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- PDB-4hj0: Crystal structure of the human GIPr ECD in complex with Gipg013 F... -

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Basic information

Entry
Database: PDB / ID: 4hj0
TitleCrystal structure of the human GIPr ECD in complex with Gipg013 Fab at 3-A resolution
Components
  • Gastric inhibitory polypeptide receptor
  • Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Heavy chain
  • Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Light chain
KeywordsIMMUNE SYSTEM / Glucagon receptor sub-family recognition fold
Function / homology
Function and homology information


gastric inhibitory peptide receptor activity / glucagon family peptide binding / gastric inhibitory peptide signaling pathway / desensitization of G protein-coupled receptor signaling pathway / endocrine pancreas development / response to fatty acid / G protein-coupled peptide receptor activity / peptide hormone binding / response to glucose / response to axon injury ...gastric inhibitory peptide receptor activity / glucagon family peptide binding / gastric inhibitory peptide signaling pathway / desensitization of G protein-coupled receptor signaling pathway / endocrine pancreas development / response to fatty acid / G protein-coupled peptide receptor activity / peptide hormone binding / response to glucose / response to axon injury / activation of adenylate cyclase activity / response to nutrient / regulation of insulin secretion / generation of precursor metabolites and energy / positive regulation of insulin secretion / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to calcium ion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / transmembrane signaling receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / cell surface receptor signaling pathway / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, gastric inhibitory polypeptide receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / 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, gastric inhibitory polypeptide receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / 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
Gastric inhibitory polypeptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMadhurantakam, C. / Ravn, P. / Gruetter, M.G. / Jackson, R.H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Pharmacological Characterization of Novel Potent and Selective Monoclonal Antibody Antagonists of Glucose-dependent Insulinotropic Polypeptide Receptor.
Authors: Ravn, P. / Madhurantakam, C. / Kunze, S. / Matthews, E. / Priest, C. / O'Brien, S. / Collinson, A. / Papworth, M. / Fritsch-Fredin, M. / Jermutus, L. / Benthem, L. / Gruetter, M. / Jackson, R.H.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gastric inhibitory polypeptide receptor
B: Gastric inhibitory polypeptide receptor
P: Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Heavy chain
Q: Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Light chain
D: Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Light chain
C: Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Heavy chain


Theoretical massNumber of molelcules
Total (without water)124,4306
Polymers124,4306
Non-polymers00
Water00
1
A: Gastric inhibitory polypeptide receptor
P: Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Heavy chain
Q: Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Light chain


Theoretical massNumber of molelcules
Total (without water)62,2153
Polymers62,2153
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-34 kcal/mol
Surface area23740 Å2
MethodPISA
2
B: Gastric inhibitory polypeptide receptor
D: Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Light chain
C: Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Heavy chain


Theoretical massNumber of molelcules
Total (without water)62,2153
Polymers62,2153
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-40 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.266, 109.850, 105.935
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gastric inhibitory polypeptide receptor / GIP-R / Glucose-dependent insulinotropic polypeptide receptor


Mass: 15764.310 Da / Num. of mol.: 2 / Fragment: Extra-cellular Domain, UNP residues 24-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIPR / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: P48546
#2: Protein Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Heavy chain


Mass: 23758.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU / Cell line (production host): CHO / Production host: Homo sapiens (human)
#3: Protein Gipg013 Fab, Antagonizing antibody to the GIP Receptor, Light chain


Mass: 22691.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU / Cell line (production host): CHO / Production host: Homo sapiens (human)
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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.02 M TAPS, 30% (w/v) PEG 10,000, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 29, 2010
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→48.665 Å / Num. obs: 21995 / % possible obs: 100 % / Observed criterion σ(I): 2.6
Reflection shellResolution: 3→3.16 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERMRphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QKH, 1GIG

2qkh

1gig


Resolution: 3→48.665 Å / SU ML: 1 / σ(F): 1.29 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3107 1997 9.08 %
Rwork0.2553 --
obs0.2603 21989 99.92 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.75 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.603 Å2-0 Å2-9.6426 Å2
2---10.7044 Å20 Å2
3---15.3074 Å2
Refinement stepCycle: LAST / Resolution: 3→48.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 0 0 7635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057855
X-RAY DIFFRACTIONf_angle_d1.1510709
X-RAY DIFFRACTIONf_dihedral_angle_d15.5992745
X-RAY DIFFRACTIONf_chiral_restr0.0771180
X-RAY DIFFRACTIONf_plane_restr0.0061384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.07510.35061410.32671403X-RAY DIFFRACTION100
3.0751-3.15820.39321410.30371412X-RAY DIFFRACTION100
3.1582-3.25110.34151450.28831460X-RAY DIFFRACTION100
3.2511-3.35610.34871390.25571385X-RAY DIFFRACTION100
3.3561-3.4760.32011430.26861435X-RAY DIFFRACTION100
3.476-3.61510.29371410.26051417X-RAY DIFFRACTION100
3.6151-3.77960.35611440.26371440X-RAY DIFFRACTION100
3.7796-3.97880.33021420.26781415X-RAY DIFFRACTION100
3.9788-4.22790.3021420.24221428X-RAY DIFFRACTION100
4.2279-4.55410.26831430.21031426X-RAY DIFFRACTION100
4.5541-5.0120.27141420.21061424X-RAY DIFFRACTION100
5.012-5.73630.27561440.2461434X-RAY DIFFRACTION100
5.7363-7.22330.31571450.27971446X-RAY DIFFRACTION100
7.2233-48.67140.30331450.25391467X-RAY DIFFRACTION100

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