HEADER TRANSPORT PROTEIN 23-FEB-24 8YEX TITLE CRYO EM STRUCTURE OF HUMAN PHOSPHATE CHANNEL XPR1 AT APO 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 8YEX 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. 3.68 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) : 3.680 REMARK 3 NUMBER OF PARTICLES : 215129 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 8YEX 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_1300045511. 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 APO REMARK 245 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 VAL B 478 OH TYR B 524 2.14 REMARK 500 OH TYR A 443 O THR A 580 2.18 REMARK 500 OD2 ASP B 529 NH2 ARG B 570 2.19 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 22.83 48.82 REMARK 500 ALA A 337 73.18 53.64 REMARK 500 SER A 340 -177.15 -171.91 REMARK 500 LYS A 427 -116.88 65.28 REMARK 500 ASP A 506 40.97 -102.93 REMARK 500 ASN A 540 36.78 -96.79 REMARK 500 LEU A 585 73.22 53.30 REMARK 500 PRO A 598 47.77 -84.40 REMARK 500 TYR B 345 40.07 -106.23 REMARK 500 LYS B 364 33.58 -97.11 REMARK 500 ASP B 424 49.37 -85.60 REMARK 500 SER B 426 -169.55 -126.01 REMARK 500 LYS B 427 -66.34 62.11 REMARK 500 THR B 444 -101.19 51.82 REMARK 500 LYS B 471 60.61 60.64 REMARK 500 THR B 580 1.62 -67.59 REMARK 500 LEU B 585 70.59 53.20 REMARK 500 PRO B 598 47.81 -86.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39204 RELATED DB: EMDB REMARK 900 A HUMAN TRANSPORTER FOR SUBSTRATE TRANSLOCATION DBREF 8YEX A 228 619 UNP Q9UBH6 S53A1_HUMAN 228 619 DBREF 8YEX B 228 619 UNP Q9UBH6 S53A1_HUMAN 228 619 SEQRES 1 A 392 PRO ALA PRO ALA TRP THR THR PHE ARG VAL GLY LEU PHE SEQRES 2 A 392 CYS GLY ILE PHE ILE VAL LEU ASN ILE THR LEU VAL LEU SEQRES 3 A 392 ALA ALA VAL PHE LYS LEU GLU THR ASP ARG SER ILE TRP SEQRES 4 A 392 PRO LEU ILE ARG ILE TYR ARG GLY GLY PHE LEU LEU ILE SEQRES 5 A 392 GLU PHE LEU PHE LEU LEU GLY ILE ASN THR TYR GLY TRP SEQRES 6 A 392 ARG GLN ALA GLY VAL ASN HIS VAL LEU ILE PHE GLU LEU SEQRES 7 A 392 ASN PRO ARG SER ASN LEU SER HIS GLN HIS LEU PHE GLU SEQRES 8 A 392 ILE ALA GLY PHE LEU GLY ILE LEU TRP CYS LEU SER LEU SEQRES 9 A 392 LEU ALA CYS PHE PHE ALA PRO ILE SER VAL ILE PRO THR SEQRES 10 A 392 TYR VAL TYR PRO LEU ALA LEU TYR GLY PHE MET VAL PHE SEQRES 11 A 392 PHE LEU ILE ASN PRO THR LYS THR PHE TYR TYR LYS SER SEQRES 12 A 392 ARG PHE TRP LEU LEU LYS LEU LEU PHE ARG VAL PHE THR SEQRES 13 A 392 ALA PRO PHE HIS LYS VAL GLY PHE ALA ASP PHE TRP LEU SEQRES 14 A 392 ALA ASP GLN LEU ASN SER LEU SER VAL ILE LEU MET ASP SEQRES 15 A 392 LEU GLU TYR MET ILE CYS PHE TYR SER LEU GLU LEU LYS SEQRES 16 A 392 TRP ASP GLU SER LYS GLY LEU LEU PRO ASN ASN SER GLU SEQRES 17 A 392 GLU SER GLY ILE CYS HIS LYS TYR THR TYR GLY VAL ARG SEQRES 18 A 392 ALA ILE VAL GLN CYS ILE PRO ALA TRP LEU ARG PHE ILE SEQRES 19 A 392 GLN CYS LEU ARG ARG TYR ARG ASP THR LYS ARG ALA PHE SEQRES 20 A 392 PRO HIS LEU VAL ASN ALA GLY LYS TYR SER THR THR PHE SEQRES 21 A 392 PHE MET VAL THR PHE ALA ALA LEU TYR SER THR HIS LYS SEQRES 22 A 392 GLU ARG GLY HIS SER ASP THR MET VAL PHE PHE TYR LEU SEQRES 23 A 392 TRP ILE VAL PHE TYR ILE ILE SER SER CYS TYR THR LEU SEQRES 24 A 392 ILE TRP ASP LEU LYS MET ASP TRP GLY LEU PHE ASP LYS SEQRES 25 A 392 ASN ALA GLY GLU ASN THR PHE LEU ARG GLU GLU ILE VAL SEQRES 26 A 392 TYR PRO GLN LYS ALA TYR TYR TYR CYS ALA ILE ILE GLU SEQRES 27 A 392 ASP VAL ILE LEU ARG PHE ALA TRP THR ILE GLN ILE SER SEQRES 28 A 392 ILE THR SER THR THR LEU LEU PRO HIS SER GLY ASP ILE SEQRES 29 A 392 ILE ALA THR VAL PHE ALA PRO LEU GLU VAL PHE ARG ARG SEQRES 30 A 392 PHE VAL TRP ASN PHE PHE ARG LEU GLU ASN GLU HIS LEU SEQRES 31 A 392 ASN ASN SEQRES 1 B 392 PRO ALA PRO ALA TRP THR THR PHE ARG VAL GLY LEU PHE SEQRES 2 B 392 CYS GLY ILE PHE ILE VAL LEU ASN ILE THR LEU VAL LEU SEQRES 3 B 392 ALA ALA VAL PHE LYS LEU GLU THR ASP ARG SER ILE TRP SEQRES 4 B 392 PRO LEU ILE ARG ILE TYR ARG GLY GLY PHE LEU LEU ILE SEQRES 5 B 392 GLU PHE LEU PHE LEU LEU GLY ILE ASN THR TYR GLY TRP SEQRES 6 B 392 ARG GLN ALA GLY VAL ASN HIS VAL LEU ILE PHE GLU LEU SEQRES 7 B 392 ASN PRO ARG SER ASN LEU SER HIS GLN HIS LEU PHE GLU SEQRES 8 B 392 ILE ALA GLY PHE LEU GLY ILE LEU TRP CYS LEU SER LEU SEQRES 9 B 392 LEU ALA CYS PHE PHE ALA PRO ILE SER VAL ILE PRO THR SEQRES 10 B 392 TYR VAL TYR PRO LEU ALA LEU TYR GLY PHE MET VAL PHE SEQRES 11 B 392 PHE LEU ILE ASN PRO THR LYS THR PHE TYR TYR LYS SER SEQRES 12 B 392 ARG PHE TRP LEU LEU LYS LEU LEU PHE ARG VAL PHE THR SEQRES 13 B 392 ALA PRO PHE HIS LYS VAL GLY PHE ALA ASP PHE TRP LEU SEQRES 14 B 392 ALA ASP GLN LEU ASN SER LEU SER VAL ILE LEU MET ASP SEQRES 15 B 392 LEU GLU TYR MET ILE CYS PHE TYR SER LEU GLU LEU LYS SEQRES 16 B 392 TRP ASP GLU SER LYS GLY LEU LEU PRO ASN ASN SER GLU SEQRES 17 B 392 GLU SER GLY ILE CYS HIS LYS TYR THR TYR GLY VAL ARG SEQRES 18 B 392 ALA ILE VAL GLN CYS ILE PRO ALA TRP LEU ARG PHE ILE SEQRES 19 B 392 GLN CYS LEU ARG ARG TYR ARG ASP THR LYS ARG ALA PHE SEQRES 20 B 392 PRO HIS LEU VAL ASN ALA GLY LYS TYR SER THR THR PHE SEQRES 21 B 392 PHE MET VAL THR PHE ALA ALA LEU TYR SER THR HIS LYS SEQRES 22 B 392 GLU ARG GLY HIS SER ASP THR MET VAL PHE PHE TYR LEU SEQRES 23 B 392 TRP ILE VAL PHE TYR ILE ILE SER SER CYS TYR THR LEU SEQRES 24 B 392 ILE TRP ASP LEU LYS MET ASP TRP GLY LEU PHE ASP LYS SEQRES 25 B 392 ASN ALA GLY GLU ASN THR PHE LEU ARG GLU GLU ILE VAL SEQRES 26 B 392 TYR PRO GLN LYS ALA TYR TYR TYR CYS ALA ILE ILE GLU SEQRES 27 B 392 ASP VAL ILE LEU ARG PHE ALA TRP THR ILE GLN ILE SER SEQRES 28 B 392 ILE THR SER THR THR LEU LEU PRO HIS SER GLY ASP ILE SEQRES 29 B 392 ILE ALA THR VAL PHE ALA PRO LEU GLU VAL PHE ARG ARG SEQRES 30 B 392 PHE VAL TRP ASN PHE PHE ARG LEU GLU ASN GLU HIS LEU SEQRES 31 B 392 ASN ASN HELIX 1 AA1 PRO A 230 LEU A 259 1 30 HELIX 2 AA2 ILE A 265 GLY A 296 1 32 HELIX 3 AA3 SER A 312 ALA A 337 1 26 HELIX 4 AA4 VAL A 346 ILE A 360 1 15 HELIX 5 AA5 LYS A 369 THR A 383 1 15 HELIX 6 AA6 ALA A 384 HIS A 387 5 4 HELIX 7 AA7 GLY A 390 SER A 402 1 13 HELIX 8 AA8 LEU A 403 LEU A 419 1 17 HELIX 9 AA9 GLY A 446 LYS A 471 1 26 HELIX 10 AB1 ARG A 472 ARG A 502 1 31 HELIX 11 AB2 THR A 507 MET A 532 1 26 HELIX 12 AB3 GLN A 555 THR A 583 1 29 HELIX 13 AB4 LEU A 585 ASN A 619 1 35 HELIX 14 AB5 PRO B 230 LEU B 259 1 30 HELIX 15 AB6 ILE B 265 GLY B 296 1 32 HELIX 16 AB7 ASN B 298 GLU B 304 1 7 HELIX 17 AB8 SER B 312 ALA B 337 1 26 HELIX 18 AB9 VAL B 346 ILE B 360 1 15 HELIX 19 AC1 TYR B 367 THR B 383 1 17 HELIX 20 AC2 GLY B 390 LEU B 403 1 14 HELIX 21 AC3 LEU B 403 LEU B 419 1 17 HELIX 22 AC4 ARG B 448 LYS B 471 1 24 HELIX 23 AC5 ALA B 473 GLY B 503 1 31 HELIX 24 AC6 ASP B 506 LEU B 530 1 25 HELIX 25 AC7 LYS B 556 THR B 583 1 28 HELIX 26 AC8 SER B 588 ALA B 597 1 10 HELIX 27 AC9 LEU B 599 ASN B 619 1 21 SSBOND 1 CYS A 415 CYS A 440 1555 1555 2.03 SSBOND 2 CYS B 415 CYS B 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