HEADER TRANSPORT PROTEIN 11-OCT-24 9JXK TITLE CRYO-EM STRUCTURE OF HUMAN XPR1 IN A CLOSED STATE AT THE INTRACELLULAR TITLE 2 GATE AND AN OPEN STATE AT THE EXTRACELLULAR GATE, OBTAINED THROUGH TITLE 3 LOCAL REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 53 MEMBER 1; COMPND 3 CHAIN: 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_TAXID: 9606 KEYWDS PHOSPHATE CHANNEL, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.WANG,Z.BAI,C.WALLIS,H.WANG,Y.HAN,R.JIN,M.LEI,C.GU,H.JESSEN, AUTHOR 2 S.SHEARS,Y.SUN,B.CORRY,Y.ZHANG REVDAT 3 17-SEP-25 9JXK 1 JRNL REVDAT 2 10-SEP-25 9JXK 1 JRNL REVDAT 1 27-AUG-25 9JXK 0 JRNL AUTH X.WANG,Z.BAI,C.WALLIS,H.WANG,Y.HAN,R.JIN,M.LEI,T.YANG,C.GU, JRNL AUTH 2 H.JESSEN,S.SHEARS,Y.SUN,B.CORRY,Y.ZHANG JRNL TITL KIDINS220 AND INSP8 SAFEGUARD THE STEPWISE REGULATION OF JRNL TITL 2 PHOSPHATE EXPORTER XPR1. JRNL REF MOL.CELL V. 85 3209 2025 JRNL REFN ISSN 1097-2765 JRNL PMID 40858110 JRNL DOI 10.1016/J.MOLCEL.2025.08.003 REMARK 2 REMARK 2 RESOLUTION. 3.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GAUTOMATCH, PHENIX, 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) : 3.380 REMARK 3 NUMBER OF PARTICLES : 385663 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 9JXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 15-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052407. 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 : HOMODIMER OF XPR1 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 : 7.40 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOCONTINUUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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) : 4941.00 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 APPLY THE FOLLOWING TO CHAINS: 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 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 B 100 REMARK 465 SER B 101 REMARK 465 THR B 102 REMARK 465 GLY B 103 REMARK 465 VAL B 104 REMARK 465 THR B 105 REMARK 465 THR B 106 REMARK 465 LEU B 107 REMARK 465 ARG B 108 REMARK 465 GLN B 109 REMARK 465 ARG B 110 REMARK 465 ARG B 111 REMARK 465 LYS B 112 REMARK 465 PRO B 113 REMARK 465 VAL B 114 REMARK 465 PHE B 115 REMARK 465 HIS B 116 REMARK 465 LEU B 117 REMARK 465 SER B 118 REMARK 465 HIS B 119 REMARK 465 GLU B 120 REMARK 465 GLU B 121 REMARK 465 ARG B 122 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 OD2 ASP B 529 NH2 ARG B 570 2.00 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 B 38 149.59 -172.81 REMARK 500 GLU B 181 46.07 -91.25 REMARK 500 LYS B 258 -164.00 -79.56 REMARK 500 LEU B 259 131.94 77.86 REMARK 500 THR B 261 -66.72 61.16 REMARK 500 TYR B 367 60.26 62.78 REMARK 500 LEU B 403 51.36 -91.39 REMARK 500 GLU B 435 57.94 30.90 REMARK 500 HIS B 441 79.01 -117.93 REMARK 500 TYR B 443 22.62 -77.97 REMARK 500 THR B 444 -116.69 37.89 REMARK 500 LYS B 471 -18.04 101.59 REMARK 500 ASN B 479 -6.29 76.33 REMARK 500 SER B 505 -169.88 -76.70 REMARK 500 ASN B 540 31.49 -96.59 REMARK 500 THR B 583 -60.21 70.99 REMARK 500 LEU B 585 -0.86 81.73 REMARK 500 ASN B 619 107.73 -18.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 THR B 470 13.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61866 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN XPR1 IN A CLOSED STATE AT THE REMARK 900 INTRACELLULAR GATE AND AN OPEN STATE AT THE EXTRACELLULAR GATE, REMARK 900 OBTAINED THROUGH LOCAL REFINEMENT DBREF 9JXK B 1 625 UNP Q9UBH6 S53A1_HUMAN 1 625 SEQRES 1 B 625 MET LYS PHE ALA GLU HIS LEU SER ALA HIS ILE THR PRO SEQRES 2 B 625 GLU TRP ARG LYS GLN TYR ILE GLN TYR GLU ALA PHE LYS SEQRES 3 B 625 ASP MET LEU TYR SER ALA GLN ASP GLN ALA PRO SER VAL SEQRES 4 B 625 GLU VAL THR ASP GLU ASP THR VAL LYS ARG TYR PHE ALA SEQRES 5 B 625 LYS PHE GLU GLU LYS PHE PHE GLN THR CYS GLU LYS GLU SEQRES 6 B 625 LEU ALA LYS ILE ASN THR PHE TYR SER GLU LYS LEU ALA SEQRES 7 B 625 GLU ALA GLN ARG ARG PHE ALA THR LEU GLN ASN GLU LEU SEQRES 8 B 625 GLN SER SER LEU ASP ALA GLN LYS GLU SER THR GLY VAL SEQRES 9 B 625 THR THR LEU ARG GLN ARG ARG LYS PRO VAL PHE HIS LEU SEQRES 10 B 625 SER HIS GLU GLU ARG VAL GLN HIS ARG ASN ILE LYS ASP SEQRES 11 B 625 LEU LYS LEU ALA PHE SER GLU PHE TYR LEU SER LEU ILE SEQRES 12 B 625 LEU LEU GLN ASN TYR GLN ASN LEU ASN PHE THR GLY PHE SEQRES 13 B 625 ARG LYS ILE LEU LYS LYS HIS ASP LYS ILE LEU GLU THR SEQRES 14 B 625 SER ARG GLY ALA ASP TRP ARG VAL ALA HIS VAL GLU VAL SEQRES 15 B 625 ALA PRO PHE TYR THR CYS LYS LYS ILE ASN GLN LEU ILE SEQRES 16 B 625 SER GLU THR GLU ALA VAL VAL THR ASN GLU LEU GLU ASP SEQRES 17 B 625 GLY ASP ARG GLN LYS ALA MET LYS ARG LEU ARG VAL PRO SEQRES 18 B 625 PRO LEU GLY ALA ALA GLN PRO ALA PRO ALA TRP THR THR SEQRES 19 B 625 PHE ARG VAL GLY LEU PHE CYS GLY ILE PHE ILE VAL LEU SEQRES 20 B 625 ASN ILE THR LEU VAL LEU ALA ALA VAL PHE LYS LEU GLU SEQRES 21 B 625 THR ASP ARG SER ILE TRP PRO LEU ILE ARG ILE TYR ARG SEQRES 22 B 625 GLY GLY PHE LEU LEU ILE GLU PHE LEU PHE LEU LEU GLY SEQRES 23 B 625 ILE ASN THR TYR GLY TRP ARG GLN ALA GLY VAL ASN HIS SEQRES 24 B 625 VAL LEU ILE PHE GLU LEU ASN PRO ARG SER ASN LEU SER SEQRES 25 B 625 HIS GLN HIS LEU PHE GLU ILE ALA GLY PHE LEU GLY ILE SEQRES 26 B 625 LEU TRP CYS LEU SER LEU LEU ALA CYS PHE PHE ALA PRO SEQRES 27 B 625 ILE SER VAL ILE PRO THR TYR VAL TYR PRO LEU ALA LEU SEQRES 28 B 625 TYR GLY PHE MET VAL PHE PHE LEU ILE ASN PRO THR LYS SEQRES 29 B 625 THR PHE TYR TYR LYS SER ARG PHE TRP LEU LEU LYS LEU SEQRES 30 B 625 LEU PHE ARG VAL PHE THR ALA PRO PHE HIS LYS VAL GLY SEQRES 31 B 625 PHE ALA ASP PHE TRP LEU ALA ASP GLN LEU ASN SER LEU SEQRES 32 B 625 SER VAL ILE LEU MET ASP LEU GLU TYR MET ILE CYS PHE SEQRES 33 B 625 TYR SER LEU GLU LEU LYS TRP ASP GLU SER LYS GLY LEU SEQRES 34 B 625 LEU PRO ASN ASN SER GLU GLU SER GLY ILE CYS HIS LYS SEQRES 35 B 625 TYR THR TYR GLY VAL ARG ALA ILE VAL GLN CYS ILE PRO SEQRES 36 B 625 ALA TRP LEU ARG PHE ILE GLN CYS LEU ARG ARG TYR ARG SEQRES 37 B 625 ASP THR LYS ARG ALA PHE PRO HIS LEU VAL ASN ALA GLY SEQRES 38 B 625 LYS TYR SER THR THR PHE PHE MET VAL THR PHE ALA ALA SEQRES 39 B 625 LEU TYR SER THR HIS LYS GLU ARG GLY HIS SER ASP THR SEQRES 40 B 625 MET VAL PHE PHE TYR LEU TRP ILE VAL PHE TYR ILE ILE SEQRES 41 B 625 SER SER CYS TYR THR LEU ILE TRP ASP LEU LYS MET ASP SEQRES 42 B 625 TRP GLY LEU PHE ASP LYS ASN ALA GLY GLU ASN THR PHE SEQRES 43 B 625 LEU ARG GLU GLU ILE VAL TYR PRO GLN LYS ALA TYR TYR SEQRES 44 B 625 TYR CYS ALA ILE ILE GLU ASP VAL ILE LEU ARG PHE ALA SEQRES 45 B 625 TRP THR ILE GLN ILE SER ILE THR SER THR THR LEU LEU SEQRES 46 B 625 PRO HIS SER GLY ASP ILE ILE ALA THR VAL PHE ALA PRO SEQRES 47 B 625 LEU GLU VAL PHE ARG ARG PHE VAL TRP ASN PHE PHE ARG SEQRES 48 B 625 LEU GLU ASN GLU HIS LEU ASN ASN CYS GLY GLU PHE ARG SEQRES 49 B 625 ALA HET PO4 B 701 5 HET PO4 B 702 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 2(O4 P 3-) HELIX 1 AA1 PHE B 3 ILE B 11 1 9 HELIX 2 AA2 THR B 12 TYR B 19 5 8 HELIX 3 AA3 GLN B 21 GLN B 35 1 15 HELIX 4 AA4 ASP B 43 LYS B 99 1 57 HELIX 5 AA5 GLN B 124 GLU B 168 1 45 HELIX 6 AA6 SER B 170 VAL B 180 1 11 HELIX 7 AA7 ALA B 183 CYS B 188 1 6 HELIX 8 AA8 LYS B 189 LEU B 206 1 18 HELIX 9 AA9 ASP B 210 ARG B 219 1 10 HELIX 10 AB1 LEU B 223 GLN B 227 5 5 HELIX 11 AB2 PRO B 230 LYS B 258 1 29 HELIX 12 AB3 ILE B 265 TYR B 272 1 8 HELIX 13 AB4 TYR B 272 GLY B 296 1 25 HELIX 14 AB5 ASN B 298 PHE B 303 1 6 HELIX 15 AB6 SER B 312 ALA B 337 1 26 HELIX 16 AB7 TYR B 345 ILE B 360 1 16 HELIX 17 AB8 TYR B 367 THR B 383 1 17 HELIX 18 AB9 GLY B 390 LEU B 403 1 14 HELIX 19 AC1 LEU B 403 GLU B 420 1 18 HELIX 20 AC2 GLY B 446 LYS B 471 1 26 HELIX 21 AC3 ALA B 480 GLY B 503 1 24 HELIX 22 AC4 ASP B 506 MET B 532 1 27 HELIX 23 AC5 LYS B 556 PHE B 571 1 16 HELIX 24 AC6 ALA B 572 THR B 583 1 12 HELIX 25 AC7 HIS B 587 THR B 594 1 8 HELIX 26 AC8 PHE B 596 ASN B 618 1 23 SSBOND 1 CYS B 415 CYS B 440 1555 1555 2.02 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 CONECT 3238 3438 CONECT 3438 3238 CONECT 5003 5004 5005 5006 5007 CONECT 5004 5003 CONECT 5005 5003 CONECT 5006 5003 CONECT 5007 5003 CONECT 5008 5009 5010 5011 5012 CONECT 5009 5008 CONECT 5010 5008 CONECT 5011 5008 CONECT 5012 5008 MASTER 191 0 2 26 0 0 0 6 5011 1 12 49 END