HEADER STRUCTURAL PROTEIN 16-JAN-25 9LK8 TITLE CRYO-EM STRUCTURE OF GAT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM- AND CHLORIDE-DEPENDENT GABA TRANSPORTER 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAT-3,SOLUTE CARRIER FAMILY 6 MEMBER 11; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SLC6A11, GABT3, GAT3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS PROTEIN STRUCTURE, STRUCTUAL PROTEIN, STRUCTURAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.ZHAO,H.XU REVDAT 2 04-MAR-26 9LK8 1 JRNL REVDAT 1 20-AUG-25 9LK8 0 JRNL AUTH H.XU,Y.ZHANG,Q.BAI,L.HE,Q.CHEN,Y.QIU,R.LI,J.YU,J.ZHAO,Y.ZHAO JRNL TITL SUBSTRATE AND INHIBITOR BINDING OF HUMAN GABA TRANSPORTER 3. JRNL REF STRUCTURE V. 33 2049 2025 JRNL REFN ISSN 0969-2126 JRNL PMID 40914153 JRNL DOI 10.1016/J.STR.2025.08.012 REMARK 2 REMARK 2 RESOLUTION. 3.40 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 : 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 32961 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9LK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055821. 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 : STRUCTURE OF GAT3 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 TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 BIOCONTINUUM (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 : 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 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 THR A 2 REMARK 465 ALA A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 LEU A 7 REMARK 465 PRO A 8 REMARK 465 LEU A 9 REMARK 465 GLY A 10 REMARK 465 ASN A 11 REMARK 465 GLY A 12 REMARK 465 LYS A 13 REMARK 465 ALA A 14 REMARK 465 ALA A 15 REMARK 465 GLU A 16 REMARK 465 GLU A 17 REMARK 465 ALA A 18 REMARK 465 ARG A 19 REMARK 465 GLU A 20 REMARK 465 SER A 21 REMARK 465 GLU A 22 REMARK 465 ALA A 23 REMARK 465 PRO A 24 REMARK 465 GLY A 25 REMARK 465 GLY A 26 REMARK 465 GLY A 27 REMARK 465 SER A 28 REMARK 465 SER A 29 REMARK 465 SER A 30 REMARK 465 GLY A 31 REMARK 465 GLY A 32 REMARK 465 ALA A 33 REMARK 465 ALA A 34 REMARK 465 PRO A 35 REMARK 465 ALA A 36 REMARK 465 ARG A 37 REMARK 465 HIS A 38 REMARK 465 PRO A 39 REMARK 465 ARG A 40 REMARK 465 VAL A 41 REMARK 465 LYS A 42 REMARK 465 ARG A 43 REMARK 465 ASP A 44 REMARK 465 LYS A 45 REMARK 465 ALA A 46 REMARK 465 VAL A 47 REMARK 465 HIS A 48 REMARK 465 GLU A 49 REMARK 465 ARG A 50 REMARK 465 GLY A 51 REMARK 465 HIS A 52 REMARK 465 TRP A 53 REMARK 465 ASN A 54 REMARK 465 ASN A 55 REMARK 465 LYS A 56 REMARK 465 VAL A 57 REMARK 465 GLU A 58 REMARK 465 PHE A 59 REMARK 465 VAL A 60 REMARK 465 LEU A 186 REMARK 465 ASN A 187 REMARK 465 VAL A 188 REMARK 465 SER A 189 REMARK 465 ASN A 190 REMARK 465 TYR A 191 REMARK 465 SER A 192 REMARK 465 HIS A 193 REMARK 465 VAL A 194 REMARK 465 SER A 195 REMARK 465 ILE A 243 REMARK 465 TRP A 244 REMARK 465 LYS A 245 REMARK 465 GLY A 246 REMARK 465 THR A 247 REMARK 465 LYS A 248 REMARK 465 SER A 249 REMARK 465 THR A 250 REMARK 465 GLY A 251 REMARK 465 LYS A 252 REMARK 465 ASN A 324 REMARK 465 ASN A 325 REMARK 465 TYR A 326 REMARK 465 ASN A 327 REMARK 465 PHE A 430 REMARK 465 ARG A 431 REMARK 465 ARG A 432 REMARK 465 GLY A 433 REMARK 465 ASP A 593 REMARK 465 LEU A 594 REMARK 465 LYS A 595 REMARK 465 MET A 596 REMARK 465 ARG A 597 REMARK 465 GLY A 598 REMARK 465 LYS A 599 REMARK 465 LEU A 600 REMARK 465 GLY A 601 REMARK 465 VAL A 602 REMARK 465 SER A 603 REMARK 465 PRO A 604 REMARK 465 ARG A 605 REMARK 465 MET A 606 REMARK 465 VAL A 607 REMARK 465 THR A 608 REMARK 465 VAL A 609 REMARK 465 ASN A 610 REMARK 465 ASP A 611 REMARK 465 SER A 612 REMARK 465 ASP A 613 REMARK 465 ALA A 614 REMARK 465 LYS A 615 REMARK 465 LEU A 616 REMARK 465 LYS A 617 REMARK 465 SER A 618 REMARK 465 ASP A 619 REMARK 465 GLY A 620 REMARK 465 THR A 621 REMARK 465 ILE A 622 REMARK 465 ALA A 623 REMARK 465 ALA A 624 REMARK 465 ILE A 625 REMARK 465 THR A 626 REMARK 465 GLU A 627 REMARK 465 LYS A 628 REMARK 465 GLU A 629 REMARK 465 THR A 630 REMARK 465 HIS A 631 REMARK 465 PHE A 632 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASP A 333 N LEU A 337 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 66 40.89 -100.87 REMARK 500 SER A 322 -149.24 60.31 REMARK 500 SER A 472 -169.00 -167.60 REMARK 500 ILE A 543 -52.28 -124.32 REMARK 500 THR A 576 -126.49 51.59 REMARK 500 THR A 579 -168.62 -126.63 REMARK 500 LEU A 580 158.51 71.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63171 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF GAT3 DBREF 9LK8 A 1 632 UNP P48066 S6A11_HUMAN 1 632 SEQADV 9LK8 SER A 28 UNP P48066 CYS 28 ENGINEERED MUTATION SEQADV 9LK8 SER A 612 UNP P48066 CYS 612 ENGINEERED MUTATION SEQRES 1 A 632 MET THR ALA GLU LYS ALA LEU PRO LEU GLY ASN GLY LYS SEQRES 2 A 632 ALA ALA GLU GLU ALA ARG GLU SER GLU ALA PRO GLY GLY SEQRES 3 A 632 GLY SER SER SER GLY GLY ALA ALA PRO ALA ARG HIS PRO SEQRES 4 A 632 ARG VAL LYS ARG ASP LYS ALA VAL HIS GLU ARG GLY HIS SEQRES 5 A 632 TRP ASN ASN LYS VAL GLU PHE VAL LEU SER VAL ALA GLY SEQRES 6 A 632 GLU ILE ILE GLY LEU GLY ASN VAL TRP ARG PHE PRO TYR SEQRES 7 A 632 LEU CYS TYR LYS ASN GLY GLY GLY ALA PHE LEU ILE PRO SEQRES 8 A 632 TYR VAL VAL PHE PHE ILE CYS CYS GLY ILE PRO VAL PHE SEQRES 9 A 632 PHE LEU GLU THR ALA LEU GLY GLN PHE THR SER GLU GLY SEQRES 10 A 632 GLY ILE THR CYS TRP ARG LYS VAL CYS PRO LEU PHE GLU SEQRES 11 A 632 GLY ILE GLY TYR ALA THR GLN VAL ILE GLU ALA HIS LEU SEQRES 12 A 632 ASN VAL TYR TYR ILE ILE ILE LEU ALA TRP ALA ILE PHE SEQRES 13 A 632 TYR LEU SER ASN CYS PHE THR THR GLU LEU PRO TRP ALA SEQRES 14 A 632 THR CYS GLY HIS GLU TRP ASN THR GLU ASN CYS VAL GLU SEQRES 15 A 632 PHE GLN LYS LEU ASN VAL SER ASN TYR SER HIS VAL SER SEQRES 16 A 632 LEU GLN ASN ALA THR SER PRO VAL MET GLU PHE TRP GLU SEQRES 17 A 632 HIS ARG VAL LEU ALA ILE SER ASP GLY ILE GLU HIS ILE SEQRES 18 A 632 GLY ASN LEU ARG TRP GLU LEU ALA LEU CYS LEU LEU ALA SEQRES 19 A 632 ALA TRP THR ILE CYS TYR PHE CYS ILE TRP LYS GLY THR SEQRES 20 A 632 LYS SER THR GLY LYS VAL VAL TYR VAL THR ALA THR PHE SEQRES 21 A 632 PRO TYR ILE MET LEU LEU ILE LEU LEU ILE ARG GLY VAL SEQRES 22 A 632 THR LEU PRO GLY ALA SER GLU GLY ILE LYS PHE TYR LEU SEQRES 23 A 632 TYR PRO ASP LEU SER ARG LEU SER ASP PRO GLN VAL TRP SEQRES 24 A 632 VAL ASP ALA GLY THR GLN ILE PHE PHE SER TYR ALA ILE SEQRES 25 A 632 CYS LEU GLY CYS LEU THR ALA LEU GLY SER TYR ASN ASN SEQRES 26 A 632 TYR ASN ASN ASN CYS TYR ARG ASP CYS ILE MET LEU CYS SEQRES 27 A 632 CYS LEU ASN SER GLY THR SER PHE VAL ALA GLY PHE ALA SEQRES 28 A 632 ILE PHE SER VAL LEU GLY PHE MET ALA TYR GLU GLN GLY SEQRES 29 A 632 VAL PRO ILE ALA GLU VAL ALA GLU SER GLY PRO GLY LEU SEQRES 30 A 632 ALA PHE ILE ALA TYR PRO LYS ALA VAL THR MET MET PRO SEQRES 31 A 632 LEU SER PRO LEU TRP ALA THR LEU PHE PHE MET MET LEU SEQRES 32 A 632 ILE PHE LEU GLY LEU ASP SER GLN PHE VAL CYS VAL GLU SEQRES 33 A 632 SER LEU VAL THR ALA VAL VAL ASP MET TYR PRO LYS VAL SEQRES 34 A 632 PHE ARG ARG GLY TYR ARG ARG GLU LEU LEU ILE LEU ALA SEQRES 35 A 632 LEU SER VAL ILE SER TYR PHE LEU GLY LEU VAL MET LEU SEQRES 36 A 632 THR GLU GLY GLY MET TYR ILE PHE GLN LEU PHE ASP SER SEQRES 37 A 632 TYR ALA ALA SER GLY MET CYS LEU LEU PHE VAL ALA ILE SEQRES 38 A 632 PHE GLU CYS ILE CYS ILE GLY TRP VAL TYR GLY SER ASN SEQRES 39 A 632 ARG PHE TYR ASP ASN ILE GLU ASP MET ILE GLY TYR ARG SEQRES 40 A 632 PRO PRO SER LEU ILE LYS TRP CYS TRP MET ILE MET THR SEQRES 41 A 632 PRO GLY ILE CYS ALA GLY ILE PHE ILE PHE PHE LEU ILE SEQRES 42 A 632 LYS TYR LYS PRO LEU LYS TYR ASN ASN ILE TYR THR TYR SEQRES 43 A 632 PRO ALA TRP GLY TYR GLY ILE GLY TRP LEU MET ALA LEU SEQRES 44 A 632 SER SER MET LEU CYS ILE PRO LEU TRP ILE CYS ILE THR SEQRES 45 A 632 VAL TRP LYS THR GLU GLY THR LEU PRO GLU LYS LEU GLN SEQRES 46 A 632 LYS LEU THR THR PRO SER THR ASP LEU LYS MET ARG GLY SEQRES 47 A 632 LYS LEU GLY VAL SER PRO ARG MET VAL THR VAL ASN ASP SEQRES 48 A 632 SER ASP ALA LYS LEU LYS SER ASP GLY THR ILE ALA ALA SEQRES 49 A 632 ILE THR GLU LYS GLU THR HIS PHE HET ABU A 701 7 HET CL A 702 1 HETNAM ABU GAMMA-AMINO-BUTANOIC ACID HETNAM CL CHLORIDE ION HETSYN ABU GAMMA(AMINO)-BUTYRIC ACID FORMUL 2 ABU C4 H9 N O2 FORMUL 3 CL CL 1- HELIX 1 AA1 GLY A 69 TRP A 74 1 6 HELIX 2 AA2 TRP A 74 GLY A 84 1 11 HELIX 3 AA3 PHE A 88 CYS A 99 1 12 HELIX 4 AA4 GLY A 100 SER A 115 1 16 HELIX 5 AA5 GLY A 117 CYS A 126 1 10 HELIX 6 AA6 GLU A 130 TYR A 147 1 18 HELIX 7 AA7 ILE A 148 ASN A 160 1 13 HELIX 8 AA8 SER A 201 ARG A 210 1 10 HELIX 9 AA9 ARG A 225 CYS A 242 1 18 HELIX 10 AB1 VAL A 254 LEU A 275 1 22 HELIX 11 AB2 GLY A 277 TYR A 287 1 11 HELIX 12 AB3 ASP A 289 SER A 294 5 6 HELIX 13 AB4 ASP A 295 ALA A 311 1 17 HELIX 14 AB5 ASN A 329 ILE A 335 1 7 HELIX 15 AB6 MET A 336 GLY A 364 1 29 HELIX 16 AB7 PRO A 366 VAL A 370 5 5 HELIX 17 AB8 LEU A 377 MET A 388 1 12 HELIX 18 AB9 LEU A 391 VAL A 423 1 33 HELIX 19 AC1 TYR A 434 GLU A 437 5 4 HELIX 20 AC2 LEU A 438 GLY A 451 1 14 HELIX 21 AC3 LEU A 452 THR A 456 5 5 HELIX 22 AC4 GLY A 458 ALA A 470 1 13 HELIX 23 AC5 GLY A 473 TRP A 489 1 17 HELIX 24 AC6 GLY A 492 GLY A 505 1 14 HELIX 25 AC7 SER A 510 ILE A 518 1 9 HELIX 26 AC8 ILE A 518 LYS A 534 1 17 HELIX 27 AC9 ASN A 541 ILE A 543 5 3 HELIX 28 AD1 PRO A 547 LEU A 563 1 17 HELIX 29 AD2 LEU A 563 LYS A 575 1 13 HELIX 30 AD3 THR A 579 LEU A 587 1 9 SHEET 1 AA1 2 LYS A 539 TYR A 540 0 SHEET 2 AA1 2 TYR A 544 THR A 545 -1 O TYR A 544 N TYR A 540 SSBOND 1 CYS A 126 CYS A 486 1555 1555 2.03 SSBOND 2 CYS A 171 CYS A 180 1555 1555 2.03 SSBOND 3 CYS A 239 CYS A 242 1555 1555 2.04 SSBOND 4 CYS A 334 CYS A 338 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 CONECT 510 3121 CONECT 876 951 CONECT 951 876 CONECT 1348 1377 CONECT 1377 1348 CONECT 1988 2018 CONECT 2018 1988 CONECT 3121 510 CONECT 3993 3994 CONECT 3994 3993 3995 CONECT 3995 3994 3996 CONECT 3996 3995 3997 CONECT 3997 3996 3998 3999 CONECT 3998 3997 CONECT 3999 3997 MASTER 266 0 2 30 2 0 0 6 3999 1 15 49 END