HEADER MEMBRANE PROTEIN 12-MAY-25 9UWD TITLE CRYO-EM STRUCTURE OF INACTIVE-DP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROSTAGLANDIN D2 RECEPTOR,SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PGD RECEPTOR,PGD2 RECEPTOR,PROSTANOID DP RECEPTOR,CYTOCHROME COMPND 5 B-562; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, ESCHERICHIA COLI; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606, 562; SOURCE 5 GENE: PTGDR, CYBC; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS GPCR, DP1, INACTIVE, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.XU,Y.XU,C.WU,H.E.XU REVDAT 2 25-JUN-25 9UWD 1 JRNL REVDAT 1 28-MAY-25 9UWD 0 JRNL AUTH J.XU,Y.WU,Y.XU,Y.LI,X.HE,H.ZHANG,J.J.WANG,J.HOU,J.LI,W.HU, JRNL AUTH 2 K.WU,Q.YUAN,C.WU,H.E.XU JRNL TITL MOLECULAR BASIS FOR LIGAND RECOGNITION AND RECEPTOR JRNL TITL 2 ACTIVATION OF THE PROSTAGLANDIN D2 RECEPTOR DP1. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 02122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 40440061 JRNL DOI 10.1073/PNAS.2501902122 REMARK 2 REMARK 2 RESOLUTION. 3.41 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) : 3.410 REMARK 3 NUMBER OF PARTICLES : 41270 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 9UWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 16-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059360. 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 : DP1 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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 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 CD2 LEU A 345 CZ PHE A 427 2.00 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 PRO A 408 C - N - CA ANGL. DEV. = -16.4 DEGREES REMARK 500 PRO A 408 CA - N - CD ANGL. DEV. = -10.3 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 SER A 19 17.99 121.85 REMARK 500 LEU A 46 7.28 -68.79 REMARK 500 ARG A 55 74.61 50.31 REMARK 500 THR A 181 -71.27 -84.07 REMARK 500 SER A 193 106.01 -8.96 REMARK 500 TYR A 375 4.47 -64.76 REMARK 500 VAL A 381 30.39 -142.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64550 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF INACTIVE-DP1 DBREF 9UWD A 1 232 UNP Q13258 PD2R_HUMAN 1 232 DBREF 9UWD A 233 337 UNP P0ABE7 C562_ECOLX 23 127 DBREF 9UWD A 346 428 UNP Q13258 PD2R_HUMAN 258 340 SEQADV 9UWD ALA A 228 UNP Q13258 MET 228 CONFLICT SEQADV 9UWD ARG A 229 UNP Q13258 HIS 229 CONFLICT SEQADV 9UWD GLN A 231 UNP Q13258 ARG 231 CONFLICT SEQADV 9UWD TRP A 239 UNP P0ABE7 MET 29 CONFLICT SEQADV 9UWD ILE A 334 UNP P0ABE7 HIS 124 CONFLICT SEQADV 9UWD LEU A 338 UNP P0ABE7 LINKER SEQADV 9UWD GLU A 339 UNP P0ABE7 LINKER SEQADV 9UWD ARG A 340 UNP P0ABE7 LINKER SEQADV 9UWD ALA A 341 UNP P0ABE7 LINKER SEQADV 9UWD ARG A 342 UNP P0ABE7 LINKER SEQADV 9UWD SER A 343 UNP P0ABE7 LINKER SEQADV 9UWD THR A 344 UNP P0ABE7 LINKER SEQADV 9UWD LEU A 345 UNP P0ABE7 LINKER SEQRES 1 A 428 MET LYS SER PRO PHE TYR ARG CYS GLN ASN THR THR SER SEQRES 2 A 428 VAL GLU LYS GLY ASN SER ALA VAL MET GLY GLY VAL LEU SEQRES 3 A 428 PHE SER THR GLY LEU LEU GLY ASN LEU LEU ALA LEU GLY SEQRES 4 A 428 LEU LEU ALA ARG SER GLY LEU GLY TRP CYS SER ARG ARG SEQRES 5 A 428 PRO LEU ARG PRO LEU PRO SER VAL PHE TYR MET LEU VAL SEQRES 6 A 428 CYS GLY LEU THR VAL THR ASP LEU LEU GLY LYS CYS LEU SEQRES 7 A 428 LEU SER PRO VAL VAL LEU ALA ALA TYR ALA GLN ASN ARG SEQRES 8 A 428 SER LEU ARG VAL LEU ALA PRO ALA LEU ASP ASN SER LEU SEQRES 9 A 428 CYS GLN ALA PHE ALA PHE PHE MET SER PHE PHE GLY LEU SEQRES 10 A 428 SER SER THR LEU GLN LEU LEU ALA MET ALA LEU GLU CYS SEQRES 11 A 428 TRP LEU SER LEU GLY HIS PRO PHE PHE TYR ARG ARG HIS SEQRES 12 A 428 ILE THR LEU ARG LEU GLY ALA LEU VAL ALA PRO VAL VAL SEQRES 13 A 428 SER ALA PHE SER LEU ALA PHE CYS ALA LEU PRO PHE MET SEQRES 14 A 428 GLY PHE GLY LYS PHE VAL GLN TYR CYS PRO GLY THR TRP SEQRES 15 A 428 CYS PHE ILE GLN MET VAL HIS GLU GLU GLY SER LEU SER SEQRES 16 A 428 VAL LEU GLY TYR SER VAL LEU TYR SER SER LEU MET ALA SEQRES 17 A 428 LEU LEU VAL LEU ALA THR VAL LEU CYS ASN LEU GLY ALA SEQRES 18 A 428 MET ARG ASN LEU TYR ALA ALA ARG ARG GLN LEU ALA ASP SEQRES 19 A 428 LEU GLU ASP ASN TRP GLU THR LEU ASN ASP ASN LEU LYS SEQRES 20 A 428 VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL LYS ASP SEQRES 21 A 428 ALA LEU THR LYS MET ARG ALA ALA ALA LEU ASP ALA GLN SEQRES 22 A 428 LYS ALA THR PRO PRO LYS LEU GLU ASP LYS SER PRO ASP SEQRES 23 A 428 SER PRO GLU MET LYS ASP PHE ARG HIS GLY PHE ASP ILE SEQRES 24 A 428 LEU VAL GLY GLN ILE ASP ASP ALA LEU LYS LEU ALA ASN SEQRES 25 A 428 GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA GLU GLN SEQRES 26 A 428 LEU LYS THR THR ARG ASN ALA TYR ILE GLN LYS TYR LEU SEQRES 27 A 428 GLU ARG ALA ARG SER THR LEU LEU GLU GLU LEU ASP HIS SEQRES 28 A 428 LEU LEU LEU LEU ALA LEU MET THR VAL LEU PHE THR MET SEQRES 29 A 428 CYS SER LEU PRO VAL ILE TYR ARG ALA TYR TYR GLY ALA SEQRES 30 A 428 PHE LYS ASP VAL LYS GLU LYS ASN ARG THR SER GLU GLU SEQRES 31 A 428 ALA GLU ASP LEU ARG ALA LEU ARG PHE LEU SER VAL ILE SEQRES 32 A 428 SER ILE VAL ASP PRO TRP ILE PHE ILE ILE PHE ARG SER SEQRES 33 A 428 PRO VAL PHE ARG ILE PHE PHE HIS LYS ILE PHE ILE HELIX 1 AA1 SER A 19 GLY A 45 1 27 HELIX 2 AA2 SER A 59 ASN A 90 1 32 HELIX 3 AA3 SER A 92 ALA A 97 1 6 HELIX 4 AA4 ASN A 102 LEU A 134 1 33 HELIX 5 AA5 HIS A 136 ILE A 144 1 9 HELIX 6 AA6 ARG A 147 CYS A 164 1 18 HELIX 7 AA7 ALA A 165 GLY A 170 1 6 HELIX 8 AA8 SER A 193 GLU A 250 1 58 HELIX 9 AA9 ASN A 254 LYS A 274 1 21 HELIX 10 AB1 SER A 287 GLU A 313 1 27 HELIX 11 AB2 VAL A 316 PHE A 378 1 63 HELIX 12 AB3 THR A 387 ARG A 415 1 29 HELIX 13 AB4 SER A 416 ILE A 428 1 13 SHEET 1 AA1 2 PHE A 174 GLN A 176 0 SHEET 2 AA1 2 CYS A 183 ILE A 185 -1 O PHE A 184 N VAL A 175 SSBOND 1 CYS A 8 CYS A 178 1555 1555 1.95 SSBOND 2 CYS A 105 CYS A 183 1555 1555 2.03 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 3356 ILE A 428 CONECT 70 1358 CONECT 780 1396 CONECT 1358 70 CONECT 1396 780 MASTER 150 0 0 13 2 0 0 6 3355 1 4 33 END