HEADER TRANSPORT PROTEIN 06-FEB-26 23IC TITLE CRYO-EM STRUCTURE OF ORYZA SATIVA VACUOLAR PHOSPHATE EFFLUX TITLE 2 TRANSPORTER 2 (OSVPE2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: OS08G0156600 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA JAPONICA GROUP; SOURCE 3 ORGANISM_COMMON: JAPANESE RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: OS08G0156600; SOURCE 6 EXPRESSION_SYSTEM: HOMO; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9605 KEYWDS VACUOLAR PHOSPHATE EFFLUX TRANSPORTER, MONOMER, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Z.LIU,S.CAO,J.ZOU REVDAT 1 12-AUG-26 23IC 0 JRNL AUTH Z.LIU,S.CAO,J.ZOU JRNL TITL DECODING PLANT VACUOLAR PHOSPHATE EFFLUX: STRUCTURAL AND JRNL TITL 2 DYNAMIC INSIGHTS FROM RICE VPE2 JRNL REF PROC.NATL.ACAD.SCI.USA 2026 JRNL REFN ESSN 1091-6490 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 155111 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 23IC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 13-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1300069969. 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 : O. SATIVA VACUOLAR PHOSPHATE REMARK 245 EFFLUX TRANSPORTER 2 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 : 8.00 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) : 1800.00 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: 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 GLU A 6 REMARK 465 MET A 7 REMARK 465 THR A 8 REMARK 465 SER A 9 REMARK 465 ARG A 10 REMARK 465 LYS A 11 REMARK 465 PRO A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 14 REMARK 465 ILE A 15 REMARK 465 ARG A 16 REMARK 465 LEU A 17 REMARK 465 PHE A 18 REMARK 465 GLY A 19 REMARK 465 GLY A 20 REMARK 465 ILE A 21 REMARK 465 THR A 22 REMARK 465 VAL A 23 REMARK 465 LEU A 24 REMARK 465 ARG A 25 REMARK 465 THR A 26 REMARK 465 ASN A 74 REMARK 465 GLY A 79 REMARK 465 GLU A 242 REMARK 465 ILE A 243 REMARK 465 ASP A 244 REMARK 465 ILE A 245 REMARK 465 ASP A 246 REMARK 465 ILE A 250 REMARK 465 SER A 251 REMARK 465 SER A 252 REMARK 465 VAL A 253 REMARK 465 LYS A 254 REMARK 465 ASP A 255 REMARK 465 THR A 256 REMARK 465 THR A 257 REMARK 465 LYS A 258 REMARK 465 GLU A 259 REMARK 465 PRO A 260 REMARK 465 LEU A 261 REMARK 465 LEU A 262 REMARK 465 GLU A 263 REMARK 465 PRO A 264 REMARK 465 GLY A 265 REMARK 465 GLN A 266 REMARK 465 GLU A 267 REMARK 465 VAL A 268 REMARK 465 LYS A 269 REMARK 465 LYS A 479 REMARK 465 ALA A 480 REMARK 465 THR A 481 REMARK 465 SER A 482 REMARK 465 ASN A 483 REMARK 465 ALA A 484 REMARK 465 SER A 485 REMARK 465 LYS A 486 REMARK 465 ASP A 487 REMARK 465 VAL A 488 REMARK 465 ALA A 489 REMARK 465 ASP A 490 REMARK 465 ALA A 491 REMARK 465 GLN A 492 REMARK 465 GLY A 493 REMARK 465 THR A 494 REMARK 465 TYR A 495 REMARK 465 SER A 496 REMARK 465 ASP A 497 REMARK 465 GLU A 498 REMARK 465 VAL A 499 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 THR A 72 58.10 36.03 REMARK 500 ASN A 144 56.02 37.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-68988 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ORYZA SATIVA VACUOLAR PHOSPHATE EFFLUX REMARK 900 TRANSPORTER 2 (OSVPE2) DBREF1 23IC A 1 499 UNP A0A0P0XCF9_ORYSJ DBREF2 23IC A A0A0P0XCF9 1 499 SEQRES 1 A 499 MET ALA HIS SER HIS GLU MET THR SER ARG LYS PRO PRO SEQRES 2 A 499 GLY ILE ARG LEU PHE GLY GLY ILE THR VAL LEU ARG THR SEQRES 3 A 499 TYR GLN THR LEU VAL LEU VAL LEU THR PHE VAL ALA TYR SEQRES 4 A 499 THR CYS PHE HIS MET THR ARG LYS ILE PRO SER ILE VAL SEQRES 5 A 499 LYS SER VAL LEU ASP PRO GLN THR LYS LEU GLY SER SER SEQRES 6 A 499 PRO TRP GLY ARG LEU HIS THR LYS ASN THR LEU ASN ILE SEQRES 7 A 499 GLY TRP LEU PRO PHE ASN THR ILE ASP GLY SER ALA LEU SEQRES 8 A 499 LEU GLY GLU ILE ASP VAL ALA PHE LEU ALA VAL TYR SER SEQRES 9 A 499 VAL GLY MET PHE PHE ALA GLY HIS LEU GLY ASP ARG MET SEQRES 10 A 499 ASP LEU ARG ILE PHE LEU THR ILE GLY MET PHE GLY THR SEQRES 11 A 499 ALA VAL PHE THR ALA LEU PHE GLY ALA GLY TYR TRP LEU SEQRES 12 A 499 ASN ILE HIS ASN PHE TYR TYR PHE LEU VAL ILE GLN MET SEQRES 13 A 499 ILE ALA GLY LEU PHE GLN ALA ILE GLY TRP PRO SER VAL SEQRES 14 A 499 VAL ALA ILE VAL GLY ASN TRP PHE GLY LYS SER LYS ARG SEQRES 15 A 499 GLY LEU ILE MET GLY ILE TRP ASN ALA HIS THR SER VAL SEQRES 16 A 499 GLY ASN ILE SER GLY SER LEU LEU ALA ALA PHE LEU LEU SEQRES 17 A 499 LYS PHE GLY TRP GLY TRP SER PHE ALA ILE PRO SER LEU SEQRES 18 A 499 ILE MET VAL ALA VAL GLY LEU LEU VAL PHE VAL PHE LEU SEQRES 19 A 499 PRO VAL SER PRO GLU VAL MET GLU ILE ASP ILE ASP ASP SEQRES 20 A 499 GLY GLU ILE SER SER VAL LYS ASP THR THR LYS GLU PRO SEQRES 21 A 499 LEU LEU GLU PRO GLY GLN GLU VAL LYS HIS ASN ALA VAL SEQRES 22 A 499 GLY PHE LEU GLU ALA TRP LYS ILE PRO GLY VAL ALA PRO SEQRES 23 A 499 PHE ALA LEU CYS LEU PHE PHE SER LYS LEU VAL ALA TYR SEQRES 24 A 499 THR PHE LEU TYR TRP LEU PRO PHE TYR ILE SER HIS THR SEQRES 25 A 499 PRO ILE GLY GLY GLU TYR LEU SER ASP ALA LEU ALA GLY SEQRES 26 A 499 SER LEU SER THR ILE PHE ASP VAL GLY GLY VAL LEU GLY SEQRES 27 A 499 GLY VAL LEU ALA GLY HIS ILE SER ASP ARG LEU ASN ALA SEQRES 28 A 499 ARG ALA VAL THR ALA ALA SER PHE MET TYR CYS ALA ILE SEQRES 29 A 499 PRO ALA LEU PHE LEU TYR ARG THR TYR GLY SER MET SER SEQRES 30 A 499 ILE MET TRP ASN ILE CYS LEU MET PHE ILE THR GLY MET SEQRES 31 A 499 PHE VAL ASN GLY PRO TYR ALA LEU ILE THR THR ALA VAL SEQRES 32 A 499 SER ALA ASP LEU GLY THR HIS SER SER LEU ASN GLY ASN SEQRES 33 A 499 SER ARG ALA LEU ALA THR VAL THR ALA ILE ILE ASP GLY SEQRES 34 A 499 THR GLY SER VAL GLY ALA ALA ILE GLY PRO LEU LEU THR SEQRES 35 A 499 GLY TYR ILE SER SER SER SER TRP SER ALA VAL PHE THR SEQRES 36 A 499 MET LEU MET ALA ALA ALA LEU LEU ALA GLY LEU LEU LEU SEQRES 37 A 499 THR GLN LEU VAL CYS SER GLU LEU LYS GLY LYS ALA THR SEQRES 38 A 499 SER ASN ALA SER LYS ASP VAL ALA ASP ALA GLN GLY THR SEQRES 39 A 499 TYR SER ASP GLU VAL HELIX 1 AA1 TYR A 27 LYS A 47 1 21 HELIX 2 AA2 LYS A 47 ASP A 57 1 11 HELIX 3 AA3 LEU A 81 THR A 85 1 5 HELIX 4 AA4 ASP A 87 MET A 117 1 31 HELIX 5 AA5 ASP A 118 ALA A 139 1 22 HELIX 6 AA6 ASN A 147 ALA A 163 1 17 HELIX 7 AA7 ILE A 164 TRP A 176 1 13 HELIX 8 AA8 LYS A 181 ASN A 190 1 10 HELIX 9 AA9 ALA A 191 LYS A 209 1 19 HELIX 10 AB1 GLY A 213 LEU A 234 1 22 HELIX 11 AB2 GLY A 283 HIS A 311 1 29 HELIX 12 AB3 PRO A 313 GLU A 317 5 5 HELIX 13 AB4 SER A 320 ASN A 350 1 31 HELIX 14 AB5 ALA A 351 SER A 375 1 25 HELIX 15 AB6 SER A 377 THR A 409 1 33 HELIX 16 AB7 HIS A 410 ASN A 414 5 5 HELIX 17 AB8 ALA A 419 GLY A 443 1 25 HELIX 18 AB9 ALA A 452 LEU A 467 1 16 HELIX 19 AC1 LEU A 468 GLY A 478 1 11 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 MASTER 200 0 0 19 0 0 0 6 3229 1 0 39 END