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- PDB-9j4s: Structural basis for recognition of SARS-CoV-2 conserved nucleoca... -

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Basic information

Entry
Database: PDB / ID: 9j4s
TitleStructural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Components
  • (T cell receptor CLA1 ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B alpha chain
  • Nucleoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / TCR / T cell receptor / SARS-CoV-2 / Nucleocapside / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / poly(U) RNA binding / Maturation of nucleoprotein ...: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / CD28 dependent PI3K/Akt signaling / detection of bacterium / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / negative regulation of receptor binding / secretory granule membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / VEGFR2 mediated vascular permeability / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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 / molecular condensate scaffold activity / 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 / defense response / 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 / Interleukin-1 signaling / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / specific granule lumen / RNA stem-loop binding / phagocytic vesicle membrane / recycling endosome membrane / 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 / late endosome membrane / sensory perception of smell / viral capsid / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / PIP3 activates AKT signaling / ER-Phagosome pathway / protein-folding chaperone binding / negative regulation of neuron projection development / Transcription of SARS-CoV-2 sgRNAs / protein refolding / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / early endosome membrane / host cell Golgi apparatus / protein homotetramerization / adaptive immune response / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / amyloid fibril formation / Induction of Cell-Cell Fusion / intracellular iron ion homeostasis / Attachment and Entry / learning or memory
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / MHC class I, alpha chain, C-terminal ...Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsYuan, P. / Wu, D.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270995 China
National Natural Science Foundation of China (NSFC)32100985 China
CitationJournal: To Be Published
Title: Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Authors: Yuan, P. / Wu, D.C.
History
DepositionAug 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: T cell receptor CLA1 beta
I: T cell receptor CLA1 alpha
A: T cell receptor CLA1 beta
B: T cell receptor CLA1 alpha
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
E: Nucleoprotein
F: HLA class I histocompatibility antigen, B alpha chain
H: Beta-2-microglobulin
J: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,10720
Polymers192,15110
Non-polymers95710
Water724
1
G: T cell receptor CLA1 beta
I: T cell receptor CLA1 alpha
F: HLA class I histocompatibility antigen, B alpha chain
H: Beta-2-microglobulin
J: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,64811
Polymers96,0755
Non-polymers5726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-113 kcal/mol
Surface area38150 Å2
MethodPISA
2
A: T cell receptor CLA1 beta
B: T cell receptor CLA1 alpha
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
E: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4609
Polymers96,0755
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-94 kcal/mol
Surface area37750 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26000 Å2
ΔGint-217 kcal/mol
Surface area72740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.978, 93.303, 261.912
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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T cell receptor CLA1 ... , 2 types, 4 molecules GAIB

#1: Protein T cell receptor CLA1 beta


Mass: 27585.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: T cell receptor beta / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein T cell receptor CLA1 alpha


Mass: 23221.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein , 2 types, 4 molecules CFDH

#3: Protein HLA class I histocompatibility antigen, B alpha chain / Human leukocyte antigen B / HLA-B


Mass: 32093.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01889
#4: Protein Beta-2-microglobulin


Mass: 11879.356 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 BL21(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules EJ

#5: Protein/peptide Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 1295.464 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9

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Non-polymers , 3 types, 14 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris-base/hydrochloric acid (pH 7.0), 0.2 M lithium sulfate, and 1.9 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.95→76.1 Å / Num. obs: 48369 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.995 / Net I/σ(I): 10.9
Reflection shellResolution: 2.95→3.06 Å / Num. unique obs: 4775 / CC1/2: 0.687

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→76.1 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU B: 16.021 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23786 2450 5.1 %RANDOM
Rwork0.19354 ---
obs0.19581 45924 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.418 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--3.31 Å2-0 Å2
3----3.03 Å2
Refinement stepCycle: 1 / Resolution: 2.95→76.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13246 0 51 4 13301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01213659
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.941.82318590
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10451632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.331597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.041102122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.21935
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9994.2016567
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.8197.5368186
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.7494.577092
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.10251.8353179
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 170 -
Rwork0.288 3343 -
obs--99.97 %

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