HEADER TRANSPORT PROTEIN 20-DEC-23 8XIU TITLE CRYO-EM STRUCTURE OF A FROG VMAT2 IN AN APO CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: XLVMAT2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_TAXID: 8355; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS VESICULAR MONOAMINE TRANSPORTER, SLC18A2, MFS, FOLD, TRANSPORT KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.LYU,C.FU,H.MA,Z.SUN,Z.SU,X.ZHOU REVDAT 1 14-AUG-24 8XIU 0 JRNL AUTH Y.LYU,C.FU,H.MA,Z.SU,Z.SUN,X.ZHOU JRNL TITL ENGINEERING OF A MAMMALIAN VMAT2 FOR CRYO-EM ANALYSIS JRNL TITL 2 RESULTS IN NON-CANONICAL PROTEIN FOLDING. JRNL REF NAT COMMUN V. 15 6511 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39095428 JRNL DOI 10.1038/S41467-024-50934-5 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : COOT, PHENIX, RELION, RELION, 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) : 4.000 REMARK 3 NUMBER OF PARTICLES : 107961 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 8XIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043568. 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 : XLVMAT2 WT REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 8.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FOR 3 S BEFORE PLUNGING REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.00 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 K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 900.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 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 SER A 2 REMARK 465 MET A 3 REMARK 465 THR A 4 REMARK 465 GLU A 5 REMARK 465 PHE A 6 REMARK 465 THR A 7 REMARK 465 LEU A 8 REMARK 465 LEU A 9 REMARK 465 ARG A 10 REMARK 465 TRP A 11 REMARK 465 LEU A 12 REMARK 465 ARG A 13 REMARK 465 GLU A 14 REMARK 465 GLY A 15 REMARK 465 ARG A 16 REMARK 465 GLN A 17 REMARK 465 SER A 50 REMARK 465 MET A 51 REMARK 465 THR A 52 REMARK 465 HIS A 53 REMARK 465 GLU A 54 REMARK 465 SER A 55 REMARK 465 ASN A 56 REMARK 465 ASN A 57 REMARK 465 THR A 58 REMARK 465 HIS A 59 REMARK 465 ASP A 60 REMARK 465 GLY A 61 REMARK 465 SER A 62 REMARK 465 ILE A 63 REMARK 465 PRO A 64 REMARK 465 PRO A 65 REMARK 465 ALA A 66 REMARK 465 ALA A 67 REMARK 465 PRO A 68 REMARK 465 SER A 69 REMARK 465 GLY A 70 REMARK 465 PHE A 71 REMARK 465 HIS A 72 REMARK 465 SER A 73 REMARK 465 ILE A 74 REMARK 465 PHE A 75 REMARK 465 SER A 76 REMARK 465 TYR A 77 REMARK 465 TYR A 78 REMARK 465 ASP A 79 REMARK 465 ASN A 80 REMARK 465 THR A 81 REMARK 465 THR A 82 REMARK 465 VAL A 83 REMARK 465 ILE A 84 REMARK 465 THR A 85 REMARK 465 THR A 86 REMARK 465 ASN A 87 REMARK 465 PHE A 88 REMARK 465 THR A 89 REMARK 465 SER A 90 REMARK 465 SER A 91 REMARK 465 ASP A 92 REMARK 465 GLN A 93 REMARK 465 LEU A 94 REMARK 465 GLN A 95 REMARK 465 GLN A 96 REMARK 465 SER A 97 REMARK 465 ALA A 98 REMARK 465 LEU A 99 REMARK 465 THR A 100 REMARK 465 PRO A 101 REMARK 465 THR A 102 REMARK 465 THR A 103 REMARK 465 SER A 104 REMARK 465 PRO A 105 REMARK 465 SER A 106 REMARK 465 LEU A 107 REMARK 465 ALA A 108 REMARK 465 THR A 109 REMARK 465 PRO A 110 REMARK 465 PRO A 111 REMARK 465 ALA A 112 REMARK 465 SER A 113 REMARK 465 ALA A 114 REMARK 465 ASP A 115 REMARK 465 CYS A 116 REMARK 465 PRO A 117 REMARK 465 LYS A 118 REMARK 465 ALA A 119 REMARK 465 ASP A 120 REMARK 465 SER A 121 REMARK 465 SER A 122 REMARK 465 LEU A 123 REMARK 465 LEU A 124 REMARK 465 VAL A 245 REMARK 465 GLY A 246 REMARK 465 LYS A 247 REMARK 465 GLN A 270 REMARK 465 PRO A 271 REMARK 465 SER A 272 REMARK 465 ARG A 273 REMARK 465 VAL A 274 REMARK 465 GLN A 275 REMARK 465 PRO A 276 REMARK 465 GLU A 277 REMARK 465 SER A 278 REMARK 465 GLN A 279 REMARK 465 THR A 280 REMARK 465 GLY A 281 REMARK 465 THR A 282 REMARK 465 PRO A 283 REMARK 465 LEU A 284 REMARK 465 CYS A 323 REMARK 465 SER A 324 REMARK 465 ARG A 325 REMARK 465 LYS A 326 REMARK 465 TRP A 327 REMARK 465 GLN A 328 REMARK 465 LEU A 329 REMARK 465 GLY A 330 REMARK 465 ILE A 446 REMARK 465 GLY A 447 REMARK 465 PHE A 448 REMARK 465 PRO A 449 REMARK 465 SER A 471 REMARK 465 PRO A 472 REMARK 465 PRO A 473 REMARK 465 ALA A 474 REMARK 465 ARG A 475 REMARK 465 GLU A 476 REMARK 465 GLU A 477 REMARK 465 LYS A 478 REMARK 465 MET A 479 REMARK 465 ALA A 480 REMARK 465 ILE A 481 REMARK 465 LEU A 482 REMARK 465 MET A 483 REMARK 465 ASP A 484 REMARK 465 HIS A 485 REMARK 465 LYS A 486 REMARK 465 CYS A 487 REMARK 465 PRO A 488 REMARK 465 VAL A 489 REMARK 465 LYS A 490 REMARK 465 THR A 491 REMARK 465 LYS A 492 REMARK 465 MET A 493 REMARK 465 TYR A 494 REMARK 465 THR A 495 REMARK 465 GLN A 496 REMARK 465 ASN A 497 REMARK 465 SER A 498 REMARK 465 GLY A 499 REMARK 465 GLN A 500 REMARK 465 PRO A 501 REMARK 465 TYR A 502 REMARK 465 TYR A 503 REMARK 465 THR A 504 REMARK 465 GLY A 505 REMARK 465 GLU A 506 REMARK 465 GLU A 507 REMARK 465 GLU A 508 REMARK 465 GLU A 509 REMARK 465 SER A 510 REMARK 465 GLU A 511 REMARK 465 SER A 512 REMARK 465 ASP A 513 REMARK 465 GLU 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 PHE A 434 43.79 -140.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38390 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF A FROG VMAT2 IN AN APO CONFORMATION DBREF 8XIU A 1 514 PDB 8XIU 8XIU 1 514 SEQRES 1 A 514 MET SER MET THR GLU PHE THR LEU LEU ARG TRP LEU ARG SEQRES 2 A 514 GLU GLY ARG GLN SER ARG LYS LEU ILE LEU LEU ILE VAL SEQRES 3 A 514 PHE ILE 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 MET THR SEQRES 5 A 514 HIS GLU SER ASN ASN THR HIS ASP GLY SER ILE PRO PRO SEQRES 6 A 514 ALA ALA PRO SER GLY PHE HIS SER ILE PHE SER TYR TYR SEQRES 7 A 514 ASP ASN THR THR VAL ILE THR THR ASN PHE THR SER SER SEQRES 8 A 514 ASP GLN LEU GLN GLN SER ALA LEU THR PRO THR THR SER SEQRES 9 A 514 PRO SER LEU ALA THR PRO PRO ALA SER ALA ASP CYS PRO SEQRES 10 A 514 LYS ALA ASP SER SER LEU LEU ASN GLU ASN VAL LYS VAL SEQRES 11 A 514 GLY LEU LEU PHE ALA SER LYS ALA THR VAL GLN LEU LEU SEQRES 12 A 514 THR ASN PRO PHE ILE GLY PRO MET THR ASN ARG ILE GLY SEQRES 13 A 514 TYR GLN ILE PRO MET PHE ALA GLY PHE CYS ILE MET PHE SEQRES 14 A 514 VAL SER THR ILE MET PHE ALA PHE SER GLY THR TYR THR SEQRES 15 A 514 LEU LEU PHE ILE ALA ARG SER LEU GLN GLY ILE GLY SER SEQRES 16 A 514 SER CYS SER SER VAL ALA GLY MET GLY MET LEU ALA SER SEQRES 17 A 514 VAL TYR THR ASP ASP GLU GLU ARG GLY ASN ALA MET GLY SEQRES 18 A 514 VAL ALA LEU GLY GLY LEU ALA MET GLY VAL LEU VAL GLY SEQRES 19 A 514 PRO PRO PHE GLY SER ILE LEU TYR GLU PHE VAL GLY LYS SEQRES 20 A 514 THR ALA PRO PHE ILE VAL LEU ALA VAL LEU VAL LEU PHE SEQRES 21 A 514 ASP GLY ALA LEU GLN LEU PHE VAL LEU GLN PRO SER ARG SEQRES 22 A 514 VAL GLN PRO GLU SER GLN THR GLY THR PRO LEU LEU THR SEQRES 23 A 514 LEU ILE ARG ASP PRO TYR ILE LEU ILE ALA ALA GLY SER SEQRES 24 A 514 ILE CYS PHE ALA ASN MET ALA ILE ALA MET LEU GLU PRO SEQRES 25 A 514 ALA LEU PRO ILE TRP MET MET GLU THR MET CYS SER ARG SEQRES 26 A 514 LYS TRP GLN LEU GLY VAL ALA PHE LEU PRO ALA SER ILE SEQRES 27 A 514 SER TYR LEU LEU GLY THR ASN ILE PHE GLY PRO LEU ALA SEQRES 28 A 514 HIS LYS MET GLY ARG TRP LEU CYS ALA PHE ILE GLY MET SEQRES 29 A 514 ILE MET VAL GLY ILE SER ILE ILE CYS VAL PRO PHE ALA SEQRES 30 A 514 ARG ASN ILE TYR GLY LEU ILE ALA PRO ASN PHE GLY VAL SEQRES 31 A 514 GLY PHE ALA ILE GLY MET VAL ASP SER SER MET MET PRO SEQRES 32 A 514 ILE MET GLY TYR LEU VAL ASP LEU ARG HIS VAL SER VAL SEQRES 33 A 514 TYR GLY SER VAL TYR ALA ILE ALA ASP VAL ALA PHE CYS SEQRES 34 A 514 MET GLY PHE ALA PHE GLY PRO SER ALA GLY GLY ALA ILE SEQRES 35 A 514 ALA LYS SER ILE GLY PHE PRO TRP LEU MET THR ILE ILE SEQRES 36 A 514 GLY VAL VAL ASP ILE LEU PHE ALA PRO LEU CYS LEU PHE SEQRES 37 A 514 LEU ARG SER PRO PRO ALA ARG GLU GLU LYS MET ALA ILE SEQRES 38 A 514 LEU MET ASP HIS LYS CYS PRO VAL LYS THR LYS MET TYR SEQRES 39 A 514 THR GLN ASN SER GLY GLN PRO TYR TYR THR GLY GLU GLU SEQRES 40 A 514 GLU GLU SER GLU SER ASP GLU HELIX 1 AA1 ARG A 19 VAL A 39 1 21 HELIX 2 AA2 ILE A 44 TYR A 49 1 6 HELIX 3 AA3 GLU A 126 ILE A 155 1 30 HELIX 4 AA4 TYR A 157 ILE A 173 1 17 HELIX 5 AA5 MET A 174 PHE A 177 5 4 HELIX 6 AA6 THR A 180 TYR A 210 1 31 HELIX 7 AA7 ASP A 212 PHE A 244 1 33 HELIX 8 AA8 PHE A 251 LEU A 269 1 19 HELIX 9 AA9 ASP A 290 MET A 322 1 33 HELIX 10 AB1 PHE A 333 GLY A 348 1 16 HELIX 11 AB2 PRO A 349 LYS A 353 5 5 HELIX 12 AB3 GLY A 355 VAL A 374 1 20 HELIX 13 AB4 ILE A 380 LEU A 383 5 4 HELIX 14 AB5 ILE A 384 ARG A 412 1 29 HELIX 15 AB6 TYR A 417 GLY A 435 1 19 HELIX 16 AB7 ALA A 438 SER A 445 1 8 HELIX 17 AB8 ILE A 454 ALA A 463 1 10 HELIX 18 AB9 PRO A 464 PHE A 468 5 5 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