HEADER MEMBRANE PROTEIN 18-JAN-24 8XXI TITLE STRUCTURE OF Y+LAT1 BOUND WITH LEU COMPND MOL_ID: 1; COMPND 2 MOLECULE: Y+L AMINO ACID TRANSPORTER 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MONOCYTE AMINO ACID PERMEASE 2,MOP-2,SOLUTE CARRIER FAMILY 7 COMPND 5 MEMBER 7,Y(+)L-TYPE AMINO ACID TRANSPORTER 1,Y+LAT1,Y+LAT-1; COMPND 6 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: SLC7A7; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS COMPLEX, MEMBRANE PROTEIN, AMINO ACID EXPDTA ELECTRON MICROSCOPY AUTHOR R.H.YAN,L.DAI,T.ZHANG REVDAT 3 02-APR-25 8XXI 1 JRNL REVDAT 2 19-MAR-25 8XXI 1 COMPND REMARK SHEET LINK REVDAT 2 2 1 ATOM REVDAT 1 22-JAN-25 8XXI 0 JRNL AUTH L.DAI,Q.ZENG,T.ZHANG,Y.ZHANG,Y.SHI,Y.LI,K.XU,J.HUANG,Z.WANG, JRNL AUTH 2 Q.ZHOU,R.YAN JRNL TITL STRUCTURAL BASIS FOR THE SUBSTRATE RECOGNITION AND TRANSPORT JRNL TITL 2 MECHANISM OF THE HUMAN Y + LAT1-4F2HC TRANSPORTER COMPLEX. JRNL REF SCI ADV V. 11 Q0558 2025 JRNL REFN ESSN 2375-2548 JRNL PMID 40106545 JRNL DOI 10.1126/SCIADV.ADQ0558 REMARK 2 REMARK 2 RESOLUTION. 3.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.040 REMARK 3 NUMBER OF PARTICLES : 427472 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 8XXI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044260. 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 THE Y+LAT1 BOUND REMARK 245 WITH LEU 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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) : 5000.00 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 ASP A -17 REMARK 465 TYR A -16 REMARK 465 LYS A -15 REMARK 465 ASP A -14 REMARK 465 ASP A -13 REMARK 465 ASP A -12 REMARK 465 ASP A -11 REMARK 465 LYS A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 PRO A -7 REMARK 465 ASP A -6 REMARK 465 GLU A -5 REMARK 465 VAL A -4 REMARK 465 ASP A -3 REMARK 465 ALA A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 ARG A 1 REMARK 465 VAL A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 TYR A 7 REMARK 465 GLU A 8 REMARK 465 VAL A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 GLN A 12 REMARK 465 PRO A 13 REMARK 465 GLU A 14 REMARK 465 VAL A 15 REMARK 465 GLU A 16 REMARK 465 THR A 17 REMARK 465 SER A 18 REMARK 465 PRO A 19 REMARK 465 LEU A 20 REMARK 465 GLY A 21 REMARK 465 ASP A 22 REMARK 465 GLY A 23 REMARK 465 ALA A 24 REMARK 465 SER A 25 REMARK 465 PRO A 26 REMARK 465 GLY A 27 REMARK 465 PRO A 28 REMARK 465 MET A 494 REMARK 465 ASP A 495 REMARK 465 LEU A 496 REMARK 465 GLU A 497 REMARK 465 ASP A 498 REMARK 465 GLY A 499 REMARK 465 GLY A 500 REMARK 465 GLU A 501 REMARK 465 MET A 502 REMARK 465 PRO A 503 REMARK 465 LYS A 504 REMARK 465 GLN A 505 REMARK 465 ARG A 506 REMARK 465 ASP A 507 REMARK 465 PRO A 508 REMARK 465 LYS A 509 REMARK 465 SER A 510 REMARK 465 ASN A 511 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 LYS A 32 141.88 -172.54 REMARK 500 LYS A 98 36.38 70.15 REMARK 500 ALA A 102 -71.76 -60.85 REMARK 500 LEU A 115 -12.76 74.20 REMARK 500 SER A 211 -70.95 -65.02 REMARK 500 THR A 212 1.11 56.37 REMARK 500 SER A 217 -179.28 -66.23 REMARK 500 ASN A 254 78.81 -161.38 REMARK 500 ASP A 289 29.42 -79.81 REMARK 500 ILE A 290 -19.35 -141.79 REMARK 500 CYS A 349 -76.46 -71.64 REMARK 500 MET A 350 68.20 37.77 REMARK 500 PRO A 358 85.73 -69.89 REMARK 500 GLU A 407 70.18 57.68 REMARK 500 GLN A 484 -69.45 -92.90 REMARK 500 ALA A 491 -141.62 62.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 243 OD1 REMARK 620 2 ASP A 243 OD2 49.2 REMARK 620 3 TYR A 389 OH 137.7 105.9 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38750 RELATED DB: EMDB REMARK 900 STRUCTURE OF Y+LAT1 BOUND WITH LEU DBREF 8XXI A 2 511 UNP Q9UM01 YLAT1_HUMAN 2 511 SEQADV 8XXI ASP A -17 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI TYR A -16 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI LYS A -15 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI ASP A -14 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI ASP A -13 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI ASP A -12 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI ASP A -11 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI LYS A -10 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI SER A -9 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI GLY A -8 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI PRO A -7 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI ASP A -6 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI GLU A -5 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI VAL A -4 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI ASP A -3 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI ALA A -2 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI SER A -1 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI GLY A 0 UNP Q9UM01 EXPRESSION TAG SEQADV 8XXI ARG A 1 UNP Q9UM01 EXPRESSION TAG SEQRES 1 A 529 ASP TYR LYS ASP ASP ASP ASP LYS SER GLY PRO ASP GLU SEQRES 2 A 529 VAL ASP ALA SER GLY ARG VAL ASP SER THR GLU TYR GLU SEQRES 3 A 529 VAL ALA SER GLN PRO GLU VAL GLU THR SER PRO LEU GLY SEQRES 4 A 529 ASP GLY ALA SER PRO GLY PRO GLU GLN VAL LYS LEU LYS SEQRES 5 A 529 LYS GLU ILE SER LEU LEU ASN GLY VAL CYS LEU ILE VAL SEQRES 6 A 529 GLY ASN MET ILE GLY SER GLY ILE PHE VAL SER PRO LYS SEQRES 7 A 529 GLY VAL LEU ILE TYR SER ALA SER PHE GLY LEU SER LEU SEQRES 8 A 529 VAL ILE TRP ALA VAL GLY GLY LEU PHE SER VAL PHE GLY SEQRES 9 A 529 ALA LEU CYS TYR ALA GLU LEU GLY THR THR ILE LYS LYS SEQRES 10 A 529 SER GLY ALA SER TYR ALA TYR ILE LEU GLU ALA PHE GLY SEQRES 11 A 529 GLY PHE LEU ALA PHE ILE ARG LEU TRP THR SER LEU LEU SEQRES 12 A 529 ILE ILE GLU PRO THR SER GLN ALA ILE ILE ALA ILE THR SEQRES 13 A 529 PHE ALA ASN TYR MET VAL GLN PRO LEU PHE PRO SER CYS SEQRES 14 A 529 PHE ALA PRO TYR ALA ALA SER ARG LEU LEU ALA ALA ALA SEQRES 15 A 529 CYS ILE CYS LEU LEU THR PHE ILE ASN CYS ALA TYR VAL SEQRES 16 A 529 LYS TRP GLY THR LEU VAL GLN ASP ILE PHE THR TYR ALA SEQRES 17 A 529 LYS VAL LEU ALA LEU ILE ALA VAL ILE VAL ALA GLY ILE SEQRES 18 A 529 VAL ARG LEU GLY GLN GLY ALA SER THR HIS PHE GLU ASN SEQRES 19 A 529 SER PHE GLU GLY SER SER PHE ALA VAL GLY ASP ILE ALA SEQRES 20 A 529 LEU ALA LEU TYR SER ALA LEU PHE SER TYR SER GLY TRP SEQRES 21 A 529 ASP THR LEU ASN TYR VAL THR GLU GLU ILE LYS ASN PRO SEQRES 22 A 529 GLU ARG ASN LEU PRO LEU SER ILE GLY ILE SER MET PRO SEQRES 23 A 529 ILE VAL THR ILE ILE TYR ILE LEU THR ASN VAL ALA TYR SEQRES 24 A 529 TYR THR VAL LEU ASP MET ARG ASP ILE LEU ALA SER ASP SEQRES 25 A 529 ALA VAL ALA VAL THR PHE ALA ASP GLN ILE PHE GLY ILE SEQRES 26 A 529 PHE ASN TRP ILE ILE PRO LEU SER VAL ALA LEU SER CYS SEQRES 27 A 529 PHE GLY GLY LEU ASN ALA SER ILE VAL ALA ALA SER ARG SEQRES 28 A 529 LEU PHE PHE VAL GLY SER ARG GLU GLY HIS LEU PRO ASP SEQRES 29 A 529 ALA ILE CYS MET ILE HIS VAL GLU ARG PHE THR PRO VAL SEQRES 30 A 529 PRO SER LEU LEU PHE ASN GLY ILE MET ALA LEU ILE TYR SEQRES 31 A 529 LEU CYS VAL GLU ASP ILE PHE GLN LEU ILE ASN TYR TYR SEQRES 32 A 529 SER PHE SER TYR TRP PHE PHE VAL GLY LEU SER ILE VAL SEQRES 33 A 529 GLY GLN LEU TYR LEU ARG TRP LYS GLU PRO ASP ARG PRO SEQRES 34 A 529 ARG PRO LEU LYS LEU SER VAL PHE PHE PRO ILE VAL PHE SEQRES 35 A 529 CYS LEU CYS THR ILE PHE LEU VAL ALA VAL PRO LEU TYR SEQRES 36 A 529 SER ASP THR ILE ASN SER LEU ILE GLY ILE ALA ILE ALA SEQRES 37 A 529 LEU SER GLY LEU PRO PHE TYR PHE LEU ILE ILE ARG VAL SEQRES 38 A 529 PRO GLU HIS LYS ARG PRO LEU TYR LEU ARG ARG ILE VAL SEQRES 39 A 529 GLY SER ALA THR ARG TYR LEU GLN VAL LEU CYS MET SER SEQRES 40 A 529 VAL ALA ALA GLU MET ASP LEU GLU ASP GLY GLY GLU MET SEQRES 41 A 529 PRO LYS GLN ARG ASP PRO LYS SER ASN HET NA A 601 1 HET LEU A 602 9 HETNAM NA SODIUM ION HETNAM LEU LEUCINE FORMUL 2 NA NA 1+ FORMUL 3 LEU C6 H13 N O2 HELIX 1 AA1 SER A 38 GLY A 52 1 15 HELIX 2 AA2 LYS A 60 SER A 66 1 7 HELIX 3 AA3 SER A 68 LYS A 98 1 31 HELIX 4 AA4 SER A 103 PHE A 111 1 9 HELIX 5 AA5 ALA A 116 ILE A 126 1 11 HELIX 6 AA6 ILE A 126 VAL A 144 1 19 HELIX 7 AA7 PRO A 154 TYR A 176 1 23 HELIX 8 AA8 TYR A 176 GLY A 209 1 34 HELIX 9 AA9 ALA A 224 TYR A 239 1 16 HELIX 10 AB1 ASP A 243 TYR A 247 5 5 HELIX 11 AB2 ASN A 254 LEU A 285 1 32 HELIX 12 AB3 MET A 287 ALA A 292 1 6 HELIX 13 AB4 ALA A 295 PHE A 305 1 11 HELIX 14 AB5 TRP A 310 GLU A 341 1 32 HELIX 15 AB6 PRO A 358 TYR A 372 1 15 HELIX 16 AB7 LEU A 373 VAL A 375 5 3 HELIX 17 AB8 PHE A 379 LYS A 406 1 28 HELIX 18 AB9 VAL A 418 ASP A 439 1 22 HELIX 19 AC1 ASP A 439 LEU A 454 1 16 HELIX 20 AC2 PRO A 455 TYR A 457 5 3 HELIX 21 AC3 PRO A 469 LEU A 483 1 15 LINK OD1 ASP A 243 NA NA A 601 1555 1555 2.35 LINK OD2 ASP A 243 NA NA A 601 1555 1555 2.83 LINK OH TYR A 389 NA NA A 601 1555 1555 2.22 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