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

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Basic information

Entry
Database: PDB / ID: 5otu
TitleExtracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Hcs/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 / hormone secretion / positive regulation of blood pressure / negative regulation of execution phase of apoptosis / post-translational protein targeting to membrane, translocation / feeding behavior / response to psychosocial stress / regulation of heart contraction ...glucagon receptor binding / glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / negative regulation of execution phase of apoptosis / post-translational protein targeting to membrane, translocation / feeding behavior / response to psychosocial stress / regulation of heart contraction / positive regulation of calcium ion import / cellular response to glucagon stimulus / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / peptide hormone binding / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / protein kinase A signaling / activation of adenylate cyclase activity / negative regulation of blood pressure / cAMP-mediated signaling / positive regulation of peptidyl-threonine phosphorylation / response to activity / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / 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 / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / learning or memory / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / 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, 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. / Hormone receptor domain ...Glucagon / : / 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. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / 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.
Similarity search - Domain/homology
Pro-glucagon / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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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)33,9394
Polymers33,9394
Non-polymers00
Water3,819212
1
A: Glucagon-like peptide 1 receptor
B: Glucagon


Theoretical massNumber of molelcules
Total (without water)16,9702
Polymers16,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-9 kcal/mol
Surface area8410 Å2
MethodPISA
2
C: Glucagon-like peptide 1 receptor
D: Glucagon


Theoretical massNumber of molelcules
Total (without water)16,9702
Polymers16,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-10 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.822, 81.038, 42.945
Angle α, β, γ (deg.)90.00, 97.92, 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: 3421.857 Da / Num. of mol.: 2 / Mutation: A8HCS, 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.: 212 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus from Molecular Dimensions, solution G1: 0.1 M Carboxylic acids, 0.1 Buffer system 1 pH 6.5, 20% (v/v) PEG500mme, 10% (w/v) PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→42.535 Å / Num. obs: 24985 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.029 / Rsym value: 0.054 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 5444 / Num. unique all: 1544 / CC1/2: 0.851 / Rpim(I) all: 0.298 / Rrim(I) all: 0.568 / % possible all: 99.68

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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: 1.8→42.535 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2106 2221 4.65 %
Rwork0.1729 --
obs0.1747 24961 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 0 212 2303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072169
X-RAY DIFFRACTIONf_angle_d0.842960
X-RAY DIFFRACTIONf_dihedral_angle_d13.556760
X-RAY DIFFRACTIONf_chiral_restr0.081294
X-RAY DIFFRACTIONf_plane_restr0.006381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83920.31661360.27092857X-RAY DIFFRACTION98
1.8392-1.88190.2831370.25012876X-RAY DIFFRACTION97
1.8819-1.9290.31371390.22862819X-RAY DIFFRACTION98
1.929-1.98120.2221530.20522864X-RAY DIFFRACTION98
1.9812-2.03950.21871260.19852864X-RAY DIFFRACTION97
2.0395-2.10530.23611420.18372874X-RAY DIFFRACTION98
2.1053-2.18050.19791560.172849X-RAY DIFFRACTION97
2.1805-2.26780.20561390.16852830X-RAY DIFFRACTION96
2.2678-2.3710.17991170.17992815X-RAY DIFFRACTION95
2.371-2.4960.24041480.17842762X-RAY DIFFRACTION94
2.496-2.65240.21151400.16542836X-RAY DIFFRACTION98
2.6524-2.85710.18261340.16612901X-RAY DIFFRACTION98
2.8571-3.14460.18721330.16972838X-RAY DIFFRACTION97
3.1446-3.59940.19921340.1682900X-RAY DIFFRACTION98
3.5994-4.53410.20661390.14712812X-RAY DIFFRACTION96
4.5341-42.54710.211480.16862864X-RAY DIFFRACTION98
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)
12.03160.03020.72860.82910.19894.02890.0127-0.0078-0.0425-0.01930.0366-0.031-0.03710.1448-0.03430.2540.018-0.01310.158-0.01530.19538.79629.64915.8856
22.16141.2765-1.66913.8948-4.00148.004-0.15340.0025-0.1968-0.23240.0652-0.05890.5059-0.2810.01850.21550.01110.00250.23-0.04650.212329.5325-0.113825.6367
32.33390.4253-0.72631.3312-0.07192.8680.0411-0.0938-0.0202-0.10240.0319-0.00320.00640.0739-0.05250.3027-0.0199-0.00990.20360.00710.203857.0878-9.86622.6577
42.08940.0222-0.03215.72236.19.1372-0.0668-0.05180.0577-0.27240.15510.0926-0.39460.153-0.12010.2502-0.0311-0.01050.21650.02010.192960.16850.29324.6224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 29 through 128)
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 35)
3X-RAY DIFFRACTION3(chain 'C' and resid 29 through 128)
4X-RAY DIFFRACTION4(chain 'D' and resid 8 through 34)

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