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- PDB-3ws3: Crystal Structure of H-2D in complex with an insulin derived peptide -

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Basic information

Entry
Database: PDB / ID: 3ws3
TitleCrystal Structure of H-2D in complex with an insulin derived peptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Insulin derived 9-mer peptide
KeywordsIMMUNE SYSTEM / Class I MHC / Major histocompatibility complex / insulin / H-2D / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
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 / transmembrane receptor protein tyrosine kinase activator activity / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / response to cAMP / Neutrophil degranulation / response to cytokine / lumenal side of endoplasmic reticulum membrane / insulin receptor binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / cellular response to glucose stimulus / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / hormone activity / positive regulation of T cell cytokine production / MHC class I protein complex / receptor internalization / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / glucose metabolic process / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / insulin receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / : / secretory granule lumen / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / receptor ligand activity / endoplasmic reticulum lumen / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
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 class I, alpha chain, C-terminal / MHC_I C-terminus ...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 class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Insulin-1 / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.335 Å
AuthorsKumar, P.R. / Mukherjee, G. / Samanta, D. / DiLorenzo, T.P. / Almo, S.C. / Immune Function Network / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: J. Immunol. / Year: 2014
Title: Compensatory mechanisms allow undersized anchor-deficient class I MHC ligands to mediate pathogenic autoreactive T cell responses
Authors: Lamont, D. / Mukherjee, G. / Kumar, P.R. / Samanta, D. / McPhee, C.G. / Kay, T.W.H. / Almo, S.C. / DiLorenzo, T.P. / Serreze, D.V.
History
DepositionFeb 28, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author
Revision 1.2Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: Insulin derived 9-mer peptide
F: Insulin derived 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)89,4846
Polymers89,4846
Non-polymers00
Water1,892105
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
E: Insulin derived 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,7423
Polymers44,7423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-21 kcal/mol
Surface area19300 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
F: Insulin derived 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,7423
Polymers44,7423
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-20 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.220, 101.130, 117.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 31804.420 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H-2Db, H2-D1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide Insulin derived 9-mer peptide


Mass: 1102.218 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to Insulin-1A, residues 101-107 followed by an artificial spacer
References: UniProt: P01325*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE CORRESPONDS TO A NATURAL VARIANT, ALLELE A WHICH HAS A A->D MUTATION.

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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: 2.9 Å3/Da / Density % sol: 57.53 %
Description: Initial data was integrated and processed by XDS. The anisotropic data was further subject to an ellipsoidal truncation and sharpening using the UCLA anisotropy server (http://services. ...Description: Initial data was integrated and processed by XDS. The anisotropic data was further subject to an ellipsoidal truncation and sharpening using the UCLA anisotropy server (http://services.mbi.ucla.edu/anisoscale/). The resulting isotropic data has ellipsoidal resolution boundaries of 3.4A along A*, 2.4A along B* and 2.6A along C*. This data set was used for final refinement.
Mosaicity: 0.27 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Ammonium Sulfate, 25% PEG 3350, 0.1M HEPES, 30% Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2013 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.335→50 Å / Num. obs: 33466 / % possible obs: 74.65 % / Redundancy: 5.7 % / Biso Wilson estimate: 39.72 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 8.4
Reflection shellResolution: 2.335→2.419 Å / Redundancy: 0.4 % / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 2.1 / % possible all: 7.01

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.14data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
CBASSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YN6

1yn6


Resolution: 2.335→46.449 Å / FOM work R set: 0.7209 / SU ML: 0.37 / σ(F): 1.36 / Phase error: 36.04 / Stereochemistry target values: ML
Details: The original processed data was further subject to ellipsoidal truncation along the three axes (a*, b* & c*) to provide the final data used for refinement. The structure factor data contains ...Details: The original processed data was further subject to ellipsoidal truncation along the three axes (a*, b* & c*) to provide the final data used for refinement. The structure factor data contains all reflections before anisotropic correction.
RfactorNum. reflection% reflection
Rfree0.2938 1692 5.06 %
Rwork0.2171 --
obs0.221 33449 74.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.83 Å2 / Biso mean: 60.75 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.335→46.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6241 0 0 105 6346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016436
X-RAY DIFFRACTIONf_angle_d1.4148723
X-RAY DIFFRACTIONf_chiral_restr0.055876
X-RAY DIFFRACTIONf_plane_restr0.0071136
X-RAY DIFFRACTIONf_dihedral_angle_d17.0612389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3351-2.40380.4626160.31562102266
2.4038-2.48140.3086300.307562765718
2.4814-2.57010.3694720.31791370144239
2.5701-2.6730.33211020.31192136223861
2.673-2.79460.37051430.28782686282977
2.7946-2.94190.3191730.27533303347694
2.9419-3.12620.34451870.264635353722100
3.1262-3.36750.33472230.24635053728100
3.3675-3.70630.28361780.208135453723100
3.7063-4.24220.26811820.18593540372299
4.2422-5.34350.24071820.16783565374799
5.3435-46.45840.2822040.194437353939100
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)
12.9560.24490.85124.5275-0.42542.0441-0.0185-0.45430.0059-0.10370.08510.07170.5929-0.0757-0.00550.78270.08250.04260.0215-0.08410.138519.626.00710.936
25.18011.4242-1.51873.393-0.36622.1773-0.1261-0.8701-0.25770.68730.0869-0.3731-0.07350.48620.00110.59480.0847-0.15510.2586-0.0290.187625.80927.67119.848
33.26620.8903-0.94822.9102-1.4243.1798-0.05890.4030.1241-0.18680.27570.1975-0.0686-0.4026-0.18080.70860.0047-0.0560.1160.08140.03478.31928.53512.933
44.0432-1.0799-0.57081.2716-1.12151.71460.28410.5645-0.7416-0.5545-0.23290.09640.9112-0.4841-0.10420.9648-0.0446-0.00130.2547-0.07770.280826.10510.707-1.691
56.7231-4.88580.20845.9060.41572.0244-0.1274-0.0991-0.24530.3140.05960.0963-0.11530.07750.01180.596-0.0953-0.03270.14750.02930.275528.4492.1811.534
62.4432-2.56950.96354.5942-0.61020.6847-0.2094-0.1172-0.28990.2699-0.0585-0.24390.18970.11370.20150.7674-0.0258-0.06790.26530.08260.380526.5935.38217.535
75.23560.35530.06614.43030.60622.69050.16680.29290.00940.3505-0.1062-0.3210.11270.10140.02280.72830.0188-0.02370.14640.00880.320417.9426.088-35.116
82.76651.5098-0.73983.39221.63241.815-0.05050.28280.38930.5961-0.14140.69470.0912-0.1430.12390.66560.06110.12420.17460.00150.457621.86819.362-40.54
93.13620.79281.10043.9242-0.9182.9803-0.0055-0.24290.29351.0453-0.02450.83220.6068-0.4439-0.01890.8903-0.07470.27060.3363-0.05480.61854.53722.934-29.234
105.1058-3.1172-1.27313.36752.93133.610.6682-0.26540.4503-1.2579-0.72140.264-0.2963-0.00220.0391.0274-0.1562-0.03520.41110.06280.353818.97712.288-25.401
112.50911.11941.27072.59940.02412.25810.2125-0.44310.34580.5853-0.32830.1702-0.9836-0.50090.18741.0730.08930.07840.3505-0.07290.185326.80447.518-15.77
122.22723.5806-0.6756.9660.53434.257-0.02730.12880.03660.2932-0.16650.55530.3835-0.11380.25760.43360.16290.1350.12830.06970.380126.73648.303-31.411
134.75173.26570.3357.5902-0.02481.32460.01850.31820.18760.1358-0.12560.36850.44990.11720.15290.4310.05590.11080.22650.0490.180524.44945.125-37.128
143.36881.1771-1.80952.14950.47934.7115-0.692-0.21970.35280.23130.56370.1617-0.3170.28110.11280.84080.119-0.14270.33670.01350.188712.24835.592915.2635
153.3882-2.8933.93725.9926-2.83946.2307-0.63760.2495-0.62590.62620.9730.5424-0.1333-0.139-0.33840.66450.07120.12260.3985-0.04850.336410.171114.8093-34.7344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 26:37 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 38:84 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 85:175 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 180:274 )
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 20:45 )
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 46:99 )
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 26:56 )
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 57:103 )
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 104:177 )
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 178:197 )
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 198:274 )
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 20:45 )
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 46:99 )
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 1:9 )
15X-RAY DIFFRACTION15CHAIN F AND (RESSEQ 1:9 )

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