HEADER MEMBRANE PROTEIN 06-FEB-24 8Y8Q TITLE CRYO-EM STRUCTURE OF AQP3 Y212T IN POPC NANODISC 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 8Y8Q 1 REMARK REVDAT 2 02-APR-25 8Y8Q 1 JRNL REVDAT 1 19-MAR-25 8Y8Q 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. 2.67 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) : 2.670 REMARK 3 NUMBER OF PARTICLES : 295521 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 8Y8Q 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_1300045003. 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 POPC REMARK 245 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 148.74000 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 148.74000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 148.74000 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 148.74000 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 4 REMARK 465 LYS A 5 REMARK 465 GLU A 6 REMARK 465 LEU A 7 REMARK 465 MET A 8 REMARK 465 ASN A 9 REMARK 465 ARG A 10 REMARK 465 CYS A 11 REMARK 465 GLY A 12 REMARK 465 GLU A 13 REMARK 465 MET A 14 REMARK 465 LEU A 15 REMARK 465 HIS A 16 REMARK 465 ILE A 17 REMARK 465 ARG A 18 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 VAL A 77 -61.30 -105.17 REMARK 500 LEU A 82 18.42 54.93 REMARK 500 ASP A 156 -179.71 -66.37 REMARK 500 SER A 205 -61.46 -100.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39055 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF AQP3 Y212T IN POPC NANODISC DBREF 8Y8Q A 1 292 UNP P47862 AQP3_RAT 1 292 SEQADV 8Y8Q MET A -18 UNP P47862 INITIATING METHIONINE SEQADV 8Y8Q HIS A -17 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q HIS A -16 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q HIS A -15 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q HIS A -14 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q HIS A -13 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q HIS A -12 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q HIS A -11 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q HIS A -10 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q ALA A -9 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q ALA A -8 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q ALA A -7 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q GLY A -6 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q LEU A -5 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q VAL A -4 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q PRO A -3 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q ARG A -2 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q GLY A -1 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q SER A 0 UNP P47862 EXPRESSION TAG SEQADV 8Y8Q 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 HELIX 1 AA1 TYR A 19 SER A 49 1 31 HELIX 2 AA2 GLY A 55 GLY A 79 1 25 HELIX 3 AA3 ASN A 83 LEU A 93 1 11 HELIX 4 AA4 ILE A 99 TYR A 123 1 25 HELIX 5 AA5 TYR A 123 ALA A 129 1 7 HELIX 6 AA6 THR A 143 PHE A 147 5 5 HELIX 7 AA7 ASP A 156 VAL A 179 1 24 HELIX 8 AA8 GLY A 189 MET A 206 1 18 HELIX 9 AA9 ASN A 215 GLY A 230 1 16 HELIX 10 AB1 SER A 233 TRP A 242 1 10 HELIX 11 AB2 TRP A 244 ILE A 265 1 22 HELIX 12 AB3 GLY A 266 LEU A 269 5 4 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 148.74001 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 148.74001 MTRIX2 3 0.000000 -1.000000 0.000000 148.74001 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 148.74001 MTRIX3 4 0.000000 0.000000 1.000000 0.00000 TER 1884 GLU A 270 MASTER 195 0 0 12 0 0 0 15 1883 1 0 24 END