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- PDB-3i6g: Newly identified epitope Mn2 from SARS-CoV M protein complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3i6g
TitleNewly identified epitope Mn2 from SARS-CoV M protein complexed withHLA-A*0201
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Membrane protein
KeywordsIMMUNE SYSTEM / HLA-A2 / SARS-CoV / membrane glycoprotein / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Envelope protein / Golgi apparatus / Viral matrix protein / Virion
Function / homology
Function and homology information


Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation ...Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / : / : / 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 / lumenal side of endoplasmic reticulum membrane / 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 / positive regulation of type II interferon production / 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 / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / structural constituent of virion / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response
Similarity search - Function
M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Membrane protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsLiu, J.
CitationJournal: J.INFECT.DIS. / Year: 2010
Title: The membrane protein of severe acute respiratory syndrome coronavirus acts as a dominant immunogen revealed by a clustering region of novel functionally and structurally defined cytotoxic T-lymphocyte epitopes.
Authors: Liu, J. / Sun, Y. / Qi, J. / Chu, F. / Wu, H. / Gao, F. / Li, T. / Yan, J. / Gao, G.F.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Membrane protein
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Membrane protein


Theoretical massNumber of molelcules
Total (without water)89,6986
Polymers89,6986
Non-polymers00
Water10,034557
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Membrane protein


Theoretical massNumber of molelcules
Total (without water)44,8493
Polymers44,8493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-25 kcal/mol
Surface area18870 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Membrane protein


Theoretical massNumber of molelcules
Total (without water)44,8493
Polymers44,8493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-24 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.871, 48.847, 137.242
Angle α, β, γ (deg.)90.00, 110.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


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 / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide Membrane protein / M protein / Membrane glycoprotein / E1 glycoprotein / Matrix glycoprotein / Peptide Mn2


Mass: 1115.344 Da / Num. of mol.: 2 / Fragment: UNP residues 88-96 / Source method: obtained synthetically
Details: Peptide Mn2 derived from membrane glycoprotein of SARS coronavirus TJF was synthesized.
References: UniProt: P59596
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O
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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Ammonium acetate, 0.1M BIS-TRIS, pH6.0, 13-17% Polyethylene glycol 10,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5478 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 10, 2008 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 2.2→27.3 Å / Num. obs: 50983 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 31.682
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 5.051 / Rsym value: 0.319 / % possible all: 100

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Processing

Software
NameClassification
CrystalCleardata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZF1

1zf1


Resolution: 2.201→27.254 Å / SU ML: 0.33 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 2589 5.08 %
Rwork0.205 --
obs0.2071 50983 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.145 Å2 / ksol: 0.356 e/Å3
Refinement stepCycle: LAST / Resolution: 2.201→27.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 0 557 6883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046513
X-RAY DIFFRACTIONf_angle_d0.8018825
X-RAY DIFFRACTIONf_dihedral_angle_d16.9342327
X-RAY DIFFRACTIONf_chiral_restr0.056894
X-RAY DIFFRACTIONf_plane_restr0.0031148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2006-2.24290.27281460.24012610X-RAY DIFFRACTION98
2.2429-2.28860.30651150.24622680X-RAY DIFFRACTION100
2.2886-2.33840.32981550.24522691X-RAY DIFFRACTION100
2.3384-2.39270.30631430.23492671X-RAY DIFFRACTION100
2.3927-2.45250.32811360.22762659X-RAY DIFFRACTION100
2.4525-2.51880.28181450.22922670X-RAY DIFFRACTION100
2.5188-2.59290.30561390.22322683X-RAY DIFFRACTION100
2.5929-2.67650.3071340.21922673X-RAY DIFFRACTION100
2.6765-2.77210.2871700.22812637X-RAY DIFFRACTION100
2.7721-2.88290.25691320.2142730X-RAY DIFFRACTION100
2.8829-3.0140.24781340.22042688X-RAY DIFFRACTION100
3.014-3.17270.24071550.21812648X-RAY DIFFRACTION100
3.1727-3.37110.24871670.20732690X-RAY DIFFRACTION100
3.3711-3.63090.21971440.18712694X-RAY DIFFRACTION100
3.6309-3.99520.18341490.17112698X-RAY DIFFRACTION100
3.9952-4.5710.18811470.15862721X-RAY DIFFRACTION100
4.571-5.75010.21291410.17342732X-RAY DIFFRACTION100
5.7501-27.25610.23871370.21072819X-RAY DIFFRACTION99

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