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- PDB-5gsr: Mouse MHC class I H-2Kd with a MERS-CoV-derived peptide I5A -

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Basic information

Entry
Database: PDB / ID: 5gsr
TitleMouse MHC class I H-2Kd with a MERS-CoV-derived peptide I5A
Components
  • 9-mer peptide from Spike protein
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-D alpha chain
KeywordsIMMUNE SYSTEM / mouse / H-2Kd / MERS-CoV / T-cell
Function / homology
Function and homology information


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 / : / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin 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 / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / : / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / endocytosis involved in viral entry into host cell / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / learning or memory / receptor-mediated virion attachment to host cell / defense response to bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane
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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / 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 speciesHomo sapiens (human)
Mus musculus (house mouse)
Middle East respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.198 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 1.0Apr 26, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Beta-2-microglobulin
B: Beta-2-microglobulin
A: H-2 class I histocompatibility antigen, K-D alpha chain
C: H-2 class I histocompatibility antigen, K-D alpha chain
P: 9-mer peptide from Spike protein
Q: 9-mer peptide from Spike protein


Theoretical massNumber of molelcules
Total (without water)89,7126
Polymers89,7126
Non-polymers00
Water6,377354
1
D: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, K-D alpha chain
Q: 9-mer peptide from Spike protein


Theoretical massNumber of molelcules
Total (without water)44,8563
Polymers44,8563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-23 kcal/mol
Surface area18990 Å2
MethodPISA
2
B: Beta-2-microglobulin
A: H-2 class I histocompatibility antigen, K-D alpha chain
P: 9-mer peptide from Spike protein


Theoretical massNumber of molelcules
Total (without water)44,8563
Polymers44,8563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-22 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.353, 79.658, 122.706
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-2-microglobulin


Mass: 11819.238 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
#2: Protein H-2 class I histocompatibility antigen, K-D alpha chain / H-2K(D)


Mass: 31985.510 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
#3: Protein/peptide 9-mer peptide from Spike protein


Mass: 1051.173 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 292-300 / Mutation: I5A / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome coronavirus
References: UniProt: A0A0U2W1D8, UniProt: K9N5Q8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES 7.5, 30 % v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97944 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: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.198→50 Å / % possible obs: 94.3 % / Redundancy: 4.8 % / Net I/σ(I): 5.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
CNSdata reduction
CNSdata scaling
PHASESphasing
RefinementResolution: 2.198→31.829 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 24.7
RfactorNum. reflection% reflection
Rfree0.2309 2390 4.94 %
Rwork0.201 --
obs0.2025 48385 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.198→31.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 0 354 6690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076530
X-RAY DIFFRACTIONf_angle_d0.7738878
X-RAY DIFFRACTIONf_dihedral_angle_d21.5452396
X-RAY DIFFRACTIONf_chiral_restr0.06900
X-RAY DIFFRACTIONf_plane_restr0.0031156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1985-2.24330.28521170.23922367X-RAY DIFFRACTION86
2.2433-2.29210.25071450.23072688X-RAY DIFFRACTION97
2.2921-2.34540.2611650.23242654X-RAY DIFFRACTION99
2.3454-2.40410.29881450.23182750X-RAY DIFFRACTION99
2.4041-2.4690.3085930.22462752X-RAY DIFFRACTION99
2.469-2.54170.30581260.23982726X-RAY DIFFRACTION98
2.5417-2.62370.24221360.23362743X-RAY DIFFRACTION99
2.6237-2.71740.31431380.23462707X-RAY DIFFRACTION99
2.7174-2.82610.28121160.23972772X-RAY DIFFRACTION99
2.8261-2.95460.21191520.23412768X-RAY DIFFRACTION99
2.9546-3.11030.26491860.23142681X-RAY DIFFRACTION100
3.1103-3.3050.26861460.21032757X-RAY DIFFRACTION100
3.305-3.55980.24521570.19872738X-RAY DIFFRACTION99
3.5598-3.91750.22841310.18972767X-RAY DIFFRACTION99
3.9175-4.4830.1621590.16682689X-RAY DIFFRACTION98
4.483-5.6430.2081210.15922702X-RAY DIFFRACTION96
5.643-31.83270.19871570.18262734X-RAY DIFFRACTION96

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