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- PDB-8rj5: P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex -

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Basic information

Entry
Database: PDB / ID: 8rj5
TitleP1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • P1-15 T-cell Receptor Alpha Chain
  • P1-15 T-cell Receptor Beta Chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM / T-cell Receptor / Peptide:HLA / NF9 / Covid-19
Function / homology
Function and homology information


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 ...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 / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / amyloid fibril formation / Induction of Cell-Cell Fusion / structural constituent of virion / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell / membrane fusion / 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 / 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 / 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 / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Beta-2-Microglobulin / : / 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 ...Beta-2-Microglobulin / : / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsWall, A. / Sewell, A.K. / Motozono, C. / Rizkallah, P.J. / Fuller, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: NF9 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex (Paper Pending)
Authors: Motozono, C. / Wall, A. / Sewell, A.K. / Rizkallah, P.J. / Fuller, A.
History
DepositionDec 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 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
C: Spike protein S1
D: P1-15 T-cell Receptor Alpha Chain
E: P1-15 T-cell Receptor Beta Chain
F: MHC class I antigen
G: Beta-2-microglobulin
H: Spike protein S1
I: P1-15 T-cell Receptor Alpha Chain
J: P1-15 T-cell Receptor Beta Chain


Theoretical massNumber of molelcules
Total (without water)190,87010
Polymers190,87010
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
D: P1-15 T-cell Receptor Alpha Chain
E: P1-15 T-cell Receptor Beta Chain


Theoretical massNumber of molelcules
Total (without water)95,4355
Polymers95,4355
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: Spike protein S1
I: P1-15 T-cell Receptor Alpha Chain
J: P1-15 T-cell Receptor Beta Chain


Theoretical massNumber of molelcules
Total (without water)95,4355
Polymers95,4355
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.439, 200.439, 156.272
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein MHC class I antigen


Mass: 31909.312 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)
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / 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
#3: Protein/peptide Spike protein S1


Mass: 1266.425 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Protein P1-15 T-cell Receptor Alpha Chain


Mass: 22836.367 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 P1-15 T-cell Receptor Beta Chain


Mass: 27543.496 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)
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: 4.75 Å3/Da / Density % sol: 74.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: di-Sodium malonate, 0.1M HEPES pH7, 0.1M Poly(acrylic acid sodium salt) 2,100, 30% w/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.02→61.63 Å / Num. obs: 71335 / % possible obs: 100 % / Redundancy: 21.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.302 / Rpim(I) all: 0.067 / Rrim(I) all: 0.309 / Net I/σ(I): 7.1
Reflection shellResolution: 3.05→3.11 Å / Rmerge(I) obs: 4.765 / Num. unique obs: 3413 / CC1/2: 0.274 / Rpim(I) all: 1.03 / Rrim(I) all: 4.876

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→61.62 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.92 / SU B: 65.149 / SU ML: 0.449 / Cross valid method: THROUGHOUT / ESU R: 0.705 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25981 3445 4.9 %RANDOM
Rwork0.21997 ---
obs0.22195 66155 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 119.997 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å2-1.34 Å20 Å2
2---2.68 Å2-0 Å2
3---8.69 Å2
Refinement stepCycle: 1 / Resolution: 3.02→61.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13408 0 0 0 13408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01313768
X-RAY DIFFRACTIONr_bond_other_d0.0010.01512286
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.65318684
X-RAY DIFFRACTIONr_angle_other_deg1.1431.58328332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85351656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.22422.152818
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.757152236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.06515102
X-RAY DIFFRACTIONr_chiral_restr0.0570.21720
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215882
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023402
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_it4.3296.7566660
X-RAY DIFFRACTIONr_mcbond_other4.3286.7566659
X-RAY DIFFRACTIONr_mcangle_it7.04110.1298304
X-RAY DIFFRACTIONr_mcangle_other7.04110.138305
X-RAY DIFFRACTIONr_scbond_it4.4147.0727108
X-RAY DIFFRACTIONr_scbond_other4.4157.0727105
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.25210.47510379
X-RAY DIFFRACTIONr_long_range_B_refined13.568127.81454356
X-RAY DIFFRACTIONr_long_range_B_other13.568127.81254355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85240.13
12F85240.13
21B29070.14
22G29070.14
31D53290.21
32I53290.21
41E74180.15
42J74180.15
LS refinement shellResolution: 3.02→3.097 Å
RfactorNum. reflection% reflection
Rfree0.403 161 -
Rwork0.386 3411 -
obs--68.36 %
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)
12.1357-0.42660.28482.7661-0.81885.10020.28060.25580.2548-0.4721-0.12540.07920.5163-0.2431-0.15521.10760.1663-0.15030.2301-0.03970.0834-0.967154.36587.549
26.43990.53361.08511.34680.77960.747-0.08340.5475-1.23240.81730.03570.49110.5487-0.34310.04772.1197-0.1267-0.08640.9992-0.03260.6502-5.548131.43958.952
34.6573-1.312-0.6034.60221.11224.87750.03770.5072-0.3216-0.3675-0.1132-0.55640.59380.26660.07551.64560.2982-0.07910.4395-0.07140.245810.639132.38175.344
41.7452-2.7111-0.21786.75743.72824.79040.12740.12330.1029-0.2426-0.16170.00940.09680.06090.03430.68570.0943-0.07170.25850.13380.2325-6.577181.275102.502
57.2119-1.15251.25152.4645-0.29133.6787-0.11040.32470.4103-0.1767-0.00260.2498-0.35240.05160.1130.69830.09150.04460.2346-0.04210.2379-3.037207.852122.999
64.1363.93962.01367.07781.03963.02860.286-0.0189-0.1414-0.09540.0195-0.2468-0.00580.1607-0.30550.65620.18580.00880.30890.0490.174311.859172.249112.211
76.1257-2.3407-1.53735.27251.69363.2595-0.0712-0.1194-0.13160.1057-0.0323-0.1016-0.04430.03960.10340.6744-0.0994-0.0150.09030.01080.01294.804195.396131.456
83.106-1.18730.8753.45110.19493.83910.22740.11890.3153-0.5262-0.4276-0.824-0.25780.42610.20020.83910.13230.10760.43830.0320.665336.357147.02100.256
90.01540.0010.0160.0018-0.00710.0545-0.01590.05130.13440.0122-0.03240.0283-0.06130.22320.04821.1578-0.030.110.9780.06981.407547.141171.94575.564
103.83150.7566-1.02093.8404-1.66532.24860.09750.29920.6671-0.4325-0.4535-0.5976-0.443-0.11120.3561.25890.23220.12830.59650.01241.07130.502172.52391.411
110.8921-0.7066-1.07567.0549-3.15824.1236-0.09230.14740.12070.00560.0193-0.08650.1546-0.05210.07290.46150.1367-0.04650.5022-0.10610.36436.361118.323112.098
126.78180.30430.08933.16591.66462.6705-0.1946-0.2173-0.66620.0851-0.03010.5530.467-0.05980.22470.80850.19960.1310.58390.00490.464928.19691.644132.08
137.26842.5263-1.75413.9401-0.52232.24870.1626-0.0560.06080.17140.0381-0.16540.00690.0589-0.20070.57790.2168-0.02130.3419-0.10290.200820.009129.827122.894
146.2602-1.68180.98575.1826-1.62281.72940.1074-0.5563-0.16440.02690.0410.41490.31160.1324-0.14840.81310.28540.14440.6635-0.01880.073722.403104.781140.576
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D0 - 115
6X-RAY DIFFRACTION5D117 - 203
7X-RAY DIFFRACTION6E1 - 115
8X-RAY DIFFRACTION7E120 - 245
9X-RAY DIFFRACTION8F1 - 180
10X-RAY DIFFRACTION8H1 - 9
11X-RAY DIFFRACTION9F181 - 276
12X-RAY DIFFRACTION10G0 - 99
13X-RAY DIFFRACTION11I0 - 115
14X-RAY DIFFRACTION12I117 - 203
15X-RAY DIFFRACTION13J1 - 115
16X-RAY DIFFRACTION14J120 - 245

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