HEADER MEMBRANE PROTEIN 04-SEP-21 7PN1 TITLE APO HSPEPT1 IN THE OUTWARD FACING OPEN CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 15 MEMBER 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INTESTINAL H(+)/PEPTIDE COTRANSPORTER,OLIGOPEPTIDE COMPND 5 TRANSPORTER,SMALL INTESTINE ISOFORM,PEPTIDE TRANSPORTER 1,HSPEPT1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: HSPEPT1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SLC15A1, PEPT1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS HSPEPT1, PEPT1, PEPTIDE TRANSPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.KILLER,J.WALD,J.PIEPRZYK,T.C.MARLOVITS,C.LOEW REVDAT 2 17-NOV-21 7PN1 1 JRNL REVDAT 1 20-OCT-21 7PN1 0 JRNL AUTH M.KILLER,J.WALD,J.PIEPRZYK,T.C.MARLOVITS,C.LOW JRNL TITL STRUCTURAL SNAPSHOTS OF HUMAN PEPT1 AND PEPT2 REVEAL JRNL TITL 2 MECHANISTIC INSIGHTS INTO SUBSTRATE AND DRUG TRANSPORT JRNL TITL 3 ACROSS EPITHELIAL MEMBRANES. JRNL REF SCI ADV V. 7 K3259 2021 JRNL REFN ESSN 2375-2548 JRNL PMID 34730990 JRNL DOI 10.1126/SCIADV.ABK3259 REMARK 2 REMARK 2 RESOLUTION. 3.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 199987 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 7PN1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1292117982. 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 PEPT1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 6600.00 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 GLY A 2 REMARK 465 MET A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 HIS A 7 REMARK 465 SER A 8 REMARK 465 PHE A 9 REMARK 465 PHE A 10 REMARK 465 GLY A 11 REMARK 465 ASP A 49 REMARK 465 HIS A 109 REMARK 465 ASN A 110 REMARK 465 HIS A 111 REMARK 465 ASP A 112 REMARK 465 GLY A 113 REMARK 465 THR A 114 REMARK 465 PRO A 115 REMARK 465 ASP A 116 REMARK 465 CYS A 189 REMARK 465 GLY A 190 REMARK 465 ILE A 191 REMARK 465 HIS A 192 REMARK 465 SER A 193 REMARK 465 LYS A 194 REMARK 465 GLU A 684 REMARK 465 ASP A 685 REMARK 465 GLU A 686 REMARK 465 LYS A 687 REMARK 465 LYS A 688 REMARK 465 ASN A 689 REMARK 465 ARG A 690 REMARK 465 LEU A 691 REMARK 465 GLU A 692 REMARK 465 LYS A 693 REMARK 465 SER A 694 REMARK 465 ASN A 695 REMARK 465 PRO A 696 REMARK 465 TYR A 697 REMARK 465 PHE A 698 REMARK 465 MET A 699 REMARK 465 SER A 700 REMARK 465 GLY A 701 REMARK 465 ALA A 702 REMARK 465 ASN A 703 REMARK 465 SER A 704 REMARK 465 GLN A 705 REMARK 465 LYS A 706 REMARK 465 GLN A 707 REMARK 465 MET A 708 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 O LEU A 39 OG1 THR A 42 2.05 REMARK 500 O LEU A 306 OG1 THR A 309 2.07 REMARK 500 OH TYR A 40 OD2 ASP A 105 2.09 REMARK 500 OH TYR A 287 OG SER A 606 2.17 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 GLN A 155 35.36 -98.33 REMARK 500 SER A 532 149.98 -172.31 REMARK 500 GLU A 549 -140.30 57.72 REMARK 500 ALA A 637 -131.28 58.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13545 RELATED DB: EMDB REMARK 900 APO HSPEPT1 IN THE OUTWARD FACING OPEN CONFORMATION DBREF 7PN1 A 1 708 UNP P46059 S15A1_HUMAN 1 708 SEQRES 1 A 708 MET GLY MET SER LYS SER HIS SER PHE PHE GLY TYR PRO SEQRES 2 A 708 LEU SER ILE PHE PHE ILE VAL VAL ASN GLU PHE CYS GLU SEQRES 3 A 708 ARG PHE SER TYR TYR GLY MET ARG ALA ILE LEU ILE LEU SEQRES 4 A 708 TYR PHE THR ASN PHE ILE SER TRP ASP ASP ASN LEU SER SEQRES 5 A 708 THR ALA ILE TYR HIS THR PHE VAL ALA LEU CYS TYR LEU SEQRES 6 A 708 THR PRO ILE LEU GLY ALA LEU ILE ALA ASP SER TRP LEU SEQRES 7 A 708 GLY LYS PHE LYS THR ILE VAL SER LEU SER ILE VAL TYR SEQRES 8 A 708 THR ILE GLY GLN ALA VAL THR SER VAL SER SER ILE ASN SEQRES 9 A 708 ASP LEU THR ASP HIS ASN HIS ASP GLY THR PRO ASP SER SEQRES 10 A 708 LEU PRO VAL HIS VAL VAL LEU SER LEU ILE GLY LEU ALA SEQRES 11 A 708 LEU ILE ALA LEU GLY THR GLY GLY ILE LYS PRO CYS VAL SEQRES 12 A 708 SER ALA PHE GLY GLY ASP GLN PHE GLU GLU GLY GLN GLU SEQRES 13 A 708 LYS GLN ARG ASN ARG PHE PHE SER ILE PHE TYR LEU ALA SEQRES 14 A 708 ILE ASN ALA GLY SER LEU LEU SER THR ILE ILE THR PRO SEQRES 15 A 708 MET LEU ARG VAL GLN GLN CYS GLY ILE HIS SER LYS GLN SEQRES 16 A 708 ALA CYS TYR PRO LEU ALA PHE GLY VAL PRO ALA ALA LEU SEQRES 17 A 708 MET ALA VAL ALA LEU ILE VAL PHE VAL LEU GLY SER GLY SEQRES 18 A 708 MET TYR LYS LYS PHE LYS PRO GLN GLY ASN ILE MET GLY SEQRES 19 A 708 LYS VAL ALA LYS CYS ILE GLY PHE ALA ILE LYS ASN ARG SEQRES 20 A 708 PHE ARG HIS ARG SER LYS ALA PHE PRO LYS ARG GLU HIS SEQRES 21 A 708 TRP LEU ASP TRP ALA LYS GLU LYS TYR ASP GLU ARG LEU SEQRES 22 A 708 ILE SER GLN ILE LYS MET VAL THR ARG VAL MET PHE LEU SEQRES 23 A 708 TYR ILE PRO LEU PRO MET PHE TRP ALA LEU PHE ASP GLN SEQRES 24 A 708 GLN GLY SER ARG TRP THR LEU GLN ALA THR THR MET SER SEQRES 25 A 708 GLY LYS ILE GLY ALA LEU GLU ILE GLN PRO ASP GLN MET SEQRES 26 A 708 GLN THR VAL ASN ALA ILE LEU ILE VAL ILE MET VAL PRO SEQRES 27 A 708 ILE PHE ASP ALA VAL LEU TYR PRO LEU ILE ALA LYS CYS SEQRES 28 A 708 GLY PHE ASN PHE THR SER LEU LYS LYS MET ALA VAL GLY SEQRES 29 A 708 MET VAL LEU ALA SER MET ALA PHE VAL VAL ALA ALA ILE SEQRES 30 A 708 VAL GLN VAL GLU ILE ASP LYS THR LEU PRO VAL PHE PRO SEQRES 31 A 708 LYS GLY ASN GLU VAL GLN ILE LYS VAL LEU ASN ILE GLY SEQRES 32 A 708 ASN ASN THR MET ASN ILE SER LEU PRO GLY GLU MET VAL SEQRES 33 A 708 THR LEU GLY PRO MET SER GLN THR ASN ALA PHE MET THR SEQRES 34 A 708 PHE ASP VAL ASN LYS LEU THR ARG ILE ASN ILE SER SER SEQRES 35 A 708 PRO GLY SER PRO VAL THR ALA VAL THR ASP ASP PHE LYS SEQRES 36 A 708 GLN GLY GLN ARG HIS THR LEU LEU VAL TRP ALA PRO ASN SEQRES 37 A 708 HIS TYR GLN VAL VAL LYS ASP GLY LEU ASN GLN LYS PRO SEQRES 38 A 708 GLU LYS GLY GLU ASN GLY ILE ARG PHE VAL ASN THR PHE SEQRES 39 A 708 ASN GLU LEU ILE THR ILE THR MET SER GLY LYS VAL TYR SEQRES 40 A 708 ALA ASN ILE SER SER TYR ASN ALA SER THR TYR GLN PHE SEQRES 41 A 708 PHE PRO SER GLY ILE LYS GLY PHE THR ILE SER SER THR SEQRES 42 A 708 GLU ILE PRO PRO GLN CYS GLN PRO ASN PHE ASN THR PHE SEQRES 43 A 708 TYR LEU GLU PHE GLY SER ALA TYR THR TYR ILE VAL GLN SEQRES 44 A 708 ARG LYS ASN ASP SER CYS PRO GLU VAL LYS VAL PHE GLU SEQRES 45 A 708 ASP ILE SER ALA ASN THR VAL ASN MET ALA LEU GLN ILE SEQRES 46 A 708 PRO GLN TYR PHE LEU LEU THR CYS GLY GLU VAL VAL PHE SEQRES 47 A 708 SER VAL THR GLY LEU GLU PHE SER TYR SER GLN ALA PRO SEQRES 48 A 708 SER ASN MET LYS SER VAL LEU GLN ALA GLY TRP LEU LEU SEQRES 49 A 708 THR VAL ALA VAL GLY ASN ILE ILE VAL LEU ILE VAL ALA SEQRES 50 A 708 GLY ALA GLY GLN PHE SER LYS GLN TRP ALA GLU TYR ILE SEQRES 51 A 708 LEU PHE ALA ALA LEU LEU LEU VAL VAL CYS VAL ILE PHE SEQRES 52 A 708 ALA ILE MET ALA ARG PHE TYR THR TYR ILE ASN PRO ALA SEQRES 53 A 708 GLU ILE GLU ALA GLN PHE ASP GLU ASP GLU LYS LYS ASN SEQRES 54 A 708 ARG LEU GLU LYS SER ASN PRO TYR PHE MET SER GLY ALA SEQRES 55 A 708 ASN SER GLN LYS GLN MET HELIX 1 AA1 TYR A 12 ASP A 48 1 37 HELIX 2 AA2 LEU A 51 TRP A 77 1 27 HELIX 3 AA3 GLY A 79 ASP A 108 1 30 HELIX 4 AA4 LEU A 118 ILE A 139 1 22 HELIX 5 AA5 ILE A 139 GLN A 150 1 12 HELIX 6 AA6 GLN A 155 ARG A 185 1 31 HELIX 7 AA7 CYS A 197 GLY A 219 1 23 HELIX 8 AA8 SER A 220 TYR A 223 5 4 HELIX 9 AA9 ASN A 231 ARG A 249 1 19 HELIX 10 AB1 TRP A 261 LYS A 266 1 6 HELIX 11 AB2 ASP A 270 LEU A 286 1 17 HELIX 12 AB3 PRO A 289 ASP A 298 1 10 HELIX 13 AB4 GLN A 300 THR A 310 1 11 HELIX 14 AB5 GLN A 321 MET A 325 5 5 HELIX 15 AB6 GLN A 326 VAL A 343 1 18 HELIX 16 AB7 VAL A 343 CYS A 351 1 9 HELIX 17 AB8 THR A 356 ASP A 383 1 28 HELIX 18 AB9 LYS A 384 LEU A 386 5 3 HELIX 19 AC1 PRO A 481 GLU A 485 5 5 HELIX 20 AC2 ASN A 580 LEU A 583 5 4 HELIX 21 AC3 GLN A 584 ALA A 610 1 27 HELIX 22 AC4 PRO A 611 ASN A 613 5 3 HELIX 23 AC5 MET A 614 ALA A 637 1 24 HELIX 24 AC6 SER A 643 ALA A 654 1 12 HELIX 25 AC7 LEU A 655 ARG A 668 1 14 HELIX 26 AC8 TYR A 670 ASN A 674 5 5 HELIX 27 AC9 PRO A 675 ALA A 680 1 6 HELIX 28 AD1 GLN A 681 ASP A 683 5 3 SHEET 1 AA1 3 SER A 422 GLN A 423 0 SHEET 2 AA1 3 GLU A 394 ASN A 401 -1 N ASN A 401 O SER A 422 SHEET 3 AA1 3 MET A 428 ASP A 431 -1 O PHE A 430 N VAL A 395 SHEET 1 AA2 4 SER A 422 GLN A 423 0 SHEET 2 AA2 4 GLU A 394 ASN A 401 -1 N ASN A 401 O SER A 422 SHEET 3 AA2 4 ARG A 459 ALA A 466 1 O LEU A 462 N LYS A 398 SHEET 4 AA2 4 HIS A 469 LYS A 474 -1 O GLN A 471 N LEU A 463 SHEET 1 AA3 4 GLU A 414 LEU A 418 0 SHEET 2 AA3 4 MET A 407 LEU A 411 -1 N LEU A 411 O GLU A 414 SHEET 3 AA3 4 ASN A 439 SER A 441 -1 O SER A 441 N ASN A 408 SHEET 4 AA3 4 THR A 448 ALA A 449 -1 O THR A 448 N ILE A 440 SHEET 1 AA4 3 ASN A 514 ALA A 515 0 SHEET 2 AA4 3 ASN A 486 ASN A 492 -1 N ASN A 492 O ASN A 514 SHEET 3 AA4 3 GLN A 519 PHE A 521 -1 O PHE A 521 N ASN A 486 SHEET 1 AA5 4 ASN A 514 ALA A 515 0 SHEET 2 AA5 4 ASN A 486 ASN A 492 -1 N ASN A 492 O ASN A 514 SHEET 3 AA5 4 ALA A 553 ARG A 560 1 O TYR A 556 N ARG A 489 SHEET 4 AA5 4 PRO A 566 ILE A 574 -1 O PHE A 571 N THR A 555 SHEET 1 AA6 4 LYS A 505 ILE A 510 0 SHEET 2 AA6 4 ILE A 498 MET A 502 -1 N ILE A 500 O TYR A 507 SHEET 3 AA6 4 GLY A 527 SER A 531 -1 O SER A 531 N THR A 499 SHEET 4 AA6 4 ASN A 542 ASN A 544 -1 O PHE A 543 N PHE A 528 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