HEADER MEMBRANE PROTEIN 18-APR-24 8Z67 TITLE CRYO-EM STRUCTURE OF THE HGPR68-GS COMPLEX IN PH6.8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: G-PROTEIN COUPLED RECEPTOR 4; COMPND 3 CHAIN: R; COMPND 4 SYNONYM: G-PROTEIN COUPLED RECEPTOR 6C.L,GPR6C.L; COMPND 5 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: GPR4; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PH6.8, HGPR68, GS, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.N.ZHONG,L.L.GUO,F.YANG,J.P.SUN REVDAT 1 23-APR-25 8Z67 0 JRNL AUTH Y.N.ZHONG,L.L.GUO,F.YANG,J.P.SUN JRNL TITL CRYO-EM STRUCTURE OF THE HGPR68-GS COMPLEX IN PH6.8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 282290 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 8Z67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 24-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300046806. 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 HGPR4-GS COMPLEX IN REMARK 245 PH6.8 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 : 6.80 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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 GLY R 2 REMARK 465 ASN R 3 REMARK 465 HIS R 4 REMARK 465 THR R 5 REMARK 465 TRP R 6 REMARK 465 GLU R 7 REMARK 465 LEU R 305 REMARK 465 ARG R 306 REMARK 465 PHE R 307 REMARK 465 LEU R 308 REMARK 465 ALA R 309 REMARK 465 SER R 310 REMARK 465 ASP R 311 REMARK 465 LYS R 312 REMARK 465 PRO R 313 REMARK 465 GLN R 314 REMARK 465 GLU R 315 REMARK 465 MET R 316 REMARK 465 ALA R 317 REMARK 465 ASN R 318 REMARK 465 ALA R 319 REMARK 465 SER R 320 REMARK 465 LEU R 321 REMARK 465 THR R 322 REMARK 465 LEU R 323 REMARK 465 GLU R 324 REMARK 465 THR R 325 REMARK 465 PRO R 326 REMARK 465 LEU R 327 REMARK 465 THR R 328 REMARK 465 SER R 329 REMARK 465 LYS R 330 REMARK 465 ARG R 331 REMARK 465 ASN R 332 REMARK 465 SER R 333 REMARK 465 THR R 334 REMARK 465 ALA R 335 REMARK 465 LYS R 336 REMARK 465 ALA R 337 REMARK 465 MET R 338 REMARK 465 THR R 339 REMARK 465 GLY R 340 REMARK 465 SER R 341 REMARK 465 TRP R 342 REMARK 465 ALA R 343 REMARK 465 ALA R 344 REMARK 465 THR R 345 REMARK 465 PRO R 346 REMARK 465 PRO R 347 REMARK 465 SER R 348 REMARK 465 GLN R 349 REMARK 465 GLY R 350 REMARK 465 ASP R 351 REMARK 465 GLN R 352 REMARK 465 VAL R 353 REMARK 465 GLN R 354 REMARK 465 LEU R 355 REMARK 465 LYS R 356 REMARK 465 MET R 357 REMARK 465 LEU R 358 REMARK 465 PRO R 359 REMARK 465 PRO R 360 REMARK 465 ALA R 361 REMARK 465 GLN R 362 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 CYS R 9 SG REMARK 470 VAL R 11 CG1 CG2 REMARK 470 ASP R 12 CG OD1 OD2 REMARK 470 SER R 13 OG REMARK 470 ARG R 14 CG CD NE CZ NH1 NH2 REMARK 470 ARG R 49 CG CD NE CZ NH1 NH2 REMARK 470 ARG R 127 CG CD NE CZ NH1 NH2 REMARK 470 LYS R 132 CG CD CE NZ REMARK 470 GLU R 157 CG CD OE1 OE2 REMARK 470 PHE R 159 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG R 160 CG CD NE CZ NH1 NH2 REMARK 470 ARG R 162 CG CD NE CZ NH1 NH2 REMARK 470 ARG R 206 CG CD NE CZ NH1 NH2 REMARK 470 ARG R 209 CG CD NE CZ NH1 NH2 REMARK 470 GLU R 215 CG CD OE1 OE2 REMARK 470 ARG R 216 CG CD NE CZ NH1 NH2 REMARK 470 GLN R 217 CG CD OE1 NE2 REMARK 470 ASP R 257 CG OD1 OD2 REMARK 470 GLU R 262 CG CD OE1 OE2 REMARK 470 ARG R 263 CG CD NE CZ NH1 NH2 REMARK 470 GLU R 291 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CB SER R 13 OD1 ASP R 16 1.71 REMARK 500 CB SER R 13 CG ASP R 16 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 GLY R 259 N - CA - C ANGL. DEV. = -19.6 DEGREES 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 12 74.72 -154.66 REMARK 500 TRP R 256 47.07 -83.33 REMARK 500 ASP R 257 59.96 -146.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39794 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE HGPR68-GS COMPLEX IN PH6.8 DBREF 8Z67 R 1 362 UNP P46093 GPR4_HUMAN 1 362 SEQRES 1 R 362 MET GLY ASN HIS THR TRP GLU GLY CYS HIS VAL ASP SER SEQRES 2 R 362 ARG VAL ASP HIS LEU PHE PRO PRO SER LEU TYR ILE PHE SEQRES 3 R 362 VAL ILE GLY VAL GLY LEU PRO THR ASN CYS LEU ALA LEU SEQRES 4 R 362 TRP ALA ALA TYR ARG GLN VAL GLN GLN ARG ASN GLU LEU SEQRES 5 R 362 GLY VAL TYR LEU MET ASN LEU SER ILE ALA ASP LEU LEU SEQRES 6 R 362 TYR ILE CYS THR LEU PRO LEU TRP VAL ASP TYR PHE LEU SEQRES 7 R 362 HIS HIS ASP ASN TRP ILE HIS GLY PRO GLY SER CYS LYS SEQRES 8 R 362 LEU PHE GLY PHE ILE PHE TYR THR ASN ILE TYR ILE SER SEQRES 9 R 362 ILE ALA PHE LEU CYS CYS ILE SER VAL ASP ARG TYR LEU SEQRES 10 R 362 ALA VAL ALA HIS PRO LEU ARG PHE ALA ARG LEU ARG ARG SEQRES 11 R 362 VAL LYS THR ALA VAL ALA VAL SER SER VAL VAL TRP ALA SEQRES 12 R 362 THR GLU LEU GLY ALA ASN SER ALA PRO LEU PHE HIS ASP SEQRES 13 R 362 GLU LEU PHE ARG ASP ARG TYR ASN HIS THR PHE CYS PHE SEQRES 14 R 362 GLU LYS PHE PRO MET GLU GLY TRP VAL ALA TRP MET ASN SEQRES 15 R 362 LEU TYR ARG VAL PHE VAL GLY PHE LEU PHE PRO TRP ALA SEQRES 16 R 362 LEU MET LEU LEU SER TYR ARG GLY ILE LEU ARG ALA VAL SEQRES 17 R 362 ARG GLY SER VAL SER THR GLU ARG GLN GLU LYS ALA LYS SEQRES 18 R 362 ILE LYS ARG LEU ALA LEU SER LEU ILE ALA ILE VAL LEU SEQRES 19 R 362 VAL CYS PHE ALA PRO TYR HIS VAL LEU LEU LEU SER ARG SEQRES 20 R 362 SER ALA ILE TYR LEU GLY ARG PRO TRP ASP CYS GLY PHE SEQRES 21 R 362 GLU GLU ARG VAL PHE SER ALA TYR HIS SER SER LEU ALA SEQRES 22 R 362 PHE THR SER LEU ASN CYS VAL ALA ASP PRO ILE LEU TYR SEQRES 23 R 362 CYS LEU VAL ASN GLU GLY ALA ARG SER ASP VAL ALA LYS SEQRES 24 R 362 ALA LEU HIS ASN LEU LEU ARG PHE LEU ALA SER ASP LYS SEQRES 25 R 362 PRO GLN GLU MET ALA ASN ALA SER LEU THR LEU GLU THR SEQRES 26 R 362 PRO LEU THR SER LYS ARG ASN SER THR ALA LYS ALA MET SEQRES 27 R 362 THR GLY SER TRP ALA ALA THR PRO PRO SER GLN GLY ASP SEQRES 28 R 362 GLN VAL GLN LEU LYS MET LEU PRO PRO ALA GLN HELIX 1 AA1 LEU R 18 GLN R 48 1 31 HELIX 2 AA2 GLU R 51 HIS R 79 1 29 HELIX 3 AA3 GLY R 86 ALA R 120 1 35 HELIX 4 AA4 ALA R 126 ARG R 129 5 4 HELIX 5 AA5 ARG R 130 ASN R 149 1 20 HELIX 6 AA6 ALA R 151 HIS R 155 5 5 HELIX 7 AA7 GLU R 175 VAL R 188 1 14 HELIX 8 AA8 PHE R 190 GLY R 210 1 21 HELIX 9 AA9 GLU R 215 ARG R 254 1 40 HELIX 10 AB1 GLY R 259 VAL R 264 1 6 HELIX 11 AB2 VAL R 264 THR R 275 1 12 HELIX 12 AB3 LEU R 277 CYS R 287 1 11 HELIX 13 AB4 ASN R 290 LEU R 304 1 15 SHEET 1 AA1 2 LEU R 158 ARG R 160 0 SHEET 2 AA1 2 THR R 166 CYS R 168 -1 O PHE R 167 N PHE R 159 SSBOND 1 CYS R 90 CYS R 168 1555 1555 2.03 CISPEP 1 PHE R 172 PRO R 173 0 2.85 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 2305 LEU R 304 CONECT 649 1254 CONECT 1254 649 MASTER 247 0 0 13 2 0 0 6 2304 1 2 28 END