HEADER TRANSPORT PROTEIN 22-SEP-25 9SQH TITLE CRYO-EM STRUCTURE OF THE ARABIDOPSIS THALIANA CAT4 TRANSPORTER IN THE TITLE 2 OUTWARD-OPEN APO STATE (WITHOUT SYNTHETIC NANOBODY) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATIONIC AMINO ACID TRANSPORTER 4, VACUOLAR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: CAT4, AT3G03720, F20H23.25; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BJ5460; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDDGFP2-LEU2D KEYWDS CATIONIC AMINO ACID TRANSPORTER, APC FOLD, LEUT FOLD, CHOLESTEROL, KEYWDS 2 OUTWARD-OPEN STATE, CATIONIC AMINO ACIDS, SLC7, MEMBRANE PROTEIN, KEYWDS 3 TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.KOLOKOURIS,Y.C.ZENG,S.NEWSTEAD REVDAT 1 08-APR-26 9SQH 0 JRNL AUTH D.KOLOKOURIS,A.BOTHRA,T.KATO,Y.C.ZENG,S.LICHTINGER, JRNL AUTH 2 J.L.PARKER,P.C.BIGGIN,S.NEWSTEAD JRNL TITL STRUCTURAL BASIS FOR PH-RESPONSIVE AMINO ACID TRANSPORT VIA JRNL TITL 2 SLC7A4. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 41904136 JRNL DOI 10.1038/S41467-026-70956-5 REMARK 2 REMARK 2 RESOLUTION. 4.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX, ISOLDE REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 9HJK REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE 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) : 4.230 REMARK 3 NUMBER OF PARTICLES : 120868 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 9SQH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1292149863. 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 : ARABIDOPSIS THALIANA CATIONIC REMARK 245 AMINO ACID TRANSPORTER 4 REMARK 245 SOLUBILISED IN LMNG REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.70 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 : 30514 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3990.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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 ASN A 2 REMARK 465 SER A 3 REMARK 465 LEU A 4 REMARK 465 VAL A 5 REMARK 465 ARG A 6 REMARK 465 ARG A 7 REMARK 465 LYS A 8 REMARK 465 GLN A 9 REMARK 465 VAL A 10 REMARK 465 ASP A 11 REMARK 465 SER A 12 REMARK 465 VAL A 13 REMARK 465 HIS A 14 REMARK 465 LEU A 15 REMARK 465 ILE A 16 REMARK 465 LYS A 17 REMARK 465 ASN A 18 REMARK 465 ASP A 19 REMARK 465 GLY A 20 REMARK 465 PRO A 21 REMARK 465 ALA A 133 REMARK 465 SER A 134 REMARK 465 PHE A 135 REMARK 465 PHE A 136 REMARK 465 GLY A 137 REMARK 465 GLY A 138 REMARK 465 LEU A 139 REMARK 465 ASP A 140 REMARK 465 ASN A 141 REMARK 465 LEU A 142 REMARK 465 PRO A 143 REMARK 465 VAL A 144 REMARK 465 PHE A 145 REMARK 465 LEU A 146 REMARK 465 ALA A 147 REMARK 465 ARG A 148 REMARK 465 GLN A 149 REMARK 465 THR A 150 REMARK 465 ILE A 151 REMARK 465 PRO A 152 REMARK 465 GLY A 153 REMARK 465 VAL A 154 REMARK 465 GLY A 155 REMARK 465 ILE A 156 REMARK 465 VAL A 157 REMARK 465 VAL A 158 REMARK 465 TYR A 214 REMARK 465 ASP A 215 REMARK 465 LEU A 216 REMARK 465 PRO A 217 REMARK 465 SER A 218 REMARK 465 GLY A 219 REMARK 465 TYR A 220 REMARK 465 TYR A 287 REMARK 465 TYR A 288 REMARK 465 SER A 289 REMARK 465 LEU A 290 REMARK 465 ASN A 291 REMARK 465 PRO A 292 REMARK 465 ASP A 293 REMARK 465 THR A 294 REMARK 465 PRO A 295 REMARK 465 ILE A 296 REMARK 465 SER A 297 REMARK 465 SER A 298 REMARK 465 ALA A 299 REMARK 465 PHE A 300 REMARK 465 GLY A 301 REMARK 465 ASP A 302 REMARK 465 SER A 303 REMARK 465 GLY A 304 REMARK 465 MET A 305 REMARK 465 PRO A 408 REMARK 465 ASP A 409 REMARK 465 GLY A 410 REMARK 465 VAL A 411 REMARK 465 PRO A 412 REMARK 465 LEU A 413 REMARK 465 SER A 414 REMARK 465 SER A 415 REMARK 465 SER A 416 REMARK 465 SER A 417 REMARK 465 GLN A 418 REMARK 465 THR A 419 REMARK 465 LEU A 420 REMARK 465 SER A 421 REMARK 465 ASP A 422 REMARK 465 THR A 423 REMARK 465 ASP A 424 REMARK 465 GLU A 425 REMARK 465 SER A 426 REMARK 465 ARG A 427 REMARK 465 ALA A 428 REMARK 465 GLU A 429 REMARK 465 THR A 430 REMARK 465 GLU A 431 REMARK 465 ASN A 432 REMARK 465 PHE A 433 REMARK 465 LEU A 434 REMARK 465 VAL A 435 REMARK 465 ASP A 436 REMARK 465 ALA A 437 REMARK 465 ILE A 438 REMARK 465 GLU A 439 REMARK 465 SER A 440 REMARK 465 SER A 441 REMARK 465 ASP A 442 REMARK 465 SER A 443 REMARK 465 PRO A 444 REMARK 465 LEU A 445 REMARK 465 LEU A 446 REMARK 465 GLY A 447 REMARK 465 ASN A 448 REMARK 465 GLU A 449 REMARK 465 THR A 450 REMARK 465 ALA A 451 REMARK 465 ARG A 452 REMARK 465 ASP A 453 REMARK 465 GLU A 454 REMARK 465 LYS A 455 REMARK 465 TYR A 456 REMARK 465 PHE A 457 REMARK 465 GLY A 458 REMARK 465 ARG A 486 REMARK 465 LEU A 487 REMARK 465 PRO A 488 REMARK 465 SER A 489 REMARK 465 PHE A 490 REMARK 465 GLY A 511 REMARK 465 TYR A 512 REMARK 465 ILE A 513 REMARK 465 ASP A 514 REMARK 465 GLU A 515 REMARK 465 ASP A 516 REMARK 465 GLU A 517 REMARK 465 GLU A 518 REMARK 465 ARG A 519 REMARK 465 HIS A 520 REMARK 465 ASN A 521 REMARK 465 PHE A 522 REMARK 465 GLY A 523 REMARK 465 HIS A 524 REMARK 465 LYS A 525 REMARK 465 GLY A 526 REMARK 465 GLY A 527 REMARK 465 LEU A 580 REMARK 465 ASN A 581 REMARK 465 ASN A 582 REMARK 465 ALA A 583 REMARK 465 VAL A 584 REMARK 465 TYR A 585 REMARK 465 VAL A 586 REMARK 465 PRO A 587 REMARK 465 THR A 588 REMARK 465 MET A 589 REMARK 465 THR A 590 REMARK 465 CYS A 591 REMARK 465 THR A 592 REMARK 465 ARG A 593 REMARK 465 LYS A 594 REMARK 465 THR A 595 REMARK 465 THR A 596 REMARK 465 ASP A 597 REMARK 465 HIS A 598 REMARK 465 LEU A 599 REMARK 465 ALA A 600 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 92 -132.65 58.48 REMARK 500 ILE A 228 -62.31 -103.80 REMARK 500 ALA A 330 -60.83 -93.24 REMARK 500 PRO A 358 78.33 -68.51 REMARK 500 TYR A 405 -1.90 -140.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-55110 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE ARABIDOPSIS THALIANA CAT4 TRANSPORTER IN REMARK 900 THE OUTWARD-OPEN APO STATE (WITHOUT SYNTHETIC NANOBODY) DBREF 9SQH A 1 600 UNP Q8W4K3 CAAT4_ARATH 1 600 SEQRES 1 A 600 MET ASN SER LEU VAL ARG ARG LYS GLN VAL ASP SER VAL SEQRES 2 A 600 HIS LEU ILE LYS ASN ASP GLY PRO HIS GLN LEU ALA LYS SEQRES 3 A 600 LYS LEU SER ALA VAL ASP LEU VAL ALA ILE GLY VAL GLY SEQRES 4 A 600 THR THR ILE GLY ALA GLY VAL TYR ILE LEU VAL GLY THR SEQRES 5 A 600 VAL ALA ARG GLU HIS THR GLY PRO ALA LEU ALA VAL SER SEQRES 6 A 600 PHE PHE ILE ALA GLY VAL ALA ALA ALA LEU SER ALA CYS SEQRES 7 A 600 CYS TYR ALA GLU LEU ALA SER ARG CYS PRO SER ALA GLY SEQRES 8 A 600 SER ALA TYR HIS TYR ALA TYR ILE CYS LEU GLY GLU GLY SEQRES 9 A 600 ILE ALA TRP LEU VAL GLY TRP ALA LEU VAL LEU ASP TYR SEQRES 10 A 600 THR ILE GLY GLY SER ALA ILE ALA ARG GLY ILE THR PRO SEQRES 11 A 600 ASN LEU ALA SER PHE PHE GLY GLY LEU ASP ASN LEU PRO SEQRES 12 A 600 VAL PHE LEU ALA ARG GLN THR ILE PRO GLY VAL GLY ILE SEQRES 13 A 600 VAL VAL ASP PRO CYS ALA ALA LEU LEU ILE MET ILE VAL SEQRES 14 A 600 THR ILE LEU LEU CYS PHE GLY ILE LYS GLU SER SER THR SEQRES 15 A 600 VAL GLN ALA ILE VAL THR SER VAL ASN VAL CYS THR LEU SEQRES 16 A 600 VAL PHE ILE ILE VAL VAL GLY GLY TYR LEU ALA CYS LYS SEQRES 17 A 600 THR GLY TRP VAL GLY TYR ASP LEU PRO SER GLY TYR PHE SEQRES 18 A 600 PRO PHE GLY LEU ASN GLY ILE LEU ALA GLY SER ALA VAL SEQRES 19 A 600 VAL PHE PHE SER TYR ILE GLY PHE ASP THR VAL THR SER SEQRES 20 A 600 THR ALA GLU GLU VAL LYS ASN PRO GLN ARG ASP LEU PRO SEQRES 21 A 600 LEU GLY ILE GLY ILE ALA LEU LEU ILE CYS CYS ILE LEU SEQRES 22 A 600 TYR MET LEU LEU SER VAL VAL ILE VAL GLY LEU VAL PRO SEQRES 23 A 600 TYR TYR SER LEU ASN PRO ASP THR PRO ILE SER SER ALA SEQRES 24 A 600 PHE GLY ASP SER GLY MET GLN TRP ALA ALA TYR ILE LEU SEQRES 25 A 600 THR THR GLY ALA ILE THR ALA LEU CYS ALA SER LEU LEU SEQRES 26 A 600 GLY SER LEU LEU ALA GLN PRO ARG ILE PHE MET ALA MET SEQRES 27 A 600 ALA ARG ASP GLY LEU LEU PRO ALA PHE PHE SER GLU ILE SEQRES 28 A 600 SER PRO ARG THR GLN VAL PRO VAL LYS SER THR ILE ALA SEQRES 29 A 600 ILE GLY VAL LEU ALA ALA ALA LEU ALA PHE PHE MET ASP SEQRES 30 A 600 VAL ALA GLN LEU SER GLU MET VAL SER VAL GLY THR LEU SEQRES 31 A 600 MET ALA PHE THR ALA VAL ALA VAL CYS VAL LEU VAL LEU SEQRES 32 A 600 ARG TYR VAL PRO PRO ASP GLY VAL PRO LEU SER SER SER SEQRES 33 A 600 SER GLN THR LEU SER ASP THR ASP GLU SER ARG ALA GLU SEQRES 34 A 600 THR GLU ASN PHE LEU VAL ASP ALA ILE GLU SER SER ASP SEQRES 35 A 600 SER PRO LEU LEU GLY ASN GLU THR ALA ARG ASP GLU LYS SEQRES 36 A 600 TYR PHE GLY LYS ARG ARG LYS ILE ALA ALA TRP SER ILE SEQRES 37 A 600 ALA LEU VAL CYS ILE GLY VAL LEU GLY LEU ALA SER ALA SEQRES 38 A 600 ALA SER ALA GLU ARG LEU PRO SER PHE PRO ARG PHE THR SEQRES 39 A 600 ILE CYS GLY VAL SER ALA VAL ILE LEU LEU GLY SER LEU SEQRES 40 A 600 ILE THR LEU GLY TYR ILE ASP GLU ASP GLU GLU ARG HIS SEQRES 41 A 600 ASN PHE GLY HIS LYS GLY GLY PHE LEU CYS PRO PHE VAL SEQRES 42 A 600 PRO TYR LEU PRO VAL LEU CYS ILE LEU ILE ASN THR TYR SEQRES 43 A 600 LEU ILE ILE ASN ILE GLY ALA GLY THR TRP ILE ARG VAL SEQRES 44 A 600 LEU ILE TRP LEU LEU ILE GLY SER MET ILE TYR ILE PHE SEQRES 45 A 600 TYR GLY ARG SER HIS SER LEU LEU ASN ASN ALA VAL TYR SEQRES 46 A 600 VAL PRO THR MET THR CYS THR ARG LYS THR THR ASP HIS SEQRES 47 A 600 LEU ALA HELIX 1 AA1 SER A 29 THR A 52 1 24 HELIX 2 AA2 VAL A 53 HIS A 57 5 5 HELIX 3 AA3 THR A 58 CYS A 87 1 30 HELIX 4 AA4 SER A 92 LEU A 101 1 10 HELIX 5 AA5 GLY A 104 ARG A 126 1 23 HELIX 6 AA6 LEU A 164 CYS A 174 1 11 HELIX 7 AA7 GLY A 176 TYR A 204 1 29 HELIX 8 AA8 LEU A 205 LYS A 208 5 4 HELIX 9 AA9 LEU A 229 ILE A 240 5 12 HELIX 10 AB1 GLY A 241 VAL A 252 5 12 HELIX 11 AB2 ASN A 254 ILE A 281 1 28 HELIX 12 AB3 TRP A 307 GLY A 326 1 20 HELIX 13 AB4 ALA A 330 GLY A 342 1 13 HELIX 14 AB5 PRO A 345 SER A 349 5 5 HELIX 15 AB6 PRO A 358 MET A 376 1 19 HELIX 16 AB7 ASP A 377 SER A 382 1 6 HELIX 17 AB8 GLU A 383 VAL A 385 5 3 HELIX 18 AB9 SER A 386 ARG A 404 1 19 HELIX 19 AC1 ARG A 460 ALA A 464 1 5 HELIX 20 AC2 ALA A 464 ALA A 484 1 21 HELIX 21 AC3 THR A 494 ALA A 500 1 7 HELIX 22 AC4 ALA A 500 ILE A 508 1 9 HELIX 23 AC5 PRO A 534 ILE A 551 1 18 HELIX 24 AC6 GLY A 552 MET A 568 1 17 HELIX 25 AC7 MET A 568 TYR A 573 1 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 MASTER 300 0 0 25 0 0 0 6 3193 1 0 47 END