HEADER TRANSPORT PROTEIN 17-NOV-23 8X5E TITLE CRYO-EM STRUCTURE OF HUMAN XPR1 IN OPEN STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 53 MEMBER 1; COMPND 3 CHAIN: A; COMPND 4 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: XPR1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS TRANSPORT OPEN STATE, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.H.JIANG,R.YAN REVDAT 1 03-JUL-24 8X5E 0 JRNL AUTH D.H.JIANG,R.YAN JRNL TITL STRUCTURE OF TRANSPORT AT 3.6 ANGSTROMS RESOLUTION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.61 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) : 3.610 REMARK 3 NUMBER OF PARTICLES : 40195 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 8X5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042654. 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 : TRANSPORT 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 : FEI TITAN 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 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 GLU A 260 REMARK 465 THR A 261 REMARK 465 ASP A 262 REMARK 465 ARG A 263 REMARK 465 SER A 264 REMARK 465 THR A 583 REMARK 465 LEU A 584 REMARK 465 LEU A 585 REMARK 465 ARG A 627 REMARK 465 ASP A 628 REMARK 465 ILE A 629 REMARK 465 SER A 630 REMARK 465 VAL A 631 REMARK 465 ALA A 632 REMARK 465 PRO A 633 REMARK 465 LEU A 634 REMARK 465 ASN A 635 REMARK 465 ALA A 636 REMARK 465 ASP A 637 REMARK 465 ASP A 638 REMARK 465 GLN A 639 REMARK 465 THR A 640 REMARK 465 LEU A 641 REMARK 465 LEU A 642 REMARK 465 GLU A 643 REMARK 465 GLN A 644 REMARK 465 MET A 645 REMARK 465 MET A 646 REMARK 465 ASP A 647 REMARK 465 GLN A 648 REMARK 465 ASP A 649 REMARK 465 ASP A 650 REMARK 465 GLY A 651 REMARK 465 VAL A 652 REMARK 465 ARG A 653 REMARK 465 ASN A 654 REMARK 465 ARG A 655 REMARK 465 GLN A 656 REMARK 465 LYS A 657 REMARK 465 ASN A 658 REMARK 465 ARG A 659 REMARK 465 SER A 660 REMARK 465 TRP A 661 REMARK 465 LYS A 662 REMARK 465 TYR A 663 REMARK 465 ASN A 664 REMARK 465 GLN A 665 REMARK 465 SER A 666 REMARK 465 ILE A 667 REMARK 465 SER A 668 REMARK 465 LEU A 669 REMARK 465 ARG A 670 REMARK 465 ARG A 671 REMARK 465 PRO A 672 REMARK 465 ARG A 673 REMARK 465 LEU A 674 REMARK 465 ALA A 675 REMARK 465 SER A 676 REMARK 465 GLN A 677 REMARK 465 SER A 678 REMARK 465 LYS A 679 REMARK 465 ALA A 680 REMARK 465 ARG A 681 REMARK 465 ASP A 682 REMARK 465 THR A 683 REMARK 465 LYS A 684 REMARK 465 VAL A 685 REMARK 465 LEU A 686 REMARK 465 ILE A 687 REMARK 465 GLU A 688 REMARK 465 ASP A 689 REMARK 465 THR A 690 REMARK 465 ASP A 691 REMARK 465 ASP A 692 REMARK 465 GLU A 693 REMARK 465 ALA A 694 REMARK 465 ASN A 695 REMARK 465 THR A 696 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 ARG A 293 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 369 CG CD CE NZ REMARK 470 LEU A 430 CG CD1 CD2 REMARK 470 ASN A 432 CG OD1 ND2 REMARK 470 ASN A 433 CG OD1 ND2 REMARK 470 SER A 434 OG REMARK 470 GLU A 435 CG CD OE1 OE2 REMARK 470 GLU A 436 CG CD OE1 OE2 REMARK 470 SER A 437 OG REMARK 470 LYS A 442 CG CD CE NZ REMARK 470 ARG A 472 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 500 CG CD CE NZ REMARK 470 GLU A 501 CG CD OE1 OE2 REMARK 470 ARG A 502 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 504 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 506 CG OD1 OD2 REMARK 470 THR A 507 OG1 CG2 REMARK 470 MET A 508 CG SD CE REMARK 470 TYR A 512 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE A 517 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 533 CG OD1 OD2 REMARK 470 ASP A 538 CG OD1 OD2 REMARK 470 LYS A 539 CG CD CE NZ REMARK 470 GLN A 555 CG CD OE1 NE2 REMARK 470 GLU A 565 CG CD OE1 OE2 REMARK 470 GLN A 576 CG CD OE1 NE2 REMARK 470 ILE A 591 CG1 CG2 CD1 REMARK 470 GLU A 622 CG CD OE1 OE2 REMARK 470 PHE A 623 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 554 CB - CA - C ANGL. DEV. = -18.6 DEGREES REMARK 500 PRO A 554 N - CA - C ANGL. DEV. = 22.0 DEGREES 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 GLU A 304 74.80 44.31 REMARK 500 ASN A 310 -56.64 69.16 REMARK 500 ALA A 337 64.47 -157.24 REMARK 500 VAL A 341 -51.82 -140.25 REMARK 500 ASN A 432 23.56 49.77 REMARK 500 SER A 434 25.69 49.23 REMARK 500 GLU A 435 -75.37 -94.19 REMARK 500 LYS A 471 -59.61 72.49 REMARK 500 HIS A 504 -59.97 70.90 REMARK 500 LYS A 531 -63.20 -105.23 REMARK 500 ALA A 541 77.98 -67.68 REMARK 500 PHE A 623 105.42 -53.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 6OU A 703 REMARK 610 6OU A 704 REMARK 610 6OU A 705 REMARK 610 6OU A 706 REMARK 610 6OU A 707 REMARK 610 6OU A 708 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38067 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN XPR1 IN OPEN STATE DBREF 8X5E A 229 696 UNP Q9UBH6 S53A1_HUMAN 229 696 SEQRES 1 A 468 ALA PRO ALA TRP THR THR PHE ARG VAL GLY LEU PHE CYS SEQRES 2 A 468 GLY ILE PHE ILE VAL LEU ASN ILE THR LEU VAL LEU ALA SEQRES 3 A 468 ALA VAL PHE LYS LEU GLU THR ASP ARG SER ILE TRP PRO SEQRES 4 A 468 LEU ILE ARG ILE TYR ARG GLY GLY PHE LEU LEU ILE GLU SEQRES 5 A 468 PHE LEU PHE LEU LEU GLY ILE ASN THR TYR GLY TRP ARG SEQRES 6 A 468 GLN ALA GLY VAL ASN HIS VAL LEU ILE PHE GLU LEU ASN SEQRES 7 A 468 PRO ARG SER ASN LEU SER HIS GLN HIS LEU PHE GLU ILE SEQRES 8 A 468 ALA GLY PHE LEU GLY ILE LEU TRP CYS LEU SER LEU LEU SEQRES 9 A 468 ALA CYS PHE PHE ALA PRO ILE SER VAL ILE PRO THR TYR SEQRES 10 A 468 VAL TYR PRO LEU ALA LEU TYR GLY PHE MET VAL PHE PHE SEQRES 11 A 468 LEU ILE ASN PRO THR LYS THR PHE TYR TYR LYS SER ARG SEQRES 12 A 468 PHE TRP LEU LEU LYS LEU LEU PHE ARG VAL PHE THR ALA SEQRES 13 A 468 PRO PHE HIS LYS VAL GLY PHE ALA ASP PHE TRP LEU ALA SEQRES 14 A 468 ASP GLN LEU ASN SER LEU SER VAL ILE LEU MET ASP LEU SEQRES 15 A 468 GLU TYR MET ILE CYS PHE TYR SER LEU GLU LEU LYS TRP SEQRES 16 A 468 ASP GLU SER LYS GLY LEU LEU PRO ASN ASN SER GLU GLU SEQRES 17 A 468 SER GLY ILE CYS HIS LYS TYR THR TYR GLY VAL ARG ALA SEQRES 18 A 468 ILE VAL GLN CYS ILE PRO ALA TRP LEU ARG PHE ILE GLN SEQRES 19 A 468 CYS LEU ARG ARG TYR ARG ASP THR LYS ARG ALA PHE PRO SEQRES 20 A 468 HIS LEU VAL ASN ALA GLY LYS TYR SER THR THR PHE PHE SEQRES 21 A 468 MET VAL THR PHE ALA ALA LEU TYR SER THR HIS LYS GLU SEQRES 22 A 468 ARG GLY HIS SER ASP THR MET VAL PHE PHE TYR LEU TRP SEQRES 23 A 468 ILE VAL PHE TYR ILE ILE SER SER CYS TYR THR LEU ILE SEQRES 24 A 468 TRP ASP LEU LYS MET ASP TRP GLY LEU PHE ASP LYS ASN SEQRES 25 A 468 ALA GLY GLU ASN THR PHE LEU ARG GLU GLU ILE VAL TYR SEQRES 26 A 468 PRO GLN LYS ALA TYR TYR TYR CYS ALA ILE ILE GLU ASP SEQRES 27 A 468 VAL ILE LEU ARG PHE ALA TRP THR ILE GLN ILE SER ILE SEQRES 28 A 468 THR SER THR THR LEU LEU PRO HIS SER GLY ASP ILE ILE SEQRES 29 A 468 ALA THR VAL PHE ALA PRO LEU GLU VAL PHE ARG ARG PHE SEQRES 30 A 468 VAL TRP ASN PHE PHE ARG LEU GLU ASN GLU HIS LEU ASN SEQRES 31 A 468 ASN CYS GLY GLU PHE ARG ALA VAL ARG ASP ILE SER VAL SEQRES 32 A 468 ALA PRO LEU ASN ALA ASP ASP GLN THR LEU LEU GLU GLN SEQRES 33 A 468 MET MET ASP GLN ASP ASP GLY VAL ARG ASN ARG GLN LYS SEQRES 34 A 468 ASN ARG SER TRP LYS TYR ASN GLN SER ILE SER LEU ARG SEQRES 35 A 468 ARG PRO ARG LEU ALA SER GLN SER LYS ALA ARG ASP THR SEQRES 36 A 468 LYS VAL LEU ILE GLU ASP THR ASP ASP GLU ALA ASN THR HET PO4 A 701 5 HET PO4 A 702 5 HET 6OU A 703 12 HET 6OU A 704 12 HET 6OU A 705 12 HET 6OU A 706 12 HET 6OU A 707 12 HET 6OU A 708 12 HETNAM PO4 PHOSPHATE ION HETNAM 6OU [(2~{R})-1-[2-AZANYLETHOXY(OXIDANYL)PHOSPHORYL]OXY-3- HETNAM 2 6OU HEXADECANOYLOXY-PROPAN-2-YL] (~{Z})-OCTADEC-9-ENOATE FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 6OU 6(C39 H76 N O8 P) HELIX 1 AA1 PRO A 230 LYS A 258 1 29 HELIX 2 AA2 TRP A 266 GLY A 296 1 31 HELIX 3 AA3 ASN A 298 PHE A 303 1 6 HELIX 4 AA4 SER A 312 PHE A 336 1 25 HELIX 5 AA5 TYR A 345 ASN A 361 1 17 HELIX 6 AA6 TYR A 367 THR A 383 1 17 HELIX 7 AA7 ALA A 384 HIS A 387 5 4 HELIX 8 AA8 GLY A 390 LEU A 403 1 14 HELIX 9 AA9 SER A 404 LEU A 419 1 16 HELIX 10 AB1 PRO A 431 LYS A 442 5 12 HELIX 11 AB2 GLY A 446 LYS A 471 1 26 HELIX 12 AB3 ALA A 473 ARG A 502 1 30 HELIX 13 AB4 THR A 507 MET A 532 1 26 HELIX 14 AB5 GLN A 555 PHE A 571 1 17 HELIX 15 AB6 ALA A 572 THR A 582 1 11 HELIX 16 AB7 GLY A 589 ASN A 619 1 31 SSBOND 1 CYS A 415 CYS A 440 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