HEADER MEMBRANE PROTEIN 06-FEB-24 8Y8X TITLE CRYO-EM STRUCTURE OF GLPF WITH P177 DELETION IN POPC NANODISC COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCEROL UPTAKE FACILITATOR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AQUAGLYCEROPORIN,GLYCEROL FACILITATOR; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: 2-9 HIS TAG 14-19 THROMBIN DIGESTION SITE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: GLPF, B3927, JW3898; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS WATER CHANNEL, AQUAPORIN, AQUAGLYCEROPORIN, GLYCEROL, MEMBRANE KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.KOZAI,S.SUZUKI,A.KAMEGAWA,K.NISHIKAWA,H.SUZUKI,Y.FUJIYOSHI REVDAT 3 02-JUL-25 8Y8X 1 REMARK REVDAT 2 02-APR-25 8Y8X 1 JRNL REVDAT 1 19-MAR-25 8Y8X 0 JRNL AUTH D.KOZAI,M.INOUE,S.SUZUKI,A.KAMEGAWA,K.NISHIKAWA,H.SUZUKI, JRNL AUTH 2 T.EKIMOTO,M.IKEGUCHI,Y.FUJIYOSHI JRNL TITL NARROWED PORE CONFORMATIONS OF AQUAGLYCEROPORINS AQP3 AND JRNL TITL 2 GLPF. JRNL REF NAT COMMUN V. 16 2653 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40113770 JRNL DOI 10.1038/S41467-025-57728-3 REMARK 2 REMARK 2 RESOLUTION. 2.26 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) : 2.260 REMARK 3 NUMBER OF PARTICLES : 462907 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 8Y8X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300045109. 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 : TETRAMER OF GLPF WITH P177 REMARK 245 DELETION IN POPC NANODISC 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 : JEOL CRYO ARM 300 REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 6340.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C4). 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 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 146.73000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 146.73000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 146.73000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 146.73000 REMARK 350 BIOMT3 4 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 -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 ALA A -9 REMARK 465 ALA A -8 REMARK 465 ALA A -7 REMARK 465 GLY A -6 REMARK 465 LEU A -5 REMARK 465 VAL A -4 REMARK 465 PRO A -3 REMARK 465 ARG A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 GLN A 3 REMARK 465 THR A 4 REMARK 465 ARG A 256 REMARK 465 HIS A 257 REMARK 465 LEU A 258 REMARK 465 PRO A 259 REMARK 465 CYS A 260 REMARK 465 ASP A 261 REMARK 465 ILE A 262 REMARK 465 CYS A 263 REMARK 465 VAL A 264 REMARK 465 VAL A 265 REMARK 465 GLU A 266 REMARK 465 GLU A 267 REMARK 465 LYS A 268 REMARK 465 GLU A 269 REMARK 465 THR A 270 REMARK 465 THR A 271 REMARK 465 THR A 272 REMARK 465 PRO A 273 REMARK 465 SER A 274 REMARK 465 GLU A 275 REMARK 465 GLN A 276 REMARK 465 LYS A 277 REMARK 465 ALA A 278 REMARK 465 SER A 279 REMARK 465 LEU A 280 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 VAL A 62 -60.79 -97.36 REMARK 500 LEU A 67 19.14 57.40 REMARK 500 PHE A 199 57.52 37.37 REMARK 500 MET A 201 9.05 59.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39063 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF GLPF WITH P177 DELETION IN POPC NANODISC DBREF 8Y8X A 1 280 UNP P0AER0 GLPF_ECOLI 1 281 SEQADV 8Y8X MET A -18 UNP P0AER0 INITIATING METHIONINE SEQADV 8Y8X HIS A -17 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X HIS A -16 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X HIS A -15 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X HIS A -14 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X HIS A -13 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X HIS A -12 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X HIS A -11 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X HIS A -10 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X ALA A -9 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X ALA A -8 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X ALA A -7 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X GLY A -6 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X LEU A -5 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X VAL A -4 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X PRO A -3 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X ARG A -2 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X GLY A -1 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X SER A 0 UNP P0AER0 EXPRESSION TAG SEQADV 8Y8X A UNP P0AER0 PRO 177 DELETION SEQRES 1 A 299 MET HIS HIS HIS HIS HIS HIS HIS HIS ALA ALA ALA GLY SEQRES 2 A 299 LEU VAL PRO ARG GLY SER MET SER GLN THR SER THR LEU SEQRES 3 A 299 LYS GLY GLN CYS ILE ALA GLU PHE LEU GLY THR GLY LEU SEQRES 4 A 299 LEU ILE PHE PHE GLY VAL GLY CYS VAL ALA ALA LEU LYS SEQRES 5 A 299 VAL ALA GLY ALA SER PHE GLY GLN TRP GLU ILE SER VAL SEQRES 6 A 299 ILE TRP GLY LEU GLY VAL ALA MET ALA ILE TYR LEU THR SEQRES 7 A 299 ALA GLY VAL SER GLY ALA HIS LEU ASN PRO ALA VAL THR SEQRES 8 A 299 ILE ALA LEU TRP LEU PHE ALA CYS PHE ASP LYS ARG LYS SEQRES 9 A 299 VAL ILE PRO PHE ILE VAL SER GLN VAL ALA GLY ALA PHE SEQRES 10 A 299 CYS ALA ALA ALA LEU VAL TYR GLY LEU TYR TYR ASN LEU SEQRES 11 A 299 PHE PHE ASP PHE GLU GLN THR HIS HIS ILE VAL ARG GLY SEQRES 12 A 299 SER VAL GLU SER VAL ASP LEU ALA GLY THR PHE SER THR SEQRES 13 A 299 TYR PRO ASN PRO HIS ILE ASN PHE VAL GLN ALA PHE ALA SEQRES 14 A 299 VAL GLU MET VAL ILE THR ALA ILE LEU MET GLY LEU ILE SEQRES 15 A 299 LEU ALA LEU THR ASP ASP GLY ASN GLY VAL PRO ARG GLY SEQRES 16 A 299 LEU ALA PRO LEU LEU ILE GLY LEU LEU ILE ALA VAL ILE SEQRES 17 A 299 GLY ALA SER MET GLY PRO LEU THR GLY PHE ALA MET ASN SEQRES 18 A 299 PRO ALA ARG ASP PHE GLY PRO LYS VAL PHE ALA TRP LEU SEQRES 19 A 299 ALA GLY TRP GLY ASN VAL ALA PHE THR GLY GLY ARG ASP SEQRES 20 A 299 ILE PRO TYR PHE LEU VAL PRO LEU PHE GLY PRO ILE VAL SEQRES 21 A 299 GLY ALA ILE VAL GLY ALA PHE ALA TYR ARG LYS LEU ILE SEQRES 22 A 299 GLY ARG HIS LEU PRO CYS ASP ILE CYS VAL VAL GLU GLU SEQRES 23 A 299 LYS GLU THR THR THR PRO SER GLU GLN LYS ALA SER LEU HELIX 1 AA1 THR A 6 ALA A 35 1 30 HELIX 2 AA2 GLY A 40 GLY A 64 1 25 HELIX 3 AA3 ASN A 68 ALA A 79 1 12 HELIX 4 AA4 ASP A 82 ARG A 84 5 3 HELIX 5 AA5 LYS A 85 TYR A 108 1 24 HELIX 6 AA6 TYR A 108 HIS A 120 1 13 HELIX 7 AA7 SER A 125 GLU A 127 5 3 HELIX 8 AA8 SER A 128 GLY A 133 1 6 HELIX 9 AA9 ASN A 144 THR A 167 1 24 HELIX 10 AB1 LEU A 177 GLY A 198 1 22 HELIX 11 AB2 ASN A 202 GLY A 217 1 16 HELIX 12 AB3 ASN A 220 GLY A 225 1 6 HELIX 13 AB4 PHE A 232 ILE A 254 1 23 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 MTRIX1 2 0.000000 -1.000000 0.000000 146.73000 MTRIX2 2 1.000000 0.000000 0.000000 0.00000 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 -1.000000 0.000000 0.000000 146.73000 MTRIX2 3 0.000000 -1.000000 0.000000 146.73000 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 MTRIX1 4 0.000000 1.000000 0.000000 0.00000 MTRIX2 4 -1.000000 0.000000 0.000000 146.73000 MTRIX3 4 0.000000 0.000000 1.000000 0.00000 TER 1872 GLY A 255 MASTER 184 0 0 13 0 0 0 15 1871 1 0 23 END