK 465 THR A 565 REMARK 465 ALA A 566 REMARK 465 VAL A 567 REMARK 465 TYR A 568 REMARK 465 TYR A 569 REMARK 465 CYS A 570 REMARK 465 ASN A 571 REMARK 465 VAL A 572 REMARK 465 ASN A 573 REMARK 465 VAL A 574 REMARK 465 GLY A 575 REMARK 465 PHE A 576 REMARK 465 GLU A 577 REMARK 465 TYR A 578 REMARK 465 TRP A 579 REMARK 465 GLY A 580 REMARK 465 GLN A 581 REMARK 465 GLY A 582 REMARK 465 THR A 583 REMARK 465 GLN A 584 REMARK 465 VAL A 585 REMARK 465 THR A 586 REMARK 465 VAL A 587 REMARK 465 SER A 588 REMARK 465 SER A 589 REMARK 465 LYS A 590 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 GLU A 54 CG CD OE1 OE2 REMARK 470 ASP A 121 CG OD1 OD2 REMARK 470 LYS A 122 CG CD CE NZ REMARK 470 ASP A 123 CG OD1 OD2 REMARK 470 LEU A 124 CG CD1 CD2 REMARK 470 LEU A 125 CG CD1 CD2 REMARK 470 ASN A 126 CG OD1 ND2 REMARK 470 GLU A 216 CG CD OE1 OE2 REMARK 470 GLU A 278 CG CD OE1 OE2 REMARK 470 SER A 279 OG REMARK 470 MET A 355 CG SD CE REMARK 470 TYR A 418 CG CD1 CD2 CE1 CE2 CZ OH 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 124 -16.11 71.98 REMARK 500 VAL A 246 -61.19 -105.17 REMARK 500 GLN A 271 50.77 -141.48 REMARK 500 PRO A 376 1.42 -69.01 REMARK 500 LEU A 470 42.86 -102.29 REMARK 500 ARG A 471 35.45 -92.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38523 RELATED DB: EMDB REMARK 900 TRANSPORTERNE-C DBREF 8XO9 A 17 474 UNP Q05940 VMAT2_HUMAN 17 474 DBREF 8XO9 A 475 590 PDB 8XO9 8XO9 475 590 SEQADV 8XO9 ALA A 214 UNP Q05940 ASP 214 CONFLICT SEQADV 8XO9 ALA A 217 UNP Q05940 ARG 217 CONFLICT SEQRES 1 A 574 ARG SER ARG LYS LEU ILE LEU PHE ILE VAL PHE LEU ALA SEQRES 2 A 574 LEU LEU LEU ASP ASN MET LEU LEU THR VAL VAL VAL PRO SEQRES 3 A 574 ILE ILE PRO SER TYR LEU TYR SER ILE LYS HIS GLU LYS SEQRES 4 A 574 ASN ALA THR GLU ILE GLN THR ALA ARG PRO VAL HIS THR SEQRES 5 A 574 ALA SER ILE SER ASP SER PHE GLN SER ILE PHE SER TYR SEQRES 6 A 574 TYR ASP ASN SER THR MET VAL THR GLY ASN ALA THR ARG SEQRES 7 A 574 ASP LEU THR LEU HIS GLN THR ALA THR GLN HIS MET VAL SEQRES 8 A 574 THR ASN ALA SER ALA VAL PRO SER ASP CYS PRO SER GLU SEQRES 9 A 574 ASP LYS ASP LEU LEU ASN GLU ASN VAL GLN VAL GLY LEU SEQRES 10 A 574 LEU PHE ALA SER LYS ALA THR VAL GLN LEU ILE THR ASN SEQRES 11 A 574 PRO PHE ILE GLY LEU LEU THR ASN ARG ILE GLY TYR PRO SEQRES 12 A 574 ILE PRO ILE PHE ALA GLY PHE CYS ILE MET PHE VAL SER SEQRES 13 A 574 THR ILE MET PHE ALA PHE SER SER SER TYR ALA PHE LEU SEQRES 14 A 574 LEU ILE ALA ARG SER LEU GLN GLY ILE GLY SER SER CYS SEQRES 15 A 574 SER SER VAL ALA GLY MET GLY MET LEU ALA SER VAL TYR SEQRES 16 A 574 THR ASP ALA GLU GLU ALA GLY ASN VAL MET GLY ILE ALA SEQRES 17 A 574 LEU GLY GLY LEU ALA MET GLY VAL LEU VAL GLY PRO PRO SEQRES 18 A 574 PHE GLY SER VAL LEU TYR GLU PHE VAL GLY LYS THR ALA SEQRES 19 A 574 PRO PHE LEU VAL LEU ALA ALA LEU VAL LEU LEU ASP GLY SEQRES 20 A 574 ALA ILE GLN LEU PHE VAL LEU GLN PRO SER ARG VAL GLN SEQRES 21 A 574 PRO GLU SER GLN LYS GLY THR PRO LEU THR THR LEU LEU SEQRES 22 A 574 LYS ASP PRO TYR ILE LEU ILE ALA ALA GLY SER ILE CYS SEQRES 23 A 574 PHE ALA ASN MET GLY ILE ALA MET LEU GLU PRO ALA LEU SEQRES 24 A 574 PRO ILE TRP MET MET GLU THR MET CYS SER ARG LYS TRP SEQRES 25 A 574 GLN LEU GLY VAL ALA PHE LEU PRO ALA SER ILE SER TYR SEQRES 26 A 574 LEU ILE GLY THR ASN ILE PHE GLY ILE LEU ALA HIS LYS SEQRES 27 A 574 MET GLY ARG TRP LEU CYS ALA LEU LEU GLY MET ILE ILE SEQRES 28 A 574 VAL GLY VAL SER ILE LEU CYS ILE PRO PHE ALA LYS ASN SEQRES 29 A 574 ILE TYR GLY LEU ILE ALA PRO ASN PHE GLY VAL GLY PHE SEQRES 30 A 574 ALA ILE GLY MET VAL ASP SER SER MET MET PRO ILE MET SEQRES 31 A 574 GLY TYR LEU VAL ASP LEU ARG HIS VAL SER VAL TYR GLY SEQRES 32 A 574 SER VAL TYR ALA ILE ALA ASP VAL ALA PHE CYS MET GLY SEQRES 33 A 574 TYR ALA ILE GLY PRO SER ALA GLY GLY ALA ILE ALA LYS SEQRES 34 A 574 ALA ILE GLY PHE PRO TRP LEU MET THR ILE ILE GLY ILE SEQRES 35 A 574 ILE ASP ILE LEU PHE ALA PRO LEU CYS PHE PHE LEU ARG SEQRES 36 A 574 SER PRO PRO GLN VAL GLN LEU VAL GLU SER GLY GLY ALA SEQRES 37 A 574 LEU VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA SEQRES 38 A 574 ALA SER GLY PHE PRO VAL ASN ARG TYR SER MET ARG TRP SEQRES 39 A 574 TYR ARG GLN ALA PRO GLY LYS GLU ARG GLU TRP VAL ALA SEQRES 40 A 574 GLY MET SER SER ALA GLY ASP ARG SER SER TYR GLU ASP SEQRES 41 A 574 SER VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASP ALA SEQRES 42 A 574 ARG ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO SEQRES 43 A 574 GLU ASP THR ALA VAL TYR TYR CYS ASN VAL ASN VAL GLY SEQRES 44 A 574 PHE GLU TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 45 A 574 SER LYS HET E5E A 601 12 HETNAM E5E NORADRENALINE FORMUL 2 E5E C8 H12 N O3 1+ HELIX 1 AA1 ARG A 19 GLU A 54 1 36 HELIX 2 AA2 LEU A 124 GLY A 157 1 34 HELIX 3 AA3 TYR A 158 PHE A 178 1 21 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 VAL A 269 1 21 HELIX 7 AA7 PRO A 284 LYS A 290 1 7 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 TRP A 328 ALA A 333 1 6 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 GLY A 383 5 4 HELIX 15 AB6 LEU A 384 HIS A 414 1 31 HELIX 16 AB7 VAL A 417 ILE A 447 1 31 HELIX 17 AB8 GLY A 448 ALA A 464 1 17 HELIX 18 AB9 PRO A 465 LEU A 470 5 6 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