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- PDB-3iol: Crystal structure of Glucagon-Like Peptide-1 in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 3iol
TitleCrystal structure of Glucagon-Like Peptide-1 in complex with the extracellular domain of the Glucagon-Like Peptide-1 Receptor
Components
  • Glucagon-like peptide 1 receptorGlucagon-like peptide-1 receptor
  • Glucagon
KeywordsSIGNALING PROTEIN/SIGNALING PROTEIN / receptor-ligand complex / Cell membrane / Disulfide bond / G-protein coupled receptor / Glycoprotein / Membrane / Receptor / Transducer / Transmembrane / Amidation / Cleavage on pair of basic residues / Hormone / Secreted / SIGNALING PROTEIN-SIGNALING PROTEIN COMPLEX
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 / : / 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 / : / regulation of heart contraction / response to psychosocial stress / cellular response to glucagon stimulus / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / peptide hormone binding / regulation of insulin secretion / cAMP-mediated signaling / Synthesis, secretion, and deacylation of Ghrelin / protein kinase A signaling / positive regulation of gluconeogenesis / activation of adenylate cyclase activity / negative regulation of blood pressure / response to activity / positive regulation of peptidyl-threonine phosphorylation / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / 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 peptidyl-serine phosphorylation / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / positive regulation of ERK1 and ERK2 cascade / learning or memory / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
GPCR, family 2, extracellular hormone receptor domain / Glucagon / 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 ...GPCR, family 2, extracellular hormone receptor domain / Glucagon / 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
Pro-glucagon / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsReedtz-Runge, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of glucagon-like peptide-1 in complex with the extracellular domain of the glucagon-like peptide-1 receptor
Authors: Underwood, C.R. / Garibay, P. / Knudsen, L.B. / Hastrup, S. / Peters, G.H. / Rudolph, R. / Reedtz-Runge, S.
History
DepositionAug 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 23, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Glucagon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5983
Polymers18,0992
Non-polymers4991
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-10 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.670, 42.670, 95.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-1-

10M

21A-191-

HOH

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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: 14739.316 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) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43220
#2: Protein/peptide Glucagon / / GLP-1 / Glucagon-like peptide 1 / Glicentin / Glicentin-related polypeptide


Mass: 3359.699 Da / Num. of mol.: 1 / Fragment: UNP residues 98-128 / Source method: obtained synthetically / Details: This peptide has been chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275
#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.: 73 / 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 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.1M N-(2-Acetamido) Iminodiacetic Acid (ADA), pH 6.9, 14 vol-% (+/-)-2-Methyl-2,4-pentanediol (MPD), 9mM n-decyl-beta-D-thiomaltoside, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→95 Å / Num. all: 10585 / Num. obs: 10348 / % possible obs: 98 % / Redundancy: 7 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.111 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 1132 / Rsym value: 0.449 / % possible all: 98

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C59 without ligand

3c59


Resolution: 2.1→28.53 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.679 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22622 429 4.9 %RANDOM
Rwork0.17816 ---
obs0.18058 8357 97.85 %-
all-8786 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.663 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2---1.42 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 33 73 1130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221074
X-RAY DIFFRACTIONr_bond_other_d0.0030.02742
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9341466
X-RAY DIFFRACTIONr_angle_other_deg1.07231788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4625124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.40623.58553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04215156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.082157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_mcbond_it1.0031.5629
X-RAY DIFFRACTIONr_mcbond_other0.2631.5249
X-RAY DIFFRACTIONr_mcangle_it1.88521015
X-RAY DIFFRACTIONr_scbond_it2.8593445
X-RAY DIFFRACTIONr_scangle_it4.7174.5448
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 35 -
Rwork0.187 581 -
obs--96.55 %
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)
10.3386-0.1889-0.17481.80180.34680.44540.01470.02360.0261-0.0322-0.0162-0.001-0.00590.03150.00140.0249-0.01080.00490.0359-0.00510.0053-5.974-16.61213.513
20.9042-2.32831.96029.3486-6.96685.36190.0231-0.08130.003-0.1982-0.0459-0.04980.1499-0.04270.02270.0381-0.01670.00310.0499-0.00790.0219-3.6673.3613.574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 128
2X-RAY DIFFRACTION2B11 - 35

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