HEADER MEMBRANE PROTEIN 01-SEP-21 7S15 TITLE GLP-1 RECEPTOR BOUND WITH PFIZER SMALL MOLECULE AGONIST COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCAGON-LIKE PEPTIDE 1 RECEPTOR; COMPND 3 CHAIN: R; COMPND 4 SYNONYM: GLP-1 RECEPTOR,GLP-1-R,GLP-1R; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GLP1R; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS GLP-1R, GPCR, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.LIU,J.M.DIAS,S.HAN REVDAT 3 06-JUL-22 7S15 1 JRNL REVDAT 2 15-JUN-22 7S15 1 JRNL REVDAT 1 08-JUN-22 7S15 0 JRNL AUTH D.A.GRIFFITH,D.J.EDMONDS,J.P.FORTIN,A.S.KALGUTKAR, JRNL AUTH 2 J.B.KUZMISKI,P.M.LORIA,A.R.SAXENA,S.W.BAGLEY,C.BUCKERIDGE, JRNL AUTH 3 J.M.CURTO,D.R.DERKSEN,J.M.DIAS,M.C.GRIFFOR,S.HAN, JRNL AUTH 4 V.M.JACKSON,M.S.LANDIS,D.LETTIERE,C.LIMBERAKIS,Y.LIU, JRNL AUTH 5 A.M.MATHIOWETZ,J.C.PATEL,D.W.PIOTROWSKI,D.A.PRICE, JRNL AUTH 6 R.B.RUGGERI,D.A.TESS JRNL TITL A SMALL-MOLECULE ORAL AGONIST OF THE HUMAN GLUCAGON-LIKE JRNL TITL 2 PEPTIDE-1 RECEPTOR. JRNL REF J.MED.CHEM. V. 65 8208 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35647711 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01856 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GAUTOMATCH, SERIALEM, GCTF, COOT, REMARK 3 RELION, RELION, RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6B3J REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 120000 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 7S15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000257997. 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 : AGONIST BOUND GLP1 RECEPTOR REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.08 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : -2 BLOTTING FORCE 4S BLOTTING REMARK 245 TIME REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : GLP1 RECEPTOR IS STABILIZED BY REMARK 245 STAR MUTATIONS REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 19000 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 200.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 29000 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 ARG R 24 REMARK 465 PRO R 25 REMARK 465 GLN R 26 REMARK 465 GLY R 27 REMARK 465 ALA R 28 REMARK 465 THR R 29 REMARK 465 SER R 129 REMARK 465 LYS R 130 REMARK 465 ARG R 131 REMARK 465 GLY R 132 REMARK 465 GLU R 133 REMARK 465 ARG R 134 REMARK 465 GLU R 339 REMARK 465 MET R 340 REMARK 465 CYS R 341 REMARK 465 LYS R 342 REMARK 465 LEU R 422 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 OH TYR R 241 OE2 GLU R 364 2.17 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 CYS R 126 CA - CB - SG ANGL. DEV. = 7.7 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 ALA R 57 -60.37 -94.51 REMARK 500 GLU R 68 -2.26 65.09 REMARK 500 PRO R 77 -177.68 -69.80 REMARK 500 GLN R 97 37.17 -99.37 REMARK 500 ASN R 115 -3.65 75.58 REMARK 500 LEU R 123 13.55 -141.41 REMARK 500 CYS R 126 37.34 -99.24 REMARK 500 GLU R 138 14.61 -140.76 REMARK 500 HIS R 171 9.55 57.55 REMARK 500 SER R 223 9.51 -69.87 REMARK 500 SER R 258 -3.86 69.07 REMARK 500 GLN R 263 -8.32 -56.06 REMARK 500 ASP R 293 -162.69 -79.15 REMARK 500 THR R 298 42.07 36.86 REMARK 500 ASN R 300 141.40 -172.73 REMARK 500 MET R 303 12.75 -141.92 REMARK 500 TRP R 306 34.84 -99.60 REMARK 500 ILE R 345 -62.13 -102.38 REMARK 500 HIS R 374 5.43 -69.29 REMARK 500 CYS R 403 -2.23 -140.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24794 RELATED DB: EMDB REMARK 900 GLP-1 RECEPTOR BOUND WITH PFIZER SMALL MOLECULE AGONIST DBREF 7S15 R 24 422 UNP P43220 GLP1R_HUMAN 24 422 SEQADV 7S15 TYR R 146 UNP P43220 ILE 146 ENGINEERED MUTATION SEQADV 7S15 ARG R 208 UNP P43220 ALA 208 ENGINEERED MUTATION SEQADV 7S15 GLU R 213 UNP P43220 GLN 213 ENGINEERED MUTATION SEQADV 7S15 ARG R 219 UNP P43220 SER 219 ENGINEERED MUTATION SEQADV 7S15 ALA R 260 UNP P43220 LEU 260 ENGINEERED MUTATION SEQADV 7S15 ALA R 291 UNP P43220 TYR 291 ENGINEERED MUTATION SEQADV 7S15 GLU R 339 UNP P43220 LEU 339 ENGINEERED MUTATION SEQADV 7S15 GLN R 346 UNP P43220 LYS 346 ENGINEERED MUTATION SEQRES 1 R 399 ARG PRO GLN GLY ALA THR VAL SER LEU TRP GLU THR VAL SEQRES 2 R 399 GLN LYS TRP ARG GLU TYR ARG ARG GLN CYS GLN ARG SER SEQRES 3 R 399 LEU THR GLU ASP PRO PRO PRO ALA THR ASP LEU PHE CYS SEQRES 4 R 399 ASN ARG THR PHE ASP GLU TYR ALA CYS TRP PRO ASP GLY SEQRES 5 R 399 GLU PRO GLY SER PHE VAL ASN VAL SER CYS PRO TRP TYR SEQRES 6 R 399 LEU PRO TRP ALA SER SER VAL PRO GLN GLY HIS VAL TYR SEQRES 7 R 399 ARG PHE CYS THR ALA GLU GLY LEU TRP LEU GLN LYS ASP SEQRES 8 R 399 ASN SER SER LEU PRO TRP ARG ASP LEU SER GLU CYS GLU SEQRES 9 R 399 GLU SER LYS ARG GLY GLU ARG SER SER PRO GLU GLU GLN SEQRES 10 R 399 LEU LEU PHE LEU TYR TYR ILE TYR THR VAL GLY TYR ALA SEQRES 11 R 399 LEU SER PHE SER ALA LEU VAL ILE ALA SER ALA ILE LEU SEQRES 12 R 399 LEU GLY PHE ARG HIS LEU HIS CYS THR ARG ASN TYR ILE SEQRES 13 R 399 HIS LEU ASN LEU PHE ALA SER PHE ILE LEU ARG ALA LEU SEQRES 14 R 399 SER VAL PHE ILE LYS ASP ALA ALA LEU LYS TRP MET TYR SEQRES 15 R 399 SER THR ARG ALA GLN GLN HIS GLU TRP ASP GLY LEU LEU SEQRES 16 R 399 ARG TYR GLN ASP SER LEU SER CYS ARG LEU VAL PHE LEU SEQRES 17 R 399 LEU MET GLN TYR CYS VAL ALA ALA ASN TYR TYR TRP LEU SEQRES 18 R 399 LEU VAL GLU GLY VAL TYR LEU TYR THR LEU LEU ALA PHE SEQRES 19 R 399 SER VAL ALA SER GLU GLN TRP ILE PHE ARG LEU TYR VAL SEQRES 20 R 399 SER ILE GLY TRP GLY VAL PRO LEU LEU PHE VAL VAL PRO SEQRES 21 R 399 TRP GLY ILE VAL LYS TYR LEU ALA GLU ASP GLU GLY CYS SEQRES 22 R 399 TRP THR ARG ASN SER ASN MET ASN TYR TRP LEU ILE ILE SEQRES 23 R 399 ARG LEU PRO ILE LEU PHE ALA ILE GLY VAL ASN PHE LEU SEQRES 24 R 399 ILE PHE VAL ARG VAL ILE CYS ILE VAL VAL SER LYS LEU SEQRES 25 R 399 LYS ALA ASN GLU MET CYS LYS THR ASP ILE GLN CYS ARG SEQRES 26 R 399 LEU ALA LYS SER THR LEU THR LEU ILE PRO LEU LEU GLY SEQRES 27 R 399 THR HIS GLU VAL ILE PHE ALA PHE VAL MET ASP GLU HIS SEQRES 28 R 399 ALA ARG GLY THR LEU ARG PHE ILE LYS LEU PHE THR GLU SEQRES 29 R 399 LEU SER PHE THR SER PHE GLN GLY LEU MET VAL ALA ILE SEQRES 30 R 399 LEU TYR CYS PHE VAL ASN ASN GLU VAL GLN LEU GLU PHE SEQRES 31 R 399 ARG LYS SER TRP GLU ARG TRP ARG LEU HET 82L R 501 43 HETNAM 82L 2-[(4-{6-[(2,4-DIFLUOROPHENYL)METHOXY]PYRIDIN-2- HETNAM 2 82L YL}PIPERIDIN-1-YL)METHYL]-1-[(1-ETHYL-1H-IMIDAZOL-5- HETNAM 3 82L YL)METHYL]-1H-BENZIMIDAZOLE-6-CARBOXYLIC ACID FORMUL 2 82L C32 H32 F2 N6 O3 HELIX 1 AA1 SER R 31 GLU R 52 1 22 HELIX 2 AA2 TRP R 91 VAL R 95 5 5 HELIX 3 AA3 GLU R 138 LEU R 166 1 29 HELIX 4 AA4 CYS R 174 LYS R 202 1 29 HELIX 5 AA5 TRP R 214 GLN R 221 1 8 HELIX 6 AA6 SER R 225 LEU R 254 1 30 HELIX 7 AA7 GLN R 263 VAL R 276 1 14 HELIX 8 AA8 PRO R 277 PHE R 280 5 4 HELIX 9 AA9 VAL R 281 GLU R 292 1 12 HELIX 10 AB1 TRP R 306 LEU R 335 1 30 HELIX 11 AB2 ILE R 345 LEU R 360 1 16 HELIX 12 AB3 HIS R 363 MET R 371 1 9 HELIX 13 AB4 GLY R 377 PHE R 393 1 17 HELIX 14 AB5 PHE R 393 PHE R 404 1 12 HELIX 15 AB6 ASN R 406 ARG R 421 1 16 SSBOND 1 CYS R 46 CYS R 71 1555 1555 2.04 SSBOND 2 CYS R 62 CYS R 104 1555 1555 2.03 SSBOND 3 CYS R 85 CYS R 126 1555 1555 2.05 SSBOND 4 CYS R 226 CYS R 296 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