HEADER MEMBRANE PROTEIN 06-FEB-24 8Y8R TITLE CRYO-EM STRUCTURE OF AQP3 Y212T IN DDM MICELLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AQUAPORIN-3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AQP-3,31.4 KDA WATER CHANNEL PROTEIN,AQUAGLYCEROPORIN-3; 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: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: AQP3; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 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 8Y8R 1 REMARK REVDAT 2 02-APR-25 8Y8R 1 JRNL REVDAT 1 19-MAR-25 8Y8R 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. 3.39 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) : 3.390 REMARK 3 NUMBER OF PARTICLES : 54899 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 8Y8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300045006. 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 AQP3 Y212T IN DDM REMARK 245 MICELLE 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 194.97000 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 194.96999 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 194.97000 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 194.97000 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 GLY A 2 REMARK 465 ARG A 3 REMARK 465 GLN A 271 REMARK 465 PRO A 272 REMARK 465 PRO A 273 REMARK 465 PRO A 274 REMARK 465 SER A 275 REMARK 465 THR A 276 REMARK 465 GLU A 277 REMARK 465 ALA A 278 REMARK 465 GLU A 279 REMARK 465 ASN A 280 REMARK 465 VAL A 281 REMARK 465 LYS A 282 REMARK 465 LEU A 283 REMARK 465 ALA A 284 REMARK 465 HIS A 285 REMARK 465 MET A 286 REMARK 465 LYS A 287 REMARK 465 HIS A 288 REMARK 465 LYS A 289 REMARK 465 GLU A 290 REMARK 465 GLN A 291 REMARK 465 ILE A 292 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 HIS A 53 31.08 -96.49 REMARK 500 LEU A 82 11.34 58.76 REMARK 500 ALA A 94 16.86 58.07 REMARK 500 ALA A 213 -64.29 -97.78 REMARK 500 VAL A 214 28.90 33.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39056 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF AQP3 Y212T IN DDM MICELLE DBREF 8Y8R A 1 292 UNP P47862 AQP3_RAT 1 292 SEQADV 8Y8R MET A -18 UNP P47862 INITIATING METHIONINE SEQADV 8Y8R HIS A -17 UNP P47862 EXPRESSION TAG SEQADV 8Y8R HIS A -16 UNP P47862 EXPRESSION TAG SEQADV 8Y8R HIS A -15 UNP P47862 EXPRESSION TAG SEQADV 8Y8R HIS A -14 UNP P47862 EXPRESSION TAG SEQADV 8Y8R HIS A -13 UNP P47862 EXPRESSION TAG SEQADV 8Y8R HIS A -12 UNP P47862 EXPRESSION TAG SEQADV 8Y8R HIS A -11 UNP P47862 EXPRESSION TAG SEQADV 8Y8R HIS A -10 UNP P47862 EXPRESSION TAG SEQADV 8Y8R ALA A -9 UNP P47862 EXPRESSION TAG SEQADV 8Y8R ALA A -8 UNP P47862 EXPRESSION TAG SEQADV 8Y8R ALA A -7 UNP P47862 EXPRESSION TAG SEQADV 8Y8R GLY A -6 UNP P47862 EXPRESSION TAG SEQADV 8Y8R LEU A -5 UNP P47862 EXPRESSION TAG SEQADV 8Y8R VAL A -4 UNP P47862 EXPRESSION TAG SEQADV 8Y8R PRO A -3 UNP P47862 EXPRESSION TAG SEQADV 8Y8R ARG A -2 UNP P47862 EXPRESSION TAG SEQADV 8Y8R GLY A -1 UNP P47862 EXPRESSION TAG SEQADV 8Y8R SER A 0 UNP P47862 EXPRESSION TAG SEQADV 8Y8R THR A 212 UNP P47862 TYR 212 ENGINEERED MUTATION SEQRES 1 A 311 MET HIS HIS HIS HIS HIS HIS HIS HIS ALA ALA ALA GLY SEQRES 2 A 311 LEU VAL PRO ARG GLY SER MET GLY ARG GLN LYS GLU LEU SEQRES 3 A 311 MET ASN ARG CYS GLY GLU MET LEU HIS ILE ARG TYR ARG SEQRES 4 A 311 LEU LEU ARG GLN ALA LEU ALA GLU CYS LEU GLY THR LEU SEQRES 5 A 311 ILE LEU VAL MET PHE GLY CYS GLY SER VAL ALA GLN VAL SEQRES 6 A 311 VAL LEU SER ARG GLY THR HIS GLY GLY PHE LEU THR ILE SEQRES 7 A 311 ASN LEU ALA PHE GLY PHE ALA VAL THR LEU ALA ILE LEU SEQRES 8 A 311 VAL ALA GLY GLN VAL SER GLY ALA HIS LEU ASN PRO ALA SEQRES 9 A 311 VAL THR PHE ALA MET CYS PHE LEU ALA ARG GLU PRO TRP SEQRES 10 A 311 ILE LYS LEU PRO ILE TYR THR LEU ALA GLN THR LEU GLY SEQRES 11 A 311 ALA PHE LEU GLY ALA GLY ILE VAL PHE GLY LEU TYR TYR SEQRES 12 A 311 ASP ALA ILE TRP ALA PHE ALA GLY ASN GLU LEU VAL VAL SEQRES 13 A 311 SER GLY PRO ASN GLY THR ALA GLY ILE PHE ALA THR TYR SEQRES 14 A 311 PRO SER GLY HIS LEU ASP MET VAL ASN GLY PHE PHE ASP SEQRES 15 A 311 GLN PHE ILE GLY THR ALA ALA LEU ILE VAL CYS VAL LEU SEQRES 16 A 311 ALA ILE VAL ASP PRO TYR ASN ASN PRO VAL PRO ARG GLY SEQRES 17 A 311 LEU GLU ALA PHE THR VAL GLY LEU VAL VAL LEU VAL ILE SEQRES 18 A 311 GLY THR SER MET GLY PHE ASN SER GLY THR ALA VAL ASN SEQRES 19 A 311 PRO ALA ARG ASP PHE GLY PRO ARG LEU PHE THR ALA LEU SEQRES 20 A 311 ALA GLY TRP GLY SER GLU VAL PHE THR THR GLY GLN ASN SEQRES 21 A 311 TRP TRP TRP VAL PRO ILE VAL SER PRO LEU LEU GLY SER SEQRES 22 A 311 ILE GLY GLY VAL PHE VAL TYR GLN LEU MET ILE GLY CYS SEQRES 23 A 311 HIS LEU GLU GLN PRO PRO PRO SER THR GLU ALA GLU ASN SEQRES 24 A 311 VAL LYS LEU ALA HIS MET LYS HIS LYS GLU GLN ILE HET LMT A 301 35 HETNAM LMT DODECYL-BETA-D-MALTOSIDE FORMUL 2 LMT C24 H46 O11 HELIX 1 AA1 GLN A 4 LEU A 15 1 12 HELIX 2 AA2 TYR A 19 SER A 49 1 31 HELIX 3 AA3 GLY A 55 GLY A 75 1 21 HELIX 4 AA4 ASN A 83 LEU A 93 1 11 HELIX 5 AA5 PRO A 97 ILE A 99 5 3 HELIX 6 AA6 LYS A 100 TYR A 123 1 24 HELIX 7 AA7 TYR A 123 ALA A 131 1 9 HELIX 8 AA8 THR A 143 PHE A 147 5 5 HELIX 9 AA9 ASP A 156 ASP A 180 1 25 HELIX 10 AB1 LEU A 190 GLY A 207 1 18 HELIX 11 AB2 ASN A 215 ALA A 229 1 15 HELIX 12 AB3 SER A 233 THR A 238 1 6 HELIX 13 AB4 ASN A 241 TRP A 243 5 3 HELIX 14 AB5 TRP A 244 LEU A 263 1 20 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 194.97000 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 194.97000 MTRIX2 3 0.000000 -1.000000 0.000000 194.97000 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 194.97000 MTRIX3 4 0.000000 0.000000 1.000000 0.00000 TER 2010 GLU A 270 HETATM 2011 C1B LMT A 301 82.387 83.704 106.656 1.00 85.56 C HETATM 2012 C2B LMT A 301 82.419 82.685 107.797 1.00 84.48 C HETATM 2013 C3B LMT A 301 81.262 81.706 107.682 1.00 83.73 C HETATM 2014 C4B LMT A 301 79.958 82.492 107.633 1.00 87.45 C HETATM 2015 C5B LMT A 301 80.001 83.458 106.445 1.00 91.51 C HETATM 2016 C6B LMT A 301 78.780 84.341 106.321 1.00 84.99 C HETATM 2017 O1B LMT A 301 82.792 83.070 105.477 1.00 79.84 O HETATM 2018 O2B LMT A 301 83.670 82.037 107.761 1.00 84.33 O HETATM 2019 O3B LMT A 301 81.327 80.845 108.791 1.00 79.78 O HETATM 2020 O4' LMT A 301 78.905 81.565 107.502 1.00 82.80 O HETATM 2021 O5B LMT A 301 81.135 84.312 106.546 1.00 92.13 O HETATM 2022 O6B LMT A 301 78.967 85.275 105.286 1.00 71.96 O HETATM 2023 C1' LMT A 301 84.212 84.215 101.752 1.00 63.29 C HETATM 2024 C2' LMT A 301 84.526 85.173 102.893 1.00 66.14 C HETATM 2025 C3' LMT A 301 84.335 84.445 104.216 1.00 72.41 C HETATM 2026 C4' LMT A 301 82.933 83.839 104.297 1.00 74.22 C HETATM 2027 C5' LMT A 301 82.726 82.927 103.085 1.00 69.07 C HETATM 2028 C6' LMT A 301 81.332 82.343 103.026 1.00 66.53 C HETATM 2029 O1' LMT A 301 84.230 84.912 100.572 1.00 59.82 O HETATM 2030 O2' LMT A 301 85.844 85.630 102.744 1.00 66.73 O HETATM 2031 O3' LMT A 301 84.601 85.379 105.230 1.00 70.92 O HETATM 2032 O5' LMT A 301 82.916 83.691 101.916 1.00 66.66 O HETATM 2033 O6' LMT A 301 81.158 81.479 104.121 1.00 70.07 O HETATM 2034 C1 LMT A 301 84.254 84.120 99.394 1.00 51.47 C HETATM 2035 C2 LMT A 301 84.368 85.028 98.187 1.00 44.26 C HETATM 2036 C3 LMT A 301 84.588 84.326 96.849 1.00 39.86 C HETATM 2037 C4 LMT A 301 84.678 85.225 95.619 1.00 39.34 C HETATM 2038 C5 LMT A 301 84.441 84.525 94.286 1.00 37.64 C HETATM 2039 C6 LMT A 301 84.416 85.451 93.074 1.00 35.16 C HETATM 2040 C7 LMT A 301 84.042 84.785 91.754 1.00 32.63 C HETATM 2041 C8 LMT A 301 84.249 85.610 90.485 1.00 29.10 C HETATM 2042 C9 LMT A 301 83.757 84.988 89.178 1.00 31.89 C HETATM 2043 C10 LMT A 301 83.811 85.897 87.955 1.00 31.15 C HETATM 2044 C11 LMT A 301 83.189 85.260 86.720 1.00 33.59 C HETATM 2045 C12 LMT A 301 83.490 86.034 85.446 1.00 34.87 C CONECT 2011 2012 2017 2021 CONECT 2012 2011 2013 2018 CONECT 2013 2012 2014 2019 CONECT 2014 2013 2015 2020 CONECT 2015 2014 2016 2021 CONECT 2016 2015 2022 CONECT 2017 2011 2026 CONECT 2018 2012 CONECT 2019 2013 CONECT 2020 2014 CONECT 2021 2011 2015 CONECT 2022 2016 CONECT 2023 2024 2029 2032 CONECT 2024 2023 2025 2030 CONECT 2025 2024 2026 2031 CONECT 2026 2017 2025 2027 CONECT 2027 2026 2028 2032 CONECT 2028 2027 2033 CONECT 2029 2023 2034 CONECT 2030 2024 CONECT 2031 2025 CONECT 2032 2023 2027 CONECT 2033 2028 CONECT 2034 2029 2035 CONECT 2035 2034 2036 CONECT 2036 2035 2037 CONECT 2037 2036 2038 CONECT 2038 2037 2039 CONECT 2039 2038 2040 CONECT 2040 2039 2041 CONECT 2041 2040 2042 CONECT 2042 2041 2043 CONECT 2043 2042 2044 CONECT 2044 2043 2045 CONECT 2045 2044 MASTER 181 0 1 14 0 0 0 15 2044 1 35 24 END