HEADER SIGNALING PROTEIN 14-MAY-25 9UXN TITLE LOCAL REFINEMENT OF SUCCINATE BOUND OXGR1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-OXOGLUTARATE RECEPTOR 1; COMPND 3 CHAIN: R; COMPND 4 SYNONYM: ALPHA-KETOGLUTARATE RECEPTOR 1,G-PROTEIN COUPLED RECEPTOR COMPND 5 80,G-PROTEIN COUPLED RECEPTOR 99,P2Y PURINOCEPTOR 15,P2Y15,P2Y-LIKE COMPND 6 GPCR,P2Y-LIKE NUCLEOTIDE RECEPTOR; COMPND 7 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: OXGR1, GPR80, GPR99, P2RY15, P2Y15; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS 2-OXOGLUTARATE, AKG, 2-OXOGLUTARATE RECEPTOR 1, OXGR1, CRYO-EM, KEYWDS 2 MEMBRANE PROTEIN, SIGNALING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.LIU,X.ZHANG,H.E.XU REVDAT 1 27-MAY-26 9UXN 0 JRNL AUTH H.LIU,X.ZHANG,H.E.XU JRNL TITL LOCAL REFINEMENT OF AKG BOUND OXGR1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.700 REMARK 3 NUMBER OF PARTICLES : 360330 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 9UXN 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_1300059454. 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 : SUCCINATE BOUND OXGR1 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 : 7.40 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 TALOS ARCTICA 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 : DARK 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ASN R 2 REMARK 465 GLU R 3 REMARK 465 PRO R 4 REMARK 465 LEU R 5 REMARK 465 ASP R 6 REMARK 465 TYR R 7 REMARK 465 LEU R 8 REMARK 465 ALA R 9 REMARK 465 ASN R 10 REMARK 465 ALA R 11 REMARK 465 SER R 12 REMARK 465 ASP R 13 REMARK 465 PHE R 14 REMARK 465 PRO R 15 REMARK 465 ASP R 16 REMARK 465 TYR R 17 REMARK 465 ALA R 18 REMARK 465 ALA R 19 REMARK 465 ALA R 20 REMARK 465 PHE R 21 REMARK 465 GLY R 22 REMARK 465 ASN R 23 REMARK 465 CYS R 24 REMARK 465 THR R 25 REMARK 465 ASP R 26 REMARK 465 GLU R 27 REMARK 465 CYS R 314 REMARK 465 SER R 315 REMARK 465 THR R 316 REMARK 465 VAL R 317 REMARK 465 ARG R 318 REMARK 465 CYS R 319 REMARK 465 LYS R 320 REMARK 465 VAL R 321 REMARK 465 SER R 322 REMARK 465 GLY R 323 REMARK 465 ASN R 324 REMARK 465 LEU R 325 REMARK 465 GLU R 326 REMARK 465 GLN R 327 REMARK 465 ALA R 328 REMARK 465 LYS R 329 REMARK 465 LYS R 330 REMARK 465 ILE R 331 REMARK 465 SER R 332 REMARK 465 TYR R 333 REMARK 465 SER R 334 REMARK 465 ASN R 335 REMARK 465 ASN R 336 REMARK 465 PRO R 337 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 ASN R 98 CG OD1 ND2 REMARK 470 LEU R 270 CG CD1 CD2 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 PHE R 207 -54.38 -120.42 REMARK 500 VAL R 303 -57.29 -123.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64587 RELATED DB: EMDB REMARK 900 LOCAL REFINEMENT OF SUCCINATE BOUND OXGR1 DBREF 9UXN R 1 337 UNP Q96P68 OXGR1_HUMAN 1 337 SEQRES 1 R 337 MET ASN GLU PRO LEU ASP TYR LEU ALA ASN ALA SER ASP SEQRES 2 R 337 PHE PRO ASP TYR ALA ALA ALA PHE GLY ASN CYS THR ASP SEQRES 3 R 337 GLU ASN ILE PRO LEU LYS MET HIS TYR LEU PRO VAL ILE SEQRES 4 R 337 TYR GLY ILE ILE PHE LEU VAL GLY PHE PRO GLY ASN ALA SEQRES 5 R 337 VAL VAL ILE SER THR TYR ILE PHE LYS MET ARG PRO TRP SEQRES 6 R 337 LYS SER SER THR ILE ILE MET LEU ASN LEU ALA CYS THR SEQRES 7 R 337 ASP LEU LEU TYR LEU THR SER LEU PRO PHE LEU ILE HIS SEQRES 8 R 337 TYR TYR ALA SER GLY GLU ASN TRP ILE PHE GLY ASP PHE SEQRES 9 R 337 MET CYS LYS PHE ILE ARG PHE SER PHE HIS PHE ASN LEU SEQRES 10 R 337 TYR SER SER ILE LEU PHE LEU THR CYS PHE SER ILE PHE SEQRES 11 R 337 ARG TYR CYS VAL ILE ILE HIS PRO MET SER CYS PHE SER SEQRES 12 R 337 ILE HIS LYS THR ARG CYS ALA VAL VAL ALA CYS ALA VAL SEQRES 13 R 337 VAL TRP ILE ILE SER LEU VAL ALA VAL ILE PRO MET THR SEQRES 14 R 337 PHE LEU ILE THR SER THR ASN ARG THR ASN ARG SER ALA SEQRES 15 R 337 CYS LEU ASP LEU THR SER SER ASP GLU LEU ASN THR ILE SEQRES 16 R 337 LYS TRP TYR ASN LEU ILE LEU THR ALA THR THR PHE CYS SEQRES 17 R 337 LEU PRO LEU VAL ILE VAL THR LEU CYS TYR THR THR ILE SEQRES 18 R 337 ILE HIS THR LEU THR HIS GLY LEU GLN THR ASP SER CYS SEQRES 19 R 337 LEU LYS GLN LYS ALA ARG ARG LEU THR ILE LEU LEU LEU SEQRES 20 R 337 LEU ALA PHE TYR VAL CYS PHE LEU PRO PHE HIS ILE LEU SEQRES 21 R 337 ARG VAL ILE ARG ILE GLU SER ARG LEU LEU SER ILE SER SEQRES 22 R 337 CYS SER ILE GLU ASN GLN ILE HIS GLU ALA TYR ILE VAL SEQRES 23 R 337 SER ARG PRO LEU ALA ALA LEU ASN THR PHE GLY ASN LEU SEQRES 24 R 337 LEU LEU TYR VAL VAL VAL SER ASP ASN PHE GLN GLN ALA SEQRES 25 R 337 VAL CYS SER THR VAL ARG CYS LYS VAL SER GLY ASN LEU SEQRES 26 R 337 GLU GLN ALA LYS LYS ILE SER TYR SER ASN ASN PRO HET SIN R 401 8 HETNAM SIN SUCCINIC ACID FORMUL 2 SIN C4 H6 O4 FORMUL 3 HOH *3(H2 O) HELIX 1 AA1 ASN R 28 PHE R 60 1 33 HELIX 2 AA2 LYS R 66 SER R 95 1 30 HELIX 3 AA3 GLY R 102 HIS R 137 1 36 HELIX 4 AA4 CYS R 141 HIS R 145 5 5 HELIX 5 AA5 LYS R 146 ILE R 166 1 21 HELIX 6 AA6 PRO R 167 PHE R 170 5 4 HELIX 7 AA7 GLU R 191 PHE R 207 1 17 HELIX 8 AA8 PHE R 207 GLY R 228 1 22 HELIX 9 AA9 SER R 233 LEU R 270 1 38 HELIX 10 AB1 SER R 273 LEU R 293 1 21 HELIX 11 AB2 LEU R 293 VAL R 303 1 11 HELIX 12 AB3 SER R 306 VAL R 313 1 8 SHEET 1 AA1 2 SER R 174 THR R 175 0 SHEET 2 AA1 2 ALA R 182 CYS R 183 -1 O ALA R 182 N THR R 175 SSBOND 1 CYS R 106 CYS R 183 1555 1555 2.25 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 CONECT 638 1258 CONECT 1258 638 CONECT 2297 2298 2299 2300 CONECT 2298 2297 CONECT 2299 2297 CONECT 2300 2297 2301 CONECT 2301 2300 2302 CONECT 2302 2301 2303 2304 CONECT 2303 2302 CONECT 2304 2302 MASTER 183 0 1 12 2 0 0 6 2306 1 10 26 END