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

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Basic information

Entry
Database: PDB / ID: 5otx
TitleExtracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Cys/Thr11Cys
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 / cellular response to glucagon stimulus / positive regulation of gluconeogenesis / 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 1.3Oct 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
A: Glucagon-like peptide 1 receptor
B: Glucagon
C: Glucagon-like peptide 1 receptor
D: Glucagon


Theoretical massNumber of molelcules
Total (without water)33,8834
Polymers33,8834
Non-polymers00
Water2,468137
1
A: Glucagon-like peptide 1 receptor
B: Glucagon


Theoretical massNumber of molelcules
Total (without water)16,9422
Polymers16,9422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9 kcal/mol
Surface area8270 Å2
MethodPISA
2
C: Glucagon-like peptide 1 receptor
D: Glucagon


Theoretical massNumber of molelcules
Total (without water)16,9422
Polymers16,9422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-11 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.870, 83.590, 42.830
Angle α, β, γ (deg.)90.00, 95.19, 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: 3393.803 Da / Num. of mol.: 2 / Mutation: A8C, T11C / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.99 Å3/Da / Density % sol: 38.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus from Molecular Dimensions solution F2: 0.12 M Monosaccharides, 0.1 M Buffer system 1 pH 6.5, 20% (v/v) Ethylene Glycol, 10% (w/v) PEG8000

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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: Jan 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2→42.66 Å / Num. obs: 16996 / % possible obs: 94.4 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rsym value: 0.083 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.071 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2312 / Mean I/σ(I) obs: 3.69 / Num. unique obs: 1622 / CC1/2: 0.895 / Rpim(I) all: 0.2228 / Rsym value: 0.3216 / % possible all: 92.26

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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→42.654 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.2398 1979 5.98 %
Rwork0.1915 --
obs0.1944 16962 93.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→42.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 0 137 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082157
X-RAY DIFFRACTIONf_angle_d1.1322949
X-RAY DIFFRACTIONf_dihedral_angle_d13.176757
X-RAY DIFFRACTIONf_chiral_restr0.1294
X-RAY DIFFRACTIONf_plane_restr0.009631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2781370.2152135X-RAY DIFFRACTION90
2.05-2.10540.27961380.18382146X-RAY DIFFRACTION91
2.1054-2.16740.17391390.18212160X-RAY DIFFRACTION92
2.1674-2.23730.26831350.21292141X-RAY DIFFRACTION89
2.2373-2.31730.34191290.24762097X-RAY DIFFRACTION89
2.3173-2.41010.26291410.19262246X-RAY DIFFRACTION94
2.4101-2.51980.21541450.1812250X-RAY DIFFRACTION94
2.5198-2.65260.26161410.18352218X-RAY DIFFRACTION95
2.6526-2.81870.24471440.18282269X-RAY DIFFRACTION96
2.8187-3.03630.25251490.18072294X-RAY DIFFRACTION96
3.0363-3.34180.21771440.18052298X-RAY DIFFRACTION96
3.3418-3.82510.21641440.17772272X-RAY DIFFRACTION96
3.8251-4.81810.18611450.18452245X-RAY DIFFRACTION96
4.8181-42.66410.29371480.2132334X-RAY DIFFRACTION98

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