HEADER MEMBRANE PROTEIN 26-FEB-24 8S61 TITLE CRYO-EM STRUCTURE OF THIAMINE-BOUND HUMAN SLC19A3 IN INWARD-OPEN STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NB3.7; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: THIAMINE TRANSPORTER 2; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: THTR-2,THTR2,SOLUTE CARRIER FAMILY 19 MEMBER 3; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: SLC19A3; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SLC19A3, VITAMIN TRANSPORTER, THIAMINE TRANSPORTER, MFS FOLD, KEYWDS 2 NANOBODY COMPLEX, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR F.GABRIEL,C.LOEW REVDAT 5 04-DEC-24 8S61 1 REMARK REVDAT 4 06-NOV-24 8S61 1 REMARK REVDAT 3 16-OCT-24 8S61 1 JRNL REVDAT 2 09-OCT-24 8S61 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQADV SEQRES HELIX SHEET REVDAT 2 3 1 SSBOND ATOM REVDAT 1 02-OCT-24 8S61 0 JRNL AUTH F.GABRIEL,L.SPRIESTERSBACH,A.FUHRMANN,K.E.J.JUNGNICKEL, JRNL AUTH 2 S.MOSTAFAVI,E.PARDON,J.STEYAERT,C.LOW JRNL TITL STRUCTURAL BASIS OF THIAMINE TRANSPORT AND DRUG RECOGNITION JRNL TITL 2 BY SLC19A3. JRNL REF NAT COMMUN V. 15 8542 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39358356 JRNL DOI 10.1038/S41467-024-52872-8 REMARK 2 REMARK 2 RESOLUTION. 3.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, ISOLDE, REMARK 3 PHENIX, CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.530 REMARK 3 NUMBER OF PARTICLES : 501165 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 8S61 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136872. 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 : SLC19A3:NB3.7:THIAMINE; REMARK 245 SLC19A3; NB3.7 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 : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 5308 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) : 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4500.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 LYS A 202 REMARK 465 PRO A 203 REMARK 465 SER A 204 REMARK 465 ARG A 205 REMARK 465 GLU A 206 REMARK 465 ILE A 207 REMARK 465 LYS A 208 REMARK 465 LYS A 209 REMARK 465 SER A 210 REMARK 465 SER A 211 REMARK 465 SER A 212 REMARK 465 VAL A 213 REMARK 465 ASN A 214 REMARK 465 PRO A 215 REMARK 465 VAL A 216 REMARK 465 LEU A 217 REMARK 465 GLU A 218 REMARK 465 GLU A 219 REMARK 465 THR A 220 REMARK 465 HIS A 221 REMARK 465 GLU A 222 REMARK 465 GLY A 223 REMARK 465 GLU A 224 REMARK 465 ALA A 225 REMARK 465 PRO A 226 REMARK 465 GLY A 227 REMARK 465 CYS A 228 REMARK 465 GLU A 229 REMARK 465 GLU A 230 REMARK 465 GLN A 231 REMARK 465 LYS A 232 REMARK 465 PRO A 233 REMARK 465 THR A 234 REMARK 465 SER A 235 REMARK 465 GLU A 236 REMARK 465 ILE A 237 REMARK 465 LEU A 238 REMARK 465 SER A 239 REMARK 465 THR A 240 REMARK 465 SER A 241 REMARK 465 GLY A 242 REMARK 465 LYS A 243 REMARK 465 LEU A 244 REMARK 465 ASN A 245 REMARK 465 LYS A 246 REMARK 465 GLY A 247 REMARK 465 GLN A 248 REMARK 465 LEU A 249 REMARK 465 ASN A 250 REMARK 465 SER A 251 REMARK 465 LEU A 252 REMARK 465 LYS A 253 REMARK 465 PRO A 254 REMARK 465 SER A 255 REMARK 465 ASN A 256 REMARK 465 VAL A 257 REMARK 465 THR A 258 REMARK 465 VAL A 259 REMARK 465 ASP A 260 REMARK 465 VAL A 261 REMARK 465 PHE A 262 REMARK 465 VAL A 263 REMARK 465 GLN A 264 REMARK 465 TRP A 265 REMARK 465 PHE A 266 REMARK 465 GLN A 267 REMARK 465 ASP A 268 REMARK 465 LEU A 269 REMARK 465 LYS A 270 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 ARG B 27 39.56 -141.06 REMARK 500 THR B 28 3.85 -67.90 REMARK 500 MET B 34 111.99 -160.55 REMARK 500 ALA B 49 -175.78 -172.54 REMARK 500 GLN B 50 147.30 -172.48 REMARK 500 ASN B 77 -14.59 79.15 REMARK 500 SER B 85 61.00 61.88 REMARK 500 SER B 122 -169.88 -160.82 REMARK 500 SER A 31 47.85 -93.62 REMARK 500 GLU A 54 -35.73 -132.16 REMARK 500 ILE A 55 -60.86 -98.97 REMARK 500 LEU A 66 51.80 -92.82 REMARK 500 HIS A 135 54.76 -92.87 REMARK 500 TYR A 171 48.44 -82.99 REMARK 500 PHE A 184 48.23 -85.70 REMARK 500 LEU A 185 -31.49 -132.68 REMARK 500 TYR A 315 65.18 -100.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19754 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THIAMINE-BOUND HUMAN SLC19A3 IN INWARD-OPEN REMARK 900 STATE DBREF 8S61 B 2 123 PDB 8S61 8S61 2 123 DBREF 8S61 A 11 459 UNP Q9BZV2 S19A3_HUMAN 11 459 SEQADV 8S61 GLN A 45 UNP Q9BZV2 ASN 45 ENGINEERED MUTATION SEQADV 8S61 GLN A 166 UNP Q9BZV2 ASN 166 ENGINEERED MUTATION SEQRES 1 B 122 VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN PRO SEQRES 2 B 122 GLY ASP SER LEU ARG LEU SER CYS ALA ALA SER GLY ARG SEQRES 3 B 122 THR PHE SER ILE ASN ALA MET ALA TRP PHE ARG GLN ALA SEQRES 4 B 122 PRO GLY LYS GLU ARG GLU TYR VAL ALA GLN ILE SER TRP SEQRES 5 B 122 THR GLY GLY ASN THR TYR TYR ALA GLU SER VAL LYS GLY SEQRES 6 B 122 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 B 122 TYR LEU GLN MET ILE SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 B 122 VAL TYR TYR CYS ALA ALA ASP SER GLY GLY ILE ARG LEU SEQRES 9 B 122 GLY ALA SER ARG TRP ASN TYR TRP GLY GLN GLY THR GLN SEQRES 10 B 122 VAL THR VAL SER SER SEQRES 1 A 449 SER TRP ILE TYR PRO THR VAL ILE LEU CYS LEU PHE GLY SEQRES 2 A 449 PHE PHE SER MET MET ARG PRO SER GLU PRO PHE LEU ILE SEQRES 3 A 449 PRO TYR LEU SER GLY PRO ASP LYS GLN LEU THR SER ALA SEQRES 4 A 449 GLU ILE THR ASN GLU ILE PHE PRO VAL TRP THR TYR SER SEQRES 5 A 449 TYR LEU VAL LEU LEU LEU PRO VAL PHE VAL LEU THR ASP SEQRES 6 A 449 TYR VAL ARG TYR LYS PRO VAL ILE ILE LEU GLN GLY ILE SEQRES 7 A 449 SER PHE ILE ILE THR TRP LEU LEU LEU LEU PHE GLY GLN SEQRES 8 A 449 GLY VAL LYS THR MET GLN VAL VAL GLU PHE PHE TYR GLY SEQRES 9 A 449 MET VAL THR ALA ALA GLU VAL ALA TYR TYR ALA TYR ILE SEQRES 10 A 449 TYR SER VAL VAL SER PRO GLU HIS TYR GLN ARG VAL SER SEQRES 11 A 449 GLY TYR CYS ARG SER VAL THR LEU ALA ALA TYR THR ALA SEQRES 12 A 449 GLY SER VAL LEU ALA GLN LEU LEU VAL SER LEU ALA GLN SEQRES 13 A 449 MET SER TYR PHE TYR LEU ASN VAL ILE SER LEU ALA SER SEQRES 14 A 449 VAL SER VAL ALA PHE LEU PHE SER LEU PHE LEU PRO MET SEQRES 15 A 449 PRO LYS LYS SER MET PHE PHE HIS ALA LYS PRO SER ARG SEQRES 16 A 449 GLU ILE LYS LYS SER SER SER VAL ASN PRO VAL LEU GLU SEQRES 17 A 449 GLU THR HIS GLU GLY GLU ALA PRO GLY CYS GLU GLU GLN SEQRES 18 A 449 LYS PRO THR SER GLU ILE LEU SER THR SER GLY LYS LEU SEQRES 19 A 449 ASN LYS GLY GLN LEU ASN SER LEU LYS PRO SER ASN VAL SEQRES 20 A 449 THR VAL ASP VAL PHE VAL GLN TRP PHE GLN ASP LEU LYS SEQRES 21 A 449 GLU CYS TYR SER SER LYS ARG LEU PHE TYR TRP SER LEU SEQRES 22 A 449 TRP TRP ALA PHE ALA THR ALA GLY PHE ASN GLN VAL LEU SEQRES 23 A 449 ASN TYR VAL GLN ILE LEU TRP ASP TYR LYS ALA PRO SER SEQRES 24 A 449 GLN ASP SER SER ILE TYR ASN GLY ALA VAL GLU ALA ILE SEQRES 25 A 449 ALA THR PHE GLY GLY ALA VAL ALA ALA PHE ALA VAL GLY SEQRES 26 A 449 TYR VAL LYS VAL ASN TRP ASP LEU LEU GLY GLU LEU ALA SEQRES 27 A 449 LEU VAL VAL PHE SER VAL VAL ASN ALA GLY SER LEU PHE SEQRES 28 A 449 LEU MET HIS TYR THR ALA ASN ILE TRP ALA CYS TYR ALA SEQRES 29 A 449 GLY TYR LEU ILE PHE LYS SER SER TYR MET LEU LEU ILE SEQRES 30 A 449 THR ILE ALA VAL PHE GLN ILE ALA VAL ASN LEU ASN VAL SEQRES 31 A 449 GLU ARG TYR ALA LEU VAL PHE GLY ILE ASN THR PHE ILE SEQRES 32 A 449 ALA LEU VAL ILE GLN THR ILE MET THR VAL ILE VAL VAL SEQRES 33 A 449 ASP GLN ARG GLY LEU ASN LEU PRO VAL SER ILE GLN PHE SEQRES 34 A 449 LEU VAL TYR GLY SER TYR PHE ALA VAL ILE ALA GLY ILE SEQRES 35 A 449 PHE LEU MET ARG SER MET TYR HET VIB A 501 18 HETNAM VIB 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY- HETNAM 2 VIB ETHYL)-4-METHYL-THIAZOL-3-IUM HETSYN VIB THIAMIN; VITAMIN B1 FORMUL 3 VIB C12 H17 N4 O S 1+ HELIX 1 AA1 TRP A 12 MET A 28 1 17 HELIX 2 AA2 LEU A 35 SER A 40 1 6 HELIX 3 AA3 THR A 47 THR A 52 1 6 HELIX 4 AA4 PHE A 56 LEU A 66 1 11 HELIX 5 AA5 LEU A 67 VAL A 77 1 11 HELIX 6 AA6 ARG A 78 LEU A 97 1 20 HELIX 7 AA7 VAL A 103 ALA A 119 1 17 HELIX 8 AA8 GLU A 120 ALA A 125 1 6 HELIX 9 AA9 ALA A 125 VAL A 131 1 7 HELIX 10 AB1 SER A 132 HIS A 135 5 4 HELIX 11 AB2 TYR A 136 VAL A 162 1 27 HELIX 12 AB3 TYR A 169 TYR A 171 5 3 HELIX 13 AB4 LEU A 172 SER A 187 1 16 HELIX 14 AB5 GLU A 271 SER A 274 5 4 HELIX 15 AB6 SER A 275 TYR A 298 1 24 HELIX 16 AB7 VAL A 299 ALA A 307 1 9 HELIX 17 AB8 TYR A 315 GLY A 335 1 21 HELIX 18 AB9 GLY A 345 THR A 366 1 22 HELIX 19 AC1 ASN A 368 ALA A 395 1 28 HELIX 20 AC2 TYR A 403 VAL A 426 1 24 HELIX 21 AC3 PRO A 434 ILE A 452 1 19 SHEET 1 AA1 4 GLU B 6 SER B 7 0 SHEET 2 AA1 4 LEU B 18 CYS B 22 -1 O SER B 21 N SER B 7 SHEET 3 AA1 4 VAL B 79 MET B 83 -1 O LEU B 81 N LEU B 20 SHEET 4 AA1 4 THR B 69 ARG B 72 -1 N THR B 69 O GLN B 82 SHEET 1 AA2 4 GLU B 46 TYR B 47 0 SHEET 2 AA2 4 PHE B 37 GLN B 39 -1 N ARG B 38 O GLU B 46 SHEET 3 AA2 4 ALA B 92 TYR B 95 -1 O TYR B 95 N PHE B 37 SHEET 4 AA2 4 THR B 117 VAL B 119 -1 O VAL B 119 N ALA B 92 SHEET 1 AA3 2 ALA B 97 ALA B 98 0 SHEET 2 AA3 2 TYR B 112 TRP B 113 -1 O TYR B 112 N ALA B 98 SHEET 1 AA4 2 ARG B 104 LEU B 105 0 SHEET 2 AA4 2 GLY A 100 GLN A 101 -1 O GLN A 101 N ARG B 104 SSBOND 1 CYS B 22 CYS B 96 1555 1555 2.03 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 146 736 CONECT 736 146 CONECT 3975 3989 CONECT 3976 3987 CONECT 3977 3984 CONECT 3978 3979 CONECT 3979 3978 3980 CONECT 3980 3979 3983 CONECT 3981 3982 3985 CONECT 3982 3981 3983 CONECT 3983 3980 3982 3984 CONECT 3984 3977 3983 3985 CONECT 3985 3981 3984 3986 CONECT 3986 3985 3992 CONECT 3987 3976 3988 3992 CONECT 3988 3987 3989 CONECT 3989 3975 3988 3990 CONECT 3990 3989 3991 CONECT 3991 3990 3992 CONECT 3992 3986 3987 3991 MASTER 214 0 1 21 12 0 0 6 3990 2 20 45 END