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- PDB-7pbe: Emergence of immune escape at dominant SARS-CoV-2 killer T-cell e... -

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Basic information

Entry
Database: PDB / ID: 7pbe
TitleEmergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope
Components
  • (Human T-cell Receptor YLQ36, ...) x 2
  • Beta-2-microglobulin
  • MHC class I antigen
  • Spike protein S1
KeywordsIMMUNE SYSTEM / MHC I / A02 / Wuhan epitope / SARS-COV-2 / Spike protein
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / 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 / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / amyloid fibril formation / Induction of Cell-Cell Fusion / structural constituent of virion / intracellular iron ion homeostasis / membrane fusion / entry receptor-mediated virion attachment to host cell / 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
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / MHC class I antigen / Spike glycoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsRizkallah, P.J. / Sewell, A.K. / Wall, A. / Fuller, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2022
Title: Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope.
Authors: Dolton, G. / Rius, C. / Hasan, M.S. / Wall, A. / Szomolay, B. / Behiry, E. / Whalley, T. / Southgate, J. / Fuller, A. / Morin, T. / Topley, K. / Tan, L.R. / Goulder, P.J.R. / Spiller, O.B. / ...Authors: Dolton, G. / Rius, C. / Hasan, M.S. / Wall, A. / Szomolay, B. / Behiry, E. / Whalley, T. / Southgate, J. / Fuller, A. / Morin, T. / Topley, K. / Tan, L.R. / Goulder, P.J.R. / Spiller, O.B. / Rizkallah, P.J. / Jones, L.C. / Connor, T.R. / Sewell, A.K.
History
DepositionAug 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Human T-cell Receptor YLQ36, alpha chain
E: Human T-cell Receptor YLQ36, beta chain
F: MHC class I antigen
G: Beta-2-microglobulin
H: Spike protein S1
I: Human T-cell Receptor YLQ36, alpha chain
J: Human T-cell Receptor YLQ36, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,53617
Polymers190,84410
Non-polymers6937
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
D: Human T-cell Receptor YLQ36, alpha chain
E: Human T-cell Receptor YLQ36, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8169
Polymers95,4225
Non-polymers3944
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: Spike protein S1
I: Human T-cell Receptor YLQ36, alpha chain
J: Human T-cell Receptor YLQ36, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7208
Polymers95,4225
Non-polymers2983
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)229.240, 46.450, 184.720
Angle α, β, γ (deg.)90.000, 96.750, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22G
13D
23I
14E
24J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPROFF1 - 2761 - 276
12METMETMETMETBB0 - 991 - 100
22METMETMETMETGG0 - 991 - 100
13GLUGLUGLUGLUDD3 - 2013 - 201
23GLUGLUGLUGLUII3 - 2013 - 201
14THRTHRASPASPEE2 - 2432 - 243
24THRTHRASPASPJJ2 - 2432 - 243

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules AFBG

#1: Protein MHC class I antigen


Mass: 31951.316 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) / References: UniProt: A0A5B8RNS7
#2: 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 (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Spike protein S1


Mass: 1151.377 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Human T-cell Receptor YLQ36, ... , 2 types, 4 molecules DIEJ

#4: Protein Human T-cell Receptor YLQ36, alpha chain


Mass: 22749.111 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 Human T-cell Receptor YLQ36, beta chain


Mass: 27690.611 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)

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Non-polymers , 2 types, 7 molecules

#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium sulphate, 0.1 M Tris, pH 8.5, and 25 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91808 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91808 Å / Relative weight: 1
ReflectionResolution: 2.68→113.83 Å / Num. obs: 55107 / % possible obs: 99.5 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.078 / Rrim(I) all: 0.155 / Net I/σ(I): 6.3 / Num. measured all: 212580 / Scaling rejects: 8
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
2.68-2.7543.4891629140490.4411.9974.0310.399.8
11.99-113.833.50.02524146920.9990.0160.02929.997.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.2 Å113.83 Å
Translation6.2 Å113.83 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P3D

7p3d


Resolution: 3→113.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.276 / WRfactor Rwork: 0.2085 / FOM work R set: 0.655 / SU B: 73.258 / SU ML: 0.544 / SU R Cruickshank DPI: 0.4684 / SU Rfree: 0.5401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.54 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2957 1931 4.9 %RANDOM
Rwork0.2281 ---
obs0.2314 37569 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 264.48 Å2 / Biso mean: 104.77 Å2 / Biso min: 50.07 Å2
Baniso -1Baniso -2Baniso -3
1--7.05 Å20 Å2-0.93 Å2
2--4.95 Å20 Å2
3---2.25 Å2
Refinement stepCycle: final / Resolution: 3→113.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13364 0 39 0 13403
Biso mean--139.07 --
Num. residues----1652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01313762
X-RAY DIFFRACTIONr_bond_other_d0.0020.01812272
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.65118686
X-RAY DIFFRACTIONr_angle_other_deg1.0391.58228278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3951642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49321.966834
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.277152224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.09315108
X-RAY DIFFRACTIONr_chiral_restr0.0320.21722
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215822
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023434
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A86740.08
12F86740.08
21B30800.07
22G30800.07
31D52530.14
32I52530.14
41E73770.09
42J73770.09
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 165 -
Rwork0.424 2795 -
all-2960 -
obs--99.87 %
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)
16.75921.65020.12434.4414-2.40535.8677-0.3307-0.9974-0.03730.18130.05210.0372-0.077-0.50580.27860.06650.0504-0.05240.20930.00910.148728.3532.60499.29
25.0864-0.2171-2.70546.3024-0.04374.35610.4876-0.93321.54941.4102-0.0272-0.6771-2.0505-0.5206-0.46051.51120.3132-0.17681.7111-0.1970.672246.1115.216127.729
35.8713-0.48152.56973.9961-1.574410.3441-0.1724-0.7851-0.12670.53110.0721-0.33850.089-0.15190.10030.1258-0.0148-0.11490.24550.03290.234853.0891.244111.123
410.5106-1.28112.16741.2294-0.42687.4650.0921-0.04980.41880.1236-0.03780.3137-0.0646-0.9582-0.05430.0599-0.00120.03960.47810.09060.4062-0.9320.41386.324
56.880.23641.10099.49851.13177.60430.1503-0.5736-0.92520.1514-0.09220.1570.7555-1.2631-0.05810.31050.08770.00391.51480.08060.6607-23.496-10.9764.35
65.18050.3891.92427.05874.4266.32890.40170.5018-0.8471-0.0754-0.03420.21020.81740.1144-0.36750.2320.0782-0.15970.3405-0.00060.361815.732-13.00776.102
78.698-4.01681.87756.6594-1.81494.788-0.0195-0.1764-0.88070.18650.38460.24830.3046-0.4068-0.36520.2867-0.0422-0.17340.8177-0.12760.3238-8.502-12.57657.114
85.8736-1.74910.17524.95792.53986.4644-0.32541.05640.0053-0.22780.0256-0.0773-0.15780.70540.29980.0809-0.0526-0.06490.292-0.02140.1627-39.17653.051-7.47
95.96070.5225-2.14126.6626-0.64271.54610.69980.56381.4699-1.703-0.22330.5892-1.12070.3382-0.47651.9517-0.2384-0.11831.57250.00210.4343-56.60865.866-36.147
105.94650.75091.81533.49081.764610.0887-0.14450.8034-0.1799-0.57820.07820.34390.04360.3540.06630.15260.0637-0.14060.3011-0.10570.2671-63.8251.9-19.484
1110.66630.77394.34270.81110.10035.50010.01550.67790.3775-0.00140.0565-0.149-0.09241.1347-0.0720.08260.04230.00370.7361-0.10470.2984-9.97949.8295.495
125.85562.21580.40648.5514-2.34456.0419-0.07430.0033-1.2727-0.045-0.1444-0.27980.65521.22340.21870.34680.12160.03681.4438-0.06630.794812.13337.0327.852
137.3796-1.11212.52556.9673-5.25928.24570.4334-0.4179-0.99490.02850.0267-0.18640.86520.1517-0.46020.19090.0179-0.14120.2888-0.10550.288-27.18637.48716.277
149.31783.94361.32517.4408-0.38983.8745-0.0074-0.3153-0.6768-0.53420.17490.03170.49910.6975-0.16750.41350.1906-0.16230.8886-0.03190.2448-2.87637.61135.254
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 DIFFRACTION4D3 - 113
6X-RAY DIFFRACTION5D114 - 200
7X-RAY DIFFRACTION6E2 - 113
8X-RAY DIFFRACTION7E114 - 243
9X-RAY DIFFRACTION8F1 - 180
10X-RAY DIFFRACTION8H1 - 9
11X-RAY DIFFRACTION9F181 - 276
12X-RAY DIFFRACTION10G0 - 99
13X-RAY DIFFRACTION11I3 - 113
14X-RAY DIFFRACTION12I114 - 200
15X-RAY DIFFRACTION13J2 - 113
16X-RAY DIFFRACTION14J114 - 243

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