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- PDB-5gsx: Mouse MHC class I H-2Kd with a MERS-CoV-derived peptide 142-2 -

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Basic information

Entry
Database: PDB / ID: 5gsx
TitleMouse MHC class I H-2Kd with a MERS-CoV-derived peptide 142-2
Components
  • 10-mer peptide from Spike protein
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-D alpha chain
KeywordsIMMUNE SYSTEM / mourse / H-2Kd / MERS-CoV / T-Cell
Function / homology
Function and homology information


antigen processing and presentation of exogenous peptide antigen via MHC class I / MHC class I protein binding / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / : / : / negative regulation of receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression ...antigen processing and presentation of exogenous peptide antigen via MHC class I / MHC class I protein binding / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / : / : / negative regulation of receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / positive regulation of protein binding / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / iron ion transport / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / membrane fusion / learning or memory / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / defense response to bacterium / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / : ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / 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
Spike glycoprotein / Spike glycoprotein / H-2 class I histocompatibility antigen, K-D alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Middle East respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLiu, K. / Chai, Y. / Qi, J. / Tan, W. / Liu, W.J. / Gao, G.F.
CitationJournal: J. Immunol. / Year: 2017
Title: Protective T Cell Responses Featured by Concordant Recognition of Middle East Respiratory Syndrome Coronavirus-Derived CD8+ T Cell Epitopes and Host MHC.
Authors: Liu, W.J. / Lan, J. / Liu, K. / Deng, Y. / Yao, Y. / Wu, S. / Chen, H. / Bao, L. / Zhang, H. / Zhao, M. / Wang, Q. / Han, L. / Chai, Y. / Qi, J. / Zhao, J. / Meng, S. / Qin, C. / Gao, G.F. / Tan, W.
History
DepositionAug 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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, K-D alpha chain
B: Beta-2-microglobulin
C: 10-mer peptide from Spike protein
D: H-2 class I histocompatibility antigen, K-D alpha chain
E: Beta-2-microglobulin
F: 10-mer peptide from Spike protein


Theoretical massNumber of molelcules
Total (without water)89,7626
Polymers89,7626
Non-polymers00
Water2,936163
1
A: H-2 class I histocompatibility antigen, K-D alpha chain
B: Beta-2-microglobulin
C: 10-mer peptide from Spike protein


Theoretical massNumber of molelcules
Total (without water)44,8813
Polymers44,8813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-20 kcal/mol
Surface area18900 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-D alpha chain
E: Beta-2-microglobulin
F: 10-mer peptide from Spike protein


Theoretical massNumber of molelcules
Total (without water)44,8813
Polymers44,8813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-20 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.623, 68.474, 145.075
Angle α, β, γ (deg.)90.00, 106.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31995.529 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 22-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01902
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide 10-mer peptide from Spike protein


Mass: 1137.281 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1191-1200 / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome coronavirus
References: UniProt: A0A0U2P195, UniProt: K9N5Q8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.0, 10% w/v Polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 123285 / % possible obs: 93.6 % / Redundancy: 2.345 % / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
CNSdata reduction
CNSdata scaling
PHASESphasing
RefinementResolution: 2.5→47.008 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25
RfactorNum. reflection% reflection
Rfree0.2419 1566 4.99 %
Rwork0.195 --
obs0.1973 31408 93.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 0 163 6509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066542
X-RAY DIFFRACTIONf_angle_d1.0838888
X-RAY DIFFRACTIONf_dihedral_angle_d15.442388
X-RAY DIFFRACTIONf_chiral_restr0.043902
X-RAY DIFFRACTIONf_plane_restr0.0051164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4997-2.58040.3841430.29842641X-RAY DIFFRACTION91
2.5804-2.67260.33661550.25952705X-RAY DIFFRACTION94
2.6726-2.77960.31471520.24912644X-RAY DIFFRACTION93
2.7796-2.90610.3041370.24762651X-RAY DIFFRACTION92
2.9061-3.05930.31851190.24012644X-RAY DIFFRACTION91
3.0593-3.25090.31731240.23182632X-RAY DIFFRACTION90
3.2509-3.50190.25591390.21242613X-RAY DIFFRACTION91
3.5019-3.85410.24641320.20082680X-RAY DIFFRACTION91
3.8541-4.41150.22351470.16622803X-RAY DIFFRACTION96
4.4115-5.55660.17961520.14222901X-RAY DIFFRACTION99
5.5566-47.01590.17391660.15922928X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 124.4473 Å / Origin y: 1.9566 Å / Origin z: 34.7004 Å
111213212223313233
T0.2206 Å20.0097 Å2-0.0054 Å2-0.2167 Å2-0.0167 Å2--0.234 Å2
L0.033 °2-0.0691 °2-0.226 °2-0.0801 °20.2441 °2--0.5812 °2
S-0.0246 Å °0.0035 Å °-0.0361 Å °0.0191 Å °-0.039 Å °0.0411 Å °0.0111 Å °-0.0535 Å °0 Å °
Refinement TLS groupSelection details: all

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