HEADER MEMBRANE PROTEIN 02-MAR-23 8GCL TITLE CRYO-EM STRUCTURE OF HAQP2 IN DDM COMPND MOL_ID: 1; COMPND 2 MOLECULE: AQUAPORIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AQP-2,ADH WATER CHANNEL,AQUAPORIN-CD,AQP-CD,COLLECTING DUCT COMPND 5 WATER CHANNEL PROTEIN,WCH-CD,WATER CHANNEL PROTEIN FOR RENAL COMPND 6 COLLECTING DUCT; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AQP2; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS CHANNEL, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.KAMEGAWA,S.SUZUKI,K.NISHIKAWA,N.NUMOTO,H.SUZUKI,Y.FUJIYOSHI REVDAT 2 05-JUL-23 8GCL 1 JRNL REVDAT 1 21-JUN-23 8GCL 0 JRNL AUTH A.KAMEGAWA,S.SUZUKI,H.SUZUKI,K.NISHIKAWA,N.NUMOTO, JRNL AUTH 2 Y.FUJIYOSHI JRNL TITL STRUCTURAL ANALYSIS OF THE WATER CHANNEL AQP2 BY JRNL TITL 2 SINGLE-PARTICLE CRYO-EM. JRNL REF J.STRUCT.BIOL. V. 215 07984 2023 JRNL REFN ESSN 1095-8657 JRNL PMID 37315821 JRNL DOI 10.1016/J.JSB.2023.107984 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 2.890 REMARK 3 NUMBER OF PARTICLES : 236700 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 8GCL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272597. 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 : TETRAMETER OF HAQP2 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 7.20 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 : JEOL CRYO ARM 300 REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 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) : 6960.00 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 99.84000 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 99.83999 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 99.84000 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 99.84000 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 1 REMARK 465 TRP A 2 REMARK 465 PRO A 242 REMARK 465 ASP A 243 REMARK 465 THR A 244 REMARK 465 ASP A 245 REMARK 465 TRP A 246 REMARK 465 GLU A 247 REMARK 465 GLU A 248 REMARK 465 ARG A 249 REMARK 465 GLU A 250 REMARK 465 VAL A 251 REMARK 465 ARG A 252 REMARK 465 ARG A 253 REMARK 465 ARG A 254 REMARK 465 GLN A 255 REMARK 465 SER A 256 REMARK 465 VAL A 257 REMARK 465 GLU A 258 REMARK 465 LEU A 259 REMARK 465 HIS A 260 REMARK 465 SER A 261 REMARK 465 PRO A 262 REMARK 465 GLN A 263 REMARK 465 SER A 264 REMARK 465 LEU A 265 REMARK 465 PRO A 266 REMARK 465 ARG A 267 REMARK 465 GLY A 268 REMARK 465 THR A 269 REMARK 465 LYS A 270 REMARK 465 ALA A 271 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 5 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 241 CG CD OE1 OE2 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 CYS A 181 74.69 59.05 REMARK 500 SER A 182 -71.71 -58.38 REMARK 500 MET A 183 3.42 58.54 REMARK 500 VAL A 222 -52.94 -124.16 REMARK 500 LYS A 238 47.19 -93.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29934 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HAQP2 IN DDM DBREF 8GCL A 1 271 UNP P41181 AQP2_HUMAN 1 271 SEQRES 1 A 271 MET TRP GLU LEU ARG SER ILE ALA PHE SER ARG ALA VAL SEQRES 2 A 271 PHE ALA GLU PHE LEU ALA THR LEU LEU PHE VAL PHE PHE SEQRES 3 A 271 GLY LEU GLY SER ALA LEU ASN TRP PRO GLN ALA LEU PRO SEQRES 4 A 271 SER VAL LEU GLN ILE ALA MET ALA PHE GLY LEU GLY ILE SEQRES 5 A 271 GLY THR LEU VAL GLN ALA LEU GLY HIS ILE SER GLY ALA SEQRES 6 A 271 HIS ILE ASN PRO ALA VAL THR VAL ALA CYS LEU VAL GLY SEQRES 7 A 271 CYS HIS VAL SER VAL LEU ARG ALA ALA PHE TYR VAL ALA SEQRES 8 A 271 ALA GLN LEU LEU GLY ALA VAL ALA GLY ALA ALA LEU LEU SEQRES 9 A 271 HIS GLU ILE THR PRO ALA ASP ILE ARG GLY ASP LEU ALA SEQRES 10 A 271 VAL ASN ALA LEU SER ASN SER THR THR ALA GLY GLN ALA SEQRES 11 A 271 VAL THR VAL GLU LEU PHE LEU THR LEU GLN LEU VAL LEU SEQRES 12 A 271 CYS ILE PHE ALA SER THR ASP GLU ARG ARG GLY GLU ASN SEQRES 13 A 271 PRO GLY THR PRO ALA LEU SER ILE GLY PHE SER VAL ALA SEQRES 14 A 271 LEU GLY HIS LEU LEU GLY ILE HIS TYR THR GLY CYS SER SEQRES 15 A 271 MET ASN PRO ALA ARG SER LEU ALA PRO ALA VAL VAL THR SEQRES 16 A 271 GLY LYS PHE ASP ASP HIS TRP VAL PHE TRP ILE GLY PRO SEQRES 17 A 271 LEU VAL GLY ALA ILE LEU GLY SER LEU LEU TYR ASN TYR SEQRES 18 A 271 VAL LEU PHE PRO PRO ALA LYS SER LEU SER GLU ARG LEU SEQRES 19 A 271 ALA VAL LEU LYS GLY LEU GLU PRO ASP THR ASP TRP GLU SEQRES 20 A 271 GLU ARG GLU VAL ARG ARG ARG GLN SER VAL GLU LEU HIS SEQRES 21 A 271 SER PRO GLN SER LEU PRO ARG GLY THR LYS ALA HELIX 1 AA1 SER A 6 ALA A 31 1 26 HELIX 2 AA2 SER A 40 GLY A 64 1 25 HELIX 3 AA3 ASN A 68 GLY A 78 1 11 HELIX 4 AA4 SER A 82 THR A 108 1 27 HELIX 5 AA5 PRO A 109 GLY A 114 1 6 HELIX 6 AA6 THR A 126 THR A 149 1 24 HELIX 7 AA7 ASP A 150 GLY A 154 5 5 HELIX 8 AA8 THR A 159 GLY A 180 1 22 HELIX 9 AA9 ASN A 184 GLY A 196 1 13 HELIX 10 AB1 TRP A 202 VAL A 222 1 21 HELIX 11 AB2 SER A 229 LYS A 238 1 10 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 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.000000 -1.000000 0.000000 99.84000 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 99.84000 MTRIX2 3 0.000000 -1.000000 0.000000 99.84000 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 99.84000 MTRIX3 4 0.000000 0.000000 1.000000 0.00000