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- PDB-6j2f: Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:... -

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Basic information

Entry
Database: PDB / ID: 6j2f
TitleCrystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV2
Components
  • HeV2
  • 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 / host cell surface / immune response ...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 / host cell surface / immune response / signaling receptor binding / fusion of virus membrane with host plasma membrane / external side of plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular space / extracellular region / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / 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 / : ...Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / 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 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
Hendra virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 23, 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: HeV2
D: Ptal-N*01:01
E: beta-2 microglobulin
F: HeV2


Theoretical massNumber of molelcules
Total (without water)89,2846
Polymers89,2846
Non-polymers00
Water11,169620
1
A: Ptal-N*01:01
B: beta-2 microglobulin
C: HeV2


Theoretical massNumber of molelcules
Total (without water)44,6423
Polymers44,6423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-19 kcal/mol
Surface area18450 Å2
MethodPISA
2
D: Ptal-N*01:01
E: beta-2 microglobulin
F: HeV2


Theoretical massNumber of molelcules
Total (without water)44,6423
Polymers44,6423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-16 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.245, 102.527, 176.312
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-502-

HOH

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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: 11474.836 Da / Num. of mol.: 2
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 HeV2


Mass: 1048.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Hendra virus / References: UniProt: O89342*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.075 M HEPES (pH 7.5), 15% (w/v) polyethylene glycol 10,000, and 25% (v/v) glycerol at a protein concentration of 10 mg/mL. Single crystals of Ptal-N*01:01/ EBOV-NP1 were grown in 0.1 M ...Details: 0.075 M HEPES (pH 7.5), 15% (w/v) polyethylene glycol 10,000, and 25% (v/v) glycerol at a protein concentration of 10 mg/mL. Single crystals of Ptal-N*01:01/ EBOV-NP1 were grown in 0.1 M 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: 0.979 Å
DetectorType: SDMS / Detector: IMAGE PLATE / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 72225 / % possible obs: 100 % / Redundancy: 13.4 % / Net I/σ(I): 3.25
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: 1.9→35.839 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 22.9
RfactorNum. reflection% reflection
Rfree0.2308 3592 5.11 %
Rwork0.2026 --
obs0.2041 70243 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 0 620 6920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016506
X-RAY DIFFRACTIONf_angle_d1.1358866
X-RAY DIFFRACTIONf_dihedral_angle_d23.6072404
X-RAY DIFFRACTIONf_chiral_restr0.074890
X-RAY DIFFRACTIONf_plane_restr0.0081184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8928-1.91770.28491000.25031803X-RAY DIFFRACTION70
1.9177-1.9440.29351130.24442153X-RAY DIFFRACTION81
1.944-1.97180.26111480.23382200X-RAY DIFFRACTION85
1.9718-2.00120.28131370.23642402X-RAY DIFFRACTION92
2.0012-2.03250.26651190.23552496X-RAY DIFFRACTION96
2.0325-2.06580.25851480.23242551X-RAY DIFFRACTION97
2.0658-2.10140.24811240.22192649X-RAY DIFFRACTION100
2.1014-2.13960.24861530.22172581X-RAY DIFFRACTION100
2.1396-2.18080.23791270.22192655X-RAY DIFFRACTION100
2.1808-2.22530.25771540.22372602X-RAY DIFFRACTION100
2.2253-2.27370.24321290.22112635X-RAY DIFFRACTION100
2.2737-2.32650.25681750.21422595X-RAY DIFFRACTION100
2.3265-2.38470.24961490.21662641X-RAY DIFFRACTION100
2.3847-2.44920.2431530.21992610X-RAY DIFFRACTION100
2.4492-2.52120.24611580.22282597X-RAY DIFFRACTION100
2.5212-2.60260.26291430.22152637X-RAY DIFFRACTION100
2.6026-2.69560.27961200.22782668X-RAY DIFFRACTION100
2.6956-2.80350.25961360.22532630X-RAY DIFFRACTION100
2.8035-2.9310.21791360.21052666X-RAY DIFFRACTION100
2.931-3.08540.241340.20732648X-RAY DIFFRACTION100
3.0854-3.27860.2011550.19682653X-RAY DIFFRACTION100
3.2786-3.53160.20411270.18842673X-RAY DIFFRACTION100
3.5316-3.88660.22171380.17542671X-RAY DIFFRACTION100
3.8866-4.44810.19471260.16542716X-RAY DIFFRACTION100
4.4481-5.60070.1871340.16122724X-RAY DIFFRACTION100
5.6007-35.8450.20251560.19152795X-RAY DIFFRACTION99

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