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- PDB-5oqi: Crystal Structure of a disulfide trapped single chain trimer comp... -

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Basic information

Entry
Database: PDB / ID: 5oqi
TitleCrystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy chain H-2Kb Y84C E63A mutant, beta-2microglobulin, 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


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 exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response ...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 exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / 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 / 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 / positive regulation of T cell cytokine production / MHC class I protein complex / peptide antigen binding / 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 / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / 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: 2.4 Å
AuthorsMikolajek, H. / Werner, J.M. / Beton, M.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/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 1.1May 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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)96,2472
Polymers96,2472
Non-polymers00
Water6,648369
1
A: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain


Theoretical massNumber of molelcules
Total (without water)48,1241
Polymers48,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain


Theoretical massNumber of molelcules
Total (without water)48,1241
Polymers48,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.130, 90.190, 89.450
Angle α, β, γ (deg.)90.00, 111.22, 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: 48123.574 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.: 369 / 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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Am sulphate, 25% PEG 4K, 0.1M Na cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→42.52 Å / Num. obs: 38095 / % possible obs: 97.9 % / Redundancy: 3.8 % / Net I/σ(I): 11.6

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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: 2.4→42.517 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.85
RfactorNum. reflection% reflection
Rfree0.2595 1902 5 %
Rwork0.2005 --
obs0.2034 38073 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→42.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6292 0 0 369 6661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026474
X-RAY DIFFRACTIONf_angle_d0.5418790
X-RAY DIFFRACTIONf_dihedral_angle_d6.3613840
X-RAY DIFFRACTIONf_chiral_restr0.041908
X-RAY DIFFRACTIONf_plane_restr0.0041140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.46010.36281240.2792531X-RAY DIFFRACTION97
2.4601-2.52660.2931280.24982536X-RAY DIFFRACTION97
2.5266-2.60090.31441310.24732581X-RAY DIFFRACTION97
2.6009-2.68490.29731300.23592571X-RAY DIFFRACTION97
2.6849-2.78080.30141410.24242567X-RAY DIFFRACTION98
2.7808-2.89210.31331100.23312579X-RAY DIFFRACTION97
2.8921-3.02370.28841370.22962574X-RAY DIFFRACTION98
3.0237-3.18310.33121430.22662571X-RAY DIFFRACTION98
3.1831-3.38240.27271500.21152581X-RAY DIFFRACTION98
3.3824-3.64350.25371460.1932581X-RAY DIFFRACTION98
3.6435-4.00990.21991550.17982597X-RAY DIFFRACTION98
4.0099-4.58950.21121370.15692606X-RAY DIFFRACTION98
4.5895-5.780.21761380.16222632X-RAY DIFFRACTION98
5.78-42.52380.23431320.1892664X-RAY DIFFRACTION98

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