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- PDB-6gb1: Crystal structure of the GLP1 receptor ECD with Peptide 11 -

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Basic information

Entry
Database: PDB / ID: 6gb1
TitleCrystal structure of the GLP1 receptor ECD with Peptide 11
Components
  • Glucagon-like peptide 1 receptorGlucagon-like peptide-1 receptor
  • Peptide 11
KeywordsPEPTIDE BINDING PROTEIN / Glucagon-like Peptide 1 Protein-Peptide complex Incretins Diabetes drug discovery
Function / homology
Function and homology information


glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / regulation of heart contraction / response to psychosocial stress / peptide hormone binding / activation of adenylate cyclase activity / negative regulation of blood pressure ...glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / regulation of heart contraction / response to psychosocial stress / peptide hormone binding / activation of adenylate cyclase activity / negative regulation of blood pressure / cAMP-mediated signaling / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / transmembrane signaling receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / learning or memory / cell surface receptor signaling pathway / membrane / plasma membrane
Similarity search - Function
: / GPCR, family 2, glucagon-like peptide-1 receptor / 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, glucagon-like peptide-1 receptor / 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
HEXANE-1,6-DIOL / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsSchreuder, H.A. / Liesum, A.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Dual Glucagon-like Peptide 1 (GLP-1)/Glucagon Receptor Agonists Specifically Optimized for Multidose Formulations.
Authors: Evers, A. / Bossart, M. / Pfeiffer-Marek, S. / Elvert, R. / Schreuder, H. / Kurz, M. / Stengelin, S. / Lorenz, M. / Herling, A. / Konkar, A. / Lukasczyk, U. / Pfenninger, A. / Lorenz, K. / ...Authors: Evers, A. / Bossart, M. / Pfeiffer-Marek, S. / Elvert, R. / Schreuder, H. / Kurz, M. / Stengelin, S. / Lorenz, M. / Herling, A. / Konkar, A. / Lukasczyk, U. / Pfenninger, A. / Lorenz, K. / Haack, T. / Kadereit, D. / Wagner, M.
History
DepositionApr 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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: Peptide 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5066
Polymers18,0772
Non-polymers4284
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-32 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.550, 55.550, 138.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

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Components

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


Mass: 14833.366 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLP1R / Plasmid: pD14 / Production host: Escherichia coli (E. coli) / References: UniProt: P43220
#2: Protein/peptide Peptide 11 /


Mass: 3243.687 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: N-terminally truncated Dual Glucagon-like Peptide 1 (GLP-1)/Glucagon Receptor Agonist
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: A 6-fold excess of peptide 11 was dissolved in a solution of 12 mg/ml GLP1R-ECD in 10 mM Tris buffer pH 7.5, 100 mM NaSulfate and 2% glycerol. 100 nl of this protein solution plus 100 nl ...Details: A 6-fold excess of peptide 11 was dissolved in a solution of 12 mg/ml GLP1R-ECD in 10 mM Tris buffer pH 7.5, 100 mM NaSulfate and 2% glycerol. 100 nl of this protein solution plus 100 nl reservoir solution were equilibrated against reservoir solution consisting of 10 mM CoCl2, 9.4 % (v/v) 1,6-hexanediol and 100 mM NaAcetate, pH 4.8. Crystals appeared after about one week.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.73→51.57 Å / Num. obs: 6336 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 95.53 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 22
Reflection shellResolution: 2.73→2.87 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.096 / Mean I/σ(I) obs: 2.3 / Rsym value: 1.096 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDS(VERSION November 3data reduction
autoPROC(Version 1.1.6)data scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c59

3c59


Resolution: 2.73→51.57 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.478 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.615 / SU Rfree Blow DPI: 0.32 / SU Rfree Cruickshank DPI: 0.308
RfactorNum. reflection% reflectionSelection details
Rfree0.262 308 4.91 %RANDOM
Rwork0.205 ---
obs0.208 6273 100 %-
Displacement parametersBiso mean: 83.65 Å2
Baniso -1Baniso -2Baniso -3
1-9.7569 Å20 Å20 Å2
2--9.7569 Å20 Å2
3----19.5139 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.73→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 33 42 1150
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011167HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.181597HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d374SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes166HARMONIC5
X-RAY DIFFRACTIONt_it1167HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion22.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion137SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1275SEMIHARMONIC4
LS refinement shellResolution: 2.73→3.05 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3134 -5.49 %
Rwork0.2439 1636 -
all0.2477 1731 -
obs--100 %

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