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- PDB-6j2g: Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:... -

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Basic information

Entry
Database: PDB / ID: 6j2g
TitleCrystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Ebola virus-derived peptide EBOV-NP2
Components
  • Beta-2-microglobulin
  • EBOV-NP2
  • Ptal-N*01:01
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 / 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 ...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 / 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 / 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 / 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 / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / ribonucleoprotein complex / signaling receptor binding / 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 / 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: 2.41 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 1.3Oct 30, 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: Ptal-N*01:01
B: Beta-2-microglobulin
C: EBOV-NP2
D: Ptal-N*01:01
E: Beta-2-microglobulin
F: EBOV-NP2


Theoretical massNumber of molelcules
Total (without water)90,2776
Polymers90,2776
Non-polymers00
Water3,081171
1
A: Ptal-N*01:01
B: Beta-2-microglobulin
C: EBOV-NP2


Theoretical massNumber of molelcules
Total (without water)45,1393
Polymers45,1393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-20 kcal/mol
Surface area19190 Å2
MethodPISA
2
D: Ptal-N*01:01
E: Beta-2-microglobulin
F: EBOV-NP2


Theoretical massNumber of molelcules
Total (without water)45,1393
Polymers45,1393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-17 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.397, 103.307, 180.057
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 Ptal-N*01:01


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-NP2


Mass: 1271.330 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.: 171 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M Tris pH 8.0, 16% w/v polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: SDMS / Detector: IMAGE PLATE / Date: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 36391 / % possible obs: 99.2 % / Redundancy: 9.7 % / Net I/σ(I): 1.98
Reflection shellResolution: 2.4→2.49 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→50 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.2333 1720 4.96 %
Rwork0.1971 --
obs0.1989 34701 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.41→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6370 0 0 171 6541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046576
X-RAY DIFFRACTIONf_angle_d0.7498942
X-RAY DIFFRACTIONf_dihedral_angle_d23.6462430
X-RAY DIFFRACTIONf_chiral_restr0.047896
X-RAY DIFFRACTIONf_plane_restr0.0041192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4105-2.48140.3309940.24921796X-RAY DIFFRACTION63
2.4814-2.56150.33661090.26342351X-RAY DIFFRACTION82
2.5615-2.6530.35871330.2552685X-RAY DIFFRACTION93
2.653-2.75920.33221660.24662788X-RAY DIFFRACTION97
2.7592-2.88470.28321430.24312857X-RAY DIFFRACTION98
2.8847-3.03680.29991390.24382907X-RAY DIFFRACTION100
3.0368-3.22690.29711700.23232837X-RAY DIFFRACTION99
3.2269-3.4760.27011370.20872913X-RAY DIFFRACTION99
3.476-3.82550.21931520.18982917X-RAY DIFFRACTION100
3.8255-4.37840.19251700.16362897X-RAY DIFFRACTION100
4.3784-5.51380.17471550.14342962X-RAY DIFFRACTION100
5.5138-38.73510.1581520.17713071X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -36.8383 Å / Origin y: -12.0515 Å / Origin z: -22.4434 Å
111213212223313233
T0.1795 Å20.04 Å20.023 Å2-0.1528 Å2-0.0103 Å2--0.1408 Å2
L0.3437 °20.0972 °2-0.0036 °2-0.1858 °2-0.0113 °2--0.1565 °2
S0.0104 Å °0.0187 Å °0.012 Å °-0.0255 Å °-0.0055 Å °-0.0007 Å °0.0233 Å °0.0123 Å °-0 Å °
Refinement TLS groupSelection details: all

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