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- PDB-6o9h: Mouse ECD with Fab1 -

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Basic information

Entry
Database: PDB / ID: 6o9h
TitleMouse ECD with Fab1
Components
  • Gastric inhibitory polypeptide receptor
  • Heavy chain
  • Light chain
KeywordsIMMUNE SYSTEM / GPCR
Function / homology
Function and homology information


gastric inhibitory peptide receptor activity / glucagon family peptide binding / gastric inhibitory peptide signaling pathway / Glucagon-type ligand receptors / G alpha (s) signalling events / desensitization of G protein-coupled receptor signaling pathway / endocrine pancreas development / response to fatty acid / G protein-coupled peptide receptor activity / peptide hormone binding ...gastric inhibitory peptide receptor activity / glucagon family peptide binding / gastric inhibitory peptide signaling pathway / Glucagon-type ligand receptors / G alpha (s) signalling events / desensitization of G protein-coupled receptor signaling pathway / endocrine pancreas development / response to fatty acid / G protein-coupled peptide receptor activity / peptide hormone binding / neuropeptide signaling pathway / response to axon injury / positive regulation of cAMP-mediated signaling / response to glucose / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / response to calcium ion / signaling receptor activity / positive regulation of cytosolic calcium ion concentration / cell surface receptor signaling pathway / 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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Gastric inhibitory polypeptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMin, X. / Wang, Z.
CitationJournal: Mabs / Year: 2020
Title: Molecular mechanism of an antagonistic antibody against glucose-dependent insulinotropic polypeptide receptor.
Authors: Min, X. / Yie, J. / Wang, J. / Chung, B.C. / Huang, C.S. / Xu, H. / Yang, J. / Deng, L. / Lin, J. / Chen, Q. / Abbott, C.M. / Gundel, C. / Thibault, S.A. / Meng, T. / Bates, D.L. / Lloyd, D. ...Authors: Min, X. / Yie, J. / Wang, J. / Chung, B.C. / Huang, C.S. / Xu, H. / Yang, J. / Deng, L. / Lin, J. / Chen, Q. / Abbott, C.M. / Gundel, C. / Thibault, S.A. / Meng, T. / Bates, D.L. / Lloyd, D.J. / Veniant, M.M. / Wang, Z.
History
DepositionMar 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain
L: Light chain
A: Heavy chain
B: Light chain
D: Gastric inhibitory polypeptide receptor
C: Gastric inhibitory polypeptide receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0108
Polymers127,9646
Non-polymers462
Water11,962664
1
H: Heavy chain
L: Light chain
D: Gastric inhibitory polypeptide receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0054
Polymers63,9823
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-37 kcal/mol
Surface area23630 Å2
MethodPISA
2
A: Heavy chain
B: Light chain
C: Gastric inhibitory polypeptide receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0054
Polymers63,9823
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-38 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.078, 48.974, 150.908
Angle α, β, γ (deg.)90.000, 101.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Heavy chain


Mass: 24085.227 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)
#2: Antibody Light chain /


Mass: 24223.713 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)
#3: Protein Gastric inhibitory polypeptide receptor / / GIP-R / Glucose-dependent insulinotropic polypeptide receptor


Mass: 15673.128 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gipr / Production host: Escherichia coli (E. coli) / References: UniProt: Q0P543
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 664 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG10000, 0.1 M sodium citrate, pH 5.0 and 15% isopropanol
PH range: 5

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2015
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.53 Å / Num. obs: 61740 / % possible obs: 98.7 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.048 / Rrim(I) all: 0.093 / Net I/σ(I): 11.6 / Num. measured all: 226792
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.556 / Num. unique obs: 4399 / CC1/2: 0.739 / Rpim(I) all: 0.34 / Rrim(I) all: 0.653 / % possible all: 95.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA0.3.6data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.934 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 3068 4.98 %
Rwork0.2031 58593 -
obs0.2054 61661 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.22 Å2 / Biso mean: 35.4202 Å2 / Biso min: 15.67 Å2
Refinement stepCycle: final / Resolution: 2.1→19.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8004 0 2 664 8670
Biso mean--24.74 38.59 -
Num. residues----1034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028239
X-RAY DIFFRACTIONf_angle_d0.63311239
X-RAY DIFFRACTIONf_chiral_restr0.0441225
X-RAY DIFFRACTIONf_plane_restr0.0041429
X-RAY DIFFRACTIONf_dihedral_angle_d16.4264873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13280.34131180.28642537265593
2.1328-2.16770.33411290.27122635276499
2.1677-2.20510.28351370.272639277699
2.2051-2.24510.33021460.27822633277998
2.2451-2.28820.34731660.27972597276399
2.2882-2.33490.30791560.25952676283299
2.3349-2.38560.33211430.2452608275199
2.3856-2.4410.29041380.24572661279999
2.441-2.50190.31871310.2472654278599
2.5019-2.56940.30791460.23842680282699
2.5694-2.64480.28911230.23732655277899
2.6448-2.730.29761260.22932707283399
2.73-2.82730.24421280.22552627275599
2.8273-2.94020.25711260.22392704283099
2.9402-3.07350.28661280.21732692282099
3.0735-3.23490.26841360.2042668280498
3.2349-3.43670.26321560.1982642279899
3.4367-3.70040.20621420.17562679282198
3.7004-4.070.19781350.17352687282298
4.07-4.65240.18911730.14942661283499
4.6524-5.8370.2021550.15792717287299
5.837-19.93540.20731300.17972834296499

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