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- PDB-5oqg: Crystal structure of a single chain trimer composed of the MHC I ... -

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Basic information

Entry
Database: PDB / ID: 5oqg
TitleCrystal structure of a single chain trimer composed of the MHC I heavy chain H-2Kb W167A, beta-2microglobulin, and and ovalbumin-derived peptide.
ComponentsBeta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / Diagnosis / Epitopes / Major Histocompatibility Complex / Mice / Models / Molecular / Molecular Conformation / Peptides / Receptors / Antigen / T-Cell / T-Lymphocytes / Vaccines
Function / homology
Function and homology information


MHC class Ib protein complex / TAP2 binding / TAP1 binding / natural killer cell lectin-like receptor binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling ...MHC class Ib protein complex / TAP2 binding / TAP1 binding / natural killer cell lectin-like receptor binding / cis-Golgi network membrane / 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 / regulation of membrane depolarization / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / inner ear development / CD8 receptor binding / beta-2-microglobulin binding / endoplasmic reticulum exit site / MHC class I protein binding / TAP binding / cellular defense response / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / Neutrophil degranulation / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / protein-folding chaperone binding / protein refolding / cellular response to lipopolysaccharide / early endosome membrane / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / early endosome / defense response to bacterium / defense response to Gram-positive bacterium / immune response / receptor ligand activity / signaling receptor binding / Golgi membrane / external side of plasma membrane / innate immune response / lysosomal membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / : / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMikolajek, H. / Werner, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BB/L010402/1 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The partial dissociation of MHC class I-bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1.
Authors: Papakyriakou, A. / Reeves, E. / Beton, M. / Mikolajek, H. / Douglas, L. / Cooper, G. / Elliott, T. / Werner, J.M. / James, E.
History
DepositionAug 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain


Theoretical massNumber of molelcules
Total (without water)96,1332
Polymers96,1332
Non-polymers00
Water13,079726
1
A: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain


Theoretical massNumber of molelcules
Total (without water)48,0661
Polymers48,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain


Theoretical massNumber of molelcules
Total (without water)48,0661
Polymers48,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.430, 89.640, 89.450
Angle α, β, γ (deg.)90.00, 111.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 48066.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m, H2-K1, H2-K / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887, UniProt: P01901
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Am sulphate, 23& PEG 8K, 0.1M Bis-tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→61.51 Å / Num. obs: 76853 / % possible obs: 99.8 % / Redundancy: 7.5 % / Net I/σ(I): 14.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QRI

2qri


Resolution: 1.9→61.506 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.52
RfactorNum. reflection% reflection
Rfree0.2388 3853 5.02 %
Rwork0.1879 --
obs0.1905 76765 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→61.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 0 726 7008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076663
X-RAY DIFFRACTIONf_angle_d0.8789076
X-RAY DIFFRACTIONf_dihedral_angle_d9.1145497
X-RAY DIFFRACTIONf_chiral_restr0.054939
X-RAY DIFFRACTIONf_plane_restr0.0051187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92320.34241420.28992556X-RAY DIFFRACTION99
1.9232-1.94750.32541360.25972611X-RAY DIFFRACTION99
1.9475-1.97320.28921250.23472560X-RAY DIFFRACTION99
1.9732-2.00020.28711290.23552614X-RAY DIFFRACTION100
2.0002-2.02880.30231380.22372596X-RAY DIFFRACTION100
2.0288-2.05910.27751230.22172597X-RAY DIFFRACTION100
2.0591-2.09120.25231330.21122585X-RAY DIFFRACTION100
2.0912-2.12550.27981310.21452597X-RAY DIFFRACTION100
2.1255-2.16220.23721490.20582577X-RAY DIFFRACTION100
2.1622-2.20150.28311410.2112612X-RAY DIFFRACTION100
2.2015-2.24380.24981300.20492592X-RAY DIFFRACTION100
2.2438-2.28960.27911500.20732610X-RAY DIFFRACTION100
2.2896-2.33940.2621340.20742589X-RAY DIFFRACTION100
2.3394-2.39380.28511400.21332612X-RAY DIFFRACTION100
2.3938-2.45370.26481300.20482601X-RAY DIFFRACTION100
2.4537-2.52010.30291260.21262585X-RAY DIFFRACTION100
2.5201-2.59420.28051560.20432609X-RAY DIFFRACTION100
2.5942-2.67790.24211370.20292593X-RAY DIFFRACTION100
2.6779-2.77370.26151450.20542612X-RAY DIFFRACTION100
2.7737-2.88470.23671510.19852619X-RAY DIFFRACTION100
2.8847-3.0160.26681450.19092593X-RAY DIFFRACTION100
3.016-3.1750.24221340.19522606X-RAY DIFFRACTION100
3.175-3.37390.25641220.17942605X-RAY DIFFRACTION100
3.3739-3.63440.24571570.16852614X-RAY DIFFRACTION100
3.6344-4.00010.18231390.15432614X-RAY DIFFRACTION100
4.0001-4.57870.16831440.13982614X-RAY DIFFRACTION100
4.5787-5.7680.20381350.16022656X-RAY DIFFRACTION100
5.768-61.53770.23861310.20952683X-RAY DIFFRACTION99

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