HEADER TRANSPORT PROTEIN 11-OCT-24 9JXP TITLE CRYO-EM STRUCTURE OF HUMAN XPR1-R570L 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; COMPND 8 MUTATION: 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;PHOSPHATE EXPORTER;PFBC, 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 9JXP 1 JRNL REVDAT 2 10-SEP-25 9JXP 1 JRNL REVDAT 1 27-AUG-25 9JXP 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. 3.53 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) : 3.530 REMARK 3 NUMBER OF PARTICLES : 229444 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 9JXP 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_1300052424. 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 MUTANT REMARK 245 (R570L) 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: 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 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 LYS A 427 REMARK 465 GLY A 428 REMARK 465 LEU A 429 REMARK 465 LEU A 430 REMARK 465 PRO A 431 REMARK 465 ASN A 432 REMARK 465 ASN A 433 REMARK 465 SER A 434 REMARK 465 GLU A 435 REMARK 465 GLU A 436 REMARK 465 SER A 437 REMARK 465 LYS B 427 REMARK 465 GLY B 428 REMARK 465 LEU B 429 REMARK 465 LEU B 430 REMARK 465 PRO B 431 REMARK 465 ASN B 432 REMARK 465 ASN B 433 REMARK 465 SER B 434 REMARK 465 GLU B 435 REMARK 465 GLU B 436 REMARK 465 SER B 437 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 OE2 GLU B 318 OH TYR B 367 2.09 REMARK 500 OE2 GLU A 318 OH TYR A 367 2.09 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 PHE A 257 -60.35 -92.59 REMARK 500 PRO A 267 4.79 -64.24 REMARK 500 GLU A 304 17.18 59.78 REMARK 500 THR A 363 -168.08 -79.88 REMARK 500 THR A 383 40.04 -105.39 REMARK 500 PRO A 385 43.94 -78.63 REMARK 500 PHE A 386 12.16 -142.42 REMARK 500 LEU A 403 51.51 -93.51 REMARK 500 TRP A 423 -64.33 -95.25 REMARK 500 ASP A 424 -5.10 -142.98 REMARK 500 HIS A 441 -7.36 75.66 REMARK 500 PRO A 475 39.86 -91.06 REMARK 500 HIS A 476 -51.03 -128.17 REMARK 500 PHE B 257 -60.40 -92.58 REMARK 500 PRO B 267 4.76 -64.22 REMARK 500 GLU B 304 17.19 59.82 REMARK 500 THR B 363 -168.08 -79.91 REMARK 500 PRO B 385 43.98 -78.67 REMARK 500 PHE B 386 12.05 -142.42 REMARK 500 LEU B 403 51.54 -93.60 REMARK 500 TRP B 423 -64.33 -95.22 REMARK 500 ASP B 424 -5.15 -142.94 REMARK 500 HIS B 441 -7.35 75.65 REMARK 500 PRO B 475 39.78 -91.02 REMARK 500 HIS B 476 -51.02 -128.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61871 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN XPR1-R570L DBREF 9JXP A 230 625 UNP Q9UBH6 S53A1_HUMAN 230 625 DBREF 9JXP B 230 625 UNP Q9UBH6 S53A1_HUMAN 230 625 SEQADV 9JXP LEU A 570 UNP Q9UBH6 ARG 570 ENGINEERED MUTATION SEQADV 9JXP LEU B 570 UNP Q9UBH6 ARG 570 ENGINEERED MUTATION SEQRES 1 A 396 PRO ALA TRP THR THR PHE ARG VAL GLY LEU PHE CYS GLY SEQRES 2 A 396 ILE PHE ILE VAL LEU ASN ILE THR LEU VAL LEU ALA ALA SEQRES 3 A 396 VAL PHE LYS LEU GLU THR ASP ARG SER ILE TRP PRO LEU SEQRES 4 A 396 ILE ARG ILE TYR ARG GLY GLY PHE LEU LEU ILE GLU PHE SEQRES 5 A 396 LEU PHE LEU LEU GLY ILE ASN THR TYR GLY TRP ARG GLN SEQRES 6 A 396 ALA GLY VAL ASN HIS VAL LEU ILE PHE GLU LEU ASN PRO SEQRES 7 A 396 ARG SER ASN LEU SER HIS GLN HIS LEU PHE GLU ILE ALA SEQRES 8 A 396 GLY PHE LEU GLY ILE LEU TRP CYS LEU SER LEU LEU ALA SEQRES 9 A 396 CYS PHE PHE ALA PRO ILE SER VAL ILE PRO THR TYR VAL SEQRES 10 A 396 TYR PRO LEU ALA LEU TYR GLY PHE MET VAL PHE PHE LEU SEQRES 11 A 396 ILE ASN PRO THR LYS THR PHE TYR TYR LYS SER ARG PHE SEQRES 12 A 396 TRP LEU LEU LYS LEU LEU PHE ARG VAL PHE THR ALA PRO SEQRES 13 A 396 PHE HIS LYS VAL GLY PHE ALA ASP PHE TRP LEU ALA ASP SEQRES 14 A 396 GLN LEU ASN SER LEU SER VAL ILE LEU MET ASP LEU GLU SEQRES 15 A 396 TYR MET ILE CYS PHE TYR SER LEU GLU LEU LYS TRP ASP SEQRES 16 A 396 GLU SER LYS GLY LEU LEU PRO ASN ASN SER GLU GLU SER SEQRES 17 A 396 GLY ILE CYS HIS LYS TYR THR TYR GLY VAL ARG ALA ILE SEQRES 18 A 396 VAL GLN CYS ILE PRO ALA TRP LEU ARG PHE ILE GLN CYS SEQRES 19 A 396 LEU ARG ARG TYR ARG ASP THR LYS ARG ALA PHE PRO HIS SEQRES 20 A 396 LEU VAL ASN ALA GLY LYS TYR SER THR THR PHE PHE MET SEQRES 21 A 396 VAL THR PHE ALA ALA LEU TYR SER THR HIS LYS GLU ARG SEQRES 22 A 396 GLY HIS SER ASP THR MET VAL PHE PHE TYR LEU TRP ILE SEQRES 23 A 396 VAL PHE TYR ILE ILE SER SER CYS TYR THR LEU ILE TRP SEQRES 24 A 396 ASP LEU LYS MET ASP TRP GLY LEU PHE ASP LYS ASN ALA SEQRES 25 A 396 GLY GLU ASN THR PHE LEU ARG GLU GLU ILE VAL TYR PRO SEQRES 26 A 396 GLN LYS ALA TYR TYR TYR CYS ALA ILE ILE GLU ASP VAL SEQRES 27 A 396 ILE LEU LEU PHE ALA TRP THR ILE GLN ILE SER ILE THR SEQRES 28 A 396 SER THR THR LEU LEU PRO HIS SER GLY ASP ILE ILE ALA SEQRES 29 A 396 THR VAL PHE ALA PRO LEU GLU VAL PHE ARG ARG PHE VAL SEQRES 30 A 396 TRP ASN PHE PHE ARG LEU GLU ASN GLU HIS LEU ASN ASN SEQRES 31 A 396 CYS GLY GLU PHE ARG ALA SEQRES 1 B 396 PRO ALA TRP THR THR PHE ARG VAL GLY LEU PHE CYS GLY SEQRES 2 B 396 ILE PHE ILE VAL LEU ASN ILE THR LEU VAL LEU ALA ALA SEQRES 3 B 396 VAL PHE LYS LEU GLU THR ASP ARG SER ILE TRP PRO LEU SEQRES 4 B 396 ILE ARG ILE TYR ARG GLY GLY PHE LEU LEU ILE GLU PHE SEQRES 5 B 396 LEU PHE LEU LEU GLY ILE ASN THR TYR GLY TRP ARG GLN SEQRES 6 B 396 ALA GLY VAL ASN HIS VAL LEU ILE PHE GLU LEU ASN PRO SEQRES 7 B 396 ARG SER ASN LEU SER HIS GLN HIS LEU PHE GLU ILE ALA SEQRES 8 B 396 GLY PHE LEU GLY ILE LEU TRP CYS LEU SER LEU LEU ALA SEQRES 9 B 396 CYS PHE PHE ALA PRO ILE SER VAL ILE PRO THR TYR VAL SEQRES 10 B 396 TYR PRO LEU ALA LEU TYR GLY PHE MET VAL PHE PHE LEU SEQRES 11 B 396 ILE ASN PRO THR LYS THR PHE TYR TYR LYS SER ARG PHE SEQRES 12 B 396 TRP LEU LEU LYS LEU LEU PHE ARG VAL PHE THR ALA PRO SEQRES 13 B 396 PHE HIS LYS VAL GLY PHE ALA ASP PHE TRP LEU ALA ASP SEQRES 14 B 396 GLN LEU ASN SER LEU SER VAL ILE LEU MET ASP LEU GLU SEQRES 15 B 396 TYR MET ILE CYS PHE TYR SER LEU GLU LEU LYS TRP ASP SEQRES 16 B 396 GLU SER LYS GLY LEU LEU PRO ASN ASN SER GLU GLU SER SEQRES 17 B 396 GLY ILE CYS HIS LYS TYR THR TYR GLY VAL ARG ALA ILE SEQRES 18 B 396 VAL GLN CYS ILE PRO ALA TRP LEU ARG PHE ILE GLN CYS SEQRES 19 B 396 LEU ARG ARG TYR ARG ASP THR LYS ARG ALA PHE PRO HIS SEQRES 20 B 396 LEU VAL ASN ALA GLY LYS TYR SER THR THR PHE PHE MET SEQRES 21 B 396 VAL THR PHE ALA ALA LEU TYR SER THR HIS LYS GLU ARG SEQRES 22 B 396 GLY HIS SER ASP THR MET VAL PHE PHE TYR LEU TRP ILE SEQRES 23 B 396 VAL PHE TYR ILE ILE SER SER CYS TYR THR LEU ILE TRP SEQRES 24 B 396 ASP LEU LYS MET ASP TRP GLY LEU PHE ASP LYS ASN ALA SEQRES 25 B 396 GLY GLU ASN THR PHE LEU ARG GLU GLU ILE VAL TYR PRO SEQRES 26 B 396 GLN LYS ALA TYR TYR TYR CYS ALA ILE ILE GLU ASP VAL SEQRES 27 B 396 ILE LEU LEU PHE ALA TRP THR ILE GLN ILE SER ILE THR SEQRES 28 B 396 SER THR THR LEU LEU PRO HIS SER GLY ASP ILE ILE ALA SEQRES 29 B 396 THR VAL PHE ALA PRO LEU GLU VAL PHE ARG ARG PHE VAL SEQRES 30 B 396 TRP ASN PHE PHE ARG LEU GLU ASN GLU HIS LEU ASN ASN SEQRES 31 B 396 CYS GLY GLU PHE ARG ALA HELIX 1 AA1 ALA A 231 LYS A 258 1 28 HELIX 2 AA2 ILE A 265 GLY A 296 1 32 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 LEU A 403 LEU A 419 1 17 HELIX 10 AB1 GLY A 446 THR A 470 1 25 HELIX 11 AB2 ALA A 473 GLY A 503 1 31 HELIX 12 AB3 ASP A 506 MET A 532 1 27 HELIX 13 AB4 LYS A 556 LEU A 570 1 15 HELIX 14 AB5 ALA A 572 SER A 581 1 10 HELIX 15 AB6 SER A 588 ASN A 619 1 32 HELIX 16 AB7 ALA B 231 LYS B 258 1 28 HELIX 17 AB8 ILE B 265 GLY B 296 1 32 HELIX 18 AB9 ASN B 298 PHE B 303 1 6 HELIX 19 AC1 SER B 312 PHE B 336 1 25 HELIX 20 AC2 TYR B 345 ASN B 361 1 17 HELIX 21 AC3 TYR B 367 THR B 383 1 17 HELIX 22 AC4 ALA B 384 HIS B 387 5 4 HELIX 23 AC5 GLY B 390 LEU B 403 1 14 HELIX 24 AC6 LEU B 403 LEU B 419 1 17 HELIX 25 AC7 GLY B 446 THR B 470 1 25 HELIX 26 AC8 ALA B 473 GLY B 503 1 31 HELIX 27 AC9 ASP B 506 MET B 532 1 27 HELIX 28 AD1 LYS B 556 LEU B 570 1 15 HELIX 29 AD2 ALA B 572 SER B 581 1 10 HELIX 30 AD3 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 2.03 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 TER 3216 ALA A 625 TER 6432 ALA B 625 CONECT 1537 1655 CONECT 1655 1537 CONECT 4753 4871 CONECT 4871 4753 MASTER 183 0 0 30 0 0 0 6 6430 2 4 62 END