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- PDB-5nx2: Crystal structure of thermostabilised full-length GLP-1R in compl... -

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Basic information

Entry
Database: PDB / ID: 5nx2
TitleCrystal structure of thermostabilised full-length GLP-1R in complex with a truncated peptide agonist at 3.7 A resolution
Components
  • Glucagon-like peptide 1 receptorGlucagon-like peptide-1 receptor
  • truncated peptide agonist
KeywordsMEMBRANE PROTEIN / 7TM / GPCR / signalling protein
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 / 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
Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsRappas, M. / Jazayeri, A. / Brown, A.J.H. / Kean, J. / Errey, J.C. / Robertson, N. / Fiez-Vandal, C. / Andrews, S.P. / Congreve, M. / Bortolato, A. ...Rappas, M. / Jazayeri, A. / Brown, A.J.H. / Kean, J. / Errey, J.C. / Robertson, N. / Fiez-Vandal, C. / Andrews, S.P. / Congreve, M. / Bortolato, A. / Mason, J.S. / Baig, A.H. / Teobald, I. / Dore, A.S. / Weir, M. / Cooke, R.M. / Marshall, F.H.
CitationJournal: Nature / Year: 2017
Title: Crystal structure of the GLP-1 receptor bound to a peptide agonist.
Authors: Jazayeri, A. / Rappas, M. / Brown, A.J.H. / Kean, J. / Errey, J.C. / Robertson, N.J. / Fiez-Vandal, C. / Andrews, S.P. / Congreve, M. / Bortolato, A. / Mason, J.S. / Baig, A.H. / Teobald, I. ...Authors: Jazayeri, A. / Rappas, M. / Brown, A.J.H. / Kean, J. / Errey, J.C. / Robertson, N.J. / Fiez-Vandal, C. / Andrews, S.P. / Congreve, M. / Bortolato, A. / Mason, J.S. / Baig, A.H. / Teobald, I. / Dore, A.S. / Weir, M. / Cooke, R.M. / Marshall, F.H.
History
DepositionMay 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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: truncated peptide agonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0887
Polymers50,5172
Non-polymers1,5715
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint9 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.435, 94.435, 163.905
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-1R


Mass: 49028.711 Da / Num. of mol.: 1 / Fragment: UNP residues 24-432
Mutation: T207E, Q211A, D215R, L232F, G295A, T298A, C329A, P358A, G361A, H363V, V405A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLP1R / Plasmid: pFastBac1-HM / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43220
#2: Protein/peptide truncated peptide agonist


Mass: 1488.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside / N-Octyl beta-D-thioglucopyranoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM

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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: 4.31 Å3/Da / Density % sol: 71.46 % / Description: Rod-like crystals
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH 8.0-9.0, 32-44% (v/v) PEG 200 / PH range: 8.0 - 9.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cryojet
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2015
Details: Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 3.7→54.6 Å / Num. obs: 9266 / % possible obs: 98.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 135 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.073 / Net I/σ(I): 6.6
Reflection shellResolution: 3.7→4.05 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.024 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2205 / CC1/2: 0.348 / Rpim(I) all: 1.078 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575-000)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IOL, 5EE7

3iol

5ee7


Resolution: 3.7→24.677 Å / SU ML: 0.81 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 46.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3341 763 4.74 %Random selection
Rwork0.2847 ---
obs0.2872 9202 92.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→24.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 209 0 3410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043518
X-RAY DIFFRACTIONf_angle_d1.0214794
X-RAY DIFFRACTIONf_dihedral_angle_d16.0781972
X-RAY DIFFRACTIONf_chiral_restr0.052532
X-RAY DIFFRACTIONf_plane_restr0.005574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7002-3.98480.42581620.38953056X-RAY DIFFRACTION92
3.9848-4.38380.38181320.31843116X-RAY DIFFRACTION93
4.3838-5.01350.32981480.2773053X-RAY DIFFRACTION92
5.0135-6.29910.38631800.32793060X-RAY DIFFRACTION92
6.2991-24.67770.2891410.24613043X-RAY DIFFRACTION92
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)
10.27080.8695-0.41220.9255-0.43561.5128-0.01471.0621-0.04940.25720.05440.80130.4979-1.5301-01.72280.25910.24711.7340.18641.7214-0.154240.4612-18.1541
21.03710.4209-1.15891.4869-1.8095.71070.60180.2175-0.0865-0.1350.00880.10160.3132-0.4639-0.00011.1270.109-0.17261.01190.07721.3676-21.162815.034810.2689
36.0722.3176-2.88454.43843.20965.546401.08810.3348-1.78720.0395-0.1232.0604-1.81980.06180.635-0.1807-0.21391.63650.25831.0128-24.361520.211526.1889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 334 )
3X-RAY DIFFRACTION3chain 'A' and (resid 335 through 417 )

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