HEADER MEMBRANE PROTEIN 16-AUG-22 7YU4 TITLE HUMAN LYSOPHOSPHATIDIC ACID RECEPTOR 1-GI COMPLEX BOUND TO ONO- TITLE 2 0740556, FOCUSED ON RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOPHOSPHATIDIC ACID RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LPA RECEPTOR 1,LPA-1,LYSOPHOSPHATIDIC ACID RECEPTOR EDG-2; 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: LPAR1, EDG2, LPA1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS GPCR, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.AKASAKA,W.SHIHOYA,O.NUREKI REVDAT 1 05-OCT-22 7YU4 0 JRNL AUTH H.AKASAKA,T.TANAKA,F.K.SANO,Y.MATSUZAKI,W.SHIHOYA,O.NUREKI JRNL TITL STRUCTURE OF THE ACTIVE G I -COUPLED HUMAN LYSOPHOSPHATIDIC JRNL TITL 2 ACID RECEPTOR 1 COMPLEXED WITH A POTENT AGONIST. JRNL REF NAT COMMUN V. 13 5417 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36109516 JRNL DOI 10.1038/S41467-022-33121-2 REMARK 2 REMARK 2 RESOLUTION. 3.30 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) : 3.700 REMARK 3 NUMBER OF PARTICLES : 181071 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 7YU4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031581. 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 : HUMAN LYSOPHOSPHATIDIC ACID REMARK 245 RECEPTOR 1 BOUND TO ONO-0740556 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 7.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K 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) : 5000.00 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 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: 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 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 ASP A -8 REMARK 465 TYR A -7 REMARK 465 LYS A -6 REMARK 465 ASP A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 ALA A -1 REMARK 465 MET A 0 REMARK 465 GLY A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 ILE A 4 REMARK 465 SER A 5 REMARK 465 THR A 6 REMARK 465 SER A 7 REMARK 465 ILE A 8 REMARK 465 PRO A 9 REMARK 465 VAL A 10 REMARK 465 ILE A 11 REMARK 465 SER A 12 REMARK 465 GLN A 13 REMARK 465 PRO A 14 REMARK 465 GLN A 15 REMARK 465 PHE A 16 REMARK 465 THR A 17 REMARK 465 ALA A 18 REMARK 465 MET A 19 REMARK 465 ASN A 20 REMARK 465 GLU A 21 REMARK 465 PRO A 22 REMARK 465 PHE A 82 REMARK 465 PHE A 151 REMARK 465 ARG A 152 REMARK 465 MET A 153 REMARK 465 GLN A 154 REMARK 465 LEU A 155 REMARK 465 HIS A 156 REMARK 465 THR A 157 REMARK 465 ARG A 158 REMARK 465 MET A 159 REMARK 465 TYR A 231 REMARK 465 VAL A 232 REMARK 465 ARG A 233 REMARK 465 GLN A 234 REMARK 465 ARG A 235 REMARK 465 THR A 236 REMARK 465 MET A 237 REMARK 465 ARG A 238 REMARK 465 MET A 239 REMARK 465 SER A 240 REMARK 465 ARG A 241 REMARK 465 HIS A 242 REMARK 465 SER A 243 REMARK 465 SER A 244 REMARK 465 GLY A 245 REMARK 465 PRO A 246 REMARK 465 ARG A 247 REMARK 465 ARG A 248 REMARK 465 ASN A 249 REMARK 465 ARG A 250 REMARK 465 ASP A 251 REMARK 465 THR A 252 REMARK 465 MET A 253 REMARK 465 MET A 254 REMARK 465 SER A 255 REMARK 465 GLN A 324 REMARK 465 ILE A 325 REMARK 465 LEU A 326 REMARK 465 CYS A 327 REMARK 465 CYS A 328 REMARK 465 GLN A 329 REMARK 465 ARG A 330 REMARK 465 SER A 331 REMARK 465 GLU A 332 REMARK 465 ASN A 333 REMARK 465 PRO A 334 REMARK 465 THR A 335 REMARK 465 GLY A 336 REMARK 465 PRO A 337 REMARK 465 THR A 338 REMARK 465 GLU A 339 REMARK 465 GLY A 340 REMARK 465 SER A 341 REMARK 465 ASP A 342 REMARK 465 ARG A 343 REMARK 465 SER A 344 REMARK 465 ALA A 345 REMARK 465 SER A 346 REMARK 465 SER A 347 REMARK 465 LEU A 348 REMARK 465 ASN A 349 REMARK 465 HIS A 350 REMARK 465 THR A 351 REMARK 465 ILE A 352 REMARK 465 LEU A 353 REMARK 465 ALA A 354 REMARK 465 GLY A 355 REMARK 465 VAL A 356 REMARK 465 HIS A 357 REMARK 465 SER A 358 REMARK 465 ASN A 359 REMARK 465 ASP A 360 REMARK 465 HIS A 361 REMARK 465 SER A 362 REMARK 465 VAL A 363 REMARK 465 VAL A 364 REMARK 465 GLU A 365 REMARK 465 ASN A 366 REMARK 465 LEU A 367 REMARK 465 TYR A 368 REMARK 465 PHE A 369 REMARK 465 GLN A 370 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 PHE A 25 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 27 CG OD1 ND2 REMARK 470 GLU A 28 CG CD OE1 OE2 REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 THR A 47 OG1 CG2 REMARK 470 LYS A 50 CG CD CE NZ REMARK 470 ILE A 61 CG1 CG2 CD1 REMARK 470 LEU A 65 CG CD1 CD2 REMARK 470 LEU A 68 CG CD1 CD2 REMARK 470 VAL A 72 CG1 CG2 REMARK 470 ILE A 74 CG1 CG2 CD1 REMARK 470 ARG A 78 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 79 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 81 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 115 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 162 CG CD NE CZ NH1 NH2 REMARK 470 THR A 173 OG1 CG2 REMARK 470 GLU A 193 CG CD OE1 OE2 REMARK 470 SER A 196 OG REMARK 470 GLN A 286 CG CD OE1 NE2 REMARK 470 LYS A 316 CG CD CE NZ REMARK 470 GLU A 317 CG CD OE1 OE2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 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 ALA A 42 66.43 60.74 REMARK 500 PHE A 80 57.89 -94.67 REMARK 500 TRP A 186 75.64 -100.02 REMARK 500 CYS A 188 32.22 -98.25 REMARK 500 ASP A 288 94.41 -68.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34098 RELATED DB: EMDB REMARK 900 HUMAN LYSOPHOSPHATIDIC ACID RECEPTOR 1 BOUND TO ONO-0740556 DBREF 7YU4 A 2 364 UNP Q92633 LPAR1_HUMAN 2 364 SEQADV 7YU4 ASP A -8 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 TYR A -7 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 LYS A -6 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 ASP A -5 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 ASP A -4 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 ASP A -3 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 ASP A -2 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 ALA A -1 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 MET A 0 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 GLY A 1 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 GLU A 365 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 ASN A 366 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 LEU A 367 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 TYR A 368 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 PHE A 369 UNP Q92633 EXPRESSION TAG SEQADV 7YU4 GLN A 370 UNP Q92633 EXPRESSION TAG SEQRES 1 A 379 ASP TYR LYS ASP ASP ASP ASP ALA MET GLY ALA ALA ILE SEQRES 2 A 379 SER THR SER ILE PRO VAL ILE SER GLN PRO GLN PHE THR SEQRES 3 A 379 ALA MET ASN GLU PRO GLN CYS PHE TYR ASN GLU SER ILE SEQRES 4 A 379 ALA PHE PHE TYR ASN ARG SER GLY LYS HIS LEU ALA THR SEQRES 5 A 379 GLU TRP ASN THR VAL SER LYS LEU VAL MET GLY LEU GLY SEQRES 6 A 379 ILE THR VAL CYS ILE PHE ILE MET LEU ALA ASN LEU LEU SEQRES 7 A 379 VAL MET VAL ALA ILE TYR VAL ASN ARG ARG PHE HIS PHE SEQRES 8 A 379 PRO ILE TYR TYR LEU MET ALA ASN LEU ALA ALA ALA ASP SEQRES 9 A 379 PHE PHE ALA GLY LEU ALA TYR PHE TYR LEU MET PHE ASN SEQRES 10 A 379 THR GLY PRO ASN THR ARG ARG LEU THR VAL SER THR TRP SEQRES 11 A 379 LEU LEU ARG GLN GLY LEU ILE ASP THR SER LEU THR ALA SEQRES 12 A 379 SER VAL ALA ASN LEU LEU ALA ILE ALA ILE GLU ARG HIS SEQRES 13 A 379 ILE THR VAL PHE ARG MET GLN LEU HIS THR ARG MET SER SEQRES 14 A 379 ASN ARG ARG VAL VAL VAL VAL ILE VAL VAL ILE TRP THR SEQRES 15 A 379 MET ALA ILE VAL MET GLY ALA ILE PRO SER VAL GLY TRP SEQRES 16 A 379 ASN CYS ILE CYS ASP ILE GLU ASN CYS SER ASN MET ALA SEQRES 17 A 379 PRO LEU TYR SER ASP SER TYR LEU VAL PHE TRP ALA ILE SEQRES 18 A 379 PHE ASN LEU VAL THR PHE VAL VAL MET VAL VAL LEU TYR SEQRES 19 A 379 ALA HIS ILE PHE GLY TYR VAL ARG GLN ARG THR MET ARG SEQRES 20 A 379 MET SER ARG HIS SER SER GLY PRO ARG ARG ASN ARG ASP SEQRES 21 A 379 THR MET MET SER LEU LEU LYS THR VAL VAL ILE VAL LEU SEQRES 22 A 379 GLY ALA PHE ILE ILE CYS TRP THR PRO GLY LEU VAL LEU SEQRES 23 A 379 LEU LEU LEU ASP VAL CYS CYS PRO GLN CYS ASP VAL LEU SEQRES 24 A 379 ALA TYR GLU LYS PHE PHE LEU LEU LEU ALA GLU PHE ASN SEQRES 25 A 379 SER ALA MET ASN PRO ILE ILE TYR SER TYR ARG ASP LYS SEQRES 26 A 379 GLU MET SER ALA THR PHE ARG GLN ILE LEU CYS CYS GLN SEQRES 27 A 379 ARG SER GLU ASN PRO THR GLY PRO THR GLU GLY SER ASP SEQRES 28 A 379 ARG SER ALA SER SER LEU ASN HIS THR ILE LEU ALA GLY SEQRES 29 A 379 VAL HIS SER ASN ASP HIS SER VAL VAL GLU ASN LEU TYR SEQRES 30 A 379 PHE GLN HET K6L A 401 28 HETNAM K6L [(2~{R})-2-[5-(2-HEXYLPHENYL)PENTANOYLAMINO]-3- HETNAM 2 K6L OXIDANYL-PROPYL] DIHYDROGEN PHOSPHATE FORMUL 2 K6L C20 H34 N O6 P HELIX 1 AA1 SER A 29 SER A 37 1 9 HELIX 2 AA2 ASN A 46 ASN A 77 1 32 HELIX 3 AA3 ILE A 84 MET A 106 1 23 HELIX 4 AA4 THR A 109 LEU A 116 5 8 HELIX 5 AA5 THR A 117 VAL A 150 1 34 HELIX 6 AA6 ASN A 161 GLY A 185 1 25 HELIX 7 AA7 SER A 203 GLY A 230 1 28 HELIX 8 AA8 LEU A 257 CYS A 284 1 28 HELIX 9 AA9 TYR A 292 TYR A 311 1 20 HELIX 10 AB1 ASP A 315 PHE A 322 1 8 SSBOND 1 CYS A 24 CYS A 190 1555 1555 2.05 SSBOND 2 CYS A 188 CYS A 195 1555 1555 2.05 SSBOND 3 CYS A 284 CYS A 287 1555 1555 2.04 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