HEADER MEMBRANE PROTEIN 21-JUL-23 8K5D TITLE CRYO-EM STRUCTURE OF GSK256073 BOUND HUMAN HYDROXY-CARBOXYLIC ACID TITLE 2 RECEPTOR 2 (LOCAL REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN HYDROXYCARBOXYLIC ACID RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: G-PROTEIN COUPLED RECEPTOR 109A,G-PROTEIN COUPLED RECEPTOR COMPND 5 HM74A,NIACIN RECEPTOR 1,NICOTINIC ACID RECEPTOR; COMPND 6 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: HCAR2, HCA2; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS GPCR, G-PROTEIN, MEMBRANE PROTEIN, SIGNALING EXPDTA ELECTRON MICROSCOPY AUTHOR J.H.PARK,N.ISHIMOTO,S.Y.PARK REVDAT 2 08-MAY-24 8K5D 1 JRNL REVDAT 1 22-NOV-23 8K5D 0 JRNL AUTH J.H.PARK,K.KAWAKAMI,N.ISHIMOTO,T.IKUTA,M.OHKI,T.EKIMOTO, JRNL AUTH 2 M.IKEGUCHI,D.S.LEE,Y.H.LEE,J.R.H.TAME,A.INOUE,S.Y.PARK JRNL TITL STRUCTURAL BASIS FOR LIGAND RECOGNITION AND SIGNALING OF JRNL TITL 2 HYDROXY-CARBOXYLIC ACID RECEPTOR 2. JRNL REF NAT COMMUN V. 14 7150 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37932263 JRNL DOI 10.1038/S41467-023-42764-8 REMARK 2 REMARK 2 RESOLUTION. 3.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, COOT, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.740 REMARK 3 NUMBER OF PARTICLES : 153633 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 8K5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039565. 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 : GSK256073 BOUND HUMAN HYDROXY REMARK 245 -CARBOXYLIC ACID RECEPTOR 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 : 7.50 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) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 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 : 105000 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 GLY A -112 REMARK 465 PRO A -111 REMARK 465 GLY A -110 REMARK 465 ALA A -109 REMARK 465 PRO A -108 REMARK 465 ALA A -107 REMARK 465 ASP A -106 REMARK 465 LEU A -105 REMARK 465 GLU A -104 REMARK 465 ASP A -103 REMARK 465 ASN A -102 REMARK 465 TRP A -101 REMARK 465 GLU A -100 REMARK 465 THR A -99 REMARK 465 LEU A -98 REMARK 465 ASN A -97 REMARK 465 ASP A -96 REMARK 465 ASN A -95 REMARK 465 LEU A -94 REMARK 465 LYS A -93 REMARK 465 VAL A -92 REMARK 465 ILE A -91 REMARK 465 GLU A -90 REMARK 465 LYS A -89 REMARK 465 ALA A -88 REMARK 465 ASP A -87 REMARK 465 ASN A -86 REMARK 465 ALA A -85 REMARK 465 ALA A -84 REMARK 465 GLN A -83 REMARK 465 VAL A -82 REMARK 465 LYS A -81 REMARK 465 ASP A -80 REMARK 465 ALA A -79 REMARK 465 LEU A -78 REMARK 465 THR A -77 REMARK 465 LYS A -76 REMARK 465 MET A -75 REMARK 465 ARG A -74 REMARK 465 ALA A -73 REMARK 465 ALA A -72 REMARK 465 ALA A -71 REMARK 465 LEU A -70 REMARK 465 ASP A -69 REMARK 465 ALA A -68 REMARK 465 GLN A -67 REMARK 465 LYS A -66 REMARK 465 ALA A -65 REMARK 465 THR A -64 REMARK 465 PRO A -63 REMARK 465 PRO A -62 REMARK 465 LYS A -61 REMARK 465 LEU A -60 REMARK 465 GLU A -59 REMARK 465 ASP A -58 REMARK 465 LYS A -57 REMARK 465 SER A -56 REMARK 465 PRO A -55 REMARK 465 ASP A -54 REMARK 465 SER A -53 REMARK 465 PRO A -52 REMARK 465 GLU A -51 REMARK 465 MET A -50 REMARK 465 LYS A -49 REMARK 465 ASP A -48 REMARK 465 PHE A -47 REMARK 465 ARG A -46 REMARK 465 HIS A -45 REMARK 465 GLY A -44 REMARK 465 PHE A -43 REMARK 465 ASP A -42 REMARK 465 ILE A -41 REMARK 465 LEU A -40 REMARK 465 VAL A -39 REMARK 465 GLY A -38 REMARK 465 GLN A -37 REMARK 465 ILE A -36 REMARK 465 ASP A -35 REMARK 465 ASP A -34 REMARK 465 ALA A -33 REMARK 465 LEU A -32 REMARK 465 LYS A -31 REMARK 465 LEU A -30 REMARK 465 ALA A -29 REMARK 465 ASN A -28 REMARK 465 GLU A -27 REMARK 465 GLY A -26 REMARK 465 LYS A -25 REMARK 465 VAL A -24 REMARK 465 LYS A -23 REMARK 465 GLU A -22 REMARK 465 ALA A -21 REMARK 465 GLN A -20 REMARK 465 ALA A -19 REMARK 465 ALA A -18 REMARK 465 ALA A -17 REMARK 465 GLU A -16 REMARK 465 GLN A -15 REMARK 465 LEU A -14 REMARK 465 LYS A -13 REMARK 465 THR A -12 REMARK 465 THR A -11 REMARK 465 ARG A -10 REMARK 465 ASN A -9 REMARK 465 ALA A -8 REMARK 465 TYR A -7 REMARK 465 ILE A -6 REMARK 465 GLN A -5 REMARK 465 LYS A -4 REMARK 465 TYR A -3 REMARK 465 LEU A -2 REMARK 465 GLU A -1 REMARK 465 PHE A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 ARG A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 LEU A 6 REMARK 465 GLN A 7 REMARK 465 ASP A 8 REMARK 465 SER A 300 REMARK 465 PHE A 301 REMARK 465 PRO A 302 REMARK 465 ASN A 303 REMARK 465 PHE A 304 REMARK 465 PHE A 305 REMARK 465 SER A 306 REMARK 465 THR A 307 REMARK 465 LEU A 308 REMARK 465 ILE A 309 REMARK 465 ASN A 310 REMARK 465 ARG A 311 REMARK 465 CYS A 312 REMARK 465 LEU A 313 REMARK 465 GLN A 314 REMARK 465 ARG A 315 REMARK 465 LYS A 316 REMARK 465 MET A 317 REMARK 465 THR A 318 REMARK 465 GLY A 319 REMARK 465 GLU A 320 REMARK 465 PRO A 321 REMARK 465 ASP A 322 REMARK 465 ASN A 323 REMARK 465 ASN A 324 REMARK 465 ARG A 325 REMARK 465 SER A 326 REMARK 465 THR A 327 REMARK 465 SER A 328 REMARK 465 VAL A 329 REMARK 465 GLU A 330 REMARK 465 LEU A 331 REMARK 465 THR A 332 REMARK 465 GLY A 333 REMARK 465 ASP A 334 REMARK 465 PRO A 335 REMARK 465 ASN A 336 REMARK 465 LYS A 337 REMARK 465 THR A 338 REMARK 465 ARG A 339 REMARK 465 GLY A 340 REMARK 465 ALA A 341 REMARK 465 PRO A 342 REMARK 465 GLU A 343 REMARK 465 ALA A 344 REMARK 465 LEU A 345 REMARK 465 MET A 346 REMARK 465 ALA A 347 REMARK 465 ASN A 348 REMARK 465 SER A 349 REMARK 465 GLY A 350 REMARK 465 GLU A 351 REMARK 465 PRO A 352 REMARK 465 TRP A 353 REMARK 465 SER A 354 REMARK 465 PRO A 355 REMARK 465 SER A 356 REMARK 465 TYR A 357 REMARK 465 LEU A 358 REMARK 465 GLY A 359 REMARK 465 PRO A 360 REMARK 465 THR A 361 REMARK 465 SER A 362 REMARK 465 PRO A 363 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 LYS A 15 CG CD CE NZ REMARK 470 CYS A 19 SG REMARK 470 ASP A 23 CG OD1 OD2 REMARK 470 PHE A 25 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 LEU A 56 CG CD1 CD2 REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 PRO A 81 CG CD REMARK 470 MET A 84 CG SD CE REMARK 470 ASP A 85 CG OD1 OD2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 MET A 106 CG SD CE REMARK 470 LYS A 166 CG CD CE NZ REMARK 470 PHE A 186 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 225 CE NZ REMARK 470 CYS A 266 SG REMARK 470 ARG A 270 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 SER A 58 111.23 -162.37 REMARK 500 HIS A 131 68.71 -118.61 REMARK 500 PHE A 180 51.29 -92.84 REMARK 500 SER A 261 -128.00 59.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36902 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF GSK256073 BOUND HUMAN HYDROXY-CARBOXYLIC ACID REMARK 900 RECEPTOR 2 (LOCAL REFINEMENT) DBREF 8K5D A -112 0 PDB 8K5D 8K5D -112 0 DBREF 8K5D A 1 363 UNP Q8TDS4 HCAR2_HUMAN 1 363 SEQRES 1 A 476 GLY PRO GLY ALA PRO ALA ASP LEU GLU ASP ASN TRP GLU SEQRES 2 A 476 THR LEU ASN ASP ASN LEU LYS VAL ILE GLU LYS ALA ASP SEQRES 3 A 476 ASN ALA ALA GLN VAL LYS ASP ALA LEU THR LYS MET ARG SEQRES 4 A 476 ALA ALA ALA LEU ASP ALA GLN LYS ALA THR PRO PRO LYS SEQRES 5 A 476 LEU GLU ASP LYS SER PRO ASP SER PRO GLU MET LYS ASP SEQRES 6 A 476 PHE ARG HIS GLY PHE ASP ILE LEU VAL GLY GLN ILE ASP SEQRES 7 A 476 ASP ALA LEU LYS LEU ALA ASN GLU GLY LYS VAL LYS GLU SEQRES 8 A 476 ALA GLN ALA ALA ALA GLU GLN LEU LYS THR THR ARG ASN SEQRES 9 A 476 ALA TYR ILE GLN LYS TYR LEU GLU PHE MET ASN ARG HIS SEQRES 10 A 476 HIS LEU GLN ASP HIS PHE LEU GLU ILE ASP LYS LYS ASN SEQRES 11 A 476 CYS CYS VAL PHE ARG ASP ASP PHE ILE VAL LYS VAL LEU SEQRES 12 A 476 PRO PRO VAL LEU GLY LEU GLU PHE ILE PHE GLY LEU LEU SEQRES 13 A 476 GLY ASN GLY LEU ALA LEU TRP ILE PHE CYS PHE HIS LEU SEQRES 14 A 476 LYS SER TRP LYS SER SER ARG ILE PHE LEU PHE ASN LEU SEQRES 15 A 476 ALA VAL ALA ASP PHE LEU LEU ILE ILE CYS LEU PRO PHE SEQRES 16 A 476 LEU MET ASP ASN TYR VAL ARG ARG TRP ASP TRP LYS PHE SEQRES 17 A 476 GLY ASP ILE PRO CYS ARG LEU MET LEU PHE MET LEU ALA SEQRES 18 A 476 MET ASN ARG GLN GLY SER ILE ILE PHE LEU THR VAL VAL SEQRES 19 A 476 ALA VAL ASP ARG TYR PHE ARG VAL VAL HIS PRO HIS HIS SEQRES 20 A 476 ALA LEU ASN LYS ILE SER ASN ARG THR ALA ALA ILE ILE SEQRES 21 A 476 SER CYS LEU LEU TRP GLY ILE THR ILE GLY LEU THR VAL SEQRES 22 A 476 HIS LEU LEU LYS LYS LYS MET PRO ILE GLN ASN GLY GLY SEQRES 23 A 476 ALA ASN LEU CYS SER SER PHE SER ILE CYS HIS THR PHE SEQRES 24 A 476 GLN TRP HIS GLU ALA MET PHE LEU LEU GLU PHE PHE LEU SEQRES 25 A 476 PRO LEU GLY ILE ILE LEU PHE CYS SER ALA ARG ILE ILE SEQRES 26 A 476 TRP SER LEU ARG GLN ARG GLN MET ASP ARG HIS ALA LYS SEQRES 27 A 476 ILE LYS ARG ALA ILE THR PHE ILE MET VAL VAL ALA ILE SEQRES 28 A 476 VAL PHE VAL ILE CYS PHE LEU PRO SER VAL VAL VAL ARG SEQRES 29 A 476 ILE ARG ILE PHE TRP LEU LEU HIS THR SER GLY THR GLN SEQRES 30 A 476 ASN CYS GLU VAL TYR ARG SER VAL ASP LEU ALA PHE PHE SEQRES 31 A 476 ILE THR LEU SER PHE THR TYR MET ASN SER MET LEU ASP SEQRES 32 A 476 PRO VAL VAL TYR TYR PHE SER SER PRO SER PHE PRO ASN SEQRES 33 A 476 PHE PHE SER THR LEU ILE ASN ARG CYS LEU GLN ARG LYS SEQRES 34 A 476 MET THR GLY GLU PRO ASP ASN ASN ARG SER THR SER VAL SEQRES 35 A 476 GLU LEU THR GLY ASP PRO ASN LYS THR ARG GLY ALA PRO SEQRES 36 A 476 GLU ALA LEU MET ALA ASN SER GLY GLU PRO TRP SER PRO SEQRES 37 A 476 SER TYR LEU GLY PRO THR SER PRO HET OKL A 401 17 HETNAM OKL 8-CHLORANYL-3-PENTYL-7H-PURINE-2,6-DIONE FORMUL 2 OKL C10 H13 CL N4 O2 HELIX 1 AA1 VAL A 29 PHE A 54 1 26 HELIX 2 AA2 LYS A 60 ARG A 89 1 30 HELIX 3 AA3 ASP A 97 VAL A 130 1 34 HELIX 4 AA4 HIS A 134 LYS A 138 5 5 HELIX 5 AA5 SER A 140 LYS A 166 1 27 HELIX 6 AA6 GLN A 187 ARG A 218 1 32 HELIX 7 AA7 HIS A 223 THR A 260 1 38 HELIX 8 AA8 CYS A 266 TYR A 294 1 29 SHEET 1 AA1 2 PHE A 10 GLU A 12 0 SHEET 2 AA1 2 ASN A 17 CYS A 19 -1 O CYS A 18 N LEU A 11 SHEET 1 AA2 2 ILE A 169 ASN A 171 0 SHEET 2 AA2 2 ALA A 174 LEU A 176 -1 O ALA A 174 N ASN A 171 SSBOND 1 CYS A 18 CYS A 183 1555 1555 2.03 SSBOND 2 CYS A 100 CYS A 177 1555 1555 2.03 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