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- PDB-7qhp: Structure of I-Ag7 with a bound hybrid insulin peptide -

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Basic information

Entry
Database: PDB / ID: 7qhp
TitleStructure of I-Ag7 with a bound hybrid insulin peptide
Components
  • H-2 class II histocompatibility antigen, A-D alpha chain
  • Insulin-1
  • Murine MHC class II I-A beta g7
KeywordsIMMUNE SYSTEM / Diabetes / MHC class II / hybrid insulin peptide / autoimmune disease
Function / homology
Function and homology information


response to dimethyl sulfoxide / Insulin processing / Synthesis, secretion, and deacylation of Ghrelin / Signaling by Insulin receptor / IRS activation / Insulin receptor signalling cascade / Signal attenuation / Insulin receptor recycling / COPI-mediated anterograde transport / D-glucose transmembrane transport ...response to dimethyl sulfoxide / Insulin processing / Synthesis, secretion, and deacylation of Ghrelin / Signaling by Insulin receptor / IRS activation / Insulin receptor signalling cascade / Signal attenuation / Insulin receptor recycling / COPI-mediated anterograde transport / D-glucose transmembrane transport / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / antigen processing and presentation of peptide antigen / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of T cell differentiation / antigen processing and presentation / response to cAMP / response to cytokine / insulin receptor binding / cellular response to glucose stimulus / MHC class II protein complex / hormone activity / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / receptor internalization / glucose metabolic process / insulin receptor signaling pathway / : / secretory granule lumen / adaptive immune response / lysosome / receptor ligand activity / endoplasmic reticulum lumen / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site ...MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Insulin-1 / H-2 class II histocompatibility antigen, A-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLopez-Sagaseta, J. / Erausquin, E.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessRTI2018-093964-B-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2017-21683 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-094894-B-I00 Spain
CitationJournal: Front Immunol / Year: 2022
Title: Structural plasticity in I-A g7 links autoreactivity to hybrid insulin peptides in type I diabetes.
Authors: Erausquin, E. / Serra, P. / Parras, D. / Santamaria, P. / Lopez-Sagaseta, J.
History
DepositionDec 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 17, 2022Group: Database references / Category: citation_author
Revision 1.3Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, A-D alpha chain
B: Murine MHC class II I-A beta g7
T: Insulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0638
Polymers50,7363
Non-polymers3265
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-69 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.996, 108.819, 98.055
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H-2 class II histocompatibility antigen, A-D alpha chain


Mass: 23027.711 Da / Num. of mol.: 1 / Mutation: I91C
Source method: isolated from a genetically manipulated source
Details: This polypeptide corresponds to the alpha chain of a murine major histocompatibility complex (MHC) class II molecule.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Cell line (production host): CHO-S / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P04228
#2: Protein Murine MHC class II I-A beta g7


Mass: 26263.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Hybrid insulin peptide covalently bound through glycine-serine linker to N-terminal of polypeptide
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): CHO-S / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster)

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Protein/peptide , 1 types, 1 molecules T

#3: Protein/peptide Insulin-1


Mass: 1445.591 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This peptide represents the result of a fusion of fragments derived from chromogranin A and insulin C.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ins1, Ins-1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01325

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Non-polymers , 4 types, 300 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.17 M ammonium sulfate, 25% w/v PEG 4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979185 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2021
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979185 Å / Relative weight: 1
ReflectionResolution: 1.82→70.254 Å / Num. obs: 44356 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 29.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Net I/σ(I): 11.6
Reflection shellResolution: 4.939→70.254 Å / Rmerge(I) obs: 0.037 / Mean I/σ(I) obs: 30.4 / Num. unique obs: 2365 / CC1/2: 0.998 / Rpim(I) all: 0.018 / Rrim(I) all: 0.042

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
REFMAC5.8.0267phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUJ

1muj


Resolution: 1.82→54.41 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219 2217 5 %
Rwork0.1829 42135 -
obs0.1847 44352 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.78 Å2
Refinement stepCycle: LAST / Resolution: 1.82→54.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 19 295 3246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923034
X-RAY DIFFRACTIONf_angle_d0.94264149
X-RAY DIFFRACTIONf_chiral_restr0.0659466
X-RAY DIFFRACTIONf_plane_restr0.0078534
X-RAY DIFFRACTIONf_dihedral_angle_d6.6951411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.31611340.27742592X-RAY DIFFRACTION100
1.86-1.90.29551430.2412607X-RAY DIFFRACTION99.96
1.9-1.950.25531240.21842631X-RAY DIFFRACTION100
1.95-20.25321220.20852624X-RAY DIFFRACTION100
2-2.060.25891530.20892592X-RAY DIFFRACTION99.96
2.06-2.130.28271300.19742613X-RAY DIFFRACTION100
2.13-2.20.2661180.18742631X-RAY DIFFRACTION99.96
2.2-2.290.23251590.18112609X-RAY DIFFRACTION100
2.29-2.40.23811250.17752633X-RAY DIFFRACTION99.86
2.4-2.520.22031460.18882609X-RAY DIFFRACTION100
2.52-2.680.23121320.19112619X-RAY DIFFRACTION99.93
2.68-2.890.22561330.1892652X-RAY DIFFRACTION99.89
2.89-3.180.22131530.18172635X-RAY DIFFRACTION99.79
3.18-3.640.18121410.16282649X-RAY DIFFRACTION99.68
3.64-4.580.18671440.15772669X-RAY DIFFRACTION99.47
4.59-54.410.21951600.18992770X-RAY DIFFRACTION99.46

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