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- PDB-9j4u: Structural basis for recognition of SARS-CoV-2 conserved nucleoca... -

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Basic information

Entry
Database: PDB / ID: 9j4u
TitleStructural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Components
  • (LLL epitope specific TCR ...) x 2
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / TCR / T cell receptor / sars-cov-2 / nuleocapside / hla-a2 / 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 / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling ...: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / negative regulation of receptor binding / 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 / 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 / molecular condensate scaffold activity / 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 / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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 / RNA stem-loop binding / specific granule lumen / Interleukin-1 signaling / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / 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 / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / early endosome membrane / protein homotetramerization / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / amyloid fibril formation / Induction of Cell-Cell Fusion / intracellular iron ion homeostasis / Attachment and Entry / learning or memory / host cell perinuclear region of cytoplasm / endoplasmic reticulum lumen / ribonucleoprotein complex / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
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, alpha1 alpha2 domains ...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, 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
Nucleoprotein / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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
A: MHC class I antigen
B: Beta-2-microglobulin
D: LLL epitope specific TCR APHLA
E: LLL epitope specific TCR BETA
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)95,2535
Polymers95,2535
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.757, 148.273, 64.210
Angle α, β, γ (deg.)90.00, 109.15, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31985.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WLS4
#2: Protein Beta-2-microglobulin


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

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Antibody / LLL epitope specific TCR ... / Protein/peptide / Non-polymers , 4 types, 255 molecules DEC

#3: Antibody LLL epitope specific TCR APHLA


Mass: 22631.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Protein LLL epitope specific TCR BETA


Mass: 27658.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein/peptide Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 1098.317 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium sodium tartrate tetrahydrate, and 20% (w/v) PEG 3350

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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: 2.17→60.7 Å / Num. obs: 51116 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.67 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 2.17→2.25 Å / Num. unique obs: 5086 / CC1/2: 0.799

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→60.66 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 2480 4.86 %
Rwork0.193 --
obs0.1952 51046 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→60.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6525 0 0 252 6777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086697
X-RAY DIFFRACTIONf_angle_d0.9229100
X-RAY DIFFRACTIONf_dihedral_angle_d6.464898
X-RAY DIFFRACTIONf_chiral_restr0.055963
X-RAY DIFFRACTIONf_plane_restr0.0081193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.210.27031230.24472652X-RAY DIFFRACTION98
2.21-2.260.30671480.23412680X-RAY DIFFRACTION100
2.26-2.30.27981380.23662690X-RAY DIFFRACTION100
2.3-2.360.29151470.23332666X-RAY DIFFRACTION100
2.36-2.420.24251440.22252667X-RAY DIFFRACTION100
2.42-2.480.30921400.22242746X-RAY DIFFRACTION100
2.48-2.560.30111420.23212682X-RAY DIFFRACTION100
2.56-2.640.32331370.24332681X-RAY DIFFRACTION100
2.64-2.730.36031330.23992699X-RAY DIFFRACTION100
2.73-2.840.30781120.2482715X-RAY DIFFRACTION100
2.84-2.970.32091380.2352708X-RAY DIFFRACTION100
2.97-3.130.27851390.21212691X-RAY DIFFRACTION100
3.13-3.320.24851510.19642687X-RAY DIFFRACTION100
3.32-3.580.21371570.19062697X-RAY DIFFRACTION100
3.58-3.940.20221280.16772720X-RAY DIFFRACTION100
3.94-4.510.1831090.14552737X-RAY DIFFRACTION100
4.51-5.680.19581440.15172713X-RAY DIFFRACTION100
5.68-60.660.18681500.17752735X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4768-0.60040.511.75970.36022.627-0.0524-0.0662-0.00660.00090.00040.0117-0.0750.12980.05830.1245-0.02130.01640.29560.09460.266844.606720.851920.3247
25.0147-0.4001-1.93581.39910.46632.3273-0.1804-0.4816-0.14010.08510.05060.27790.0681-0.03780.15740.40190.06120.02390.30330.03540.318724.681535.781144.2693
33.49830.70590.71753.9810.59674.72560.173-0.1699-0.14610.94640.1253-0.0394-0.1077-0.2614-0.29110.43240.14340.01780.34850.1180.467328.327641.65628.6992
41.7187-0.29480.24214.27751.60692.9049-0.21170.08630.2482-0.01070.2060.4005-0.8074-0.12440.00270.4470.0277-0.00590.35070.14040.363630.060842.207821.6031
55.00181.23191.33316.46783.00726.80450.2846-0.56850.35220.3276-0.13760.6721-0.9001-1.55240.06390.5790.2150.1450.74540.21440.605121.797447.265229.6078
65.4984-2.92650.20067.18540.31223.9825-0.541-1.62410.05880.46890.4334-0.30090.47060.1903-0.02870.42030.18820.02750.96250.09830.391675.48323.554322.7102
73.5082-1.807-1.04423.12710.78933.2313-0.1829-1.06330.09090.23020.3129-0.24550.27770.3918-0.04740.20990.04120.00990.61890.11480.336464.513110.57718.9637
85.0944-1.5327-0.0985.85490.21384.2014-0.3701-0.485-0.3794-0.22230.23950.10240.82550.63270.02190.32150.01440.01150.50170.11370.431167.89591.573710.467
91.7915-1.050.04227.16332.49984.8789-0.6119-0.9063-0.26730.84160.21070.92820.6108-0.5401-0.33920.57610.3640.1291.4350.32020.574964.24234.193326.3657
103.9366-1.7460.77792.07780.02012.128-0.4212-0.7805-0.33280.14840.59730.00540.42730.0877-0.21440.31260.09530.08020.56130.14550.362370.96063.43316.01
112.93530.23680.44113.1972-0.12192.6189-0.16430.011-0.2168-0.8119-0.2121-0.11890.54060.38610.19160.96820.2772-0.00590.36540.06040.466194.7604-14.46859.4534
122.76880.60770.45792.8903-0.91482.65690.120.0661-0.238-0.401-0.2138-0.43380.92660.3970.19010.80230.2481-0.00750.40050.0640.480595.0189-14.08079.3291
137.1360.4568-0.66463.6996-1.09494.9237-0.23170.4769-0.6479-0.7083-0.0942-0.22590.67020.22540.10780.37420.0588-0.02260.3693-0.03770.222871.76228.7792-9.0421
145.3997-0.7557-1.31321.4529-0.6344.532-0.0418-0.02310.1889-0.03930.05980.05040.1182-0.2475-0.02980.18620.0074-0.01570.15020.01990.209163.637714.4725-0.7769
152.5172-1.41030.73592.54080.69310.91320.16970.4910.6082-0.9412-0.3737-0.56850.45020.92570.06290.51610.17820.16490.55210.16620.393384.85238.0175-10.1283
161.8184-0.78280.43762.641-0.41541.1420.36330.2719-0.3215-0.4071-0.2385-0.1431.30390.4106-0.04151.16580.4488-0.05140.2843-0.0490.459387.8032-15.0541-1.4257
173.4507-0.83650.59282.69440.76322.47630.26780.12440.4633-0.1703-0.22610.19480.42460.2045-0.04370.68060.11540.00880.3044-0.00930.456286.2789-5.1516-0.7071
182.3869-0.93790.0891.46670.35770.28360.19550.1411-0.6171-0.0388-0.1331-0.04021.02130.0028-0.12861.22370.2303-0.09460.2901-0.03230.429185.9728-19.29221.3699
193.3402-0.70890.18172.34771.29341.49520.43710.7547-0.002-0.8111-0.52040.09760.5080.08770.0471.10380.3453-0.02990.6235-0.07010.276383.4046-7.9286-13.4566
200.56550.09290.02851.32180.95172.41730.0647-0.2136-0.2588-0.1260.04390.08680.1801-0.1391-0.11870.2162-0.0486-0.00340.36020.08610.371449.736616.139516.9712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 274 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 19 )
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 90 )
5X-RAY DIFFRACTION5chain 'B' and (resid 91 through 99 )
6X-RAY DIFFRACTION6chain 'D' and (resid 3 through 25 )
7X-RAY DIFFRACTION7chain 'D' and (resid 26 through 38 )
8X-RAY DIFFRACTION8chain 'D' and (resid 39 through 50 )
9X-RAY DIFFRACTION9chain 'D' and (resid 51 through 75 )
10X-RAY DIFFRACTION10chain 'D' and (resid 76 through 108 )
11X-RAY DIFFRACTION11chain 'D' and (resid 109 through 150 )
12X-RAY DIFFRACTION12chain 'D' and (resid 151 through 199 )
13X-RAY DIFFRACTION13chain 'E' and (resid 2 through 18 )
14X-RAY DIFFRACTION14chain 'E' and (resid 19 through 107 )
15X-RAY DIFFRACTION15chain 'E' and (resid 108 through 122 )
16X-RAY DIFFRACTION16chain 'E' and (resid 123 through 160 )
17X-RAY DIFFRACTION17chain 'E' and (resid 161 through 186 )
18X-RAY DIFFRACTION18chain 'E' and (resid 187 through 201 )
19X-RAY DIFFRACTION19chain 'E' and (resid 202 through 241 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 9 )

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