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- PDB-6kjv: Structure of thermal-stabilised(M9) human GLP-1 receptor transmem... -

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Basic information

Entry
Database: PDB / ID: 6kjv
TitleStructure of thermal-stabilised(M9) 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 / regulation of heart contraction / response to psychosocial stress / 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 / regulation of heart contraction / response to psychosocial stress / peptide hormone binding / activation of adenylate cyclase activity / viral release from host cell by cytolysis / cAMP-mediated signaling / 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 / 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. / : / 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. / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-97Y / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 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

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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)106,9116
Polymers105,1672
Non-polymers1,7444
Water1448
1
A: Glucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4553
Polymers52,5831
Non-polymers8722
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)53,4553
Polymers52,5831
Non-polymers8722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.030, 68.300, 83.430
Angle α, β, γ (deg.)91.53, 90.34, 106.49
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: 52583.305 Da / Num. of mol.: 2
Mutation: S193C,I196F,S225A,S271A,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
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 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: Mar 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.2 Å / Num. obs: 30099 / % possible obs: 88.8 % / Redundancy: 2.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.57 / Num. unique obs: 3968 / CC1/2: 0.62 / % possible all: 79.7

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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→29.8 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / Phase error: 37.27
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1324 4.4 %Ramdon selection
Rwork0.247 28712 --
obs0.249 30036 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.23 Å2 / Biso mean: 84.0806 Å2 / Biso min: 25.01 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6607 0 124 8 6739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046893
X-RAY DIFFRACTIONf_angle_d0.7349379
X-RAY DIFFRACTIONf_chiral_restr0.0391085
X-RAY DIFFRACTIONf_plane_restr0.0051141
X-RAY DIFFRACTIONf_dihedral_angle_d10.5273979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.91210.46531140.41012842295679
2.9121-3.04450.38141060.36523026313283
3.0445-3.20480.36981050.31993153325886
3.2048-3.40530.32071670.26693195336289
3.4053-3.66780.25411650.24453203336890
3.6678-4.03610.27311770.24263314349193
4.0361-4.61830.28741470.23273361350893
4.6183-5.81150.24341550.22923355351094
5.8115-29.78050.25871880.21093263345192
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)
10.3346-0.1735-0.11280.1637-0.24130.11270.02230.0066-0.06580.0991-0.03710.0512-0.0965-0.051-00.3782-0.00020.01940.2745-0.01940.28256.533836.098143.7195
20.76570.01020.2174-0.16320.28760.39660.23470.3479-0.1058-0.0445-0.06010.1748-0.14390.040900.36060.128-0.08370.5961-0.0060.373310.32427.46338.215
30.5074-0.20960.2507-0.1206-0.25930.0571-0.0658-0.2073-0.1758-0.0223-0.0472-0.0747-0.40070.3059-00.3357-0.00540.01470.47080.00240.3467-2.9818.298-0.901
40.25890.10270.32820.66960.32420.17220.03080.26310.0093-0.0938-0.0092-0.0297-0.21080.324700.3413-0.02440.04460.30480.00890.37633.17128.7783.918
50.39010.05950.26910.1347-0.01050.19270.02730.0360.0711-0.04170.07570.18570.217-0.350200.409-0.0716-0.06610.1907-0.01240.300538.61795.741239.2095
6-0.03240.0543-0.15930.071-0.16190.04510.6035-0.5591-0.6348-1.38590.77860.62011.1283-0.31620-0.58620.04560.62070.5474-0.03960.423933.94320.33133.683
70.1492-0.0149-0.0578-0.0409-0.06990.03990.0269-0.17410.15440.13350.19080.03660.020.3687-00.4815-0.11050.01940.70260.05070.384349.03618.50456.371
80.01670.1287-0.0170.0888-0.09530.04660.4626-0.7707-0.4470.14440.2106-0.02580.4771-0.3498-00.8052-0.34630.00120.67690.20980.457951.27612.30734.58
90.30270.43060.44150.24070.16860.06430.0189-0.1462-0.129-0.06470.0082-0.07030.2022-0.383700.2861-0.00670.02420.31080.0210.338441.937-4.35760.632
100.1665-0.1397-0.02490.08480.024-0.0059-0.01720.09220.1491-0.025-0.1359-0.00230.24810.2482-00.33870.0364-0.01780.4257-0.04640.421728.57229.32581.047
110.17340.0038-0.08890.36740.12170.1047-0.0225-0.03230.00470.06970.01830.05630.07970.113500.29890.0156-0.02880.1509-0.03140.32137.6127.03583.293
120.0487-0.0531-0.02070.00370.02240.0644-0.1442-0.18670.140.33840.23750.12160.37110.233-01.1070-0.01010.59090.1590.52131.129.22478.485
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 1001:1059 )A1001 - 1059
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1060:1160 )A1060 - 1160
5X-RAY DIFFRACTION5( CHAIN B AND RESID 136:256 )B136 - 256
6X-RAY DIFFRACTION6( CHAIN B AND RESID 257:315 )B257 - 315
7X-RAY DIFFRACTION7( CHAIN B AND RESID 316:361 )B316 - 361
8X-RAY DIFFRACTION8( CHAIN B AND RESID 362:398 )B362 - 398
9X-RAY DIFFRACTION9( CHAIN B AND RESID 399:422 )B399 - 422
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1001:1033 )B1001 - 1033
11X-RAY DIFFRACTION11( CHAIN B AND RESID 1034:1099 )B1034 - 1099
12X-RAY DIFFRACTION12( CHAIN B AND RESID 1100:1160 )B1100 - 1160

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