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- PDB-9hlj: Crystal structure of GV37-TCR in complex with HLA-C*12:02 with KA... -

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Basic information

Entry
Database: PDB / ID: 9hlj
TitleCrystal structure of GV37-TCR in complex with HLA-C*12:02 with KAYNVTQAF (KF9), a 9-mer epitope from SARS-CoV-2 Nucleocapsid (N266-274)
Components
  • Beta-2-microglobulin
  • GV37-TCR alpha chain
  • GV37-TCR beta chain
  • MHC class I antigen
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-C12 / HLA-C*12:02 / SARS-CoV-2 / Nucleocapsid / T cells
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein binding ...: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / antigen processing and presentation of peptide antigen via MHC class I / 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 / 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 / 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 / positive regulation of T cell activation / Interleukin-1 signaling / 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 / 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 / Translation of Structural Proteins / Virion Assembly and Release / amyloid fibril formation / host extracellular space / Induction of Cell-Cell Fusion / intracellular iron ion homeostasis / learning or memory / Attachment and Entry / host cell perinuclear region of cytoplasm / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / ribonucleoprotein complex / 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
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
MHC class I antigen / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsAhn, Y.M. / Maddumage, J.C. / Chatzileontiadou, D.S.M. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Crystal structure of GV37-TCR in complex with HLA-C*12:02 with KAYNVTQAF (KF9), a 9-mer epitope from SARS-CoV-2 Nucleocapsid (N266-274)
Authors: Ahn, Y.M. / Maddumage, J.C. / Chatzileontiadou, D.S.M. / Gras, S.
History
DepositionDec 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: GV37-TCR alpha chain
E: GV37-TCR beta chain
A: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5798
Polymers101,3595
Non-polymers2203
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-61 kcal/mol
Surface area37450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.006, 59.468, 109.847
Angle α, β, γ (deg.)90.000, 109.907, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 4 types, 4 molecules DEAB

#1: Protein GV37-TCR alpha chain


Mass: 22760.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein GV37-TCR beta chain


Mass: 27399.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Protein MHC class I antigen


Mass: 38277.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A3S6RG30
#4: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

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


Mass: 1042.164 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9

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Non-polymers , 3 types, 28 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium formate dihydrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.54→45.46 Å / Num. obs: 29890 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 50.37 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.6
Reflection shellResolution: 2.54→2.66 Å / Redundancy: 6.9 % / Num. unique obs: 3299 / CC1/2: 0.691 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→45.46 Å / SU ML: 0.4381 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2574 1490 5 %
Rwork0.2106 28284 -
obs0.2129 29774 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.03 Å2
Refinement stepCycle: LAST / Resolution: 2.54→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6490 0 13 25 6528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00166695
X-RAY DIFFRACTIONf_angle_d0.44329095
X-RAY DIFFRACTIONf_chiral_restr0.0388955
X-RAY DIFFRACTIONf_plane_restr0.00271198
X-RAY DIFFRACTIONf_dihedral_angle_d12.04632464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.630.39741170.3872132X-RAY DIFFRACTION82.71
2.63-2.720.36691370.31852610X-RAY DIFFRACTION99.93
2.72-2.830.34411380.282605X-RAY DIFFRACTION99.82
2.83-2.960.33381320.25972556X-RAY DIFFRACTION99.96
2.96-3.110.27531390.26042624X-RAY DIFFRACTION99.93
3.11-3.310.28981390.26372603X-RAY DIFFRACTION99.85
3.31-3.560.2791370.22232605X-RAY DIFFRACTION99.85
3.56-3.920.24161380.19622599X-RAY DIFFRACTION99.93
3.92-4.490.22051340.17922606X-RAY DIFFRACTION100
4.49-5.650.21371390.15642647X-RAY DIFFRACTION99.93
5.65-45.460.2221400.17452697X-RAY DIFFRACTION99.72
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)
14.341325357270.4667918663593.135365501542.33869717244-1.276628168914.98727024247-0.622383309902-0.1609680193040.619542771448-0.5785849425570.1412113398790.95490500335-0.491391084734-1.128329544590.4380810232790.7003857063660.0810773847931-0.3037950384190.452800973243-0.04176408044810.765140496877-37.5147755899-0.255216751786-62.2269930182
23.74606072625-0.0111407945311.04573471325.42546410241-2.131085873636.04370506173-0.4556136424040.02555352840760.32600801747-0.660617315759-0.04868497527570.276100248477-0.640027096233-0.06892290830270.4273463084210.398785207525-0.0289673386498-0.08508999866570.2285301344010.007713426738690.402356759643-30.9616966003-4.47850112933-58.888027846
32.06172925215-1.305034531092.055420181541.532679846960.06718114904254.4677756139-0.4669518329951.0263010820.612540553891-1.666516301671.280790055041.243973645870.08811457546920.2854018501580.5658761807681.7961599491-0.572992047499-0.626786568620.7157912813790.3544357778960.615818375374-42.4377898015-5.78772052648-82.1750715148
40.8107822431030.271698591433-0.9197845571498.917416630891.434470104781.53728037389-0.8115238218360.4122635076170.308222033808-0.2491173467360.2261483239852.553290600170.193327922389-0.5435238626380.4926949948672.12285638822-0.521925708099-0.7838201816981.04355043212-0.04358589828951.62890216177-54.2394124779-16.6040077546-86.671894373
58.231558401241.68507152315-0.1283749592787.520581101360.1760942857195.97486969101-0.7042296892770.2550963141280.702111758859-1.511958203560.7384415571580.318479714943-0.8494719652720.0521863797311-0.07680622368271.41339267375-0.404661578111-0.3891822226250.612456533231-0.0598231534460.790254906923-46.9285795253-15.047206541-83.2558889969
61.28210265978-2.10612946772-1.232666582075.360314837-2.098345391671.99509543701-0.236963179511.63899702750.200543525625-1.40362723465-0.5889478975452.241357047650.925518722375-1.225674220860.4255680457461.74914202267-0.415900454328-0.7037607314012.269969190610.4254721010451.94688400911-64.7835576558-19.5263046882-86.8519738071
74.363462208832.042045983760.7056244126953.706509015760.4381583676192.631267547540.676664575089-0.0541936664353-1.1510073442-0.0805166021429-0.4368752942330.02513569022631.96515785581-0.811233737543-0.00872759610620.604800874676-0.262158751255-0.03245621074650.502636713377-0.06112369045760.509212531222-39.124579405-26.8070847875-52.6126292756
83.376479486351.726506914541.981994872222.688823458992.578170215163.973164770120.191496929291-0.33611434237-0.1214013716250.523984933738-0.3714011518750.3841384914671.06369256086-1.20713616640.0004019887973320.420551738351-0.2785347956730.09144536131430.62493074387-0.003852537415440.453247837288-41.6555999749-23.4001167928-49.3678176765
94.139002313331.36972651763-0.1466642308682.63572788634-0.8465491373834.39454508563-0.7596710237730.676772246224-0.0876603604672-1.307304435940.07083956150070.249425510289-0.8828528509450.2119405679080.4033819103851.18253745669-0.371075646063-0.2078241986890.702453860696-0.1383070300750.713390708509-47.495290131-24.9291855318-83.3910964419
109.18337690014-0.3788147498-1.714348922113.36285641684-0.02139963886983.5005109595-0.0085887728847-0.7283713213780.451827234538-0.416427017098-0.06626972632030.374828001077-0.747980953840.002427562485710.1250746954980.77058771616-0.287002002577-0.1413762802180.731222511268-0.2133581491060.716377760242-50.1157386739-22.4399272805-74.1269356718
112.719687882190.3703612704071.298889629325.04331037011.048251127246.58139331296-0.6676440954250.145188874907-0.913065835462-1.48216060810.376929282486-0.3387561492211.051403817410.664317002139-0.08990305072970.865186610865-0.461124335806-0.02648972418210.554181028847-0.2777499090770.498210018611-45.2457097028-30.965524796-78.4431370541
122.10209894764-0.577868953811.89003728563.361616700691.734689771443.39420826399-0.3066039091420.293368079991-0.7892823421-0.8543668057120.470646626615-0.1568708209741.07357539558-0.752069143475-0.1894353736781.01981901515-0.419013354985-0.0738570128310.584279582069-0.1968259331710.803683753075-50.7066674385-37.4475709824-75.6444359704
133.87503535973-0.5739014562131.67828848584.1257384140.8205660432044.76847161315-0.0188198097021-0.5771505413960.08082220979220.304970101877-0.2820716725220.6895492896480.205294427782-0.8140351987090.2053093591830.365742525233-0.02189398318010.1095284360750.446335762536-0.1082433603280.306880275979-29.2913102074-9.28534063636-26.8526982721
143.9721583946-0.8080989675930.2228408157593.600542045361.824915429813.97856797581-0.1478200505730.08900485462210.619135423043-0.00598208546789-0.0893268986886-0.414834057393-0.5224671343740.208391939860.1079871468050.336275840026-0.0400190677486-0.03565546883750.2581372295960.0001875434957810.318576129145-17.7645973063-4.09199977404-35.407813146
153.573973642950.5734558694760.4385086399874.020912991661.435245846164.680059117620.0345906867047-0.5015514767510.5122777784790.409675160556-0.389465382069-0.07910976558-0.9069516096890.08276834626090.3964442982580.720083697891-0.0546537787592-0.06542374292970.585578991724-0.2328933761760.580264303538-17.027806047413.1498645581-1.49991053052
169.12396852967-0.27791198198-4.483499184937.927838259453.281267520813.44325850351-0.8706560815971.06536031962-1.57738836206-0.3242605102360.58289909501-0.8811533562742.67527802013-0.890853697279-0.02709713960561.144081868770.0253036511437-0.01021885127820.703313820884-0.1046818432870.541720801743-15.4422692526-16.0007433508-11.71217054
175.42029853396-1.48353498112-2.648093689331.60524348522-0.855409566845.17373552969-0.0176005003526-0.66933077594-0.1806279546560.620646336371-0.2940028890010.5016578077860.917234311203-2.05796504270.3551279033450.562013239101-0.1982252224640.2167868412311.20908624868-0.1894625402230.385257127835-31.0187332545-5.00212373358-2.57179753448
182.0933846373-0.692312957825-3.23663474441.956247815360.1871954420196.571126597441.08502850601-0.7883056369780.9229243038820.0068497077937-0.7203479155280.4951106291690.346229429685-1.272805515130.07694628889130.412108124784-0.1935420603990.1882057666620.802328920657-0.2200561164350.407753286197-27.0957446121-5.1079814741-12.0559238224
193.1546178424-1.08823925359-0.2950308055966.781587232231.015244742936.67307145886-0.196225677635-1.16612153262-0.01274287095171.25968055376-0.03376897783590.7220723247871.08643019347-1.033732554610.221912760020.85529816784-0.2939339225860.09161559777731.08642388056-0.1153316079730.467081382528-26.9541411743-7.802556145314.15912781333
201.86837159871-0.5677931224850.9849323869853.225899802990.7995536918532.714468388570.3371682348870.5100700224070.08418373663190.677104265477-0.752849373741-0.01460425704450.417829674698-0.1584252204560.2424380213280.324939559689-0.09026004470380.1655069090470.41205022469-0.001789920784930.375772960148-25.6566453838-9.87213536935-36.3486273889
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 6 through 30 )DA6 - 301 - 25
22chain 'D' and (resid 31 through 102 )DA31 - 10226 - 97
33chain 'D' and (resid 103 through 119 )DA103 - 11998 - 114
44chain 'D' and (resid 120 through 149 )DA120 - 149115 - 144
55chain 'D' and (resid 150 through 176 )DA150 - 176145 - 171
66chain 'D' and (resid 177 through 184 )DA177 - 184172 - 179
77chain 'E' and (resid 1 through 37 )EC1 - 371 - 37
88chain 'E' and (resid 38 through 125 )EC38 - 12538 - 125
99chain 'E' and (resid 126 through 163 )EC126 - 163126 - 163
1010chain 'E' and (resid 164 through 189 )EC164 - 189164 - 189
1111chain 'E' and (resid 190 through 226 )EC190 - 226190 - 226
1212chain 'E' and (resid 227 through 244 )EC227 - 244227 - 244
1313chain 'A' and (resid 1 through 104 )AE1 - 1041 - 104
1414chain 'A' and (resid 105 through 174 )AE105 - 174105 - 174
1515chain 'A' and (resid 175 through 276 )AE175 - 276175 - 276
1616chain 'B' and (resid 0 through 5 )BF0 - 51 - 6
1717chain 'B' and (resid 6 through 51 )BF6 - 517 - 52
1818chain 'B' and (resid 52 through 71 )BF52 - 7153 - 72
1919chain 'B' and (resid 72 through 99 )BF72 - 9973 - 100
2020chain 'C' and (resid 1 through 9 )CG1 - 91 - 9

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