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- PDB-6j2h: Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:... -

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Basic information

Entry
Database: PDB / ID: 6j2h
TitleCrystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 mutant (Met52 Asp53 Leu54 deleted) in complex with Hendra virus-derived peptide HeV1
Components
  • Beta-2-microglobulin
  • HeV1
  • Ptal-N*01:01 (Met52 Asp53 Leu54 deleted)
KeywordsIMMUNE SYSTEM
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 / 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 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 / disordered domain specific binding / 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 / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / 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 / protein-containing complex / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / 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 / Phosphoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
Homo sapiens (human)
Hendra virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Assembly

Deposited unit
A: Ptal-N*01:01 (Met52 Asp53 Leu54 deleted)
B: Beta-2-microglobulin
C: HeV1
D: Ptal-N*01:01 (Met52 Asp53 Leu54 deleted)
E: Beta-2-microglobulin
F: HeV1


Theoretical massNumber of molelcules
Total (without water)89,3146
Polymers89,3146
Non-polymers00
Water5,585310
1
A: Ptal-N*01:01 (Met52 Asp53 Leu54 deleted)
B: Beta-2-microglobulin
C: HeV1


Theoretical massNumber of molelcules
Total (without water)44,6573
Polymers44,6573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-19 kcal/mol
Surface area18780 Å2
MethodPISA
2
D: Ptal-N*01:01 (Met52 Asp53 Leu54 deleted)
E: Beta-2-microglobulin
F: HeV1


Theoretical massNumber of molelcules
Total (without water)44,6573
Polymers44,6573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-19 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.651, 102.504, 178.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

21D-397-

HOH

31D-398-

HOH

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Components

#1: Protein Ptal-N*01:01 (Met52 Asp53 Leu54 deleted)


Mass: 31759.811 Da / Num. of mol.: 2 / Mutation: 52-54 deletion
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: 11973.386 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 HeV1


Mass: 924.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Hendra virus / References: UniProt: O55778*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium formate, 20%(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: 0.97918 Å
DetectorType: SDMS / Detector: IMAGE PLATE / Date: Dec 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 40730 / % possible obs: 98 % / Redundancy: 11.8 % / Net I/σ(I): 3.807
Reflection shellResolution: 2.3→2.38 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: 2.3→50 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.1
RfactorNum. reflection% reflection
Rfree0.2278 2039 5.03 %
Rwork0.1966 --
obs0.1982 40524 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6298 0 0 310 6608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076488
X-RAY DIFFRACTIONf_angle_d0.7568826
X-RAY DIFFRACTIONf_dihedral_angle_d25.4782390
X-RAY DIFFRACTIONf_chiral_restr0.052884
X-RAY DIFFRACTIONf_plane_restr0.0041174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34870.26671280.23522318X-RAY DIFFRACTION89
2.3487-2.40750.31211360.22532456X-RAY DIFFRACTION94
2.38-5.6540.19081510.1812752X-RAY DIFFRACTION99
2.4075-2.47250.27421340.22922481X-RAY DIFFRACTION95
2.4725-2.54530.25911260.25232499X-RAY DIFFRACTION96
2.5453-2.62740.29171250.23422522X-RAY DIFFRACTION97
2.6274-2.72130.3111160.23962552X-RAY DIFFRACTION97
2.7213-2.83020.26391270.22632583X-RAY DIFFRACTION98
2.8302-2.9590.26321560.22472550X-RAY DIFFRACTION98
2.959-3.11490.25951460.22122610X-RAY DIFFRACTION100
3.1149-3.30990.25961240.21082631X-RAY DIFFRACTION100
3.3099-3.56530.23941120.19572653X-RAY DIFFRACTION100
3.5653-3.92360.19971570.18272600X-RAY DIFFRACTION100
3.9236-4.49050.17491500.15642616X-RAY DIFFRACTION98
4.4905-5.6540.18571510.15642662X-RAY DIFFRACTION100

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