HEADER SIGNALING PROTEIN 23-APR-15 4ZGM TITLE CRYSTAL STRUCTURE OF SEMAGLUTIDE PEPTIDE BACKBONE IN COMPLEX WITH THE TITLE 2 GLP-1 RECEPTOR EXTRACELLULAR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCAGON-LIKE PEPTIDE 1 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLP-1R; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SEMAGLUTIDE PEPTIDE BACKBONE; 8AIB,34R-GLP-1(7-37)-OH; COMPND 8 CHAIN: B; COMPND 9 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: GLP1R; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS GLP-1, RECEPTOR, COMPLEX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.REEDTZ-RUNGE REVDAT 4 10-JAN-24 4ZGM 1 REMARK REVDAT 3 07-OCT-15 4ZGM 1 JRNL REVDAT 2 23-SEP-15 4ZGM 1 JRNL REVDAT 1 09-SEP-15 4ZGM 0 JRNL AUTH J.LAU,P.BLOCH,L.SCHAFFER,I.PETTERSSON,J.SPETZLER,J.KOFOED, JRNL AUTH 2 K.MADSEN,L.B.KNUDSEN,J.MCGUIRE,D.B.STEENSGAARD,H.M.STRAUSS, JRNL AUTH 3 D.X.GRAM,S.M.KNUDSEN,F.S.NIELSEN,P.THYGESEN,S.REEDTZ-RUNGE, JRNL AUTH 4 T.KRUSE JRNL TITL DISCOVERY OF THE ONCE-WEEKLY GLUCAGON-LIKE PEPTIDE-1 (GLP-1) JRNL TITL 2 ANALOGUE SEMAGLUTIDE. JRNL REF J.MED.CHEM. V. 58 7370 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 26308095 JRNL DOI 10.1021/ACS.JMEDCHEM.5B00726 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1938 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 14072 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 705 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.6539 - 3.0771 1.00 2827 150 0.1617 0.1803 REMARK 3 2 3.0771 - 2.4428 1.00 2704 141 0.1704 0.2115 REMARK 3 3 2.4428 - 2.1341 1.00 2628 139 0.1525 0.1849 REMARK 3 4 2.1341 - 1.9390 0.99 2634 139 0.1545 0.1949 REMARK 3 5 1.9390 - 1.8001 0.98 2574 136 0.1827 0.2326 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 1144 REMARK 3 ANGLE : 1.346 1545 REMARK 3 CHIRALITY : 0.051 149 REMARK 3 PLANARITY : 0.007 194 REMARK 3 DIHEDRAL : 15.983 437 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ZGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209063. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 28.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3IOL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.24 M SODIUM MALONATE PH 7.0, 20% REMARK 280 (W/V) PEG3350 (JCSG SCREEN QIAGEN) AND 10 MM HEXAETHYLENE GLYCOL REMARK 280 MONOOCTYL ETHER (DETERGENT SCREEN HT HAMPTON RESEARCH)., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 47.80500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.89500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.80500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.89500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 A 24 REMARK 465 PRO A 25 REMARK 465 GLN A 26 REMARK 465 GLY A 27 REMARK 465 ALA A 28 REMARK 465 SER A 129 REMARK 465 LYS A 130 REMARK 465 ARG A 131 REMARK 465 GLY A 132 REMARK 465 GLU A 133 REMARK 465 ARG A 134 REMARK 465 SER A 135 REMARK 465 SER A 136 REMARK 465 PRO A 137 REMARK 465 GLU A 138 REMARK 465 GLU A 139 REMARK 465 GLN A 140 REMARK 465 LEU A 141 REMARK 465 LEU A 142 REMARK 465 PHE A 143 REMARK 465 LEU A 144 REMARK 465 TYR A 145 REMARK 465 HIS B 7 REMARK 465 AIB B 8 REMARK 465 GLU B 9 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 O HOH A 349 O HOH A 354 2.05 REMARK 500 OE2 GLU A 34 O HOH A 301 2.16 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 GLU A 68 -18.84 86.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 32M A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 32M B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IOL RELATED DB: PDB REMARK 900 SAME RECEPTOR IN COMPLEX WITH A DIFFERENT PEPTIDE LIGAND DBREF 4ZGM A 24 145 UNP P43220 GLP1R_HUMAN 24 145 DBREF 4ZGM B 7 37 PDB 4ZGM 4ZGM 7 37 SEQRES 1 A 122 ARG PRO GLN GLY ALA THR VAL SER LEU TRP GLU THR VAL SEQRES 2 A 122 GLN LYS TRP ARG GLU TYR ARG ARG GLN CYS GLN ARG SER SEQRES 3 A 122 LEU THR GLU ASP PRO PRO PRO ALA THR ASP LEU PHE CYS SEQRES 4 A 122 ASN ARG THR PHE ASP GLU TYR ALA CYS TRP PRO ASP GLY SEQRES 5 A 122 GLU PRO GLY SER PHE VAL ASN VAL SER CYS PRO TRP TYR SEQRES 6 A 122 LEU PRO TRP ALA SER SER VAL PRO GLN GLY HIS VAL TYR SEQRES 7 A 122 ARG PHE CYS THR ALA GLU GLY LEU TRP LEU GLN LYS ASP SEQRES 8 A 122 ASN SER SER LEU PRO TRP ARG ASP LEU SER GLU CYS GLU SEQRES 9 A 122 GLU SER LYS ARG GLY GLU ARG SER SER PRO GLU GLU GLN SEQRES 10 A 122 LEU LEU PHE LEU TYR SEQRES 1 B 31 HIS AIB GLU GLY THR PHE THR SER ASP VAL SER SER TYR SEQRES 2 B 31 LEU GLU GLY GLN ALA ALA LYS GLU PHE ILE ALA TRP LEU SEQRES 3 B 31 VAL ARG GLY ARG GLY HET 32M A 201 69 HET 32M B 101 69 HETNAM 32M 3,6,9,12,15,18-HEXAOXAHEXACOSAN-1-OL HETSYN 32M HEXAETHYLENE GLYCOL MONOOCTYL ETHER FORMUL 3 32M 2(C20 H42 O7) FORMUL 5 HOH *88(H2 O) HELIX 1 AA1 SER A 31 ASP A 53 1 23 HELIX 2 AA2 TRP A 91 VAL A 95 5 5 HELIX 3 AA3 LEU A 123 GLU A 127 5 5 HELIX 4 AA4 PHE B 12 ARG B 34 1 23 SHEET 1 AA1 2 THR A 65 PHE A 66 0 SHEET 2 AA1 2 CYS A 71 TRP A 72 -1 O TRP A 72 N THR A 65 SHEET 1 AA2 2 SER A 79 SER A 84 0 SHEET 2 AA2 2 HIS A 99 CYS A 104 -1 O CYS A 104 N SER A 79 SSBOND 1 CYS A 46 CYS A 71 1555 1555 2.11 SSBOND 2 CYS A 62 CYS A 104 1555 1555 2.04 SSBOND 3 CYS A 85 CYS A 126 1555 1555 2.01 SITE 1 AC1 1 HOH A 302 SITE 1 AC2 3 LEU B 20 ALA B 24 ARG B 36 CRYST1 95.610 35.790 42.680 90.00 90.00 90.00 P 21 21 2 4 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 0.010459 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023430 0.00000