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- PDB-6dkj: human GIPR ECD and Fab complex -

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Basic information

Entry
Database: PDB / ID: 6dkj
Titlehuman GIPR ECD and Fab complex
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Gastric inhibitory polypeptide receptor
KeywordsSIGNALING PROTEIN / GPCR
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 / immunoglobulin complex / peptide hormone binding / regulation of insulin secretion ...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 / immunoglobulin complex / peptide hormone binding / regulation of insulin secretion / response to axon injury / positive regulation of cAMP-mediated signaling / response to glucose / activation of adenylate cyclase activity / response to nutrient / generation of precursor metabolites and energy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / Glucagon-type ligand receptors / response to calcium ion / transmembrane signaling receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / adaptive immune response / cell surface receptor signaling pathway / extracellular region / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, gastric inhibitory polypeptide receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / 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 superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like ...GPCR, family 2, gastric inhibitory polypeptide receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / 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 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. / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Gastric inhibitory polypeptide receptor / Epididymis luminal protein 213
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMin, X. / Wang, Z.
CitationJournal: Sci Transl Med / Year: 2018
Title: Anti-obesity effects of GIPR antagonists alone and in combination with GLP-1R agonists in preclinical models.
Authors: Killion, E.A. / Wang, J. / Yie, J. / Shi, S.D. / Bates, D. / Min, X. / Komorowski, R. / Hager, T. / Deng, L. / Atangan, L. / Lu, S.C. / Kurzeja, R.J.M. / Sivits, G. / Lin, J. / Chen, Q. / ...Authors: Killion, E.A. / Wang, J. / Yie, J. / Shi, S.D. / Bates, D. / Min, X. / Komorowski, R. / Hager, T. / Deng, L. / Atangan, L. / Lu, S.C. / Kurzeja, R.J.M. / Sivits, G. / Lin, J. / Chen, Q. / Wang, Z. / Thibault, S.A. / Abbott, C.M. / Meng, T. / Clavette, B. / Murawsky, C.M. / Foltz, I.N. / Rottman, J.B. / Hale, C. / Veniant, M.M. / Lloyd, D.J.
History
DepositionMay 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
C: Gastric inhibitory polypeptide receptor
A: Fab heavy chain
B: Fab light chain
D: Gastric inhibitory polypeptide receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0478
Polymers120,9236
Non-polymers1242
Water18,0691003
1
H: Fab heavy chain
L: Fab light chain
C: Gastric inhibitory polypeptide receptor


Theoretical massNumber of molelcules
Total (without water)60,4613
Polymers60,4613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-35 kcal/mol
Surface area24580 Å2
MethodPISA
2
A: Fab heavy chain
B: Fab light chain
D: Gastric inhibitory polypeptide receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5855
Polymers60,4613
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-33 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.907, 63.649, 159.099
Angle α, β, γ (deg.)90.000, 92.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 23806.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5
#2: Antibody Fab light chain / Fragment antigen-binding


Mass: 23206.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HEL-213 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: V9HW34
#3: Protein Gastric inhibitory polypeptide receptor / / GIP-R / Glucose-dependent insulinotropic polypeptide receptor


Mass: 13447.896 Da / Num. of mol.: 2 / Fragment: residues 22-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIPR / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P48546
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1003 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 4000 and 20% isopropanol

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→19.74 Å / Num. obs: 79376 / % possible obs: 97.6 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.057 / Rrim(I) all: 0.111 / Net I/σ(I): 9.7 / Num. measured all: 294866
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-1.993.80.63345370.8170.3750.73797.1
9.94-19.743.60.0285630.9990.0170.03386.3

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Processing

Software
NameVersionClassification
PHENIX(dev-2328_1692)refinement
XDSdata reduction
Aimless0.5.12data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.719 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.43
RfactorNum. reflection% reflection
Rfree0.2384 3838 4.84 %
Rwork0.1986 --
obs0.2005 79290 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.65 Å2 / Biso mean: 26.4336 Å2 / Biso min: 8.16 Å2
Refinement stepCycle: final / Resolution: 1.95→19.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8259 0 8 1003 9270
Biso mean--23.22 33.96 -
Num. residues----1077

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