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- PDB-8dnt: SARS-CoV-2 specific T cell receptor -

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Open data


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Basic information

Entry
Database: PDB / ID: 8dnt
TitleSARS-CoV-2 specific T cell receptor
Components
  • Beta-2-microglobulin
  • MHC class I antigen alpha chain
  • Nucleoprotein
  • T-cell receptor alpha chain
  • T-cell receptor beta chain
KeywordsIMMUNE SYSTEM / TCR complex / MHC / HLA / SARS-CoV-2
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded 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 ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded 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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / Interleukin-1 signaling / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / viral capsid / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / PIP3 activates AKT signaling / MHC class II protein complex binding / late endosome membrane / Transcription of SARS-CoV-2 sgRNAs / iron ion transport / ER-Phagosome pathway / host cell endoplasmic reticulum-Golgi intermediate compartment / early endosome membrane / T cell differentiation in thymus / protein refolding / host cell Golgi apparatus / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / amyloid fibril formation / Induction of Cell-Cell Fusion / membrane => GO:0016020 / Attachment and Entry / learning or memory / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid / MHC class I alpha chain, alpha1 alpha2 domains ...Nucleocapsid protein, betacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid / 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: 3.18 Å
Model detailscomplex with HLA-A2 and peptide
AuthorsGallagher, D.T. / Wu, D. / Gowthaman, R. / Pierce, B.G. / Mariuzza, R.A. / Weng, N.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government1131030_SEED_01_RM United States
CitationJournal: Nat Commun / Year: 2023
Title: SARS-CoV-2 infection establishes a stable and age-independent CD8 + T cell response against a dominant nucleocapsid epitope using restricted T cell receptors.
Authors: Choy, C. / Chen, J. / Li, J. / Gallagher, D.T. / Lu, J. / Wu, D. / Zou, A. / Hemani, H. / Baptiste, B.A. / Wichmann, E. / Yang, Q. / Ciffelo, J. / Yin, R. / McKelvy, J. / Melvin, D. / ...Authors: Choy, C. / Chen, J. / Li, J. / Gallagher, D.T. / Lu, J. / Wu, D. / Zou, A. / Hemani, H. / Baptiste, B.A. / Wichmann, E. / Yang, Q. / Ciffelo, J. / Yin, R. / McKelvy, J. / Melvin, D. / Wallace, T. / Dunn, C. / Nguyen, C. / Chia, C.W. / Fan, J. / Ruffolo, J. / Zukley, L. / Shi, G. / Amano, T. / An, Y. / Meirelles, O. / Wu, W.W. / Chou, C.K. / Shen, R.F. / Willis, R.A. / Ko, M.S.H. / Liu, Y.T. / De, S. / Pierce, B.G. / Ferrucci, L. / Egan, J. / Mariuzza, R. / Weng, N.P.
History
DepositionJul 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell receptor alpha chain
B: T-cell receptor beta chain
D: Nucleoprotein
E: MHC class I antigen alpha chain
F: Beta-2-microglobulin
H: T-cell receptor alpha chain
I: T-cell receptor beta chain
J: Nucleoprotein
K: MHC class I antigen alpha chain
L: Beta-2-microglobulin
M: T-cell receptor alpha chain
P: T-cell receptor beta chain
Q: Nucleoprotein
R: MHC class I antigen alpha chain
T: Beta-2-microglobulin
V: T-cell receptor alpha chain
W: T-cell receptor beta chain
X: Nucleoprotein
Y: MHC class I antigen alpha chain
Z: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)379,02420
Polymers379,02420
Non-polymers00
Water00
1
A: T-cell receptor alpha chain
B: T-cell receptor beta chain
D: Nucleoprotein
E: MHC class I antigen alpha chain
F: Beta-2-microglobulin


  • defined by author
  • Evidence: surface plasmon resonance
  • 94.8 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)94,7565
Polymers94,7565
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: T-cell receptor alpha chain
I: T-cell receptor beta chain
J: Nucleoprotein
K: MHC class I antigen alpha chain
L: Beta-2-microglobulin


  • defined by author
  • 94.8 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)94,7565
Polymers94,7565
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: T-cell receptor alpha chain
P: T-cell receptor beta chain
Q: Nucleoprotein
R: MHC class I antigen alpha chain
T: Beta-2-microglobulin


  • defined by author
  • 94.8 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)94,7565
Polymers94,7565
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
V: T-cell receptor alpha chain
W: T-cell receptor beta chain
X: Nucleoprotein
Y: MHC class I antigen alpha chain
Z: Beta-2-microglobulin


  • defined by author
  • 94.8 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)94,7565
Polymers94,7565
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.158, 121.827, 210.555
Angle α, β, γ (deg.)90.000, 100.020, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
T-cell receptor alpha chain


Mass: 22544.775 Da / Num. of mol.: 4 / Fragment: TCR alpha from TRAV 12-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein
T-cell receptor beta chain


Mass: 27076.891 Da / Num. of mol.: 4 / Fragment: TCR beta from TRBV 7-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide
Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 1098.317 Da / Num. of mol.: 4 / Fragment: LLL peptide from nucleocapsid protein 222-230 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9
#4: Protein
MHC class I antigen alpha chain


Mass: 32156.553 Da / Num. of mol.: 4 / Fragment: Human Leukocyte Antigen HLA-A*02:01
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: U5YKE0
#5: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119
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

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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: 3.03 Å3/Da / Density % sol: 59.47 % / Description: bars in clusters
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.5 / Details: 13.5% (w/v) PEG 20,000, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.11→48.7 Å / Num. obs: 64385 / % possible obs: 79.2 % / Redundancy: 2.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.071 / Rrim(I) all: 0.121 / Net I/σ(I): 8 / Num. measured all: 163220 / Scaling rejects: 68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.11-3.191.61.381429627080.2491.3771.950.445.5
13.91-48.72.90.02425108730.9990.0170.02937.591.5

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VRN

6vrn


Resolution: 3.18→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.876 / SU B: 116.722 / SU ML: 0.786 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.775 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3126 2857 5 %RANDOM
Rwork0.221 ---
obs0.2256 54229 74.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 322.76 Å2 / Biso mean: 154.18 Å2 / Biso min: 64.08 Å2
Baniso -1Baniso -2Baniso -3
1-11.6 Å20 Å23.88 Å2
2---5.08 Å20 Å2
3----7.42 Å2
Refinement stepCycle: final / Resolution: 3.18→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26214 0 0 0 26214
Num. residues----3300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01226915
X-RAY DIFFRACTIONr_angle_refined_deg0.8311.6436588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71153280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70522.2071559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.904154238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.97915191
X-RAY DIFFRACTIONr_chiral_restr0.0680.23399
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0221133
LS refinement shellResolution: 3.18→3.262 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 120 -
Rwork0.344 2345 -
all-2465 -
obs--44.53 %
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)
10.1489-0.2879-0.06060.9873-0.43410.81210.0063-0.03430.028-0.02710.0302-0.03770.0393-0.0261-0.03650.0422-0.02860.03570.0975-0.00450.045260.573718.627963.0183
20.1744-0.07690.16060.19530.19050.5733-0.0548-0.04490.02910.06280.0425-0.03170.0072-0.02730.01220.0638-0.01160.0130.1174-0.01420.035858.798527.188785.2853
30.0557-0.05870.01440.14520.14810.3388-0.02420.01820.07580.0016-0.0462-0.0604-0.0068-0.03410.07040.0619-0.01350.01910.0344-0.00030.150157.969552.252862.6814
40.06170.066-0.02880.1175-0.07110.08430.0004-0.0069-0.0359-0.02240.0002-0.0336-0.01720.0163-0.00060.0423-0.01740.01440.09580.02330.078453.7035-15.500981.1941
50.1313-0.0633-0.21670.6986-0.3250.66780.023-0.0530.05590.07870.0395-0.1184-0.0450.0616-0.06250.0678-0.0277-0.04380.08170.02040.081557.3051-23.77298.0088
60.130.02950.16570.1289-0.16870.6131-0.0451-0.0409-0.025-0.0362-0.0039-0.0209-0.0158-0.02280.0490.0469-0.01940.01020.07630.0450.068911.0904-79.729642.2347
70.22010.11980.21710.64490.53430.5493-0.03190.0299-0.10410.01590.03570.0459-0.05350.0073-0.00380.0635-0.01020.01360.0922-0.00770.07924.6655-85.123519.9007
80.3660.10410.10820.0990.10.10430.0158-0.0798-0.0739-0.0188-0.03640.0137-0.0234-0.02270.02060.0403-0.02440.00930.08390.03840.1045-16.3905-98.962842.29
90.04720.04870.02070.13520.00350.04070.01060.0152-0.01860.02920.0044-0.01790.0023-0.0159-0.0150.0181-0.01190.01270.06210.00630.117834.9177-53.935324.263
100.3681-0.01-0.05080.1131-0.16430.29260.0246-0.05250.0031-0.02690.00570.0245-0.00350.0333-0.03030.0507-0.01630.00830.0598-0.00890.104944.9741-52.83818.099
110.21120.09890.19870.25390.19090.2336-0.03680.0377-0.0140.08540.04190.03290.01820.0486-0.00510.0649-0.020.03470.0826-0.01710.064764.782916.161840.0086
120.92110.1067-0.0810.58-0.1210.0291-0.02180.0297-0.01380.00170.0096-0.03940.0016-0.00570.01220.0266-0.02080.03270.0886-0.00450.074571.916120.232417.6005
130.27380.1683-0.12420.1086-0.04980.30640.019-0.04970.00060.0142-0.04880.0036-0.03630.03090.02990.0178-0.02280.02690.0981-0.00760.091192.196635.538539.5525
140.12520.08770.04990.14340.04920.05320.0265-0.0048-0.00380.0236-0.01810.0067-0.0114-0.0015-0.00840.0246-0.01130.02140.07120.00870.104541.5819-10.713422.7881
150.79090.02840.15270.03120.08050.24840.0188-0.03260.0044-0.01150.0022-0.01650.0101-0.0179-0.0210.0475-0.01980.01610.04310.02170.120933.1855-13.236.1424
160.16870.04710.18250.34310.0550.2023-0.00070.0132-0.04270.04480.0250.0365-0.02120.0258-0.02440.0526-0.02570.00790.06890.02680.091515.3617-81.777365.2523
170.02360.0473-0.01080.310.06870.04550.0193-0.0111-0.0070.038-0.0224-0.00490.00150.00880.00310.0621-0.0064-0.00170.0860.01480.073119.0221-63.302489.3455
180.14880.02490.11730.1211-0.08590.19590.0551-0.00830.0225-0.0102-0.01680.04260.05390.0013-0.03840.0523-0.0041-0.00010.06690.00660.09217.9806-115.28266.1144
190.06950.03860.08070.6697-0.00550.0982-0.0141-0.01720.0065-0.049-0.0015-0.0247-0.016-0.0240.01560.0433-0.02290.02990.08360.01270.060324.677-38.880179.5782
200.1255-0.28970.71251.4197-3.58389.0528-0.4585-0.13340.1771-0.2434-0.1832-0.4180.6478-0.47030.64170.38020.0954-0.04220.2296-0.17840.360438.1121-52.275995.8097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 109
2X-RAY DIFFRACTION2B3 - 115
3X-RAY DIFFRACTION3A110 - 201
4X-RAY DIFFRACTION3B116 - 244
5X-RAY DIFFRACTION4D1 - 9
6X-RAY DIFFRACTION4E1 - 275
7X-RAY DIFFRACTION5F1 - 100
8X-RAY DIFFRACTION6H4 - 109
9X-RAY DIFFRACTION7I3 - 115
10X-RAY DIFFRACTION8H110 - 201
11X-RAY DIFFRACTION8I116 - 244
12X-RAY DIFFRACTION9J1 - 9
13X-RAY DIFFRACTION9K1 - 276
14X-RAY DIFFRACTION10L1 - 100
15X-RAY DIFFRACTION11M4 - 109
16X-RAY DIFFRACTION12P3 - 115
17X-RAY DIFFRACTION13M110 - 201
18X-RAY DIFFRACTION13P116 - 244
19X-RAY DIFFRACTION14Q1 - 9
20X-RAY DIFFRACTION14R1 - 278
21X-RAY DIFFRACTION15T1 - 100
22X-RAY DIFFRACTION16V4 - 109
23X-RAY DIFFRACTION17V0
24X-RAY DIFFRACTION18V110 - 201
25X-RAY DIFFRACTION18W116 - 244
26X-RAY DIFFRACTION19X1 - 9
27X-RAY DIFFRACTION19Y1 - 274
28X-RAY DIFFRACTION20Z1 - 100

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