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- PDB-3c5t: Crystal structure of the ligand-bound glucagon-like peptide-1 rec... -

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Basic information

Entry
Database: PDB / ID: 3c5t
TitleCrystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain
Components
  • Exendin-4
  • Glucagon-like peptide 1 receptorGlucagon-like peptide-1 receptor
KeywordsSignaling protein/Signaling protein / ligand-bound G protein-coupled receptor extracellular domain / G-protein coupled receptor / Glycoprotein / Membrane / Transducer / Transmembrane / Amidation / Cleavage on pair of basic residues / Secreted / Signaling protein-Signaling protein COMPLEX
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 / cAMP-mediated signaling / activation of adenylate cyclase activity ...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 / cAMP-mediated signaling / activation of adenylate cyclase activity / negative regulation of blood pressure / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / Glucagon-type ligand receptors / regulation of blood pressure / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / transmembrane signaling receptor activity / positive regulation of cytosolic calcium ion concentration / toxin activity / 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. / 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Exendin-4 / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRunge, S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of the Ligand-bound Glucagon-like Peptide-1 Receptor Extracellular Domain
Authors: Runge, S. / Thogersen, H. / Madsen, K. / Lau, J. / Rudolph, R.
History
DepositionFeb 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Exendin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1983
Polymers17,7002
Non-polymers4991
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-9 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.910, 75.910, 87.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 14325.841 Da / Num. of mol.: 1
Fragment: N-terminal extracellular domain, UNP residues 24-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Glucagon-like peptide-1 receptor(GLP1R) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43220
#2: Protein/peptide Exendin-4 / Exenatide


Mass: 3373.765 Da / Num. of mol.: 1 / Fragment: UNP residues 56-86 / Source method: obtained synthetically
Details: Exendin-4(9-39) was generated by chemical synthesis; this sequence occurs naturally in Heloderma suspectum.
References: UniProt: P26349
#3: Sugar ChemComp-10M / decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside / (2R,3R,4S,5S,6R)-2-((2R,3S,4R,5R,6S)-6-Decylsulfanyl-4,5-dihydroxy-2-hydroxymethyl-tetrahydro-pyran-3-yloxy)-6-hydroxymethyl-tetrahydro-pyran-3,4,5-triol, n-Decyl-beta-D-thiomaltoside


Type: D-saccharide / Mass: 498.628 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O10S / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 4.12 Å3/Da / Density % sol: 70.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 0.1M MgCl2, 0.4M MgTartrate, 9mM n-Decyl-beta-D-thiomaltoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 17572 / Num. obs: 17273 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 27.1
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 7.3 / Num. unique all: 2205 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C59 without the ligand present

3c59


Resolution: 2.1→36.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.608 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23809 909 5.3 %RANDOM
Rwork0.20328 ---
obs0.20503 16321 98.28 %-
all-16607 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.54 Å20 Å2
2--1.07 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 33 126 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9631535
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7475127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39323.92956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01615170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.422158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02861
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.2484
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2760
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3591.5664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29821045
X-RAY DIFFRACTIONr_scbond_it2.7373553
X-RAY DIFFRACTIONr_scangle_it4.3854.5490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 69 -
Rwork0.211 1182 -
obs--97.96 %
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)
10.86460.61330.72930.7244-0.1332.08420.02690.0777-0.0110.024-0.07370.0131-0.09120.18690.0469-0.03670.0106-0.01270.00270.0053-0.0846-32.34622.494-7.541
214.62087.8112-2.87264.651-2.08453.21370.02080.0843-0.72220.0043-0.003-0.3740.573-0.1396-0.01790.09770.0402-0.0544-0.0642-0.0313-0.0301-39.975.955-6.971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA28 - 1315 - 108
2X-RAY DIFFRACTION2BB9 - 331 - 25

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