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- PDB-5ee7: Crystal structure of the human glucagon receptor (GCGR) in comple... -

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Basic information

Entry
Database: PDB / ID: 5ee7
TitleCrystal structure of the human glucagon receptor (GCGR) in complex with the antagonist MK-0893
ComponentsGlucagon receptor,Endolysin,Glucagon receptor
KeywordsSIGNALING PROTEIN / GPCR / 7TM
Function / homology
Function and homology information


regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / exocytosis / peptide hormone binding / viral release from host cell by cytolysis / hormone-mediated signaling pathway / peptidoglycan catabolic process / response to nutrient / cellular response to glucagon stimulus ...regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / exocytosis / peptide hormone binding / viral release from host cell by cytolysis / hormone-mediated signaling pathway / peptidoglycan catabolic process / response to nutrient / cellular response to glucagon stimulus / guanyl-nucleotide exchange factor activity / cellular response to starvation / generation of precursor metabolites and energy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / regulation of blood pressure / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Glucagon-type ligand receptors / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / glucose homeostasis / G alpha (s) signalling events / G alpha (q) signalling events / host cell cytoplasm / cell surface receptor signaling pathway / endosome / defense response to bacterium / positive regulation of gene expression / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, glucagon receptor / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. ...GPCR, family 2, glucagon receptor / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5MV / OLEIC ACID / L(+)-TARTARIC ACID / Endolysin / Glucagon receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJazayeri, A. / Dore, A.S. / Lamb, D. / Krishnamurthy, H. / Southall, S.M. / Baig, A.H. / Bortolato, A. / Koglin, M. / Robertson, N.J. / Errey, J.C. ...Jazayeri, A. / Dore, A.S. / Lamb, D. / Krishnamurthy, H. / Southall, S.M. / Baig, A.H. / Bortolato, A. / Koglin, M. / Robertson, N.J. / Errey, J.C. / Andrews, S.P. / Brown, A.J.H. / Cooke, R.M. / Weir, M. / Marshall, F.H.
CitationJournal: Nature / Year: 2016
Title: Extra-helical binding site of a glucagon receptor antagonist.
Authors: Jazayeri, A. / Dore, A.S. / Lamb, D. / Krishnamurthy, H. / Southall, S.M. / Baig, A.H. / Bortolato, A. / Koglin, M. / Robertson, N.J. / Errey, J.C. / Andrews, S.P. / Teobald, I. / Brown, A.J. ...Authors: Jazayeri, A. / Dore, A.S. / Lamb, D. / Krishnamurthy, H. / Southall, S.M. / Baig, A.H. / Bortolato, A. / Koglin, M. / Robertson, N.J. / Errey, J.C. / Andrews, S.P. / Teobald, I. / Brown, A.J. / Cooke, R.M. / Weir, M. / Marshall, F.H.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucagon receptor,Endolysin,Glucagon receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,37118
Polymers51,2791
Non-polymers5,09217
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint46 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.583, 71.476, 183.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glucagon receptor,Endolysin,Glucagon receptor / GL-R / Lysis protein / Lysozyme / Muramidase / GL-R


Mass: 51279.461 Da / Num. of mol.: 1
Mutation: G154A R173A A182L S190A G223A M276A E362F G207E K344A F387A V193F,G154A R173A A182L S190A G223A M276A E362F G207E K344A F387A V193F,G154A R173A A182L S190A G223A M276A E362F G207E K344A F387A V193F
Source method: isolated from a genetically manipulated source
Details: Chimeric fusion of human Glucagon receptor and T4-Lysozyme
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GCGR / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P47871, UniProt: P00720, lysozyme

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Non-polymers , 5 types, 41 molecules

#2: Chemical ChemComp-5MV / 3-[[4-[(1~{S})-1-[3-[3,5-bis(chloranyl)phenyl]-5-(6-methoxynaphthalen-2-yl)pyrazol-1-yl]ethyl]phenyl]carbonylamino]propanoic acid


Mass: 588.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H27Cl2N3O4
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: OVAL SHAPED
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 6 / Details: ADA BUFFER, SODIUM POTASSIUM TARTRATE, PEG 400 / PH range: 5.5 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→32.73 Å / Num. obs: 16065 / % possible obs: 91.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 1.6 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L6R

4l6r


Resolution: 2.5→19.971 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 777 4.86 %Random
Rwork0.2256 ---
obs0.2275 15996 89.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 264 24 3619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043661
X-RAY DIFFRACTIONf_angle_d0.7964888
X-RAY DIFFRACTIONf_dihedral_angle_d13.5451344
X-RAY DIFFRACTIONf_chiral_restr0.029531
X-RAY DIFFRACTIONf_plane_restr0.004594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.65640.3151310.27572489X-RAY DIFFRACTION90
2.6564-2.8610.26831400.26552537X-RAY DIFFRACTION92
2.861-3.14790.29441270.24462560X-RAY DIFFRACTION91
3.1479-3.60110.24341230.23362502X-RAY DIFFRACTION89
3.6011-4.52820.22871340.19732556X-RAY DIFFRACTION90
4.5282-19.97150.27931220.21532575X-RAY DIFFRACTION86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53340.6391-0.30891.1018-0.2169-0.08690.04970.019-0.02910.04090.0187-0.03170.0340.052200.18020.0184-0.01220.2131-0.00130.2355-22.887614.8775-54.3628
20.0199-0.05870.0570.1399-0.02680.0161-0.48630.2893-0.48580.39440.38520.4384-0.7040.91900.420.0960.04610.3210.06350.2479-16.950717.2713-29.6347
3-1.084-0.72950.2788-0.1881-0.7766-0.4311-0.14160.0740.12530.076-0.0831-0.1991-0.06890.2283-00.239-0.0017-0.01310.18730.00760.2806-13.96912.896-46.2249
40.03570.00760.0612-0.0433-0.0217-0.0517-0.6143-0.7292-0.27830.3475-0.3756-0.10240.7634-0.9375-00.4028-0.06040.07530.5019-0.03910.2446-15.621817.6143-65.7095
50.2429-0.26310.0946-0.15550.06230.1-0.12040.2763-0.4136-0.2797-0.21370.6029-0.05060.4991-00.43010.00640.02380.40540.03210.5568-5.061817.841-68.0404
60.5616-0.2704-0.1797-0.2587-0.665-0.0686-0.2150.129-0.1264-0.0057-0.1593-0.29580.1853-0.30100.1998-0.02920.01260.1881-0.00290.2175-11.2633.4815-41.4619
70.2028-0.0616-0.19860.317-0.01290.0374-0.51550.2031-0.57860.3436-0.1151-0.14660.42430.8286-00.20140.0582-0.03320.25840.14360.4059-3.80635.2315-33.0144
80.08840.1386-0.1098-0.11180.0406-0.0213-0.1626-0.4494-0.0591-0.52830.14920.4460.56310.366900.21180.0063-0.00610.27430.06910.28950.52843.7386-53.4429
90.3388-0.23890.27370.155-0.1573-0.1012-0.9174-0.3382-0.9611-0.68080.2638-0.24310.4405-0.3278-00.5292-0.00930.1010.58210.00980.4799-4.34395.6859-64.0427
100.5454-0.0440.106-0.3128-0.6553-0.17160.1588-0.01580.08680.08160.0881-0.15020.00280.055200.17970.01050.02150.1476-0.03290.2346-14.0358-7.5055-41.545
110.1718-0.1734-0.44480.130.02680.0075-0.57140.53080.57731.64730.40160.5192-0.01810.043200.7380.15090.22240.2816-0.05750.3037-26.474-3.7054-22.4966
12-0.4899-0.3403-0.0490.13630.5193-0.21160.1042-0.0379-0.0677-0.08540.0350.0406-0.2164-0.334300.1928-0.0105-0.01050.27570.02140.1962-22.0492-0.8325-41.4661
130.08360.0280.03570.1351-0.11610.0637-0.83270.66640.3147-0.01290.4026-0.6611-0.73240.7425-00.3666-0.0488-0.01260.43910.07560.3511-16.7591-5.5674-62.4409
140.0158-0.2065-0.03480.0526-0.15020.15960.11790.459-0.15430.5839-0.33580.78930.67711.0471-00.35190.0231-0.0330.4481-0.13470.3802-24.1711.2353-62.1255
15-0.1995-0.54950.2346-0.2708-0.298-0.0440.1157-0.06470.19070.07870.16750.04180.06410.0745-00.16440.0163-0.01430.1865-0.00690.2351-24.46049.6661-43.1324
160.14220.24560.2230.14460.206-0.0956-0.2433-1.3458-2.20760.04340.503-0.8305-0.53570.01-00.55750.11720.12620.2296-0.2685-0.4902-28.479820.7096-26.5461
17-0.1311-0.7273-0.08770.07240.3286-0.2948-0.12710.21140.30250.6224-0.2444-0.41190.00340.1704-00.7137-0.0266-0.14540.71510.13180.5984-2.1014-7.1879-13.5009
180.07520.05060.00330.1197-0.01140.0476-0.86070.34380.08491.141.55570.14110.8339-0.505401.08950.2026-0.28010.82540.01690.54352.4454-9.1852-3.1713
190.11270.0554-0.1516-0.1470.16570.0446-0.8851-0.83030.00950.69860.18860.12790.4721-0.193301.2340.096-0.18060.94840.10150.71294.4492-17.42810.3288
20-0.003-0.0197-0.03330.079-0.00380.0019-0.61450.20540.23721.1426-0.5138-0.01060.78340.1895-00.88250.08770.10960.83480.25380.72832.8982-22.8781-7.5463
210.7060.0730.66930.1327-0.1820.1449-0.8907-0.11-1.23360.2137-0.18371.5596-0.35951.2032-01.0178-0.1011-0.06420.89830.3280.815-11.6013-10.7938-6.6293
220.062-0.11630.06360.009-0.0341-0.03091.08971.4810.40520.5785-0.2345-0.0833-0.2657-0.1818-01.27830.204-0.08511.13010.0650.8988-20.10175.4733-2.7434
23-0.0209-0.02250.11370.2720.0892-0.0113-0.1491-0.2727-0.45280.7536-0.26810.2299-0.72740.059301.02510.0252-0.06140.83040.08720.511-11.72422.1946-8.7191
24-0.0802-0.1250.09040.00950.15740.00340.3155-1.01540.2190.8377-0.0952-0.04210.5706-0.060401.47010.2372-0.02091.2234-0.01021.2026-13.434811.1604-1.8133
250.11710.1292-0.21670.08670.07340.18811.1508-0.03780.0655-0.0759-0.8865-0.144-1.15590.2682-01.4912-0.0884-0.10321.29010.15951.0375-5.551114.5094-7.9817
260.08160.2342-0.2487-0.02850.09150.0935-0.5157-0.27091.13651.1177-0.1484-1.1365-1.24240.0747-01.0297-0.0851-0.08040.74480.10960.702-5.43078.1906-14.4428
270.04690.05790.03180.0273-0.1141-0.05640.13140.39860.49190.181-1.0881-0.0906-1.2955-0.769901.332-0.139-0.02980.56810.13040.4332-11.99875.8869-20.6738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 138 through 160 )
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 172 )
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 194 )
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 200 )
5X-RAY DIFFRACTION5chain 'A' and (resid 212 through 226 )
6X-RAY DIFFRACTION6chain 'A' and (resid 227 through 255 )
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 272 )
8X-RAY DIFFRACTION8chain 'A' and (resid 273 through 285 )
9X-RAY DIFFRACTION9chain 'A' and (resid 286 through 305 )
10X-RAY DIFFRACTION10chain 'A' and (resid 306 through 331 )
11X-RAY DIFFRACTION11chain 'A' and (resid 332 through 343 )
12X-RAY DIFFRACTION12chain 'A' and (resid 344 through 364 )
13X-RAY DIFFRACTION13chain 'A' and (resid 365 through 372 )
14X-RAY DIFFRACTION14chain 'A' and (resid 378 through 387 )
15X-RAY DIFFRACTION15chain 'A' and (resid 388 through 404 )
16X-RAY DIFFRACTION16chain 'A' and (resid 405 through 418 )
17X-RAY DIFFRACTION17chain 'A' and (resid 1000 through 1018 )
18X-RAY DIFFRACTION18chain 'A' and (resid 1022 through 1034 )
19X-RAY DIFFRACTION19chain 'A' and (resid 1035 through 1048 )
20X-RAY DIFFRACTION20chain 'A' and (resid 1049 through 1057 )
21X-RAY DIFFRACTION21chain 'A' and (resid 1058 through 1078 )
22X-RAY DIFFRACTION22chain 'A' and (resid 1079 through 1090 )
23X-RAY DIFFRACTION23chain 'A' and (resid 1091 through 1104 )
24X-RAY DIFFRACTION24chain 'A' and (resid 1105 through 1122 )
25X-RAY DIFFRACTION25chain 'A' and (resid 1123 through 1139 )
26X-RAY DIFFRACTION26chain 'A' and (resid 1140 through 1152 )
27X-RAY DIFFRACTION27chain 'A' and (resid 1153 through 1159 )

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