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- PDB-6j2d: Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:... -

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Basic information

Entry
Database: PDB / ID: 6j2d
TitleCrystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV1
Components
  • HeV1
  • Ptal-N*01:01
  • beta-2 microglobulin
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / disordered domain specific binding / amyloid fibril formation ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / disordered domain specific binding / amyloid fibril formation / immune response / signaling receptor binding / external side of plasma membrane / protein-containing complex / extracellular space / extracellular region
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 / Nucleic acid-binding, OB-fold / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / Phosphoprotein
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
Hendra virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.313 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 20, 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: HeV1


Theoretical massNumber of molelcules
Total (without water)44,5183
Polymers44,5183
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-14 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.458, 86.272, 134.728
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.: 1
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: 11474.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: PAL_GLEAN10023531 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: L5K3Y9
#3: Protein/peptide HeV1


Mass: 924.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hendra virus / References: UniProt: O55778*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaCl, 0.1 M Bis-Tris (pH 5.5), and 25% (w/v) polyethylene glycol 3,350 at a concentration of 7.5 mg/mL.

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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: SDMS / Detector: IMAGE PLATE / Date: Jan 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18451 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 2.21
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.313→42.828 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 30.9
RfactorNum. reflection% reflection
Rfree0.2824 822 4.93 %
Rwork0.2208 --
obs0.2238 16690 88.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.313→42.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 84 3222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083235
X-RAY DIFFRACTIONf_angle_d1.0554406
X-RAY DIFFRACTIONf_dihedral_angle_d25.151193
X-RAY DIFFRACTIONf_chiral_restr0.057441
X-RAY DIFFRACTIONf_plane_restr0.007588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3131-2.4580.3574920.28121730X-RAY DIFFRACTION59
2.458-2.64780.32961240.27682380X-RAY DIFFRACTION81
2.6478-2.91420.3451380.26442746X-RAY DIFFRACTION93
2.9142-3.33580.33751530.25092957X-RAY DIFFRACTION100
3.3358-4.20210.2551660.19882961X-RAY DIFFRACTION100
4.2021-42.8350.23431490.18873094X-RAY DIFFRACTION99

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