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- PDB-8zv9: Complex structure of HLA2402 with recognizing SARS-CoV-2 Y453F ep... -

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Basic information

Entry
Database: PDB / ID: 8zv9
TitleComplex structure of HLA2402 with recognizing SARS-CoV-2 Y453F epitope NYNYLFRLF
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Spike protein S1
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / MHC / Complex / epitope
Function / homology
Function and homology information


antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / : / : / 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 ...antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / : / : / 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 / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / amyloid fibril formation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / 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 / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / fusion of virus membrane with host plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / 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
Similarity search - Function
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. ...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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / 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
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 / Resolution: 2.6 Å
AuthorsDeng, S.S. / Jin, T.C. / Xu, Z.H. / Wang, M.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82272301 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants.
Authors: Deng, S. / Xu, Z. / Wang, M. / Hu, J. / Liu, Z. / Zhu, F. / Zheng, P. / Kombe Kombe, A.J. / Zhang, H. / Wu, S. / Jin, T.
History
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
SupersessionAug 28, 2024ID: 8IF1
Revision 1.1Aug 28, 2024Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Nov 13, 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

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
D: MHC class I antigen
E: Beta-2-microglobulin
F: Spike protein S1
G: MHC class I antigen
H: Beta-2-microglobulin
I: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,92311
Polymers135,7999
Non-polymers1242
Water6,810378
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3905
Polymers45,2663
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-14 kcal/mol
Surface area18870 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)45,2663
Polymers45,2663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-20 kcal/mol
Surface area18870 Å2
MethodPISA
3
G: MHC class I antigen
H: Beta-2-microglobulin
I: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)45,2663
Polymers45,2663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-20 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.060, 167.490, 168.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen


Mass: 32136.467 Da / Num. of mol.: 3
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: A0A7T3RIT5
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Spike protein S1


Mass: 1250.425 Da / Num. of mol.: 3 / Mutation: Y453F / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG8000, 0.1 M HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.6→45.33 Å / Num. obs: 42070 / % possible obs: 99.9 % / Redundancy: 14.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.111 / Net I/σ(I): 18.43
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.6-2.671.18130200.8451.231
2.67-2.740.96729890.89611
2.74-2.820.829130.9280.8311
2.82-2.910.64328340.9490.6691
2.91-30.46627310.9740.4851
3-3.110.38726710.9840.4041
3.11-3.220.29225500.9870.3041
3.22-3.360.2125000.9950.2191
3.36-3.50.15723530.9970.1631
3.5-3.680.1222780.9980.1251
3.68-3.870.09921800.9980.1031
3.87-4.110.0820480.9990.0841
4.11-4.390.06619590.9990.0691
4.39-4.750.05918350.9990.0611
4.75-5.20.05616710.9990.0591
5.2-5.810.05415340.9990.0571
5.81-6.710.05213720.9990.0551
6.71-8.220.04211600.9990.0441
8.22-11.620.0369310.9990.0381

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGD

5hgd


Resolution: 2.6→45.33 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 2034 4.84 %
Rwork0.2442 --
obs0.2464 42031 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9300 0 8 383 9691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d19.0563541
X-RAY DIFFRACTIONf_chiral_restr0.0541319
X-RAY DIFFRACTIONf_plane_restr0.011716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.42851600.39842562X-RAY DIFFRACTION99
2.66-2.730.41181130.35352632X-RAY DIFFRACTION100
2.73-2.80.3811650.34642606X-RAY DIFFRACTION100
2.8-2.880.39281190.31142636X-RAY DIFFRACTION100
2.88-2.980.33261480.30342633X-RAY DIFFRACTION100
2.98-3.080.38271240.30922624X-RAY DIFFRACTION100
3.08-3.20.35511410.32212628X-RAY DIFFRACTION100
3.21-3.350.30921430.29462674X-RAY DIFFRACTION100
3.35-3.530.34361240.26692633X-RAY DIFFRACTION100
3.53-3.750.27561280.24892656X-RAY DIFFRACTION100
3.75-4.040.28741170.23422702X-RAY DIFFRACTION100
4.04-4.440.26411310.2082682X-RAY DIFFRACTION100
4.44-5.090.24251500.19442701X-RAY DIFFRACTION100
5.09-6.40.25051320.21632746X-RAY DIFFRACTION100
6.4-45.330.24731390.20352882X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.6713 Å / Origin y: -65.4645 Å / Origin z: -24.7766 Å
111213212223313233
T0.2468 Å2-0.0517 Å2-0.0338 Å2-0.3842 Å20.0014 Å2--0.3733 Å2
L0.0692 °20.111 °2-0.1415 °2-0.4212 °2-0.002 °2--0.5694 °2
S-0.0033 Å °0.1035 Å °-0.0433 Å °0.0497 Å °0.1307 Å °0.0394 Å °0.1108 Å °-0.1131 Å °0.0006 Å °
Refinement TLS groupSelection details: all

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