HEADER MEMBRANE PROTEIN 07-MAY-24 8ZF7 TITLE CRYO-EM STRUCTURE OF THE RECEPTOR OF XGPR4-GS COMPLEX IN PH6.7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: G-PROTEIN COUPLED RECEPTOR 4; COMPND 3 CHAIN: R; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS TROPICALIS; SOURCE 3 ORGANISM_COMMON: TROPICAL CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8364; SOURCE 5 GENE: GPR4; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PH6.7, XGPR4, RECEPTOR, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR N.K.RONG,X.WEN,F.YANG,J.P.SUN REVDAT 2 23-JUL-25 8ZF7 1 REMARK REVDAT 1 26-FEB-25 8ZF7 0 JRNL AUTH X.WEN,P.SHANG,H.CHEN,L.GUO,N.RONG,X.JIANG,X.LI,J.LIU,G.YANG, JRNL AUTH 2 J.ZHANG,K.ZHU,Q.MENG,X.HE,Z.WANG,Z.LIU,H.CHENG,Y.ZHENG, JRNL AUTH 3 B.ZHANG,J.PANG,Z.LIU,P.XIAO,Y.CHEN,L.LIU,F.LUO,X.YU,F.YI, JRNL AUTH 4 P.ZHANG,F.YANG,C.DENG,J.P.SUN JRNL TITL EVOLUTIONARY STUDY AND STRUCTURAL BASIS OF PROTON SENSING BY JRNL TITL 2 MUS GPR4 AND XENOPUS GPR4. JRNL REF CELL V. 188 653 2025 JRNL REFN ISSN 1097-4172 JRNL PMID 39753131 JRNL DOI 10.1016/J.CELL.2024.12.001 REMARK 2 REMARK 2 RESOLUTION. 3.15 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) : 3.150 REMARK 3 NUMBER OF PARTICLES : 543772 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8ZF7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 15-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1300047485. 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 : CRYO-EM STRUCTURE OF THE REMARK 245 RECEPTOR OF XGPR4-GS COMPLEX IN REMARK 245 PH6.7 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 : 6.70 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : DIFFRACTION REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 187.50 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 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: R 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 R 1 REMARK 465 SER R 2 REMARK 465 ASN R 3 REMARK 465 PHE R 4 REMARK 465 THR R 5 REMARK 465 PRO R 6 REMARK 465 ASP R 7 REMARK 465 ALA R 8 REMARK 465 CYS R 9 REMARK 465 ASN R 10 REMARK 465 VAL R 11 REMARK 465 ASP R 12 REMARK 465 GLY R 255 REMARK 465 GLY R 256 REMARK 465 GLY R 257 REMARK 465 SER R 258 REMARK 465 VAL R 259 REMARK 465 ASP R 260 REMARK 465 ALA R 261 REMARK 465 GLY R 262 REMARK 465 GLY R 309 REMARK 465 GLY R 310 REMARK 465 VAL R 311 REMARK 465 VAL R 312 REMARK 465 ALA R 313 REMARK 465 TRP R 314 REMARK 465 ALA R 315 REMARK 465 MET R 316 REMARK 465 GLY R 317 REMARK 465 LYS R 318 REMARK 465 GLU R 319 REMARK 465 ARG R 320 REMARK 465 ARG R 321 REMARK 465 ALA R 322 REMARK 465 TRP R 323 REMARK 465 GLY R 324 REMARK 465 GLU R 325 REMARK 465 ARG R 326 REMARK 465 GLY R 327 REMARK 465 GLY R 328 REMARK 465 ASN R 329 REMARK 465 GLY R 330 REMARK 465 ARG R 331 REMARK 465 GLY R 332 REMARK 465 CYS R 333 REMARK 465 GLY R 334 REMARK 465 GLU R 335 REMARK 465 GLY R 336 REMARK 465 GLU R 337 REMARK 465 GLU R 338 REMARK 465 VAL R 339 REMARK 465 GLY R 340 REMARK 465 MET R 341 REMARK 465 VAL R 342 REMARK 465 GLU R 343 REMARK 465 LEU R 344 REMARK 465 ARG R 345 REMARK 465 GLY R 346 REMARK 465 ASN R 347 REMARK 465 GLY R 348 REMARK 465 ARG R 349 REMARK 465 GLU R 350 REMARK 465 PHE R 351 REMARK 465 VAL R 352 REMARK 465 VAL R 353 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 LEU R 26 CG CD1 CD2 REMARK 470 THR R 29 OG1 CG2 REMARK 470 LEU R 32 CG CD1 CD2 REMARK 470 LEU R 44 CG CD1 CD2 REMARK 470 ARG R 47 CG CD NE CZ NH1 NH2 REMARK 470 ASP R 63 CG OD1 OD2 REMARK 470 LEU R 64 CG CD1 CD2 REMARK 470 ILE R 67 CG1 CG2 CD1 REMARK 470 LEU R 70 CG CD1 CD2 REMARK 470 ASP R 75 CG OD1 OD2 REMARK 470 ARG R 80 CG CD NE CZ NH1 NH2 REMARK 470 LEU R 92 CG CD1 CD2 REMARK 470 VAL R 96 CG1 CG2 REMARK 470 ASN R 100 CG OD1 ND2 REMARK 470 ILE R 131 CG1 CG2 CD1 REMARK 470 ASN R 149 CG OD1 ND2 REMARK 470 LEU R 153 CG CD1 CD2 REMARK 470 LEU R 154 CG CD1 CD2 REMARK 470 ARG R 160 CG CD NE CZ NH1 NH2 REMARK 470 ARG R 162 CG CD NE CZ NH1 NH2 REMARK 470 THR R 166 OG1 CG2 REMARK 470 ARG R 186 CG CD NE CZ NH1 NH2 REMARK 470 LEU R 192 CG CD1 CD2 REMARK 470 LEU R 206 CG CD1 CD2 REMARK 470 ARG R 210 CG CD NE CZ NH1 NH2 REMARK 470 GLN R 217 CG CD OE1 NE2 REMARK 470 ARG R 218 CG CD NE CZ NH1 NH2 REMARK 470 LEU R 250 CG CD1 CD2 REMARK 470 CYS R 265 SG REMARK 470 GLU R 268 CG CD OE1 OE2 REMARK 470 GLU R 269 CG CD OE1 OE2 REMARK 470 ASP R 289 CG OD1 OD2 REMARK 470 LEU R 295 CG CD1 CD2 REMARK 470 CYS R 297 SG REMARK 470 ARG R 301 CG CD NE CZ NH1 NH2 REMARK 470 GLU R 303 CG CD OE1 OE2 REMARK 470 VAL R 304 CG1 CG2 REMARK 470 LYS R 306 CG CD CE NZ REMARK 470 VAL R 307 CG1 CG2 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 LYS R 48 48.18 -92.61 REMARK 500 ASP R 81 -6.11 79.65 REMARK 500 ARG R 129 70.46 46.04 REMARK 500 TYR R 163 50.32 -92.83 REMARK 500 ARG R 177 -12.70 71.64 REMARK 500 LEU R 192 -13.73 71.75 REMARK 500 ASN R 285 49.93 -85.39 REMARK 500 CYS R 294 -54.56 -120.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60052 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE RECEPTOR OF XGPR4-GS COMPLEX IN PH6.7 REMARK 900 RELATED ID: EMD-60051 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE XGPR4-GS COMPLEX IN PH6.7 DBREF1 8ZF7 R 1 353 UNP A0A6I8PUB9_XENTR DBREF2 8ZF7 R A0A6I8PUB9 1 353 SEQRES 1 R 353 MET SER ASN PHE THR PRO ASP ALA CYS ASN VAL ASP SER SEQRES 2 R 353 GLY LEU ASP SER VAL LEU PRO PRO SER LEU TYR ALA LEU SEQRES 3 R 353 VAL PHE THR LEU GLY LEU PRO ALA ASN LEU LEU ALA LEU SEQRES 4 R 353 TRP ALA ALA TRP LEU GLN VAL ARG LYS GLY ARG GLU LEU SEQRES 5 R 353 GLY VAL TYR LEU LEU ASN LEU SER LEU SER ASP LEU LEU SEQRES 6 R 353 LEU ILE CYS ALA LEU PRO PRO TRP THR ASP TYR TYR LEU SEQRES 7 R 353 ARG ARG ASP VAL TRP GLY TYR GLY PRO GLY ALA CYS ARG SEQRES 8 R 353 LEU PHE GLY PHE VAL PHE TYR THR ASN LEU TYR VAL GLY SEQRES 9 R 353 ALA ALA PHE LEU SER CYS VAL SER ALA ASP ARG TYR LEU SEQRES 10 R 353 ALA VAL ALA HIS PRO LEU ARG PHE PRO GLY ALA ARG PRO SEQRES 11 R 353 ILE ARG SER ALA ALA ALA VAL SER ALA LEU ILE TRP MET SEQRES 12 R 353 LEU GLU LEU ALA ALA ASN ALA PRO PRO LEU LEU GLY GLU SEQRES 13 R 353 ALA ILE HIS ARG ASP ARG TYR ASN HIS THR PHE CYS TYR SEQRES 14 R 353 GLU SER TYR PRO LEU SER GLY ARG GLY ALA ALA LEU ALA SEQRES 15 R 353 ASN VAL GLY ARG VAL LEU ALA GLY PHE LEU LEU PRO TRP SEQRES 16 R 353 GLY VAL MET MET LEU CYS TYR ALA GLY LEU LEU ARG ALA SEQRES 17 R 353 LEU ARG GLY SER ALA SER CYS GLU GLN ARG GLU ARG ARG SEQRES 18 R 353 ARG VAL ARG ARG LEU ALA LEU GLY LEU PRO CYS VAL ALA SEQRES 19 R 353 LEU LEU CYS TYR GLY PRO TYR HIS ALA LEU LEU LEU LEU SEQRES 20 R 353 ARG SER LEU VAL PHE LEU VAL GLY GLY GLY SER VAL ASP SEQRES 21 R 353 ALA GLY GLY GLY CYS ALA LEU GLU GLU ARG LEU PHE PRO SEQRES 22 R 353 ALA TYR HIS ALA SER LEU ALA LEU ALA THR LEU ASN CYS SEQRES 23 R 353 LEU ALA ASP PRO ALA LEU TYR CYS LEU ALA CYS PRO GLY SEQRES 24 R 353 ALA ARG GLY GLU VAL ALA LYS VAL VAL GLY GLY VAL VAL SEQRES 25 R 353 ALA TRP ALA MET GLY LYS GLU ARG ARG ALA TRP GLY GLU SEQRES 26 R 353 ARG GLY GLY ASN GLY ARG GLY CYS GLY GLU GLY GLU GLU SEQRES 27 R 353 VAL GLY MET VAL GLU LEU ARG GLY ASN GLY ARG GLU PHE SEQRES 28 R 353 VAL VAL HELIX 1 AA1 VAL R 18 ARG R 47 1 30 HELIX 2 AA2 GLU R 51 ARG R 79 1 29 HELIX 3 AA3 GLY R 86 HIS R 121 1 36 HELIX 4 AA4 PRO R 122 PHE R 125 5 4 HELIX 5 AA5 ARG R 129 ALA R 150 1 22 HELIX 6 AA6 PRO R 151 GLY R 155 5 5 HELIX 7 AA7 ARG R 177 PHE R 191 1 15 HELIX 8 AA8 LEU R 193 LEU R 209 1 17 HELIX 9 AA9 GLU R 216 LEU R 253 1 38 HELIX 10 AB1 CYS R 265 LEU R 284 1 20 HELIX 11 AB2 LEU R 287 LEU R 295 1 9 HELIX 12 AB3 CYS R 297 VAL R 308 1 12 SHEET 1 AA1 2 ILE R 158 HIS R 159 0 SHEET 2 AA1 2 PHE R 167 CYS R 168 -1 O PHE R 167 N HIS R 159 SSBOND 1 CYS R 90 CYS R 168 1555 1555 2.03 CISPEP 1 PHE R 125 PRO R 126 0 -8.91 CISPEP 2 TYR R 172 PRO R 173 0 0.56 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 TER 2077 VAL R 308 CONECT 572 1149 CONECT 1149 572 MASTER 242 0 0 12 2 0 0 6 2076 1 2 28 END