HEADER TRANSPORT PROTEIN 24-FEB-24 8YF4 TITLE CRYO EM STRUCTURE OF HUMAN PHOSPHATE CHANNEL XPR1 AT OPEN AND INWARD- TITLE 2 FACING STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 53 MEMBER 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHATE EXPORTER SLC53A1,PROTEIN SYG1 HOMOLOG,XENOTROPIC COMPND 5 AND POLYTROPIC MURINE LEUKEMIA VIRUS RECEPTOR X3,X-RECEPTOR, COMPND 6 XENOTROPIC AND POLYTROPIC RETROVIRUS RECEPTOR 1; 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: XPR1, SLC53A1, SYG1, X3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS PHOSPHATE CHANNEL, MEMBRANE PROTEIN, PHOSPHATE HOMEOSTASIS, TRANSPORT KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.LU,C.YUE,L.ZHANG,D.YAO,Y.YU,Y.CAO REVDAT 1 09-OCT-24 8YF4 0 JRNL AUTH Y.LU,C.X.YUE,L.ZHANG,D.YAO,Y.XIA,Q.ZHANG,X.ZHANG,S.LI, JRNL AUTH 2 Y.SHEN,M.CAO,C.R.GUO,A.QIN,J.ZHAO,L.ZHOU,Y.YU,Y.CAO JRNL TITL STRUCTURAL BASIS FOR INOSITOL PYROPHOSPHATE GATING OF THE JRNL TITL 2 PHOSPHATE CHANNEL XPR1. JRNL REF SCIENCE P3252 2024 JRNL REFN ESSN 1095-9203 JRNL PMID 39325866 JRNL DOI 10.1126/SCIENCE.ADP3252 REMARK 2 REMARK 2 RESOLUTION. 3.41 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) : 3.410 REMARK 3 NUMBER OF PARTICLES : 447733 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 8YF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 28-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300045512. 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 : CRYO EM STRUCTURE OF HUMAN REMARK 245 PHOSPHATE CHANNEL XPR1 AT OPEN REMARK 245 AND INWARD-FACING 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 : 7.50 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2600.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 ILE A 575 OG SER A 578 2.06 REMARK 500 O SER B 578 OG1 THR B 582 2.09 REMARK 500 O ILE A 271 OH TYR A 352 2.18 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 SER A 340 51.93 -93.11 REMARK 500 LYS A 427 -66.56 61.45 REMARK 500 THR A 444 -111.10 50.67 REMARK 500 PRO A 598 46.52 -80.82 REMARK 500 ALA B 337 72.71 52.90 REMARK 500 THR B 344 -4.32 -143.51 REMARK 500 SER B 426 -169.54 -126.33 REMARK 500 LYS B 427 -70.11 63.77 REMARK 500 THR B 444 -102.04 50.61 REMARK 500 ASN B 540 36.13 -98.87 REMARK 500 LEU B 585 72.16 53.32 REMARK 500 PRO B 598 45.63 -81.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39210 RELATED DB: EMDB REMARK 900 A HUMAN TRANSPORTER FOR SUBSTRATE TRANSLOCATION DBREF 8YF4 A 227 619 UNP Q9UBH6 S53A1_HUMAN 227 619 DBREF 8YF4 B 227 619 UNP Q9UBH6 S53A1_HUMAN 227 619 SEQRES 1 A 393 GLN PRO ALA PRO ALA TRP THR THR PHE ARG VAL GLY LEU SEQRES 2 A 393 PHE CYS GLY ILE PHE ILE VAL LEU ASN ILE THR LEU VAL SEQRES 3 A 393 LEU ALA ALA VAL PHE LYS LEU GLU THR ASP ARG SER ILE SEQRES 4 A 393 TRP PRO LEU ILE ARG ILE TYR ARG GLY GLY PHE LEU LEU SEQRES 5 A 393 ILE GLU PHE LEU PHE LEU LEU GLY ILE ASN THR TYR GLY SEQRES 6 A 393 TRP ARG GLN ALA GLY VAL ASN HIS VAL LEU ILE PHE GLU SEQRES 7 A 393 LEU ASN PRO ARG SER ASN LEU SER HIS GLN HIS LEU PHE SEQRES 8 A 393 GLU ILE ALA GLY PHE LEU GLY ILE LEU TRP CYS LEU SER SEQRES 9 A 393 LEU LEU ALA CYS PHE PHE ALA PRO ILE SER VAL ILE PRO SEQRES 10 A 393 THR TYR VAL TYR PRO LEU ALA LEU TYR GLY PHE MET VAL SEQRES 11 A 393 PHE PHE LEU ILE ASN PRO THR LYS THR PHE TYR TYR LYS SEQRES 12 A 393 SER ARG PHE TRP LEU LEU LYS LEU LEU PHE ARG VAL PHE SEQRES 13 A 393 THR ALA PRO PHE HIS LYS VAL GLY PHE ALA ASP PHE TRP SEQRES 14 A 393 LEU ALA ASP GLN LEU ASN SER LEU SER VAL ILE LEU MET SEQRES 15 A 393 ASP LEU GLU TYR MET ILE CYS PHE TYR SER LEU GLU LEU SEQRES 16 A 393 LYS TRP ASP GLU SER LYS GLY LEU LEU PRO ASN ASN SER SEQRES 17 A 393 GLU GLU SER GLY ILE CYS HIS LYS TYR THR TYR GLY VAL SEQRES 18 A 393 ARG ALA ILE VAL GLN CYS ILE PRO ALA TRP LEU ARG PHE SEQRES 19 A 393 ILE GLN CYS LEU ARG ARG TYR ARG ASP THR LYS ARG ALA SEQRES 20 A 393 PHE PRO HIS LEU VAL ASN ALA GLY LYS TYR SER THR THR SEQRES 21 A 393 PHE PHE MET VAL THR PHE ALA ALA LEU TYR SER THR HIS SEQRES 22 A 393 LYS GLU ARG GLY HIS SER ASP THR MET VAL PHE PHE TYR SEQRES 23 A 393 LEU TRP ILE VAL PHE TYR ILE ILE SER SER CYS TYR THR SEQRES 24 A 393 LEU ILE TRP ASP LEU LYS MET ASP TRP GLY LEU PHE ASP SEQRES 25 A 393 LYS ASN ALA GLY GLU ASN THR PHE LEU ARG GLU GLU ILE SEQRES 26 A 393 VAL TYR PRO GLN LYS ALA TYR TYR TYR CYS ALA ILE ILE SEQRES 27 A 393 GLU ASP VAL ILE LEU ARG PHE ALA TRP THR ILE GLN ILE SEQRES 28 A 393 SER ILE THR SER THR THR LEU LEU PRO HIS SER GLY ASP SEQRES 29 A 393 ILE ILE ALA THR VAL PHE ALA PRO LEU GLU VAL PHE ARG SEQRES 30 A 393 ARG PHE VAL TRP ASN PHE PHE ARG LEU GLU ASN GLU HIS SEQRES 31 A 393 LEU ASN ASN SEQRES 1 B 393 GLN PRO ALA PRO ALA TRP THR THR PHE ARG VAL GLY LEU SEQRES 2 B 393 PHE CYS GLY ILE PHE ILE VAL LEU ASN ILE THR LEU VAL SEQRES 3 B 393 LEU ALA ALA VAL PHE LYS LEU GLU THR ASP ARG SER ILE SEQRES 4 B 393 TRP PRO LEU ILE ARG ILE TYR ARG GLY GLY PHE LEU LEU SEQRES 5 B 393 ILE GLU PHE LEU PHE LEU LEU GLY ILE ASN THR TYR GLY SEQRES 6 B 393 TRP ARG GLN ALA GLY VAL ASN HIS VAL LEU ILE PHE GLU SEQRES 7 B 393 LEU ASN PRO ARG SER ASN LEU SER HIS GLN HIS LEU PHE SEQRES 8 B 393 GLU ILE ALA GLY PHE LEU GLY ILE LEU TRP CYS LEU SER SEQRES 9 B 393 LEU LEU ALA CYS PHE PHE ALA PRO ILE SER VAL ILE PRO SEQRES 10 B 393 THR TYR VAL TYR PRO LEU ALA LEU TYR GLY PHE MET VAL SEQRES 11 B 393 PHE PHE LEU ILE ASN PRO THR LYS THR PHE TYR TYR LYS SEQRES 12 B 393 SER ARG PHE TRP LEU LEU LYS LEU LEU PHE ARG VAL PHE SEQRES 13 B 393 THR ALA PRO PHE HIS LYS VAL GLY PHE ALA ASP PHE TRP SEQRES 14 B 393 LEU ALA ASP GLN LEU ASN SER LEU SER VAL ILE LEU MET SEQRES 15 B 393 ASP LEU GLU TYR MET ILE CYS PHE TYR SER LEU GLU LEU SEQRES 16 B 393 LYS TRP ASP GLU SER LYS GLY LEU LEU PRO ASN ASN SER SEQRES 17 B 393 GLU GLU SER GLY ILE CYS HIS LYS TYR THR TYR GLY VAL SEQRES 18 B 393 ARG ALA ILE VAL GLN CYS ILE PRO ALA TRP LEU ARG PHE SEQRES 19 B 393 ILE GLN CYS LEU ARG ARG TYR ARG ASP THR LYS ARG ALA SEQRES 20 B 393 PHE PRO HIS LEU VAL ASN ALA GLY LYS TYR SER THR THR SEQRES 21 B 393 PHE PHE MET VAL THR PHE ALA ALA LEU TYR SER THR HIS SEQRES 22 B 393 LYS GLU ARG GLY HIS SER ASP THR MET VAL PHE PHE TYR SEQRES 23 B 393 LEU TRP ILE VAL PHE TYR ILE ILE SER SER CYS TYR THR SEQRES 24 B 393 LEU ILE TRP ASP LEU LYS MET ASP TRP GLY LEU PHE ASP SEQRES 25 B 393 LYS ASN ALA GLY GLU ASN THR PHE LEU ARG GLU GLU ILE SEQRES 26 B 393 VAL TYR PRO GLN LYS ALA TYR TYR TYR CYS ALA ILE ILE SEQRES 27 B 393 GLU ASP VAL ILE LEU ARG PHE ALA TRP THR ILE GLN ILE SEQRES 28 B 393 SER ILE THR SER THR THR LEU LEU PRO HIS SER GLY ASP SEQRES 29 B 393 ILE ILE ALA THR VAL PHE ALA PRO LEU GLU VAL PHE ARG SEQRES 30 B 393 ARG PHE VAL TRP ASN PHE PHE ARG LEU GLU ASN GLU HIS SEQRES 31 B 393 LEU ASN ASN HET Y01 A 701 35 HET Y01 B 701 35 HETNAM Y01 CHOLESTEROL HEMISUCCINATE FORMUL 3 Y01 2(C31 H50 O4) HELIX 1 AA1 PRO A 230 LYS A 258 1 29 HELIX 2 AA2 ILE A 265 ALA A 295 1 31 HELIX 3 AA3 SER A 312 ALA A 337 1 26 HELIX 4 AA4 TYR A 345 ILE A 360 1 16 HELIX 5 AA5 TYR A 367 THR A 383 1 17 HELIX 6 AA6 GLY A 390 SER A 402 1 13 HELIX 7 AA7 LEU A 403 LEU A 419 1 17 HELIX 8 AA8 VAL A 447 LYS A 471 1 25 HELIX 9 AA9 HIS A 476 GLU A 501 1 26 HELIX 10 AB1 ASP A 506 MET A 532 1 27 HELIX 11 AB2 GLN A 555 PHE A 571 1 17 HELIX 12 AB3 PHE A 571 THR A 583 1 13 HELIX 13 AB4 SER A 588 ALA A 597 1 10 HELIX 14 AB5 LEU A 599 ASN A 619 1 21 HELIX 15 AB6 PRO B 230 LYS B 258 1 29 HELIX 16 AB7 ILE B 265 GLY B 296 1 32 HELIX 17 AB8 ASN B 298 PHE B 303 1 6 HELIX 18 AB9 SER B 312 ALA B 337 1 26 HELIX 19 AC1 VAL B 346 ILE B 360 1 15 HELIX 20 AC2 TYR B 367 THR B 383 1 17 HELIX 21 AC3 GLY B 390 LEU B 403 1 14 HELIX 22 AC4 SER B 404 LEU B 419 1 16 HELIX 23 AC5 ARG B 448 LYS B 471 1 24 HELIX 24 AC6 ALA B 473 GLY B 503 1 31 HELIX 25 AC7 ASP B 506 LYS B 531 1 26 HELIX 26 AC8 GLN B 555 THR B 583 1 29 HELIX 27 AC9 SER B 588 ASN B 619 1 32 SSBOND 1 CYS A 415 CYS A 440 1555 1555 2.03 SSBOND 2 CYS B 415 CYS B 440 1555 1555 2.04 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