HEADER TRANSPORT PROTEIN/IMMUNE SYSTEM 30-SEP-23 8WLJ TITLE CRYO-EM STRUCTURE OF HUMAN APO VMAT2 WITH NANOBODY IN AN OUTWARD- TITLE 2 FACING CONFORMATION 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,VESICULAR MONOAMINE TRANSPORTER 2, COMPND 6 VAT2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NANOBODY; COMPND 10 CHAIN: D; COMPND 11 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; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 9 EXPRESSION_SYSTEM_CELL: HEK293F; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 12 ORGANISM_TAXID: 30538; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN VMAT2, OUTWARD-FACING CONFORMATION, TRANSPORT PROTEIN, KEYWDS 2 TRANSPORT PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Q.QU,Y.WANG,Z.ZHOU REVDAT 1 12-JUN-24 8WLJ 0 JRNL AUTH Q.QU,Y.WANG,Z.ZHOU JRNL TITL CRYO-EM STRUCTURE OF HUMAN APO VMAT2 IN AN OUTWARD-FACING JRNL TITL 2 CONFORMATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.60 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 : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 220731 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 8WLJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300040980. 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 : VESICULAR MONOAMINE TRANSPORTER REMARK 245 2; VMAT2; NANOBODY 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 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 GLY A 488 REMARK 465 SER A 489 REMARK 465 SER A 490 REMARK 465 ASP A 491 REMARK 465 LEU A 492 REMARK 465 GLU A 493 REMARK 465 VAL A 494 REMARK 465 LEU A 495 REMARK 465 PHE A 496 REMARK 465 GLN A 497 REMARK 465 MET D -1 REMARK 465 GLY D 0 REMARK 465 SER D 1 REMARK 465 SER D 2 REMARK 465 GLU D 3 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 SER D 23 OG REMARK 470 SER D 27 OG 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 180 -64.26 -135.27 REMARK 500 VAL A 246 -62.78 -108.42 REMARK 500 PRO A 272 49.21 -86.29 REMARK 500 ARG A 326 -169.87 -126.54 REMARK 500 SER A 472 81.60 -150.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37621 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN APO VMAT2 WITH NANOBODY IN AN OUTWARD- REMARK 900 FACING CONFORMATION DBREF 8WLJ A 1 474 UNP Q05940 VMAT2_HUMAN 1 474 DBREF 8WLJ D -1 124 PDB 8WLJ 8WLJ -1 124 SEQADV 8WLJ SER A 475 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ ARG A 476 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ LEU A 477 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ GLU A 478 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ GLU A 479 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ GLU A 480 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ LEU A 481 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ ARG A 482 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ ARG A 483 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ ARG A 484 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ THR A 485 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ GLU A 486 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ GLY A 487 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ GLY A 488 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ SER A 489 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ SER A 490 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ ASP A 491 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ LEU A 492 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ GLU A 493 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ VAL A 494 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ LEU A 495 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ PHE A 496 UNP Q05940 EXPRESSION TAG SEQADV 8WLJ GLN A 497 UNP Q05940 EXPRESSION TAG SEQRES 1 A 497 MET ALA LEU SER GLU LEU ALA LEU VAL ARG TRP LEU GLN SEQRES 2 A 497 GLU SER ARG ARG SER ARG LYS LEU ILE LEU PHE ILE VAL SEQRES 3 A 497 PHE LEU ALA LEU LEU LEU ASP ASN MET LEU LEU THR VAL SEQRES 4 A 497 VAL VAL PRO ILE ILE PRO SER TYR LEU TYR SER ILE LYS SEQRES 5 A 497 HIS GLU LYS ASN ALA THR GLU ILE GLN THR ALA ARG PRO SEQRES 6 A 497 VAL HIS THR ALA SER ILE SER ASP SER PHE GLN SER ILE SEQRES 7 A 497 PHE SER TYR TYR ASP ASN SER THR MET VAL THR GLY ASN SEQRES 8 A 497 ALA THR ARG ASP LEU THR LEU HIS GLN THR ALA THR GLN SEQRES 9 A 497 HIS MET VAL THR ASN ALA SER ALA VAL PRO SER ASP CYS SEQRES 10 A 497 PRO SER GLU ASP LYS ASP LEU LEU ASN GLU ASN VAL GLN SEQRES 11 A 497 VAL GLY LEU LEU PHE ALA SER LYS ALA THR VAL GLN LEU SEQRES 12 A 497 ILE THR ASN PRO PHE ILE GLY LEU LEU THR ASN ARG ILE SEQRES 13 A 497 GLY TYR PRO ILE PRO ILE PHE ALA GLY PHE CYS ILE MET SEQRES 14 A 497 PHE VAL SER THR ILE MET PHE ALA PHE SER SER SER TYR SEQRES 15 A 497 ALA PHE LEU LEU ILE ALA ARG SER LEU GLN GLY ILE GLY SEQRES 16 A 497 SER SER CYS SER SER VAL ALA GLY MET GLY MET LEU ALA SEQRES 17 A 497 SER VAL TYR THR ASP ASP GLU GLU ARG GLY ASN VAL MET SEQRES 18 A 497 GLY ILE ALA LEU GLY GLY LEU ALA MET GLY VAL LEU VAL SEQRES 19 A 497 GLY PRO PRO PHE GLY SER VAL LEU TYR GLU PHE VAL GLY SEQRES 20 A 497 LYS THR ALA PRO PHE LEU VAL LEU ALA ALA LEU VAL LEU SEQRES 21 A 497 LEU ASP GLY ALA ILE GLN LEU PHE VAL LEU GLN PRO SER SEQRES 22 A 497 ARG VAL GLN PRO GLU SER GLN LYS GLY THR PRO LEU THR SEQRES 23 A 497 THR LEU LEU LYS ASP PRO TYR ILE LEU ILE ALA ALA GLY SEQRES 24 A 497 SER ILE CYS PHE ALA ASN MET GLY ILE ALA MET LEU GLU SEQRES 25 A 497 PRO ALA LEU PRO ILE TRP MET MET GLU THR MET CYS SER SEQRES 26 A 497 ARG LYS TRP GLN LEU GLY VAL ALA PHE LEU PRO ALA SER SEQRES 27 A 497 ILE SER TYR LEU ILE GLY THR ASN ILE PHE GLY ILE LEU SEQRES 28 A 497 ALA HIS LYS MET GLY ARG TRP LEU CYS ALA LEU LEU GLY SEQRES 29 A 497 MET ILE ILE VAL GLY VAL SER ILE LEU CYS ILE PRO PHE SEQRES 30 A 497 ALA LYS ASN ILE TYR GLY LEU ILE ALA PRO ASN PHE GLY SEQRES 31 A 497 VAL GLY PHE ALA ILE GLY MET VAL ASP SER SER MET MET SEQRES 32 A 497 PRO ILE MET GLY TYR LEU VAL ASP LEU ARG HIS VAL SER SEQRES 33 A 497 VAL TYR GLY SER VAL TYR ALA ILE ALA ASP VAL ALA PHE SEQRES 34 A 497 CYS MET GLY TYR ALA ILE GLY PRO SER ALA GLY GLY ALA SEQRES 35 A 497 ILE ALA LYS ALA ILE GLY PHE PRO TRP LEU MET THR ILE SEQRES 36 A 497 ILE GLY ILE ILE ASP ILE LEU PHE ALA PRO LEU CYS PHE SEQRES 37 A 497 PHE LEU ARG SER PRO PRO SER ARG LEU GLU GLU GLU LEU SEQRES 38 A 497 ARG ARG ARG THR GLU GLY GLY SER SER ASP LEU GLU VAL SEQRES 39 A 497 LEU PHE GLN SEQRES 1 D 126 MET GLY SER SER GLU VAL GLN LEU GLN GLU SER GLY GLY SEQRES 2 D 126 GLY LEU VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS SEQRES 3 D 126 THR ALA SER GLY VAL THR ILE SER ALA LEU ASN ALA MET SEQRES 4 D 126 ALA MET GLY TRP TYR ARG GLN ALA PRO GLY GLU ARG ARG SEQRES 5 D 126 VAL MET VAL ALA ALA VAL SER GLU ARG GLY ASN ALA MET SEQRES 6 D 126 TYR ARG GLU SER VAL GLN GLY ARG PHE THR VAL THR ARG SEQRES 7 D 126 ASP PHE THR ASN LYS MET VAL SER LEU GLN MET ASP ASN SEQRES 8 D 126 LEU LYS PRO GLU ASP THR ALA VAL TYR TYR CYS HIS VAL SEQRES 9 D 126 LEU GLU ASP ARG VAL ASP SER PHE HIS ASP TYR TRP GLY SEQRES 10 D 126 GLN GLY THR GLN VAL THR VAL SER SER 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 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 CYS A 324 1 34 HELIX 9 AA9 TRP A 328 GLY A 356 1 29 HELIX 10 AB1 GLY A 356 ALA A 378 1 23 HELIX 11 AB2 ASN A 380 HIS A 414 1 35 HELIX 12 AB3 TYR A 418 GLY A 436 1 19 HELIX 13 AB4 GLY A 436 ILE A 447 1 12 HELIX 14 AB5 GLY A 448 ALA A 464 1 17 HELIX 15 AB6 PRO A 465 ARG A 471 5 7 HELIX 16 AB7 SER A 475 GLY A 487 1 13 HELIX 17 AB8 THR D 30 MET D 37 1 8 HELIX 18 AB9 LYS D 91 THR D 95 5 5 SHEET 1 AA1 4 GLN D 7 SER D 9 0 SHEET 2 AA1 4 LEU D 20 THR D 25 -1 O THR D 25 N GLN D 7 SHEET 3 AA1 4 MET D 82 MET D 87 -1 O LEU D 85 N LEU D 22 SHEET 4 AA1 4 PHE D 72 ARG D 76 -1 N THR D 73 O GLN D 86 SHEET 1 AA2 5 GLY D 12 VAL D 14 0 SHEET 2 AA2 5 THR D 118 VAL D 122 1 O GLN D 119 N GLY D 12 SHEET 3 AA2 5 ALA D 96 LEU D 103 -1 N TYR D 98 O THR D 118 SHEET 4 AA2 5 ALA D 38 GLN D 44 -1 N GLN D 44 O VAL D 97 SHEET 5 AA2 5 ALA D 54 VAL D 56 -1 O VAL D 56 N MET D 39 SSBOND 1 CYS D 24 CYS D 100 1555 1555 2.04 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