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- PDB-6kk1: Structure of thermal-stabilised(M8) human GLP-1 receptor transmem... -

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Basic information

Entry
Database: PDB / ID: 6kk1
TitleStructure of thermal-stabilised(M8) human GLP-1 receptor transmembrane domain
ComponentsGlucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor
KeywordsSIGNALING PROTEIN / GPCR / seven-transmembrane / allosteric modulators / diabetes
Function / homology
Function and homology information


glucagon-like peptide 1 receptor activity / glucagon receptor activity / positive regulation of blood pressure / hormone secretion / 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 / positive regulation of blood pressure / hormone secretion / 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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / Glucagon-type ligand receptors / lysozyme / lysozyme activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / transmembrane signaling receptor 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. / : / 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 ...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. / : / 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. / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-97Y / Endolysin / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSong, G.
CitationJournal: Iucrj / Year: 2019
Title: Mutagenesis facilitated crystallization of GLP-1R.
Authors: Xu, Y. / Wang, Y. / Wang, Y. / Liu, K. / Peng, Y. / Yao, D. / Tao, H. / Liu, H. / Song, G.
History
DepositionJul 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.pdbx_database_id_PubMed ..._audit_author.name / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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


Theoretical massNumber of molelcules
Total (without water)106,1664
Polymers105,1342
Non-polymers1,0312
Water1267
1
A: Glucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0832
Polymers52,5671
Non-polymers5161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0832
Polymers52,5671
Non-polymers5161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.930, 67.350, 83.680
Angle α, β, γ (deg.)91.07, 90.10, 107.96
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 52567.238 Da / Num. of mol.: 2
Mutation: I196F,S225A,S271A,I317C,G318I,K346A,C347F,G361C,205-214deletion,R1011G,C1053T,C1096A,I1136R,I196F,S225A,S271A,I317C,G318I,K346A,C347F,G361C,205-214deletion
Source method: isolated from a genetically manipulated source
Details: HUMAN
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GLP1R / Plasmid: Pfastbac / Cell (production host): SF9 / Cell line (production host): IPLB-Sf-21-AE
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P43220, UniProt: P00720
#2: Chemical ChemComp-97Y / N-{4-[(R)-(3,3-dimethylcyclobutyl)({6-[4-(trifluoromethyl)-1H-imidazol-1-yl]pyridin-3-yl}amino)methyl]benzene-1-carbonyl}-beta-alanine


Mass: 515.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28F3N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.43 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.4-0.45 M ammonium acetate, 0.1 M sodium cacodylate, pH 6.2-6.6, 35-38% PEG400, 3% w/v aminohexanoic acid

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.5 Å / Num. obs: 25859 / % possible obs: 77.9 % / Redundancy: 3.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3446 / CC1/2: 0.76 / % possible all: 70.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VEW

5vew


Resolution: 2.8→49.504 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 39.29
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1136 4.4 %RAMDON SELECTION
Rwork0.2437 24660 --
obs0.2458 25796 77.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 271.17 Å2 / Biso mean: 90.7109 Å2 / Biso min: 30.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6617 0 74 7 6698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096856
X-RAY DIFFRACTIONf_angle_d1.4419342
X-RAY DIFFRACTIONf_chiral_restr0.0971083
X-RAY DIFFRACTIONf_plane_restr0.0051138
X-RAY DIFFRACTIONf_dihedral_angle_d13.1932337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.92750.4003940.39712766286069
2.9275-3.08180.3461040.3712983308774
3.0818-3.27480.33891210.32632995311676
3.2748-3.52760.3141650.24993036320177
3.5276-3.88250.30071570.24213142329980
3.8825-4.4440.31521480.23373144329279
4.444-5.59770.24751540.21793271342582
5.5977-49.51160.27511930.21323323351685
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)
10.3054-0.06850.5533-0.0884-0.1471-0.0844-0.00210.0446-0.06970.01520.0063-0.022-0.0282-0.3465-00.3675-0.0060.03680.3157-0.02160.26666.115135.876843.3587
21.02740.1105-0.0389-0.1689-0.14210.18740.15950.2969-0.03640.08710.06410.0746-0.1319-0.059700.35880.0733-0.04840.45020.02370.351110.04827.39137.85
30.13570.03860.08660.0806-0.09350.0050.0821-0.15060.0436-0.15460.04110.05060.09830.274300.3447-0.0109-0.01030.47540.00560.4362-2.8668.159-1.073
4-0.55630.05520.24280.138-0.13-0.0776-0.21730.7666-0.0004-0.10620.4374-0.1447-0.48721.010100.3976-0.02250.05270.23730.01350.41952.69328.7423.522
5-0.02320.19790.13840.05490.0272-0.01010.0386-0.15670.05130.04140.06990.10510.2161-0.371700.4692-0.0223-0.040.2154-0.0210.368638.66926.322139.0456
60.00220.00070.1747-0.02810.08470.09780.409-0.49670.0358-0.0095-0.03910.0202-0.0376-0.012500.5506-0.06340.20420.602-0.11480.673437.4521.51138.502
70.26390.15430.24260.26370.04570.04260.1406-0.0667-0.09180.09540.06880.07040.277-0.3228-00.4347-0.115-0.01390.6330.09080.396347.6818.350.173
80.0043-0.0151-0.0558-0.0061-0.0334-0.0039-0.35020.4364-0.17890.22940.3007-0.27280.123-0.0400.4522-0.0116-0.01740.23810.00380.457927.91629.43679.829
90.1554-0.1578-0.05550.10170.00070.00710.3463-0.07380.29010.1361-0.19230.35880.35510.562100.44660.0416-0.02910.34340.01890.506430.85238.4187.343
100.1683-0.3652-0.0030.61730.64270.28820.0245-0.08960.00720.1816-0.00420.01550.1948-0.0922-00.44720.0349-0.05810.3570.00720.488235.05513.4578.963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 136:256 )A136 - 256
2X-RAY DIFFRACTION2( CHAIN A AND RESID 257:422 )A257 - 422
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1001:1060 )A1001 - 1060
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1061:1160 )A1061 - 1160
5X-RAY DIFFRACTION5( CHAIN B AND RESID 136:256 )B136 - 256
6X-RAY DIFFRACTION6( CHAIN B AND RESID 257:335 )B257 - 335
7X-RAY DIFFRACTION7( CHAIN B AND RESID 336:422 )B336 - 422
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1001:1027 )B1001 - 1027
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1028:1060 )B1028 - 1060
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1061:1160 )B1061 - 1160

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