HEADER TRANSPORT PROTEIN 16-MAY-23 8JF0 TITLE HUMAN SODIUM-DEPENDENT VITAMIN C TRANSPORTER 1 IN AN INTERMEDIATE TITLE 2 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 23 MEMBER 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NA(+)/L-ASCORBIC ACID TRANSPORTER 1,SODIUM-DEPENDENT VITAMIN COMPND 5 C TRANSPORTER 1,HSVCT1,YOLK SAC PERMEASE-LIKE MOLECULE 3; 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: SLC23A1, SVCT1, YSPL3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293S GNTI- CELLS; SOURCE 9 EXPRESSION_SYSTEM_ATCC_NUMBER: 3216; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PEG BACMAM KEYWDS TRANSPORTER, SOLUTE CARRIER, ASCORBIC ACID, VITAMIN C, SODIUM, KEYWDS 2 TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.A.KOBAYASHI,T.KUSAKIZAKO,O.NUREKI REVDAT 1 22-MAY-24 8JF0 0 JRNL AUTH T.A.KOBAYASHI,T.KUSAKIZAKO,O.NUREKI JRNL TITL CRYO-EM STRUCTURES OF HUMAN SODIUM-DEPENDENT VITAMIN C JRNL TITL 2 TRANSPORTER 1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, RELION, COOT, RELION, REMARK 3 RELION, RELION, SERVALCAT REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8JEZ 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 149304 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 8JF0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300037750. 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 : HUMAN SVCT1 DIMER IN AN REMARK 245 INTERMEDIATE STATE 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 : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 5907 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) : 5090.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C2). 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: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 298.80090 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 298.80090 REMARK 350 BIOMT3 2 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 ARG A 2 REMARK 465 ALA A 3 REMARK 465 GLN A 4 REMARK 465 GLU A 5 REMARK 465 ASP A 6 REMARK 465 LEU A 7 REMARK 465 GLU A 8 REMARK 465 GLY A 9 REMARK 465 ARG A 10 REMARK 465 THR A 11 REMARK 465 GLN A 12 REMARK 465 HIS A 13 REMARK 465 GLU A 14 REMARK 465 THR A 15 REMARK 465 THR A 16 REMARK 465 ARG A 17 REMARK 465 ASP A 18 REMARK 465 PRO A 19 REMARK 465 SER A 20 REMARK 465 THR A 21 REMARK 465 PRO A 22 REMARK 465 LEU A 23 REMARK 465 PRO A 24 REMARK 465 THR A 25 REMARK 465 GLU A 26 REMARK 465 PRO A 27 REMARK 465 LYS A 28 REMARK 465 PHE A 29 REMARK 465 ASP A 30 REMARK 465 MET A 31 REMARK 465 LEU A 32 REMARK 465 TYR A 33 REMARK 465 LYS A 34 REMARK 465 ILE A 35 REMARK 465 GLU A 36 REMARK 465 ASP A 37 REMARK 465 VAL A 38 REMARK 465 PRO A 39 REMARK 465 PRO A 40 REMARK 465 TRP A 41 REMARK 465 TYR A 42 REMARK 465 LEU A 43 REMARK 465 CYS A 44 REMARK 465 ILE A 45 REMARK 465 LEU A 231 REMARK 465 THR A 232 REMARK 465 PHE A 233 REMARK 465 LEU A 234 REMARK 465 LEU A 235 REMARK 465 PRO A 236 REMARK 465 VAL A 237 REMARK 465 TYR A 238 REMARK 465 ARG A 239 REMARK 465 TRP A 240 REMARK 465 GLY A 241 REMARK 465 LYS A 242 REMARK 465 GLY A 243 REMARK 465 LEU A 244 REMARK 465 THR A 245 REMARK 465 LEU A 246 REMARK 465 LEU A 247 REMARK 465 ARG A 248 REMARK 465 ILE A 249 REMARK 465 GLN A 250 REMARK 465 ILE A 251 REMARK 465 PHE A 252 REMARK 465 LYS A 253 REMARK 465 ALA A 346 REMARK 465 GLY A 347 REMARK 465 ALA A 348 REMARK 465 PRO A 349 REMARK 465 PRO A 350 REMARK 465 PRO A 351 REMARK 465 PRO A 352 REMARK 465 SER A 382 REMARK 465 SER A 383 REMARK 465 PRO A 384 REMARK 465 ASN A 385 REMARK 465 ILE A 386 REMARK 465 GLY A 387 REMARK 465 VAL A 388 REMARK 465 LEU A 389 REMARK 465 GLY A 390 REMARK 465 ILE A 391 REMARK 465 THR A 392 REMARK 465 LYS A 393 REMARK 465 VAL A 394 REMARK 465 ILE A 525 REMARK 465 GLN A 526 REMARK 465 TRP A 527 REMARK 465 LYS A 528 REMARK 465 ALA A 529 REMARK 465 GLY A 530 REMARK 465 ALA A 531 REMARK 465 HIS A 532 REMARK 465 ALA A 533 REMARK 465 ASN A 534 REMARK 465 SER A 535 REMARK 465 ASP A 536 REMARK 465 MET A 537 REMARK 465 SER A 538 REMARK 465 SER A 539 REMARK 465 SER A 540 REMARK 465 LEU A 541 REMARK 465 LYS A 542 REMARK 465 SER A 543 REMARK 465 TYR A 544 REMARK 465 ASP A 545 REMARK 465 PHE A 546 REMARK 465 PRO A 547 REMARK 465 ILE A 548 REMARK 465 GLY A 549 REMARK 465 MET A 550 REMARK 465 GLY A 551 REMARK 465 ILE A 552 REMARK 465 VAL A 553 REMARK 465 LYS A 554 REMARK 465 ARG A 555 REMARK 465 ILE A 556 REMARK 465 THR A 557 REMARK 465 PHE A 558 REMARK 465 LEU A 559 REMARK 465 LYS A 560 REMARK 465 TYR A 561 REMARK 465 ILE A 562 REMARK 465 PRO A 563 REMARK 465 ILE A 564 REMARK 465 CYS A 565 REMARK 465 PRO A 566 REMARK 465 VAL A 567 REMARK 465 PHE A 568 REMARK 465 LYS A 569 REMARK 465 GLY A 570 REMARK 465 PHE A 571 REMARK 465 SER A 572 REMARK 465 SER A 573 REMARK 465 SER A 574 REMARK 465 SER A 575 REMARK 465 LYS A 576 REMARK 465 ASP A 577 REMARK 465 GLN A 578 REMARK 465 ILE A 579 REMARK 465 ALA A 580 REMARK 465 ILE A 581 REMARK 465 PRO A 582 REMARK 465 GLU A 583 REMARK 465 ASP A 584 REMARK 465 THR A 585 REMARK 465 PRO A 586 REMARK 465 GLU A 587 REMARK 465 ASN A 588 REMARK 465 THR A 589 REMARK 465 GLU A 590 REMARK 465 THR A 591 REMARK 465 ALA A 592 REMARK 465 SER A 593 REMARK 465 VAL A 594 REMARK 465 CYS A 595 REMARK 465 THR A 596 REMARK 465 LYS A 597 REMARK 465 VAL A 598 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 CYS A 71 -5.51 71.03 REMARK 500 PHE A 200 -57.51 -122.41 REMARK 500 MET A 258 -2.84 65.92 REMARK 500 THR A 514 -57.56 -120.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36205 RELATED DB: EMDB REMARK 900 HUMAN SODIUM-DEPENDENT VITAMIN C TRANSPORTER 1 IN AN INTERMEDIATE REMARK 900 STATE REMARK 900 RELATED ID: 8JEW RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN A DIFFERENT STATE. REMARK 900 RELATED ID: 8JEZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN A DIFFERENT STATE. REMARK 900 RELATED ID: 8JF0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN A DIFFERENT STATE. DBREF 8JF0 A 1 598 UNP Q9UHI7 S23A1_HUMAN 1 598 SEQRES 1 A 598 MET ARG ALA GLN GLU ASP LEU GLU GLY ARG THR GLN HIS SEQRES 2 A 598 GLU THR THR ARG ASP PRO SER THR PRO LEU PRO THR GLU SEQRES 3 A 598 PRO LYS PHE ASP MET LEU TYR LYS ILE GLU ASP VAL PRO SEQRES 4 A 598 PRO TRP TYR LEU CYS ILE LEU LEU GLY PHE GLN HIS TYR SEQRES 5 A 598 LEU THR CYS PHE SER GLY THR ILE ALA VAL PRO PHE LEU SEQRES 6 A 598 LEU ALA GLU ALA LEU CYS VAL GLY HIS ASP GLN HIS MET SEQRES 7 A 598 VAL SER GLN LEU ILE GLY THR ILE PHE THR CYS VAL GLY SEQRES 8 A 598 ILE THR THR LEU ILE GLN THR THR VAL GLY ILE ARG LEU SEQRES 9 A 598 PRO LEU PHE GLN ALA SER ALA PHE ALA PHE LEU VAL PRO SEQRES 10 A 598 ALA LYS ALA ILE LEU ALA LEU GLU ARG TRP LYS CYS PRO SEQRES 11 A 598 PRO GLU GLU GLU ILE TYR GLY ASN TRP SER LEU PRO LEU SEQRES 12 A 598 ASN THR SER HIS ILE TRP HIS PRO ARG ILE ARG GLU VAL SEQRES 13 A 598 GLN GLY ALA ILE MET VAL SER SER VAL VAL GLU VAL VAL SEQRES 14 A 598 ILE GLY LEU LEU GLY LEU PRO GLY ALA LEU LEU ASN TYR SEQRES 15 A 598 ILE GLY PRO LEU THR VAL THR PRO THR VAL SER LEU ILE SEQRES 16 A 598 GLY LEU SER VAL PHE GLN ALA ALA GLY ASP ARG ALA GLY SEQRES 17 A 598 SER HIS TRP GLY ILE SER ALA CYS SER ILE LEU LEU ILE SEQRES 18 A 598 ILE LEU PHE SER GLN TYR LEU ARG ASN LEU THR PHE LEU SEQRES 19 A 598 LEU PRO VAL TYR ARG TRP GLY LYS GLY LEU THR LEU LEU SEQRES 20 A 598 ARG ILE GLN ILE PHE LYS MET PHE PRO ILE MET LEU ALA SEQRES 21 A 598 ILE MET THR VAL TRP LEU LEU CYS TYR VAL LEU THR LEU SEQRES 22 A 598 THR ASP VAL LEU PRO THR ASP PRO LYS ALA TYR GLY PHE SEQRES 23 A 598 GLN ALA ARG THR ASP ALA ARG GLY ASP ILE MET ALA ILE SEQRES 24 A 598 ALA PRO TRP ILE ARG ILE PRO TYR PRO CYS GLN TRP GLY SEQRES 25 A 598 LEU PRO THR VAL THR ALA ALA ALA VAL LEU GLY MET PHE SEQRES 26 A 598 SER ALA THR LEU ALA GLY ILE ILE GLU SER ILE GLY ASP SEQRES 27 A 598 TYR TYR ALA CYS ALA ARG LEU ALA GLY ALA PRO PRO PRO SEQRES 28 A 598 PRO VAL HIS ALA ILE ASN ARG GLY ILE PHE THR GLU GLY SEQRES 29 A 598 ILE CYS CYS ILE ILE ALA GLY LEU LEU GLY THR GLY ASN SEQRES 30 A 598 GLY SER THR SER SER SER PRO ASN ILE GLY VAL LEU GLY SEQRES 31 A 598 ILE THR LYS VAL GLY SER ARG ARG VAL VAL GLN TYR GLY SEQRES 32 A 598 ALA ALA ILE MET LEU VAL LEU GLY THR ILE GLY LYS PHE SEQRES 33 A 598 THR ALA LEU PHE ALA SER LEU PRO ASP PRO ILE LEU GLY SEQRES 34 A 598 GLY MET PHE CYS THR LEU PHE GLY MET ILE THR ALA VAL SEQRES 35 A 598 GLY LEU SER ASN LEU GLN PHE VAL ASP MET ASN SER SER SEQRES 36 A 598 ARG ASN LEU PHE VAL LEU GLY PHE SER MET PHE PHE GLY SEQRES 37 A 598 LEU THR LEU PRO ASN TYR LEU GLU SER ASN PRO GLY ALA SEQRES 38 A 598 ILE ASN THR GLY ILE LEU GLU VAL ASP GLN ILE LEU ILE SEQRES 39 A 598 VAL LEU LEU THR THR GLU MET PHE VAL GLY GLY CYS LEU SEQRES 40 A 598 ALA PHE ILE LEU ASP ASN THR VAL PRO GLY SER PRO GLU SEQRES 41 A 598 GLU ARG GLY LEU ILE GLN TRP LYS ALA GLY ALA HIS ALA SEQRES 42 A 598 ASN SER ASP MET SER SER SER LEU LYS SER TYR ASP PHE SEQRES 43 A 598 PRO ILE GLY MET GLY ILE VAL LYS ARG ILE THR PHE LEU SEQRES 44 A 598 LYS TYR ILE PRO ILE CYS PRO VAL PHE LYS GLY PHE SER SEQRES 45 A 598 SER SER SER LYS ASP GLN ILE ALA ILE PRO GLU ASP THR SEQRES 46 A 598 PRO GLU ASN THR GLU THR ALA SER VAL CYS THR LYS VAL HELIX 1 AA1 LEU A 46 THR A 59 1 14 HELIX 2 AA2 ILE A 60 LEU A 70 1 11 HELIX 3 AA3 ASP A 75 VAL A 100 1 26 HELIX 4 AA4 PHE A 114 LEU A 122 1 9 HELIX 5 AA5 PRO A 131 TYR A 136 1 6 HELIX 6 AA6 THR A 145 GLY A 174 1 30 HELIX 7 AA7 GLY A 174 ILE A 183 1 10 HELIX 8 AA8 GLY A 184 VAL A 199 1 16 HELIX 9 AA9 PHE A 200 SER A 209 1 10 HELIX 10 AB1 HIS A 210 GLN A 226 1 17 HELIX 11 AB2 ALA A 260 THR A 274 1 15 HELIX 12 AB3 THR A 317 LEU A 345 1 29 HELIX 13 AB4 HIS A 354 GLY A 374 1 21 HELIX 14 AB5 SER A 396 ILE A 413 1 18 HELIX 15 AB6 ILE A 413 ALA A 421 1 9 HELIX 16 AB7 PRO A 424 LEU A 444 1 21 HELIX 17 AB8 SER A 455 ASN A 478 1 24 HELIX 18 AB9 PRO A 479 ILE A 482 5 4 HELIX 19 AC1 ILE A 486 THR A 498 1 13 HELIX 20 AC2 THR A 499 VAL A 515 1 17 HELIX 21 AC3 SER A 518 GLY A 523 1 6 CISPEP 1 LEU A 141 PRO A 142 0 5.16 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -1.000000 0.000000 0.000000 298.80090 MTRIX2 2 0.000000 -1.000000 0.000000 298.80090 MTRIX3 2 0.000000 0.000000 1.000000 0.00000