HEADER TRANSPORT PROTEIN 05-DEC-24 9KVV TITLE CRYO-EM STRUCTURE OF HUMAN G6PT IN COMPLEX WITH G6P COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSE-6-PHOSPHATE EXCHANGER SLC37A4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUCOSE-5-PHOSPHATE TRANSPORTER,GLUCOSE-6-PHOSPHATE COMPND 5 TRANSLOCASE,SOLUTE CARRIER FAMILY 37 MEMBER 4,TRANSFORMATION-RELATED COMPND 6 GENE 19 PROTEIN,TRG-19; COMPND 7 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: SLC37A4, G6PT, G6PT1, PRO0685, TRG19; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS G6PT, CRYO-EM, G6P, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.H.JIANG,Z.Y.XIA REVDAT 1 12-NOV-25 9KVV 0 JRNL AUTH Z.XIA,Y.WANG,D.WU,C.CHI,C.LI,L.CHEN,D.JIANG JRNL TITL STRUCTURAL BASIS FOR TRANSPORT AND INHIBITION OF THE HUMAN JRNL TITL 2 GLUCOSE-6-PHOSPHATE TRANSPORTER G6PT. JRNL REF NAT COMMUN V. 16 9420 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41136424 JRNL DOI 10.1038/S41467-025-64464-1 REMARK 2 REMARK 2 RESOLUTION. 3.60 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 151770 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 9KVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 10-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300054367. 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 : G6PT-G6P 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 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 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 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 ALA A 2 REMARK 465 ALA A 3 REMARK 465 GLN A 4 REMARK 465 GLY A 5 REMARK 465 PRO A 203 REMARK 465 SER A 204 REMARK 465 GLU A 205 REMARK 465 GLY A 206 REMARK 465 LYS A 207 REMARK 465 LYS A 208 REMARK 465 GLY A 209 REMARK 465 SER A 210 REMARK 465 LEU A 211 REMARK 465 LYS A 212 REMARK 465 LYS A 426 REMARK 465 LYS A 427 REMARK 465 ALA A 428 REMARK 465 GLU A 429 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 161 CG CD OE1 NE2 REMARK 470 TYR A 163 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 389 CG CD CE NZ REMARK 470 HIS A 390 CG ND1 CD2 CE1 NE2 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 OD1 ASN A 27 OG SER A 172 2.14 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 LEU A 116 46.57 -89.50 REMARK 500 LEU A 222 31.61 -95.38 REMARK 500 ALA A 380 31.49 -98.22 REMARK 500 TYR A 391 -63.52 -96.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62602 RELATED DB: EMDB REMARK 900 6P TRANSPORTER IN COMPLEX WITH 6P DBREF 9KVV A 1 429 UNP O43826 G6PT1_HUMAN 1 429 SEQRES 1 A 429 MET ALA ALA GLN GLY TYR GLY TYR TYR ARG THR VAL ILE SEQRES 2 A 429 PHE SER ALA MET PHE GLY GLY TYR SER LEU TYR TYR PHE SEQRES 3 A 429 ASN ARG LYS THR PHE SER PHE VAL MET PRO SER LEU VAL SEQRES 4 A 429 GLU GLU ILE PRO LEU ASP LYS ASP ASP LEU GLY PHE ILE SEQRES 5 A 429 THR SER SER GLN SER ALA ALA TYR ALA ILE SER LYS PHE SEQRES 6 A 429 VAL SER GLY VAL LEU SER ASP GLN MET SER ALA ARG TRP SEQRES 7 A 429 LEU PHE SER SER GLY LEU LEU LEU VAL GLY LEU VAL ASN SEQRES 8 A 429 ILE PHE PHE ALA TRP SER SER THR VAL PRO VAL PHE ALA SEQRES 9 A 429 ALA LEU TRP PHE LEU ASN GLY LEU ALA GLN GLY LEU GLY SEQRES 10 A 429 TRP PRO PRO CYS GLY LYS VAL LEU ARG LYS TRP PHE GLU SEQRES 11 A 429 PRO SER GLN PHE GLY THR TRP TRP ALA ILE LEU SER THR SEQRES 12 A 429 SER MET ASN LEU ALA GLY GLY LEU GLY PRO ILE LEU ALA SEQRES 13 A 429 THR ILE LEU ALA GLN SER TYR SER TRP ARG SER THR LEU SEQRES 14 A 429 ALA LEU SER GLY ALA LEU CYS VAL VAL VAL SER PHE LEU SEQRES 15 A 429 CYS LEU LEU LEU ILE HIS ASN GLU PRO ALA ASP VAL GLY SEQRES 16 A 429 LEU ARG ASN LEU ASP PRO MET PRO SER GLU GLY LYS LYS SEQRES 17 A 429 GLY SER LEU LYS GLU GLU SER THR LEU GLN GLU LEU LEU SEQRES 18 A 429 LEU SER PRO TYR LEU TRP VAL LEU SER THR GLY TYR LEU SEQRES 19 A 429 VAL VAL PHE GLY VAL LYS THR CYS CYS THR ASP TRP GLY SEQRES 20 A 429 GLN PHE PHE LEU ILE GLN GLU LYS GLY GLN SER ALA LEU SEQRES 21 A 429 VAL GLY SER SER TYR MET SER ALA LEU GLU VAL GLY GLY SEQRES 22 A 429 LEU VAL GLY SER ILE ALA ALA GLY TYR LEU SER ASP ARG SEQRES 23 A 429 ALA MET ALA LYS ALA GLY LEU SER ASN TYR GLY ASN PRO SEQRES 24 A 429 ARG HIS GLY LEU LEU LEU PHE MET MET ALA GLY MET THR SEQRES 25 A 429 VAL SER MET TYR LEU PHE ARG VAL THR VAL THR SER ASP SEQRES 26 A 429 SER PRO LYS LEU TRP ILE LEU VAL LEU GLY ALA VAL PHE SEQRES 27 A 429 GLY PHE SER SER TYR GLY PRO ILE ALA LEU PHE GLY VAL SEQRES 28 A 429 ILE ALA ASN GLU SER ALA PRO PRO ASN LEU CYS GLY THR SEQRES 29 A 429 SER HIS ALA ILE VAL GLY LEU MET ALA ASN VAL GLY GLY SEQRES 30 A 429 PHE LEU ALA GLY LEU PRO PHE SER THR ILE ALA LYS HIS SEQRES 31 A 429 TYR SER TRP SER THR ALA PHE TRP VAL ALA GLU VAL ILE SEQRES 32 A 429 CYS ALA ALA SER THR ALA ALA PHE PHE LEU LEU ARG ASN SEQRES 33 A 429 ILE ARG THR LYS MET GLY ARG VAL SER LYS LYS ALA GLU HET BG6 A 501 16 HETNAM BG6 6-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE HETSYN BG6 BETA-D-GLUCOSE-6-PHOSPHATE; 6-O-PHOSPHONO-BETA-D- HETSYN 2 BG6 GLUCOSE; 6-O-PHOSPHONO-D-GLUCOSE; 6-O-PHOSPHONO- HETSYN 3 BG6 GLUCOSE FORMUL 2 BG6 C6 H13 O9 P HELIX 1 AA1 TYR A 6 VAL A 34 1 29 HELIX 2 AA2 VAL A 34 GLU A 40 1 7 HELIX 3 AA3 ASP A 45 ASP A 72 1 28 HELIX 4 AA4 SER A 75 ALA A 95 1 21 HELIX 5 AA5 THR A 99 GLN A 114 1 16 HELIX 6 AA6 GLY A 117 PHE A 129 1 13 HELIX 7 AA7 GLU A 130 TYR A 163 1 34 HELIX 8 AA8 TRP A 165 ILE A 187 1 23 HELIX 9 AA9 GLU A 190 GLY A 195 1 6 HELIX 10 AB1 THR A 216 LEU A 222 1 7 HELIX 11 AB2 SER A 223 GLU A 254 1 32 HELIX 12 AB3 SER A 258 ALA A 291 1 34 HELIX 13 AB4 ARG A 300 VAL A 322 1 23 HELIX 14 AB5 PRO A 327 ALA A 357 1 31 HELIX 15 AB6 PRO A 358 ASN A 360 5 3 HELIX 16 AB7 LEU A 361 ALA A 380 1 20 HELIX 17 AB8 GLY A 381 TYR A 391 1 11 HELIX 18 AB9 SER A 392 LEU A 414 1 23 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 3116 SER A 425 HETATM 3117 C1 BG6 A 501 134.360 138.633 139.314 1.00 53.64 C HETATM 3118 C2 BG6 A 501 133.926 137.192 139.025 1.00 53.64 C HETATM 3119 O1 BG6 A 501 133.287 139.332 139.805 1.00 53.64 O HETATM 3120 O5 BG6 A 501 134.854 139.299 138.102 1.00 53.64 O HETATM 3121 C3 BG6 A 501 135.015 136.414 138.409 1.00 53.64 C HETATM 3122 O2 BG6 A 501 133.542 136.571 140.263 1.00 53.64 O HETATM 3123 C4 BG6 A 501 135.547 137.067 137.200 1.00 53.64 C HETATM 3124 O3 BG6 A 501 134.499 135.084 138.039 1.00 53.64 O HETATM 3125 C5 BG6 A 501 135.924 138.538 137.437 1.00 53.64 C HETATM 3126 O4 BG6 A 501 136.721 136.352 136.769 1.00 53.64 O HETATM 3127 C6 BG6 A 501 136.213 139.176 136.119 1.00 53.64 C HETATM 3128 O6 BG6 A 501 135.179 140.062 135.819 1.00 53.64 O HETATM 3129 P BG6 A 501 135.436 141.671 136.037 1.00 53.64 P HETATM 3130 O1P BG6 A 501 136.000 141.907 137.418 1.00 53.64 O HETATM 3131 O2P BG6 A 501 134.131 142.416 135.895 1.00 53.64 O HETATM 3132 O3P BG6 A 501 136.415 142.168 135.002 1.00 53.64 O CONECT 3117 3118 3119 3120 CONECT 3118 3117 3121 3122 CONECT 3119 3117 CONECT 3120 3117 3125 CONECT 3121 3118 3123 3124 CONECT 3122 3118 CONECT 3123 3121 3125 3126 CONECT 3124 3121 CONECT 3125 3120 3123 3127 CONECT 3126 3123 CONECT 3127 3125 3128 CONECT 3128 3127 3129 CONECT 3129 3128 3130 3131 3132 CONECT 3130 3129 CONECT 3131 3129 CONECT 3132 3129 MASTER 167 0 1 18 0 0 0 6 3131 1 16 33 END