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- PDB-5ott: Extracellular domain of GLP-1 receptor in complex with exendin-4 ... -

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Basic information

Entry
Database: PDB / ID: 5ott
TitleExtracellular domain of GLP-1 receptor in complex with exendin-4 variant Gly2Hcs/Thr5Hcs
Components
  • Exendin-4
  • Glucagon-like peptide 1 receptor
KeywordsSIGNALING PROTEIN / glucagon-like peptide 1 / GPCR / cyclic peptides
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 / response to psychosocial stress / regulation of heart contraction / 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 / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / activation of adenylate cyclase activity / negative regulation of blood pressure / hormone activity / regulation of blood pressure / 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 / toxin activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / learning or memory / cell surface receptor signaling pathway / extracellular region / membrane / plasma membrane
Similarity search - Function
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 / 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
Exendin-4 / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Heloderma suspectum (Gila monster)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 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

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Assembly

Deposited unit
A: Glucagon-like peptide 1 receptor
B: Exendin-4


Theoretical massNumber of molelcules
Total (without water)17,8162
Polymers17,8162
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-12 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.690, 62.920, 118.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-282-

HOH

21B-111-

HOH

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Components

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


Mass: 13547.892 Da / Num. of mol.: 1 / 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 Exendin-4


Mass: 4267.772 Da / Num. of mol.: 1 / Mutation: G2HCS, T5HCS / Source method: obtained synthetically / Source: (synth.) Heloderma suspectum (Gila monster) / References: UniProt: P26349
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Imidazole pH 6.5, 1.0 M Sodium acetate trihydrate

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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 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.92→47.382 Å / Num. obs: 15019 / % possible obs: 99 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rsym value: 0.108 / Net I/σ(I): 19.8
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 12.66 % / Rmerge(I) obs: 1.145 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 9519 / Num. unique all: 752 / Rpim(I) all: 0.33 / Rrim(I) all: 1.193 / % possible all: 97.41

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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: 1.92→47.382 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.2088 2704 9.56 %
Rwork0.1796 --
obs0.1824 15001 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.92→47.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 0 118 1210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151132
X-RAY DIFFRACTIONf_angle_d1.2531542
X-RAY DIFFRACTIONf_dihedral_angle_d7.852660
X-RAY DIFFRACTIONf_chiral_restr0.07151
X-RAY DIFFRACTIONf_plane_restr0.009201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.95490.34381360.34351308X-RAY DIFFRACTION97
1.9549-1.99250.27341420.22821347X-RAY DIFFRACTION97
1.9925-2.03320.24671400.19561334X-RAY DIFFRACTION100
2.0332-2.07740.22471460.21061362X-RAY DIFFRACTION99
2.0774-2.12570.23691470.18691347X-RAY DIFFRACTION100
2.1257-2.17890.22771420.18891346X-RAY DIFFRACTION99
2.1789-2.23780.1721460.16381357X-RAY DIFFRACTION100
2.2378-2.30370.23181450.18871338X-RAY DIFFRACTION100
2.3037-2.3780.24681400.17851356X-RAY DIFFRACTION100
2.378-2.4630.20461420.17431365X-RAY DIFFRACTION100
2.463-2.56160.18681420.17131351X-RAY DIFFRACTION99
2.5616-2.67820.21661440.17031341X-RAY DIFFRACTION100
2.6782-2.81940.21911420.17991353X-RAY DIFFRACTION99
2.8194-2.9960.2081490.18981371X-RAY DIFFRACTION100
2.996-3.22730.22741400.17881336X-RAY DIFFRACTION99
3.2273-3.55190.18821440.1611332X-RAY DIFFRACTION98
3.5519-4.06570.18171400.15661315X-RAY DIFFRACTION98
4.0657-5.12130.18121360.15851350X-RAY DIFFRACTION98
5.1213-47.39630.2031410.19611366X-RAY DIFFRACTION100

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