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- PDB-5vex: Structure of the human GLP-1 receptor complex with NNC0640 -

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Basic information

Entry
Database: PDB / ID: 5vex
TitleStructure of the human GLP-1 receptor complex with NNC0640
ComponentsGlucagon-like peptide 1 receptor, Endolysin chimera
KeywordsSIGNALING PROTEIN / GPCR / class B / 7TM domain / treatment of type 2 diabetes
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 / viral release from host cell by cytolysis / 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 / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / viral release from host cell by cytolysis / activation of adenylate cyclase activity / negative regulation of blood pressure / peptidoglycan catabolic process / 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 / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / host cell cytoplasm / learning or memory / cell surface receptor signaling pathway / defense response to bacterium / 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. / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-97V / Endolysin / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSong, G. / Yang, D. / Wang, Y. / Graaf, C.D. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. ...Song, G. / Yang, D. / Wang, Y. / Graaf, C.D. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. / Liu, D. / Wu, F. / Wu, Y. / Zhao, S. / Ye, L. / Han, G.W. / Lau, J. / Wu, B. / Hanson, M.A. / Liu, Z.-J. / Wang, M.-W. / Stevens, R.C.
CitationJournal: Nature / Year: 2017
Title: Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators.
Authors: Song, G. / Yang, D. / Wang, Y. / de Graaf, C. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. / Liu, D. / Wu, F. / Wu, Y. / Zhao, S. / Ye, L. / Han, G.W. / Lau, J. / Wu, B. / ...Authors: Song, G. / Yang, D. / Wang, Y. / de Graaf, C. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. / Liu, D. / Wu, F. / Wu, Y. / Zhao, S. / Ye, L. / Han, G.W. / Lau, J. / Wu, B. / Hanson, M.A. / Liu, Z.J. / Wang, M.W. / Stevens, R.C.
History
DepositionApr 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: 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

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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, Endolysin chimera
B: Glucagon-like peptide 1 receptor, Endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3224
Polymers105,1752
Non-polymers1,1472
Water00
1
A: Glucagon-like peptide 1 receptor, Endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1612
Polymers52,5871
Non-polymers5741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucagon-like peptide 1 receptor, Endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1612
Polymers52,5871
Non-polymers5741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.810, 67.510, 83.660
Angle α, β, γ (deg.)91.55, 89.88, 107.56
Int Tables number1
Space group name H-MP1
DetailsTHE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

#1: Protein Glucagon-like peptide 1 receptor, Endolysin chimera / GLP-1R / Lysis protein / Lysozyme / Muramidase


Mass: 52587.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GLP1R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43220, UniProt: P00720, lysozyme
#2: Chemical ChemComp-97V / 4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl)phenyl]carbamoyl}amino]methyl}-N-(1H-tetrazol-5-yl)benzamide


Mass: 573.666 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31N7O4S

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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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.4-0.45 M ammonium acetate, 0.1 M sodium acetate, pH 5.0-5.8, 38-40% PEG400

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 24745 / % possible obs: 91.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 92.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.6 / CC1/2: 0.66 / % possible all: 87.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5ee7 and 212L

5ee7

212l


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.389
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1060 4.29 %RANDOM
Rwork0.233 ---
obs0.234 24728 91.4 %-
Displacement parametersBiso mean: 111.74 Å2
Baniso -1Baniso -2Baniso -3
1-11.7226 Å2-1.9677 Å2-0.6183 Å2
2---27.3262 Å23.1345 Å2
3---15.6036 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: 1 / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6609 0 98 0 6707
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016877HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.869372HARMONIC2.5
X-RAY DIFFRACTIONt_dihedral_angle_d3056SINUSOIDAL15
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1015HARMONIC5
X-RAY DIFFRACTIONt_it6877HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion1.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion910SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8120SEMIHARMONIC4
LS refinement shellResolution: 3→3.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.289 135 4.6 %
Rwork0.243 2801 -
all0.245 2936 -
obs--87.76 %
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)
11.46190.1438-0.37741.0720.21664.49360.2313-0.2453-0.03920.07610.00780.120.54380.0765-0.2391-0.3862-0.0781-0.01650.1968-0.0359-0.39966.2031-22.8618-27.7299
21.9858-0.03050.98911.22240.20774.07450.19150.18550.2117-0.0524-0.0660.1148-0.47030.0496-0.1255-0.43680.00890.06450.228-0.0246-0.382838.558-10.2411-58.0396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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