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- PDB-6j2e: Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:... -

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Basic information

Entry
Database: PDB / ID: 6j2e
TitleCrystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Ebola virus-derived peptide EBOV-NP1
Components
  • Beta-2-microglobulin
  • EBOV-NP1
  • MHC class I antigen
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / 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 ...viral RNA genome packaging / helical viral capsid / 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 / 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 / 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 / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / ribonucleoprotein complex / external side of plasma membrane / Golgi membrane / signaling receptor binding / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein / 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 / : ...Ebola nucleoprotein / Ebola nucleoprotein / 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
MHC class I antigen / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
Homo sapiens (human)
Ebola virus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLu, D. / Liu, K.F. / Yue, C. / Lu, Q. / Cheng, H. / Chai, Y. / Qi, J.X. / Gao, G.F. / Liu, W.J.
CitationJournal: Plos Biol. / Year: 2019
Title: Peptide presentation by bat MHC class I provides new insight into the antiviral immunity of bats.
Authors: Lu, D. / Liu, K. / Zhang, D. / Yue, C. / Lu, Q. / Cheng, H. / Wang, L. / Chai, Y. / Qi, J. / Wang, L.F. / Gao, G.F. / Liu, W.J.
History
DepositionJan 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Structure summary / Category: entity / struct / Item: _entity.pdbx_description / _struct.title
Revision 1.2Dec 4, 2019Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: EBOV-NP1
D: MHC class I antigen
E: Beta-2-microglobulin
F: EBOV-NP1


Theoretical massNumber of molelcules
Total (without water)90,0516
Polymers90,0516
Non-polymers00
Water6,666370
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: EBOV-NP1


Theoretical massNumber of molelcules
Total (without water)45,0263
Polymers45,0263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-16 kcal/mol
Surface area18680 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: EBOV-NP1


Theoretical massNumber of molelcules
Total (without water)45,0263
Polymers45,0263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-16 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.740, 102.596, 177.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MHC class I antigen


Mass: 32119.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: Ptal-N / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A125R585
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P61769
#3: Protein/peptide EBOV-NP1


Mass: 1158.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Ebola virus sp. / References: UniProt: O72142*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M succinic acid pH 7.0, 15%(w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: SDMS / Detector: IMAGE PLATE / Date: Aug 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 54243 / % possible obs: 100 % / Redundancy: 9.9 % / Net I/σ(I): 2.365
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.284 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 26.75
RfactorNum. reflection% reflection
Rfree0.2572 2702 5.1 %
Rwork0.2057 --
obs0.2084 52961 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6356 0 0 370 6726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086542
X-RAY DIFFRACTIONf_angle_d0.9098894
X-RAY DIFFRACTIONf_dihedral_angle_d8.9033844
X-RAY DIFFRACTIONf_chiral_restr0.056892
X-RAY DIFFRACTIONf_plane_restr0.0051184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0946-2.13270.3183990.25761770X-RAY DIFFRACTION66
2.1327-2.17370.32591140.25422382X-RAY DIFFRACTION89
2.1737-2.21810.30611480.24072594X-RAY DIFFRACTION98
2.2181-2.26630.31051640.23512660X-RAY DIFFRACTION100
2.2663-2.3190.30741300.23892737X-RAY DIFFRACTION100
2.319-2.3770.29251580.23292645X-RAY DIFFRACTION100
2.377-2.44130.32411340.23092693X-RAY DIFFRACTION100
2.4413-2.51310.26731570.23112693X-RAY DIFFRACTION100
2.5131-2.59420.26051420.22642694X-RAY DIFFRACTION100
2.5942-2.68690.34821480.23312717X-RAY DIFFRACTION100
2.6869-2.79450.26451240.22532721X-RAY DIFFRACTION100
2.7945-2.92170.33911350.23522711X-RAY DIFFRACTION100
2.9217-3.07570.28481500.22112693X-RAY DIFFRACTION100
3.0757-3.26840.24121490.21442737X-RAY DIFFRACTION100
3.2684-3.52060.25321430.19552712X-RAY DIFFRACTION100
3.5206-3.87480.21831510.18372720X-RAY DIFFRACTION100
3.8748-4.43520.20961570.16872742X-RAY DIFFRACTION100
4.4352-5.58660.20861540.1682765X-RAY DIFFRACTION100
5.5866-49.29750.22541450.18492873X-RAY DIFFRACTION99

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