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- PDB-5e94: Antibody-bound Glucagon-like Peptide-1 receptor extracellular domain -

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Basic information

Entry
Database: PDB / ID: 5.0E+94
TitleAntibody-bound Glucagon-like Peptide-1 receptor extracellular domain
Components
  • Antibody Fab fragment heavy chain
  • Antibody Fab fragment light chain
  • Glucagon-like peptide 1 receptor
KeywordsMEMBRANE PROTEIN / Antibody antagonist GLP-1 receptor / immune system
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 / activation of adenylate cyclase activity / negative regulation of blood pressure ...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 / 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, extracellular hormone receptor domain / Hormone receptor fold / 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 ...GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / 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. / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSoroka, V. / Schluckebier, G. / Reedtz-Runge, S.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insight into antibody-mediated antagonism of the Glucagon-like peptide-1 Receptor.
Authors: Hennen, S. / Kodra, J.T. / Soroka, V. / Krogh, B.O. / Wu, X. / Kaastrup, P. / Orskov, C. / Ronn, S.G. / Schluckebier, G. / Barbateskovic, S. / Gandhi, P.S. / Reedtz-Runge, S.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody Fab fragment light chain
B: Antibody Fab fragment heavy chain
C: Antibody Fab fragment light chain
D: Antibody Fab fragment heavy chain
G: Glucagon-like peptide 1 receptor
H: Glucagon-like peptide 1 receptor


Theoretical massNumber of molelcules
Total (without water)125,3816
Polymers125,3816
Non-polymers00
Water8,413467
1
A: Antibody Fab fragment light chain
B: Antibody Fab fragment heavy chain
G: Glucagon-like peptide 1 receptor


Theoretical massNumber of molelcules
Total (without water)62,6903
Polymers62,6903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-38 kcal/mol
Surface area25330 Å2
MethodPISA
2
C: Antibody Fab fragment light chain
D: Antibody Fab fragment heavy chain
H: Glucagon-like peptide 1 receptor


Theoretical massNumber of molelcules
Total (without water)62,6903
Polymers62,6903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-37 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.201, 65.692, 88.351
Angle α, β, γ (deg.)111.61, 97.47, 91.28
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Antibody Fab fragment light chain


Mass: 23516.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Antibody Fab fragment heavy chain


Mass: 24434.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein Glucagon-like peptide 1 receptor / GLP-1R


Mass: 14739.316 Da / Num. of mol.: 2
Fragment: N-terminal extracellular domain, UNP residues 24-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLP1R / Production host: Escherichia coli (E. coli) / References: UniProt: P43220
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium dihydrogen Phosphate monohydrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→32 Å / Num. obs: 72374 / % possible obs: 90 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 3.8 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IOL and 1BZ7

3iol

1bz7


Resolution: 2→32.09 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 3616 5.01 %
Rwork0.188 --
obs0.1902 72223 90.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→32.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8488 0 0 467 8955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088749
X-RAY DIFFRACTIONf_angle_d1.12111944
X-RAY DIFFRACTIONf_dihedral_angle_d13.8813119
X-RAY DIFFRACTIONf_chiral_restr0.0491319
X-RAY DIFFRACTIONf_plane_restr0.0051521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02630.27031450.21732633X-RAY DIFFRACTION93
2.0263-2.05410.2641350.21152857X-RAY DIFFRACTION95
2.0541-2.08340.26961680.20962644X-RAY DIFFRACTION95
2.0834-2.11450.25721390.22052830X-RAY DIFFRACTION95
2.1145-2.14760.27131470.21912756X-RAY DIFFRACTION94
2.1476-2.18280.31361520.24272729X-RAY DIFFRACTION94
2.1828-2.22040.28711390.25932690X-RAY DIFFRACTION92
2.2204-2.26080.42121130.31992749X-RAY DIFFRACTION93
2.2608-2.30420.31931280.26472627X-RAY DIFFRACTION92
2.3042-2.35120.31521500.24732765X-RAY DIFFRACTION94
2.3512-2.40240.26551370.21542757X-RAY DIFFRACTION94
2.4024-2.45820.29521490.20632743X-RAY DIFFRACTION94
2.4582-2.51970.27691580.20152742X-RAY DIFFRACTION94
2.5197-2.58780.24131390.19452701X-RAY DIFFRACTION93
2.5878-2.66390.26151490.19612723X-RAY DIFFRACTION94
2.6639-2.74980.23071290.19832728X-RAY DIFFRACTION93
2.7498-2.8480.26531570.20052717X-RAY DIFFRACTION93
2.848-2.9620.26621440.2062652X-RAY DIFFRACTION92
2.962-3.09670.23281420.19742659X-RAY DIFFRACTION92
3.0967-3.25980.24291460.19092666X-RAY DIFFRACTION91
3.2598-3.46380.26241360.18972639X-RAY DIFFRACTION90
3.4638-3.73090.1974990.1691982X-RAY DIFFRACTION68
3.7309-4.10570.20361150.15612025X-RAY DIFFRACTION69
4.1057-4.69820.16141500.13112563X-RAY DIFFRACTION88
4.6982-5.91320.1571170.13872561X-RAY DIFFRACTION88
5.9132-32.09370.15931330.15032469X-RAY DIFFRACTION85

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