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- PDB-6kk7: Structure of thermal-stabilised(M6) human GLP-1 receptor transmem... -

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Basic information

Entry
Database: PDB / ID: 6kk7
TitleStructure of thermal-stabilised(M6) 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 / 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 / activation of adenylate cyclase activity / viral release from host cell by cytolysis ...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 / activation of adenylate cyclase activity / viral release from host cell by cytolysis / negative regulation of blood pressure / peptidoglycan catabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cell wall macromolecule catabolic process / transmembrane signaling receptor activity / 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. / : / 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: 3.1 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 1.3Oct 16, 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

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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)106,1304
Polymers105,0982
Non-polymers1,0312
Water00
1
A: Glucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0652
Polymers52,5491
Non-polymers5161
Water0
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)53,0652
Polymers52,5491
Non-polymers5161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.230, 71.060, 81.000
Angle α, β, γ (deg.)92.48, 92.61, 105.10
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: 52549.227 Da / Num. of mol.: 2
Mutation: S225A,I317C,G318I,K346A,C347F,G361C,205-214deletion,R1011G,C1053T,C1096A,I1136R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GLP1R / Plasmid: pfasctbac / 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
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: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→41.2 Å / Num. obs: 20302 / % possible obs: 79.9 % / Redundancy: 2.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.6
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2761 / CC1/2: 0.61 / % possible all: 74.5

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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: 3.1→40.392 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 39.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3032 955 4.72 %
Rwork0.2568 19263 -
obs0.2589 20218 79.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 266.65 Å2 / Biso mean: 104.4108 Å2 / Biso min: 37.02 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 74 0 6664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136825
X-RAY DIFFRACTIONf_angle_d1.5579295
X-RAY DIFFRACTIONf_chiral_restr0.0851085
X-RAY DIFFRACTIONf_plane_restr0.0091132
X-RAY DIFFRACTIONf_dihedral_angle_d4.9323932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1001-3.26340.53061360.44422525266173
3.2634-3.46780.39071450.35332700284579
3.4678-3.73540.30061350.30022739287479
3.7354-4.11090.31841650.2662847301283
4.1109-4.7050.27721390.22742806294581
4.705-5.92480.29551220.24092905302783
5.9248-40.39520.23491130.20682741285479
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)
14.4940.1224-3.08431.2808-0.68353.73830.0320.7402-0.524-0.1901-0.3115-0.19410.70140.0498-0.09180.86720.0787-0.03230.7879-0.0720.685711.7186-40.0325-47.1605
21.9420.0732-0.00662.7056-0.22864.61790.14071.0666-1.13870.0288-0.09250.61480.33661.0834-0.23720.8962-0.1051-0.0354-0.5187-0.12340.80562.1522-34.4071-39.6093
31.6711-0.1464-0.00492.39371.26511.73280.21891.59870.7739-0.5813-0.80370.5326-0.04040.01110.16550.5708-0.4375-0.1776-1.7397-0.48550.47783.1924-25.7883-46.9925
41.1709-0.02590.39712.4222-0.31780.26190.3551-1.30840.51340.23870.24970.3598-0.69340.3009-0.33290.7178-0.14610.17081.3335-0.20630.8379-0.982-18.707-48.661
53.3327-0.85610.02581.8552-0.09163.09790.1263-0.81470.20750.17640.371-0.01210.02590.3296-0.13170.5462-0.02060.02261.02420.10670.494614.652-19.129-35.715
62.10871.3360.12282.5799-2.02282.7640.0645-0.42960.07420.37891.25480.36740.5078-0.6771-0.20930.2352-0.52950.17872.01770.36630.806714.378-34.514-38.543
71.37190.0013-0.15031.2479-0.09234.5854-0.04290.3082-0.1116-0.1877-0.1555-0.0413-0.42020.04330.08810.40.05280.01250.58250.05420.47934.152-50.509-19.612
83.4428-0.87143.41231.8527-2.17026.38770.36940.51520.3003-0.0098-0.07770.12440.83820.9627-0.12470.44290.05130.11980.50440.06250.5186-5.775-10.053-3.342
91.62550.0273-0.59691.628-0.19072.0021-0.0104-0.5645-0.0512-0.2178-0.0482-0.04540.05520.70250.14810.59160.0462-0.02390.6325-0.07160.7383.107-12.638-1.128
104.76751.65740.14327.62180.44244.25110.5138-0.3793-0.30571.03120.21430.10411.35760.1616-0.22411.5016-0.02740.17541.5946-0.01221.348-3.627-29.982-6.484
112.96511.33511.86371.21391.19524.33710.2242-0.29770.003-0.04570.4163-0.7207-0.64870.0781-0.33890.8235-0.22110.13421.2112-0.60841.268845.67084.788-36.0783
121.9568-0.44910.07491.7908-0.55581.85610.1896-0.42430.34840.1039-0.07560.2386-0.39040.7392-0.13750.53290.00820.03730.5596-0.10260.561336.3167-5.2934-40.8685
131.76571.05731.02592.50140.45691.57620.20730.770.0214-0.57780.02440.3490.5266-0.1714-0.17820.87580.1183-0.19261.0201-0.10040.875331.417-16.035-35.132
143.90792.65640.87029.0931.36172.24350.05860.5835-1.1581-0.8032-0.0044-0.73980.67940.2287-0.44910.80020.1524-0.03891.1249-0.24660.890445.093-20.249-45.487
151.4-0.0077-0.44312.1828-0.03012.50120.32360.7652-0.1919-0.59150.0475-0.0354-0.750.974-0.19680.480.02450.03941.18920.1140.544149.877-10.711-57.915
163.339-0.43060.78071.1239-0.04591.02250.13730.27330.5592-0.1775-0.06760.6731-0.3834-0.3449-0.05260.90260.00220.00291.81150.18020.736150.938-9.418-34.104
172.61930.2468-0.63923.706-2.33414.1746-0.2548-0.52820.46430.25170.33920.15180.1146-0.36530.05670.4999-0.0099-0.03580.89430.24050.691446.571-58.935
181.52050.6294-0.50641.137-0.82862.10220.0913-1.13480.2520.3522-0.44280.0138-0.55610.06990.08860.55350.03190.03331.1568-0.13890.577939.37622.277-64.341
193.88480.6785-2.31912.3012-2.21353.89930.068-0.43580.10240.11030.0732-0.0217-0.32970.6887-0.05640.5047-0.0823-0.00790.3498-0.06540.64829.544-24.566-80.447
202.48820.29560.152.24850.70840.557-0.27981.51930.26230.17920.6378-0.1625-0.5042-0.35980.11040.45940.32210.0344-0.02490.17710.615132.376-34.81-86.043
210.53720.3640.08352.01440.55750.0121-0.78630.42-0.21910.39920.1126-1.4285-0.12280.06470.38180.7330.0321-0.06061.3025-0.1920.922943.726-13.06-79.654
221.7555-3.88721.43528.3381-3.55421.55590.0720.77570.326-0.8714-0.0296-0.0145-1.0946-0.49410.12191.56410.0792-0.04941.1235-0.01570.836433.19-4.904-77.406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 136:168 )A136 - 168
2X-RAY DIFFRACTION2( CHAIN A AND RESID 169:201 )A169 - 201
3X-RAY DIFFRACTION3( CHAIN A AND RESID 202:256 )A202 - 256
4X-RAY DIFFRACTION4( CHAIN A AND RESID 257:304 )A257 - 304
5X-RAY DIFFRACTION5( CHAIN A AND RESID 305:381 )A305 - 381
6X-RAY DIFFRACTION6( CHAIN A AND RESID 382:411 )A382 - 411
7X-RAY DIFFRACTION7( CHAIN A AND RESID 412:422 )A412 - 422
8X-RAY DIFFRACTION8( CHAIN A AND RESID 1001:1033 )A1001 - 1033
9X-RAY DIFFRACTION9( CHAIN A AND RESID 1034:1099 )A1034 - 1099
10X-RAY DIFFRACTION10( CHAIN A AND RESID 1100:1160 )A1100 - 1160
11X-RAY DIFFRACTION11( CHAIN B AND RESID 136:168 )B136 - 168
12X-RAY DIFFRACTION12( CHAIN B AND RESID 169:256 )B169 - 256
13X-RAY DIFFRACTION13( CHAIN B AND RESID 257:304 )B257 - 304
14X-RAY DIFFRACTION14( CHAIN B AND RESID 305:335 )B305 - 335
15X-RAY DIFFRACTION15( CHAIN B AND RESID 336:361 )B336 - 361
16X-RAY DIFFRACTION16( CHAIN B AND RESID 362:398 )B362 - 398
17X-RAY DIFFRACTION17( CHAIN B AND RESID 399:419 )B399 - 419
18X-RAY DIFFRACTION18( CHAIN B AND RESID 420:422 )B420 - 422
19X-RAY DIFFRACTION19( CHAIN B AND RESID 1001:1033 )B1001 - 1033
20X-RAY DIFFRACTION20( CHAIN B AND RESID 1034:1063 )B1034 - 1063
21X-RAY DIFFRACTION21( CHAIN B AND RESID 1064:1098 )B1064 - 1098
22X-RAY DIFFRACTION22( CHAIN B AND RESID 1099:1160 )B1099 - 1160

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