HEADER MEMBRANE PROTEIN 07-MAY-24 8ZFE TITLE CRYO-EM STRUCTURE OF THE MMGPR4-GS RECEPTOR IN PH7.2 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: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: GPR4; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PH7.2, MMGPR4, RECEPTOR, MEMBRANE PROTEIN/IMMUNE SYSTEM, MEMBRANE KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.WEN,N.K.RONG,F.YANG,J.P.SUN REVDAT 2 16-JUL-25 8ZFE 1 REMARK REVDAT 1 26-FEB-25 8ZFE 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. 2.56 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) : 2.560 REMARK 3 NUMBER OF PARTICLES : 709807 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 8ZFE 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_1300047646. 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 MMGPR4 REMARK 245 -GS RECEPTOR IN PH7.2 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 : 7.20 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 ASP R 2 REMARK 465 ASN R 3 REMARK 465 SER R 4 REMARK 465 THR R 5 REMARK 465 GLY R 6 REMARK 465 THR R 7 REMARK 465 GLY R 8 REMARK 465 GLU R 9 REMARK 465 GLY R 10 REMARK 465 CYS R 11 REMARK 465 HIS R 12 REMARK 465 LEU R 306 REMARK 465 LEU R 307 REMARK 465 ARG R 308 REMARK 465 PHE R 309 REMARK 465 LEU R 310 REMARK 465 ALA R 311 REMARK 465 SER R 312 REMARK 465 ASN R 313 REMARK 465 LYS R 314 REMARK 465 PRO R 315 REMARK 465 GLN R 316 REMARK 465 GLU R 317 REMARK 465 MET R 318 REMARK 465 ALA R 319 REMARK 465 ASN R 320 REMARK 465 ALA R 321 REMARK 465 SER R 322 REMARK 465 LEU R 323 REMARK 465 THR R 324 REMARK 465 LEU R 325 REMARK 465 GLU R 326 REMARK 465 THR R 327 REMARK 465 PRO R 328 REMARK 465 LEU R 329 REMARK 465 THR R 330 REMARK 465 SER R 331 REMARK 465 LYS R 332 REMARK 465 ARG R 333 REMARK 465 SER R 334 REMARK 465 THR R 335 REMARK 465 THR R 336 REMARK 465 GLY R 337 REMARK 465 LYS R 338 REMARK 465 SER R 339 REMARK 465 SER R 340 REMARK 465 GLY R 341 REMARK 465 ALA R 342 REMARK 465 VAL R 343 REMARK 465 TRP R 344 REMARK 465 ALA R 345 REMARK 465 VAL R 346 REMARK 465 PRO R 347 REMARK 465 PRO R 348 REMARK 465 THR R 349 REMARK 465 ALA R 350 REMARK 465 GLN R 351 REMARK 465 GLY R 352 REMARK 465 ASP R 353 REMARK 465 GLN R 354 REMARK 465 VAL R 355 REMARK 465 PRO R 356 REMARK 465 LEU R 357 REMARK 465 LYS R 358 REMARK 465 VAL R 359 REMARK 465 LEU R 360 REMARK 465 LEU R 361 REMARK 465 PRO R 362 REMARK 465 PRO R 363 REMARK 465 ALA R 364 REMARK 465 GLN R 365 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 SER R 15 OG REMARK 470 ARG R 16 CG CD NE CZ NH1 NH2 REMARK 470 VAL R 17 CG1 CG2 REMARK 470 ASP R 18 CG OD1 OD2 REMARK 470 LEU R 20 CG CD1 CD2 REMARK 470 PRO R 23 CG CD REMARK 470 ARG R 49 CG CD NE CZ NH1 NH2 REMARK 470 HIS R 51 CG ND1 CD2 CE1 NE2 REMARK 470 ASP R 77 CG OD1 OD2 REMARK 470 ILE R 86 CG1 CG2 CD1 REMARK 470 LEU R 94 CG CD1 CD2 REMARK 470 PHE R 95 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG R 129 CG CD NE CZ NH1 NH2 REMARK 470 LYS R 134 CG CD CE NZ REMARK 470 GLU R 147 CG CD OE1 OE2 REMARK 470 ASP R 158 CG OD1 OD2 REMARK 470 LEU R 160 CG CD1 CD2 REMARK 470 PHE R 161 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG R 162 CG CD NE CZ NH1 NH2 REMARK 470 ARG R 164 CG CD NE CZ NH1 NH2 REMARK 470 TYR R 165 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN R 166 CG OD1 ND2 REMARK 470 CYS R 170 SG REMARK 470 PHE R 171 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS R 173 CG CD CE NZ REMARK 470 GLU R 177 CG CD OE1 OE2 REMARK 470 ARG R 178 CG CD NE CZ NH1 NH2 REMARK 470 GLN R 211 CG CD OE1 NE2 REMARK 470 SER R 212 OG REMARK 470 GLU R 217 CG CD OE1 OE2 REMARK 470 ARG R 218 CG CD NE CZ NH1 NH2 REMARK 470 VAL R 222 CG1 CG2 REMARK 470 ARG R 256 CG CD NE CZ NH1 NH2 REMARK 470 TRP R 258 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP R 258 CZ3 CH2 REMARK 470 ASP R 259 CG OD1 OD2 REMARK 470 CYS R 260 SG REMARK 470 GLU R 264 CG CD OE1 OE2 REMARK 470 ARG R 265 CG CD NE CZ NH1 NH2 REMARK 470 CYS R 289 SG REMARK 470 GLU R 293 CG CD OE1 OE2 REMARK 470 ASP R 298 CG OD1 OD2 REMARK 470 LYS R 301 CG CD CE NZ REMARK 470 HIS R 304 CG ND1 CD2 CE1 NE2 REMARK 470 ASN R 305 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER R 152 C ALA R 153 N 0.193 REMARK 500 REMARK 500 REMARK: NULL 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 ASP R 18 63.08 -101.24 REMARK 500 PRO R 22 35.44 -87.04 REMARK 500 GLN R 50 49.38 -94.05 REMARK 500 CYS R 92 46.98 -81.28 REMARK 500 LYS R 93 -16.45 -141.06 REMARK 500 SER R 101 29.53 -140.18 REMARK 500 LEU R 125 -4.24 74.35 REMARK 500 CYS R 170 -64.03 -94.97 REMARK 500 ARG R 256 87.14 -158.19 REMARK 500 CYS R 289 17.34 -140.29 REMARK 500 LEU R 290 -4.06 -140.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60058 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE MMGPR4-GS RECEPTOR IN PH7.2 REMARK 900 RELATED ID: EMD-60053 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE MMGPR4-GS COMPLEX IN PH7.2 DBREF 8ZFE R 1 365 UNP Q8BUD0 GPR4_MOUSE 1 365 SEQRES 1 R 365 MET ASP ASN SER THR GLY THR GLY GLU GLY CYS HIS VAL SEQRES 2 R 365 ASP SER ARG VAL ASP HIS LEU PHE PRO PRO SER LEU TYR SEQRES 3 R 365 ILE PHE VAL ILE GLY VAL GLY LEU PRO THR ASN CYS LEU SEQRES 4 R 365 ALA LEU TRP ALA ALA TYR ARG GLN VAL ARG GLN HIS ASN SEQRES 5 R 365 GLU LEU GLY VAL TYR LEU MET ASN LEU SER ILE ALA ASP SEQRES 6 R 365 LEU LEU TYR ILE CYS THR LEU PRO LEU TRP VAL ASP TYR SEQRES 7 R 365 PHE LEU HIS HIS ASP ASN TRP ILE HIS GLY PRO GLY SER SEQRES 8 R 365 CYS LYS LEU PHE GLY PHE ILE PHE TYR SER ASN ILE TYR SEQRES 9 R 365 ILE SER ILE ALA PHE LEU CYS CYS ILE SER VAL ASP ARG SEQRES 10 R 365 TYR LEU ALA VAL ALA HIS PRO LEU ARG PHE ALA ARG LEU SEQRES 11 R 365 ARG ARG VAL LYS THR ALA VAL ALA VAL SER SER VAL VAL SEQRES 12 R 365 TRP ALA THR GLU LEU GLY ALA ASN SER ALA PRO LEU PHE SEQRES 13 R 365 HIS ASP GLU LEU PHE ARG ASP ARG TYR ASN HIS THR PHE SEQRES 14 R 365 CYS PHE GLU LYS PHE PRO MET GLU ARG TRP VAL ALA TRP SEQRES 15 R 365 MET ASN LEU TYR ARG VAL PHE VAL GLY PHE LEU PHE PRO SEQRES 16 R 365 TRP ALA LEU MET LEU LEU CYS TYR ARG GLY ILE LEU ARG SEQRES 17 R 365 ALA VAL GLN SER SER VAL SER THR GLU ARG GLN GLU LYS SEQRES 18 R 365 VAL LYS ILE LYS ARG LEU ALA LEU SER LEU ILE ALA ILE SEQRES 19 R 365 VAL LEU VAL CYS PHE ALA PRO TYR HIS ALA LEU LEU LEU SEQRES 20 R 365 SER ARG SER ALA VAL TYR LEU GLY ARG PRO TRP ASP CYS SEQRES 21 R 365 GLY PHE GLU GLU ARG VAL PHE SER ALA TYR HIS SER SER SEQRES 22 R 365 LEU ALA PHE THR SER LEU ASN CYS VAL ALA ASP PRO ILE SEQRES 23 R 365 LEU TYR CYS LEU VAL ASN GLU GLY ALA ARG SER ASP VAL SEQRES 24 R 365 ALA LYS ALA LEU HIS ASN LEU LEU ARG PHE LEU ALA SER SEQRES 25 R 365 ASN LYS PRO GLN GLU MET ALA ASN ALA SER LEU THR LEU SEQRES 26 R 365 GLU THR PRO LEU THR SER LYS ARG SER THR THR GLY LYS SEQRES 27 R 365 SER SER GLY ALA VAL TRP ALA VAL PRO PRO THR ALA GLN SEQRES 28 R 365 GLY ASP GLN VAL PRO LEU LYS VAL LEU LEU PRO PRO ALA SEQRES 29 R 365 GLN HELIX 1 AA1 SER R 24 GLN R 50 1 27 HELIX 2 AA2 ASN R 52 ASP R 65 1 14 HELIX 3 AA3 TYR R 68 CYS R 70 5 3 HELIX 4 AA4 THR R 71 HIS R 81 1 11 HELIX 5 AA5 ASN R 102 ALA R 122 1 21 HELIX 6 AA6 ALA R 128 ARG R 131 5 4 HELIX 7 AA7 ARG R 132 ASN R 151 1 20 HELIX 8 AA8 SER R 152 HIS R 157 1 6 HELIX 9 AA9 GLU R 177 PHE R 192 1 16 HELIX 10 AB1 PHE R 192 GLN R 211 1 20 HELIX 11 AB2 GLN R 219 TYR R 253 1 35 HELIX 12 AB3 VAL R 266 THR R 277 1 12 HELIX 13 AB4 LEU R 279 LEU R 290 1 12 HELIX 14 AB5 ASN R 292 LYS R 301 1 10 SHEET 1 AA1 2 PHE R 161 ARG R 162 0 SHEET 2 AA1 2 THR R 168 PHE R 169 -1 O PHE R 169 N PHE R 161 CISPEP 1 PHE R 174 PRO R 175 0 0.46 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 2199 ASN R 305 MASTER 276 0 0 14 2 0 0 6 2198 1 0 29 END