HEADER MEMBRANE PROTEIN 09-MAY-25 9OKG TITLE CRYO-EM STRUCTURE OF HUMAN SV2A IN COMPLEX WITH LEVETIRACETAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTIC VESICLE GLYCOPROTEIN 2A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SLC TRANSPORTER, SLC22 FAMILY, MEMBRANE PROTEIN, INHIBITOR EXPDTA ELECTRON MICROSCOPY AUTHOR S.PIDATHALA,Y.DAI,C.H.LEE REVDAT 1 10-DEC-25 9OKG 0 JRNL AUTH S.PIDATHALA,X.CHEN,Y.DAI,L.N.NGUYEN,C.GORGULLA,Y.NIU,F.LIU, JRNL AUTH 2 C.H.LEE JRNL TITL STRUCTURAL PHARMACOLOGY OF SV2A REVEALS AN ALLOSTERIC JRNL TITL 2 MODULATION MECHANISM IN THE MAJOR FACILITATOR SUPERFAMILY. JRNL REF NAT COMMUN V. 16 10748 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41315229 JRNL DOI 10.1038/S41467-025-65781-1 REMARK 2 REMARK 2 RESOLUTION. 2.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, 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) : 2.580 REMARK 3 NUMBER OF PARTICLES : 890424 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 9OKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000295778. 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 SV2A IN COMPLEX WITH REMARK 245 LEVETIRACETAM 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1100.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2100.00 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) : 7050.00 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 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 324 REMARK 465 GLY A 325 REMARK 465 SER A 326 REMARK 465 ALA A 327 REMARK 465 TYR A 328 REMARK 465 GLN A 402 REMARK 465 GLU A 403 REMARK 465 ASP A 404 REMARK 465 GLU A 405 REMARK 465 LEU A 406 REMARK 465 ILE A 407 REMARK 465 GLU A 408 REMARK 465 ILE A 409 REMARK 465 GLN A 410 REMARK 465 SER A 411 REMARK 465 ASP A 412 REMARK 465 THR A 413 REMARK 465 GLY A 414 REMARK 465 ARG A 483 REMARK 465 THR A 484 REMARK 465 LYS A 485 REMARK 465 VAL A 486 REMARK 465 PHE A 487 REMARK 465 PRO A 488 REMARK 465 GLY A 489 REMARK 465 GLU A 490 REMARK 465 ARG A 491 REMARK 465 VAL A 492 REMARK 465 GLU A 493 REMARK 465 HIS A 494 REMARK 465 VAL A 495 REMARK 465 THR A 496 REMARK 465 PHE A 497 REMARK 465 ASN A 498 REMARK 465 PHE A 499 REMARK 465 THR A 500 REMARK 465 LEU A 501 REMARK 465 GLU A 502 REMARK 465 ASN A 503 REMARK 465 GLN A 504 REMARK 465 ILE A 505 REMARK 465 HIS A 506 REMARK 465 ARG A 507 REMARK 465 GLY A 508 REMARK 465 GLY A 509 REMARK 465 GLN A 510 REMARK 465 TYR A 511 REMARK 465 PHE A 512 REMARK 465 ASN A 513 REMARK 465 ASP A 514 REMARK 465 LYS A 515 REMARK 465 PHE A 516 REMARK 465 ILE A 517 REMARK 465 GLY A 518 REMARK 465 LEU A 519 REMARK 465 ARG A 520 REMARK 465 LEU A 521 REMARK 465 LYS A 522 REMARK 465 SER A 523 REMARK 465 VAL A 524 REMARK 465 SER A 525 REMARK 465 PHE A 526 REMARK 465 GLU A 527 REMARK 465 ASP A 528 REMARK 465 SER A 529 REMARK 465 LEU A 530 REMARK 465 PHE A 531 REMARK 465 GLU A 532 REMARK 465 GLU A 533 REMARK 465 CYS A 534 REMARK 465 TYR A 535 REMARK 465 PHE A 536 REMARK 465 GLU A 537 REMARK 465 ASP A 538 REMARK 465 VAL A 539 REMARK 465 THR A 540 REMARK 465 SER A 541 REMARK 465 SER A 542 REMARK 465 ASN A 543 REMARK 465 THR A 544 REMARK 465 PHE A 545 REMARK 465 PHE A 546 REMARK 465 ARG A 547 REMARK 465 ASN A 548 REMARK 465 CYS A 549 REMARK 465 THR A 550 REMARK 465 PHE A 551 REMARK 465 ILE A 552 REMARK 465 ASN A 553 REMARK 465 THR A 554 REMARK 465 VAL A 555 REMARK 465 PHE A 556 REMARK 465 TYR A 557 REMARK 465 ASN A 558 REMARK 465 THR A 559 REMARK 465 ASP A 560 REMARK 465 LEU A 561 REMARK 465 PHE A 562 REMARK 465 GLU A 563 REMARK 465 TYR A 564 REMARK 465 LYS A 565 REMARK 465 PHE A 566 REMARK 465 VAL A 567 REMARK 465 ASN A 568 REMARK 465 SER A 569 REMARK 465 ARG A 570 REMARK 465 LEU A 571 REMARK 465 ILE A 572 REMARK 465 ASN A 573 REMARK 465 SER A 574 REMARK 465 THR A 575 REMARK 465 PHE A 576 REMARK 465 LEU A 577 REMARK 465 HIS A 578 REMARK 465 ASN A 579 REMARK 465 LYS A 580 REMARK 465 GLU A 581 REMARK 465 GLY A 582 REMARK 465 CYS A 583 REMARK 465 PRO A 584 REMARK 465 LEU A 585 REMARK 465 ASP A 586 REMARK 465 VAL A 587 REMARK 465 THR A 588 REMARK 465 GLY A 589 REMARK 465 THR A 590 REMARK 465 GLY A 591 REMARK 465 GLU A 592 REMARK 465 GLY A 593 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 PRO A 191 13.36 -67.61 REMARK 500 GLU A 194 -38.87 -131.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70563 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN SV2A IN COMPLEX WITH LEVETIRACETAM DBREF 9OKG A 139 742 PDB 9OKG 9OKG 139 742 SEQRES 1 A 604 ALA GLN ARG ARG LYS GLU ARG GLU GLU LEU ALA GLN GLN SEQRES 2 A 604 TYR GLU ALA ILE LEU ARG GLU CYS GLY HIS GLY ARG PHE SEQRES 3 A 604 GLN TRP THR LEU TYR PHE VAL LEU GLY LEU ALA LEU MET SEQRES 4 A 604 ALA ASP GLY VAL GLU VAL PHE VAL VAL GLY PHE VAL LEU SEQRES 5 A 604 PRO SER ALA GLU LYS ASP MET CYS LEU SER ASP SER ASN SEQRES 6 A 604 LYS GLY MET LEU GLY LEU ILE VAL TYR LEU GLY MET MET SEQRES 7 A 604 VAL GLY ALA PHE LEU TRP GLY GLY LEU ALA ASP ARG LEU SEQRES 8 A 604 GLY ARG ARG GLN CYS LEU LEU ILE SER LEU SER VAL ASN SEQRES 9 A 604 SER VAL PHE ALA PHE PHE SER SER PHE VAL GLN GLY TYR SEQRES 10 A 604 GLY THR PHE LEU PHE CYS ARG LEU LEU SER GLY VAL GLY SEQRES 11 A 604 ILE GLY GLY SER ILE PRO ILE VAL PHE SER TYR PHE SER SEQRES 12 A 604 GLU PHE LEU ALA GLN GLU LYS ARG GLY GLU HIS LEU SER SEQRES 13 A 604 TRP LEU CYS MET PHE TRP MET ILE GLY GLY VAL TYR ALA SEQRES 14 A 604 ALA ALA MET ALA TRP ALA ILE ILE PRO HIS TYR GLY TRP SEQRES 15 A 604 SER PHE GLN MET GLY SER ALA TYR GLN PHE HIS SER TRP SEQRES 16 A 604 ARG VAL PHE VAL LEU VAL CYS ALA PHE PRO SER VAL PHE SEQRES 17 A 604 ALA ILE GLY ALA LEU THR THR GLN PRO GLU SER PRO ARG SEQRES 18 A 604 PHE PHE LEU GLU ASN GLY LYS HIS ASP GLU ALA TRP MET SEQRES 19 A 604 VAL LEU LYS GLN VAL HIS ASP THR ASN MET ARG ALA LYS SEQRES 20 A 604 GLY HIS PRO GLU ARG VAL PHE SER VAL THR HIS ILE LYS SEQRES 21 A 604 THR ILE HIS GLN GLU ASP GLU LEU ILE GLU ILE GLN SER SEQRES 22 A 604 ASP THR GLY THR TRP TYR GLN ARG TRP GLY VAL ARG ALA SEQRES 23 A 604 LEU SER LEU GLY GLY GLN VAL TRP GLY ASN PHE LEU SER SEQRES 24 A 604 CYS PHE GLY PRO GLU TYR ARG ARG ILE THR LEU MET MET SEQRES 25 A 604 MET GLY VAL TRP PHE THR MET SER PHE SER TYR TYR GLY SEQRES 26 A 604 LEU THR VAL TRP PHE PRO ASP MET ILE ARG HIS LEU GLN SEQRES 27 A 604 ALA VAL ASP TYR ALA SER ARG THR LYS VAL PHE PRO GLY SEQRES 28 A 604 GLU ARG VAL GLU HIS VAL THR PHE ASN PHE THR LEU GLU SEQRES 29 A 604 ASN GLN ILE HIS ARG GLY GLY GLN TYR PHE ASN ASP LYS SEQRES 30 A 604 PHE ILE GLY LEU ARG LEU LYS SER VAL SER PHE GLU ASP SEQRES 31 A 604 SER LEU PHE GLU GLU CYS TYR PHE GLU ASP VAL THR SER SEQRES 32 A 604 SER ASN THR PHE PHE ARG ASN CYS THR PHE ILE ASN THR SEQRES 33 A 604 VAL PHE TYR ASN THR ASP LEU PHE GLU TYR LYS PHE VAL SEQRES 34 A 604 ASN SER ARG LEU ILE ASN SER THR PHE LEU HIS ASN LYS SEQRES 35 A 604 GLU GLY CYS PRO LEU ASP VAL THR GLY THR GLY GLU GLY SEQRES 36 A 604 ALA TYR MET VAL TYR PHE VAL SER PHE LEU GLY THR LEU SEQRES 37 A 604 ALA VAL LEU PRO GLY ASN ILE VAL SER ALA LEU LEU MET SEQRES 38 A 604 ASP LYS ILE GLY ARG LEU ARG MET LEU ALA GLY SER SER SEQRES 39 A 604 VAL MET SER CYS VAL SER CYS PHE PHE LEU SER PHE GLY SEQRES 40 A 604 ASN SER GLU SER ALA MET ILE ALA LEU LEU CYS LEU PHE SEQRES 41 A 604 GLY GLY VAL SER ILE ALA SER TRP ASN ALA LEU ASP VAL SEQRES 42 A 604 LEU THR VAL GLU LEU TYR PRO SER ASP LYS ARG THR THR SEQRES 43 A 604 ALA PHE GLY PHE LEU ASN ALA LEU CYS LYS LEU ALA ALA SEQRES 44 A 604 VAL LEU GLY ILE SER ILE PHE THR SER PHE VAL GLY ILE SEQRES 45 A 604 THR LYS ALA ALA PRO ILE LEU PHE ALA SER ALA ALA LEU SEQRES 46 A 604 ALA LEU GLY SER SER LEU ALA LEU LYS LEU PRO GLU THR SEQRES 47 A 604 ARG GLY GLN VAL LEU GLN HET UKX A 801 12 HETNAM UKX (2S)-2-(2-OXIDANYLIDENEPYRROLIDIN-1-YL)BUTANAMIDE HETSYN UKX LEVETIRACETAM FORMUL 2 UKX C8 H14 N2 O2 HELIX 1 AA1 ALA A 139 GLY A 160 1 22 HELIX 2 AA2 GLY A 162 VAL A 189 1 28 HELIX 3 AA3 SER A 200 GLY A 230 1 31 HELIX 4 AA4 GLY A 230 VAL A 252 1 23 HELIX 5 AA5 GLY A 254 GLY A 270 1 17 HELIX 6 AA6 GLY A 271 GLU A 282 1 12 HELIX 7 AA7 LYS A 288 TRP A 295 1 8 HELIX 8 AA8 CYS A 297 ILE A 315 1 19 HELIX 9 AA9 HIS A 331 CYS A 340 1 10 HELIX 10 AB1 ALA A 341 THR A 352 1 12 HELIX 11 AB2 SER A 357 ASN A 364 1 8 HELIX 12 AB3 LYS A 366 LYS A 385 1 20 HELIX 13 AB4 TRP A 416 CYS A 438 1 23 HELIX 14 AB5 TYR A 443 SER A 482 1 40 HELIX 15 AB6 TYR A 595 ALA A 607 1 13 HELIX 16 AB7 ALA A 607 GLY A 623 1 17 HELIX 17 AB8 GLY A 623 PHE A 641 1 19 HELIX 18 AB9 LEU A 642 GLY A 645 5 4 HELIX 19 AC1 SER A 647 TYR A 677 1 31 HELIX 20 AC2 LYS A 681 VAL A 708 1 28 HELIX 21 AC3 ALA A 713 LEU A 731 1 19 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 TER 3724 GLN A 742 HETATM 3725 O1 UKX A 801 146.623 139.955 131.523 1.00 35.07 O HETATM 3726 O2 UKX A 801 144.339 139.034 134.003 1.00 31.13 O HETATM 3727 N1 UKX A 801 146.012 137.774 131.374 1.00 26.78 N HETATM 3728 C1 UKX A 801 146.871 138.790 131.223 1.00 29.24 C HETATM 3729 C2 UKX A 801 148.136 138.259 130.596 1.00 24.56 C HETATM 3730 C3 UKX A 801 148.058 136.776 130.845 1.00 24.96 C HETATM 3731 C4 UKX A 801 146.564 136.493 130.929 1.00 26.11 C HETATM 3732 C5 UKX A 801 144.674 137.994 133.428 1.00 29.72 C HETATM 3733 C6 UKX A 801 144.663 137.936 131.904 1.00 25.98 C HETATM 3734 C7 UKX A 801 143.700 136.880 131.375 1.00 29.05 C HETATM 3735 C8 UKX A 801 142.252 137.192 131.719 1.00 30.58 C HETATM 3736 N2 UKX A 801 145.046 136.910 134.076 1.00 25.84 N CONECT 3725 3728 CONECT 3726 3732 CONECT 3727 3728 3731 3733 CONECT 3728 3725 3727 3729 CONECT 3729 3728 3730 CONECT 3730 3729 3731 CONECT 3731 3727 3730 CONECT 3732 3726 3733 3736 CONECT 3733 3727 3732 3734 CONECT 3734 3733 3735 CONECT 3735 3734 CONECT 3736 3732 MASTER 255 0 1 21 0 0 0 6 3735 1 12 47 END