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- PDB-5otv: Extracellular domain of GLP-1 receptor in complex with GLP-1 vari... -

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Basic information

Entry
Database: PDB / ID: 5otv
TitleExtracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Cyc/Thr11Hcs
Components
  • Glucagon
  • Glucagon-like peptide 1 receptor
KeywordsSIGNALING PROTEIN / glucagon-like peptide 1 / GPCR / cyclic peptides
Function / homology
Function and homology information


glucagon receptor binding / glucagon-like peptide 1 receptor activity / glucagon receptor activity / : / positive regulation of blood pressure / hormone secretion / post-translational protein targeting to membrane, translocation / negative regulation of execution phase of apoptosis / feeding behavior / response to psychosocial stress ...glucagon receptor binding / glucagon-like peptide 1 receptor activity / glucagon receptor activity / : / positive regulation of blood pressure / hormone secretion / post-translational protein targeting to membrane, translocation / negative regulation of execution phase of apoptosis / feeding behavior / response to psychosocial stress / regulation of heart contraction / positive regulation of calcium ion import / peptide hormone binding / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of insulin secretion involved in cellular response to glucose stimulus / activation of adenylate cyclase activity / negative regulation of blood pressure / positive regulation of gluconeogenesis / cellular response to glucagon stimulus / regulation of insulin secretion / response to activity / gluconeogenesis / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / transmembrane signaling receptor activity / glucose homeostasis / positive regulation of cytosolic calcium ion concentration / secretory granule lumen / G alpha (s) signalling events / G alpha (q) signalling events / learning or memory / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Glucagon / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / GPCR, family 2, glucagon-like peptide-1 receptor / : / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / GPCR, family 2, glucagon-like peptide-1/glucagon receptor ...Glucagon / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / GPCR, family 2, glucagon-like peptide-1 receptor / : / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Pro-glucagon / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMortensen, S.
CitationJournal: Biochemistry / Year: 2018
Title: alpha-Helix or beta-Turn? An Investigation into N-Terminally Constrained Analogues of Glucagon-like Peptide 1 (GLP-1) and Exendin-4.
Authors: Oddo, A. / Mortensen, S. / Thogersen, H. / De Maria, L. / Hennen, S. / McGuire, J.N. / Kofoed, J. / Linderoth, L. / Reedtz-Runge, S.
History
DepositionAug 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Mar 6, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Oct 23, 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
C: Glucagon-like peptide 1 receptor
D: Glucagon
A: Glucagon-like peptide 1 receptor
B: Glucagon


Theoretical massNumber of molelcules
Total (without water)33,9114
Polymers33,9114
Non-polymers00
Water2,828157
1
C: Glucagon-like peptide 1 receptor
D: Glucagon


Theoretical massNumber of molelcules
Total (without water)16,9562
Polymers16,9562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-11 kcal/mol
Surface area8170 Å2
MethodPISA
2
A: Glucagon-like peptide 1 receptor
B: Glucagon


Theoretical massNumber of molelcules
Total (without water)16,9562
Polymers16,9562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-10 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.815, 83.998, 42.815
Angle α, β, γ (deg.)90.00, 95.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucagon-like peptide 1 receptor / GLP-1R


Mass: 13547.892 Da / Num. of mol.: 2 / Fragment: extracellular domain, UNP residues 24-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLP1R / Production host: Escherichia coli (E. coli) / References: UniProt: P43220
#2: Protein/peptide Glucagon


Mass: 3407.830 Da / Num. of mol.: 2 / Mutation: A8C, T11HCS / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus from Molecular Dimensions, solution E5: 0.12 M Ethylene Glycols, 0.1 M Buffer System 2 pH 7.5, 205 (v/v) PEg500mme, 10% (w/v) PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2→42.62 Å / Num. obs: 17691 / % possible obs: 98 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.092 / Rsym value: 0.204 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.04 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 5.8 / Num. measured obs: 8233 / Num. unique all: 1170 / CC1/2: 0.962 / Rpim(I) all: 0.158 / Rrim(I) all: 0.428 / % possible all: 91.98

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Processing

Software
NameVersionClassification
PHENIX(dev_2689: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZGM

4zgm


Resolution: 2→42.616 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.246 2893 8.44 %
Rwork0.2077 --
obs0.211 17658 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→42.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 0 157 2241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022160
X-RAY DIFFRACTIONf_angle_d0.6082950
X-RAY DIFFRACTIONf_dihedral_angle_d10.4791241
X-RAY DIFFRACTIONf_chiral_restr0.035295
X-RAY DIFFRACTIONf_plane_restr0.003379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.03290.3241340.32061454X-RAY DIFFRACTION94
2.0329-2.06790.35051360.30981455X-RAY DIFFRACTION95
2.0679-2.10550.25941420.29081504X-RAY DIFFRACTION95
2.1055-2.1460.3341380.26511490X-RAY DIFFRACTION96
2.146-2.18980.31691330.26051474X-RAY DIFFRACTION97
2.1898-2.23740.37791390.32761435X-RAY DIFFRACTION93
2.2374-2.28950.43071230.35531379X-RAY DIFFRACTION90
2.2895-2.34670.29841360.25871476X-RAY DIFFRACTION95
2.3467-2.41020.24521370.23891490X-RAY DIFFRACTION97
2.4102-2.48110.28261420.22791525X-RAY DIFFRACTION98
2.4811-2.56120.29831390.2221527X-RAY DIFFRACTION98
2.5612-2.65270.29351390.21141495X-RAY DIFFRACTION99
2.6527-2.75890.22051390.21211521X-RAY DIFFRACTION99
2.7589-2.88440.27751430.21231559X-RAY DIFFRACTION99
2.8844-3.03640.22961390.20061538X-RAY DIFFRACTION99
3.0364-3.22660.22671380.18651536X-RAY DIFFRACTION99
3.2266-3.47560.21511420.17351526X-RAY DIFFRACTION99
3.4756-3.82520.20341390.15771517X-RAY DIFFRACTION97
3.8252-4.37820.18311350.15481481X-RAY DIFFRACTION97
4.3782-5.51430.18491410.15981493X-RAY DIFFRACTION96
5.5143-42.62610.21121390.18791496X-RAY DIFFRACTION97
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)
12.70090.32370.6131.55470.28714.10080.05560.0749-0.02220.0029-0.0046-0.02890.07920.1682-0.02470.10960.01570.00730.1297-0.01730.146237.37479.19775.2909
22.07390.0788-0.92621.73580.19284.52590.06150.01580.02070.00470.01180.02280.0081-0.1206-0.02750.108-0.00050.00050.10180.01690.145755.4652-11.94253.103
30.99440.5191-0.51136.6638-6.09636.5416-0.1651-0.0738-0.1378-0.28490.2274-0.24030.2132-0.2391-0.16770.1375-0.02080.01610.2404-0.05420.210230.1251-1.056725.3658
42.4346-1.0598-0.99586.6324.71983.4373-0.09280.06020.08090.01730.17910.2065-0.1243-0.0223-0.02090.19240.0049-0.02630.20.04210.197759.0503-3.008924.0503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 28 through 128)
2X-RAY DIFFRACTION2(chain 'C' and resid 29 through 129)
3X-RAY DIFFRACTION3(chain 'B' and resid 7 through 35)
4X-RAY DIFFRACTION4(chain 'D' and resid 9 through 35)

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