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- PDB-2qkh: Crystal structure of the extracellular domain of human GIP recept... -

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Basic information

Entry
Database: PDB / ID: 2qkh
TitleCrystal structure of the extracellular domain of human GIP receptor in complex with the hormone GIP
Components
  • Glucose-dependent insulinotropic polypeptide
  • Glucose-dependent insulinotropic polypeptide receptor
KeywordsSIGNALING PROTEIN/HORMONE / GPCR / incretin / hormone-GPCR complex / extracellular domain / ligand binding domain / ECD / glugacon receptor family / hormone recognition fold / diabetes / helix formation / Cleavage on pair of basic residues / Polymorphism / Alternative splicing / G-protein coupled receptor / Glycoprotein / Membrane / Transducer / Transmembrane / SIGNALING PROTEIN-HORMONE COMPLEX
Function / homology
Function and homology information


gastric inhibitory polypeptide receptor binding / gastric inhibitory peptide receptor activity / glucagon family peptide binding / digestive system development / gastric inhibitory peptide signaling pathway / glucagon receptor binding / regulation of fatty acid biosynthetic process / desensitization of G protein-coupled receptor signaling pathway / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / endocrine pancreas development ...gastric inhibitory polypeptide receptor binding / gastric inhibitory peptide receptor activity / glucagon family peptide binding / digestive system development / gastric inhibitory peptide signaling pathway / glucagon receptor binding / regulation of fatty acid biosynthetic process / desensitization of G protein-coupled receptor signaling pathway / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / endocrine pancreas development / response to selenium ion / response to fatty acid / triglyceride homeostasis / G protein-coupled peptide receptor activity / response to acidic pH / positive regulation of glucose transmembrane transport / exploration behavior / response to lipid / response to starvation / peptide hormone binding / regulation of insulin secretion / response to axon injury / response to amino acid / positive regulation of cAMP-mediated signaling / response to glucose / sensory perception of pain / activation of adenylate cyclase activity / adult locomotory behavior / response to nutrient / generation of precursor metabolites and energy / long-term synaptic potentiation / female pregnancy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / positive regulation of insulin secretion / response to organic cyclic compound / memory / response to peptide hormone / Glucagon-type ligand receptors / response to calcium ion / transmembrane signaling receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / secretory granule lumen / cell surface receptor signaling pathway / response to xenobiotic stimulus / endoplasmic reticulum lumen / neuronal cell body / signal transduction / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Gastric inhibitory polypeptide / GPCR, family 2, gastric inhibitory polypeptide receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain ...Gastric inhibitory polypeptide / GPCR, family 2, gastric inhibitory polypeptide receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
methyl-beta-cyclodextrin / D(-)-TARTARIC ACID / Gastric inhibitory polypeptide / Gastric inhibitory polypeptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsParthier, C. / Kleinschmidt, M. / Neumann, P. / Rudolph, R. / Manhart, S. / Schlenzig, D. / Fanghanel, J. / Rahfeld, J.-U. / Demuth, H.-U. / Stubbs, M.T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structure of the incretin-bound extracellular domain of a G protein-coupled receptor
Authors: Parthier, C. / Kleinschmidt, M. / Neumann, P. / Rudolph, R. / Manhart, S. / Schlenzig, D. / Fanghanel, J. / Rahfeld, J.-U. / Demuth, H.-U. / Stubbs, M.T.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Glucose-dependent insulinotropic polypeptide
A: Glucose-dependent insulinotropic polypeptide receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7834
Polymers20,3822
Non-polymers1,4012
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.007, 84.007, 180.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 4990.586 Da / Num. of mol.: 1 / Fragment: Sequence database residues 52-93 / Source method: obtained synthetically
Details: The peptide is naturally found in Homo Sapiens (human).
References: UniProt: P09681
#2: Protein Glucose-dependent insulinotropic polypeptide receptor / Gastric inhibitory polypeptide receptor / GIP-R


Mass: 15390.996 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 29-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIPR / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P48546
#3: Polysaccharide Cyclic 2,3-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-2,6-di-O- ...Cyclic 2,3-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-2,6-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-3-O-methyl-alpha-D-glucopyranose / methyl-beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1251.185 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: methyl-beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/5,7,7/[a2122h-1a_1-5_2*OC_3*OC][a2122h-1a_1-5_3*OC][a2122h-1a_1-5][a2122h-1a_1-5_2*OC][a2122h-1a_1-5_2*OC_6*OC]/1-2-3-3-4-5-4/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100 mM HEPES, 1 M potassium-sodium tartrate, 9% Methyl-beta-cyclodextrin, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 28, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 49.2 % / Av σ(I) over netI: 9.3 / Number: 1342132 / Rmerge(I) obs: 0.109 / Χ2: 0.92 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 27297 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665010010.070.87250.1
2.913.6610010.0790.90651
2.542.9110010.1071.0150.8
2.312.5410010.1431.03550.4
2.142.3110010.21.01149.9
2.022.1410010.2830.89649.8
1.912.0210010.4550.96249.2
1.831.9110010.5990.77748.9
1.761.8310010.7750.79148.4
1.71.7610010.9670.9343.2
ReflectionResolution: 1.9→50 Å / Num. all: 19684 / Num. obs: 19647 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 50.1 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.024 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 48.9 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 8.2 / Num. unique all: 1942 / Χ2: 1.009 / % possible all: 100

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Phasing

Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 27296
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.72-10023.70.816506
5.25-6.7226.10.884512
4.56-5.2522.30.922501
4.09-4.5620.20.931567
3.74-4.0920.10.928633
3.46-3.7420.60.92667
3.24-3.4623.10.922715
3.06-3.2425.10.913784
2.9-3.0627.40.899788
2.77-2.9270.905837
2.65-2.7727.10.902869
2.55-2.65260.9924
2.46-2.5527.40.897963
2.37-2.46290.892969
2.3-2.3726.80.9031027
2.23-2.329.50.9041027
2.17-2.2326.70.9111065
2.11-2.1726.30.8981107
2.06-2.1125.20.9091136
2.01-2.0625.50.9031162
1.96-2.0126.30.9031177
1.92-1.9628.20.8661201
1.88-1.9227.40.8981240
1.84-1.8828.80.8951253
1.81-1.8428.10.8951299
1.77-1.8128.20.8961301
1.74-1.7731.10.8761337
1.7-1.7438.20.8361729

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
DM5phasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.667 / SU ML: 0.057 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.092
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1004 5.1 %RANDOM
Rwork0.166 ---
all0.18329 19684 --
obs0.167 18643 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.771 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.54 Å20 Å2
2--1.07 Å20 Å2
3----1.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.092 Å0.127 Å
Refinement stepCycle: LAST / Resolution: 1.9→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 84 138 1250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211162
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9891593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1135128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.15823.3959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10115154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.139158
X-RAY DIFFRACTIONr_chiral_restr0.080.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02868
X-RAY DIFFRACTIONr_nbd_refined0.2180.3529
X-RAY DIFFRACTIONr_nbtor_refined0.320.5837
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.5189
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4220.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.523
X-RAY DIFFRACTIONr_mcbond_it1.712646
X-RAY DIFFRACTIONr_mcangle_it2.533999
X-RAY DIFFRACTIONr_scbond_it1.7462606
X-RAY DIFFRACTIONr_scangle_it2.6343592
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 62 -
Rwork0.179 1349 -
obs-1411 97.65 %
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)
13.1797-0.48961.79141.3689-0.72153.6442-0.11530.06710.11380.01870.0394-0.1025-0.11510.32910.0759-0.3064-0.2748-0.2459-0.2534-0.2451-0.23729.4329.56646.108
220.7615-7.88445.08294.2071-1.70332.48740.06740.0101-0.1530.0756-0.07180.1306-0.0179-0.05020.0045-0.2996-0.2708-0.2259-0.2506-0.2353-0.23918.7427.60643.542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB29 - 12226 - 119
2X-RAY DIFFRACTION2BA1 - 321 - 32

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