HEADER TRANSPORT PROTEIN 14-JUN-24 8ZXM TITLE CRYO-EM STRUCTURE OF HUMAN GLUT9 BOUND TO URATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER COMPND 3 MEMBER 9; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: GLUCOSE TRANSPORTER TYPE 9,GLUT-9,URATE TRANSPORTER; 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: SLC2A9, GLUT9; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293F KEYWDS URATE, TRANSPORTER, HYPOURICEMIA, RHUC, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.MATSUSHITA,Y.LEE,T.NISHIZAWA REVDAT 1 16-APR-25 8ZXM 0 JRNL AUTH D.MATSUSHITA,Y.TOYODA,Y.LEE,M.AOI,H.MATSUO,T.TAKADA, JRNL AUTH 2 T.NISHIZAWA JRNL TITL STRUCTURAL BASIS OF URATE TRANSPORT BY GLUCOSE TRANSPORTER JRNL TITL 2 9. JRNL REF CELL REP V. 44 15514 2025 JRNL REFN ESSN 2211-1247 JRNL PMID 40186864 JRNL DOI 10.1016/J.CELREP.2025.115514 REMARK 2 REMARK 2 RESOLUTION. 3.39 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) : 3.390 REMARK 3 NUMBER OF PARTICLES : 180531 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 8ZXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1300048615. 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 : GLUCOSE TRANSPORTER 9 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 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) : 5100.00 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ARG A 3 REMARK 465 LYS A 4 REMARK 465 GLN A 5 REMARK 465 ASN A 6 REMARK 465 ARG A 7 REMARK 465 ASN A 8 REMARK 465 SER A 9 REMARK 465 LYS A 10 REMARK 465 GLU A 11 REMARK 465 LEU A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 LEU A 17 REMARK 465 THR A 18 REMARK 465 ASP A 19 REMARK 465 ASP A 20 REMARK 465 THR A 21 REMARK 465 SER A 22 REMARK 465 HIS A 23 REMARK 465 ALA A 24 REMARK 465 GLY A 25 REMARK 465 PRO A 26 REMARK 465 PRO A 27 REMARK 465 GLY A 28 REMARK 465 PRO A 29 REMARK 465 GLY A 30 REMARK 465 ARG A 31 REMARK 465 ALA A 32 REMARK 465 LEU A 33 REMARK 465 LEU A 34 REMARK 465 GLU A 35 REMARK 465 CYS A 36 REMARK 465 ASP A 37 REMARK 465 HIS A 38 REMARK 465 LEU A 39 REMARK 465 ARG A 40 REMARK 465 SER A 41 REMARK 465 GLY A 42 REMARK 465 VAL A 43 REMARK 465 PRO A 44 REMARK 465 GLY A 45 REMARK 465 GLY A 46 REMARK 465 ARG A 47 REMARK 465 ARG A 48 REMARK 465 ARG A 49 REMARK 465 LYS A 50 REMARK 465 ASP A 51 REMARK 465 PRO A 523 REMARK 465 GLU A 524 REMARK 465 GLU A 525 REMARK 465 LYS A 526 REMARK 465 ILE A 527 REMARK 465 ASP A 528 REMARK 465 SER A 529 REMARK 465 ALA A 530 REMARK 465 VAL A 531 REMARK 465 THR A 532 REMARK 465 ASP A 533 REMARK 465 GLY A 534 REMARK 465 LYS A 535 REMARK 465 ILE A 536 REMARK 465 ASN A 537 REMARK 465 GLY A 538 REMARK 465 ARG A 539 REMARK 465 PRO A 540 REMARK 465 GLY A 541 REMARK 465 THR A 542 REMARK 465 GLU A 543 REMARK 465 ASN A 544 REMARK 465 LEU A 545 REMARK 465 TYR A 546 REMARK 465 PHE A 547 REMARK 465 GLN A 548 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 67 -33.25 -139.10 REMARK 500 ARG A 96 -41.92 -130.12 REMARK 500 LYS A 195 21.98 -78.12 REMARK 500 LEU A 224 -125.11 -105.27 REMARK 500 SER A 248 -50.50 -135.67 REMARK 500 GLU A 262 -35.96 -130.33 REMARK 500 LEU A 404 30.97 -94.67 REMARK 500 ASP A 477 -116.74 55.00 REMARK 500 VAL A 498 -52.69 -132.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60544 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN GLUT9 BOUND TO URATE DBREF 8ZXM A 1 540 UNP Q9NRM0 GTR9_HUMAN 1 540 SEQADV 8ZXM GLY A 541 UNP Q9NRM0 EXPRESSION TAG SEQADV 8ZXM THR A 542 UNP Q9NRM0 EXPRESSION TAG SEQADV 8ZXM GLU A 543 UNP Q9NRM0 EXPRESSION TAG SEQADV 8ZXM ASN A 544 UNP Q9NRM0 EXPRESSION TAG SEQADV 8ZXM LEU A 545 UNP Q9NRM0 EXPRESSION TAG SEQADV 8ZXM TYR A 546 UNP Q9NRM0 EXPRESSION TAG SEQADV 8ZXM PHE A 547 UNP Q9NRM0 EXPRESSION TAG SEQADV 8ZXM GLN A 548 UNP Q9NRM0 EXPRESSION TAG SEQRES 1 A 548 MET ALA ARG LYS GLN ASN ARG ASN SER LYS GLU LEU GLY SEQRES 2 A 548 LEU VAL PRO LEU THR ASP ASP THR SER HIS ALA GLY PRO SEQRES 3 A 548 PRO GLY PRO GLY ARG ALA LEU LEU GLU CYS ASP HIS LEU SEQRES 4 A 548 ARG SER GLY VAL PRO GLY GLY ARG ARG ARG LYS ASP TRP SEQRES 5 A 548 SER CYS SER LEU LEU VAL ALA SER LEU ALA GLY ALA PHE SEQRES 6 A 548 GLY SER SER PHE LEU TYR GLY TYR ASN LEU SER VAL VAL SEQRES 7 A 548 ASN ALA PRO THR PRO TYR ILE LYS ALA PHE TYR ASN GLU SEQRES 8 A 548 SER TRP GLU ARG ARG HIS GLY ARG PRO ILE ASP PRO ASP SEQRES 9 A 548 THR LEU THR LEU LEU TRP SER VAL THR VAL SER ILE PHE SEQRES 10 A 548 ALA ILE GLY GLY LEU VAL GLY THR LEU ILE VAL LYS MET SEQRES 11 A 548 ILE GLY LYS VAL LEU GLY ARG LYS HIS THR LEU LEU ALA SEQRES 12 A 548 ASN ASN GLY PHE ALA ILE SER ALA ALA LEU LEU MET ALA SEQRES 13 A 548 CYS SER LEU GLN ALA GLY ALA PHE GLU MET LEU ILE VAL SEQRES 14 A 548 GLY ARG PHE ILE MET GLY ILE ASP GLY GLY VAL ALA LEU SEQRES 15 A 548 SER VAL LEU PRO MET TYR LEU SER GLU ILE SER PRO LYS SEQRES 16 A 548 GLU ILE ARG GLY SER LEU GLY GLN VAL THR ALA ILE PHE SEQRES 17 A 548 ILE CYS ILE GLY VAL PHE THR GLY GLN LEU LEU GLY LEU SEQRES 18 A 548 PRO GLU LEU LEU GLY LYS GLU SER THR TRP PRO TYR LEU SEQRES 19 A 548 PHE GLY VAL ILE VAL VAL PRO ALA VAL VAL GLN LEU LEU SEQRES 20 A 548 SER LEU PRO PHE LEU PRO ASP SER PRO ARG TYR LEU LEU SEQRES 21 A 548 LEU GLU LYS HIS ASN GLU ALA ARG ALA VAL LYS ALA PHE SEQRES 22 A 548 GLN THR PHE LEU GLY LYS ALA ASP VAL SER GLN GLU VAL SEQRES 23 A 548 GLU GLU VAL LEU ALA GLU SER ARG VAL GLN ARG SER ILE SEQRES 24 A 548 ARG LEU VAL SER VAL LEU GLU LEU LEU ARG ALA PRO TYR SEQRES 25 A 548 VAL ARG TRP GLN VAL VAL THR VAL ILE VAL THR MET ALA SEQRES 26 A 548 CYS TYR GLN LEU CYS GLY LEU ASN ALA ILE TRP PHE TYR SEQRES 27 A 548 THR ASN SER ILE PHE GLY LYS ALA GLY ILE PRO PRO ALA SEQRES 28 A 548 LYS ILE PRO TYR VAL THR LEU SER THR GLY GLY ILE GLU SEQRES 29 A 548 THR LEU ALA ALA VAL PHE SER GLY LEU VAL ILE GLU HIS SEQRES 30 A 548 LEU GLY ARG ARG PRO LEU LEU ILE GLY GLY PHE GLY LEU SEQRES 31 A 548 MET GLY LEU PHE PHE GLY THR LEU THR ILE THR LEU THR SEQRES 32 A 548 LEU GLN ASP HIS ALA PRO TRP VAL PRO TYR LEU SER ILE SEQRES 33 A 548 VAL GLY ILE LEU ALA ILE ILE ALA SER PHE CYS SER GLY SEQRES 34 A 548 PRO GLY GLY ILE PRO PHE ILE LEU THR GLY GLU PHE PHE SEQRES 35 A 548 GLN GLN SER GLN ARG PRO ALA ALA PHE ILE ILE ALA GLY SEQRES 36 A 548 THR VAL ASN TRP LEU SER ASN PHE ALA VAL GLY LEU LEU SEQRES 37 A 548 PHE PRO PHE ILE GLN LYS SER LEU ASP THR TYR CYS PHE SEQRES 38 A 548 LEU VAL PHE ALA THR ILE CYS ILE THR GLY ALA ILE TYR SEQRES 39 A 548 LEU TYR PHE VAL LEU PRO GLU THR LYS ASN ARG THR TYR SEQRES 40 A 548 ALA GLU ILE SER GLN ALA PHE SER LYS ARG ASN LYS ALA SEQRES 41 A 548 TYR PRO PRO GLU GLU LYS ILE ASP SER ALA VAL THR ASP SEQRES 42 A 548 GLY LYS ILE ASN GLY ARG PRO GLY THR GLU ASN LEU TYR SEQRES 43 A 548 PHE GLN HET NAG B 1 14 HET NAG B 2 14 HET URC A 601 12 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM URC URIC ACID HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN URC 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 URC C5 H4 N4 O3 HELIX 1 AA1 SER A 53 PHE A 65 1 13 HELIX 2 AA2 SER A 68 LEU A 75 1 8 HELIX 3 AA3 PRO A 81 GLY A 98 1 18 HELIX 4 AA4 ASP A 102 GLY A 132 1 31 HELIX 5 AA5 GLY A 136 ASN A 144 1 9 HELIX 6 AA6 ASN A 144 ALA A 156 1 13 HELIX 7 AA7 CYS A 157 GLY A 162 1 6 HELIX 8 AA8 PHE A 164 SER A 193 1 30 HELIX 9 AA9 SER A 200 LEU A 219 1 20 HELIX 10 AB1 TRP A 231 VAL A 237 1 7 HELIX 11 AB2 ILE A 238 LEU A 247 1 10 HELIX 12 AB3 SER A 248 LEU A 252 5 5 HELIX 13 AB4 ARG A 257 GLU A 262 1 6 HELIX 14 AB5 ASN A 265 GLY A 278 1 14 HELIX 15 AB6 VAL A 282 ARG A 297 1 16 HELIX 16 AB7 SER A 303 LEU A 308 1 6 HELIX 17 AB8 ALA A 310 TYR A 312 5 3 HELIX 18 AB9 VAL A 313 CYS A 330 1 18 HELIX 19 AC1 GLY A 331 TYR A 338 1 8 HELIX 20 AC2 TYR A 338 GLY A 347 1 10 HELIX 21 AC3 LYS A 352 PHE A 370 1 19 HELIX 22 AC4 SER A 371 GLY A 379 1 9 HELIX 23 AC5 ARG A 380 LEU A 404 1 25 HELIX 24 AC6 VAL A 411 SER A 428 1 18 HELIX 25 AC7 GLY A 429 GLY A 432 5 4 HELIX 26 AC8 ILE A 433 PHE A 441 1 9 HELIX 27 AC9 GLN A 446 LEU A 467 1 22 HELIX 28 AD1 LEU A 468 ASP A 477 1 10 HELIX 29 AD2 THR A 478 CYS A 480 5 3 HELIX 30 AD3 PHE A 481 LEU A 499 1 19 HELIX 31 AD4 THR A 506 LYS A 519 1 14 LINK ND2 ASN A 90 C1 NAG B 1 1555 1555 1.42 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.39 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 297 3627 CONECT 3627 297 3628 3638 CONECT 3628 3627 3629 3635 CONECT 3629 3628 3630 3636 CONECT 3630 3629 3631 3637 CONECT 3631 3630 3632 3638 CONECT 3632 3631 3639 CONECT 3633 3634 3635 3640 CONECT 3634 3633 CONECT 3635 3628 3633 CONECT 3636 3629 CONECT 3637 3630 3641 CONECT 3638 3627 3631 CONECT 3639 3632 CONECT 3640 3633 CONECT 3641 3637 3642 3652 CONECT 3642 3641 3643 3649 CONECT 3643 3642 3644 3650 CONECT 3644 3643 3645 3651 CONECT 3645 3644 3646 3652 CONECT 3646 3645 3653 CONECT 3647 3648 3649 3654 CONECT 3648 3647 CONECT 3649 3642 3647 CONECT 3650 3643 CONECT 3651 3644 CONECT 3652 3641 3645 CONECT 3653 3646 CONECT 3654 3647 CONECT 3655 3656 3657 CONECT 3656 3655 3658 3659 CONECT 3657 3655 3661 3663 CONECT 3658 3656 3660 CONECT 3659 3656 CONECT 3660 3658 3661 3662 CONECT 3661 3657 3660 3664 CONECT 3662 3660 3665 CONECT 3663 3657 CONECT 3664 3661 3665 CONECT 3665 3662 3664 3666 CONECT 3666 3665 MASTER 208 0 3 31 0 0 0 6 3665 1 41 43 END