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- PDB-8ye4: The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448... -

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Basic information

Entry
Database: PDB / ID: 8ye4
TitleThe complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF
Components
  • Beta-2-microglobulin
  • MHC class I antigen precusor
  • Spike protein S1
  • TCR NYN-I alpha chain
  • TCR NYN-I beta chain
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / TCR-pMHC complex / CD8 T cell epitope
Function / homology
Function and homology information


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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / 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 / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / symbiont-mediated disruption of host tissue / protein homotetramerization / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / amyloid fibril formation / Induction of Cell-Cell Fusion / structural constituent of virion / intracellular iron ion homeostasis / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / learning or memory / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / symbiont entry into host cell / virion attachment to host cell / 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
Similarity search - Function
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. ...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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / Beta-2-microglobulin / MHC class I antigen precusor
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDeng, S.S. / Jin, T.C. / Xu, Z.H. / Wang, M.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82272301 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants.
Authors: Deng, S. / Xu, Z. / Wang, M. / Hu, J. / Liu, Z. / Zhu, F. / Zheng, P. / Kombe Kombe, A.J. / Zhang, H. / Wu, S. / Jin, T.
History
DepositionFeb 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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: MHC class I antigen precusor
B: Beta-2-microglobulin
E: Spike protein S1
C: MHC class I antigen precusor
D: Beta-2-microglobulin
F: Spike protein S1
G: TCR NYN-I alpha chain
H: TCR NYN-I beta chain
I: TCR NYN-I alpha chain
J: TCR NYN-I beta chain


Theoretical massNumber of molelcules
Total (without water)184,24010
Polymers184,24010
Non-polymers00
Water1448
1
A: MHC class I antigen precusor
B: Beta-2-microglobulin
E: Spike protein S1
G: TCR NYN-I alpha chain
H: TCR NYN-I beta chain


Theoretical massNumber of molelcules
Total (without water)92,1205
Polymers92,1205
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MHC class I antigen precusor
D: Beta-2-microglobulin
F: Spike protein S1
I: TCR NYN-I alpha chain
J: TCR NYN-I beta chain


Theoretical massNumber of molelcules
Total (without water)92,1205
Polymers92,1205
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.002, 148.096, 196.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules ACBDGIHJ

#1: Protein MHC class I antigen precusor


Mass: 31551.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IVJ7
#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein TCR NYN-I alpha chain


Mass: 20701.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein TCR NYN-I beta chain


Mass: 26851.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 10 molecules EF

#3: Protein/peptide Spike protein S1


Mass: 1266.425 Da / Num. of mol.: 2 / Fragment: 448-456 peptide / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 8% Tacsimate 7.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→49.37 Å / Num. obs: 34048 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.991 / Net I/σ(I): 11
Reflection shellResolution: 3.2→3.36 Å / Num. unique obs: 4447 / CC1/2: 0.742 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 3.2→39.98 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3098 1649 4.86 %
Rwork0.2659 --
obs0.2681 33951 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12286 0 0 8 12294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d13.8724655
X-RAY DIFFRACTIONf_chiral_restr0.0421827
X-RAY DIFFRACTIONf_plane_restr0.0052283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.290.4491300.39362651X-RAY DIFFRACTION100
3.29-3.40.4041200.35812641X-RAY DIFFRACTION100
3.4-3.520.37991240.32862667X-RAY DIFFRACTION100
3.52-3.660.33251450.32512656X-RAY DIFFRACTION100
3.66-3.830.39391220.2962664X-RAY DIFFRACTION100
3.83-4.030.28931370.27532663X-RAY DIFFRACTION100
4.03-4.280.29851530.26482664X-RAY DIFFRACTION100
4.28-4.610.30541510.23772675X-RAY DIFFRACTION100
4.61-5.080.26211430.2342679X-RAY DIFFRACTION100
5.08-5.810.3021320.24162736X-RAY DIFFRACTION100
5.81-7.310.321390.27032737X-RAY DIFFRACTION100
7.31-39.980.25981530.21632869X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 3.0101 Å / Origin y: 2.1491 Å / Origin z: 7.6375 Å
111213212223313233
T0.661 Å20.0903 Å20.0746 Å2-0.3917 Å20.1047 Å2--0.6566 Å2
L0.8625 °20.1131 °20.3207 °2-0.1639 °20.2695 °2--1.3522 °2
S-0.0732 Å °-0.1009 Å °-0.043 Å °0.0496 Å °0.0103 Å °-0.0064 Å °-0.0477 Å °-0.2103 Å °0.0629 Å °
Refinement TLS groupSelection details: all

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