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- PDB-5gsb: Mouse MHC class I H-2Kd with a MERS-CoV-derived peptide 37-3 -

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Basic information

Entry
Database: PDB / ID: 5gsb
TitleMouse MHC class I H-2Kd with a MERS-CoV-derived peptide 37-3
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, K-D alpha chain
  • MERS-CoV peptide 37-3
KeywordsIMMUNE SYSTEM / mouse / H-2Kd / MERS-CoV / T-cell
Function / homology
Function and homology information


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / inner ear development / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / detection of bacterium / T cell receptor binding / 14-3-3 protein binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / endocytosis involved in viral entry into host cell / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response
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 / MHC class I-like antigen recognition-like ...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 / 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 / SYNCHROTRON / Resolution: 1.801 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 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

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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: MERS-CoV peptide 37-3


Theoretical massNumber of molelcules
Total (without water)44,9663
Polymers44,9663
Non-polymers00
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-20 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.225, 76.039, 122.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 1 / 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 / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
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 MERS-CoV peptide 37-3


Mass: 1222.433 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome coronavirus
References: UniProt: K9N5Q8*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.5 , 16% w v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 274523 / % possible obs: 98.9 % / Redundancy: 6.3 % / Net I/σ(I): 20.033

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CNSdata reduction
CNSdata scaling
PHASERphasing
RefinementResolution: 1.801→47.666 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.72
RfactorNum. reflection% reflection
Rfree0.2216 2203 5.04 %
Rwork0.193 --
obs0.1944 43677 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→47.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 0 358 3528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083268
X-RAY DIFFRACTIONf_angle_d1.1714439
X-RAY DIFFRACTIONf_dihedral_angle_d15.0841192
X-RAY DIFFRACTIONf_chiral_restr0.047450
X-RAY DIFFRACTIONf_plane_restr0.006580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.84020.27881320.24332465X-RAY DIFFRACTION96
1.8402-1.8830.2341610.21492572X-RAY DIFFRACTION100
1.883-1.93010.23531360.20742599X-RAY DIFFRACTION100
1.9301-1.98230.24981210.19832575X-RAY DIFFRACTION100
1.9823-2.04060.27271370.19342579X-RAY DIFFRACTION100
2.0406-2.10650.24011430.22591X-RAY DIFFRACTION100
2.1065-2.18180.22031230.20222618X-RAY DIFFRACTION100
2.1818-2.26910.23051520.1932576X-RAY DIFFRACTION100
2.2691-2.37240.25221390.20662611X-RAY DIFFRACTION100
2.3724-2.49750.24171280.2112610X-RAY DIFFRACTION100
2.4975-2.65390.26171230.21112630X-RAY DIFFRACTION100
2.6539-2.85880.24081240.21532638X-RAY DIFFRACTION100
2.8588-3.14640.22781540.20412644X-RAY DIFFRACTION100
3.1464-3.60160.21711430.19092613X-RAY DIFFRACTION99
3.6016-4.53710.20321470.16732581X-RAY DIFFRACTION97
4.5371-47.68320.18011400.17612572X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -17.6737 Å / Origin y: 4.3112 Å / Origin z: -8.2453 Å
111213212223313233
T0.2217 Å20.0003 Å2-0.0032 Å2-0.2214 Å2-0.0151 Å2--0.2449 Å2
L0.5282 °2-0.0556 °20.0818 °2-0.4184 °20.0952 °2--1.0369 °2
S0.0169 Å °0.0541 Å °-0.0542 Å °-0.0334 Å °0.0067 Å °-0.0159 Å °0.1187 Å °0.0257 Å °-0 Å °
Refinement TLS groupSelection details: all

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