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- PDB-6ilc: CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.2 ANGSTROM -

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Basic information

Entry
Database: PDB / ID: 6ilc
TitleCRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.2 ANGSTROM
Components
  • Beta-2-microglobulin
  • HEV-1
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / IMMUNOLOGY / VIRUS
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 / immune response / signaling receptor binding ...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 / immune response / signaling receptor binding / external side of plasma membrane / extracellular space / extracellular region
Similarity search - Function
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 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
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
Hendra virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQu, Z.H. / Zhang, N.Z. / Xia, C.
CitationJournal: J Immunol. / Year: 2019
Title: Structure and Peptidome of the Bat MHC Class I Molecule Reveal a Novel Mechanism Leading to High-Affinity Peptide Binding.
Authors: Qu, Z. / Li, Z. / Ma, L. / Wei, X. / Zhang, L. / Liang, R. / Meng, G. / Zhang, N. / Xia, C.
History
DepositionOct 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: HEV-1


Theoretical massNumber of molelcules
Total (without water)44,7443
Polymers44,7443
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-16 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.660, 86.930, 135.540
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
11B-146-

HOH

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Components

#1: Protein MHC class I antigen


Mass: 32345.482 Da / Num. of mol.: 1 / Fragment: UNP residues 25-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: Ptal-N / Production host: Escherichia coli (E. coli) / 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 (E. coli) / References: UniProt: L5K3Y9*PLUS
#3: Protein/peptide HEV-1


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


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA NCBI Reference Sequence for Beta-2-microglobulin is XP_006920478.1.

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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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS ph6.5, 25%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 4, 2017
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.93→135.54 Å / Num. obs: 23392 / % possible obs: 99.8 % / Redundancy: 2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 0.248 / Num. unique obs: 2127

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VFN

3vfn


Resolution: 2.2→14.9 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57
RfactorNum. reflection% reflection
Rfree0.23 1110 5.04 %
Rwork0.1844 --
obs0.1867 22020 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 204 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073258
X-RAY DIFFRACTIONf_angle_d0.9084439
X-RAY DIFFRACTIONf_dihedral_angle_d11.4441917
X-RAY DIFFRACTIONf_chiral_restr0.056443
X-RAY DIFFRACTIONf_plane_restr0.006595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.29980.26451530.23542563X-RAY DIFFRACTION100
2.2998-2.42060.26971380.23052593X-RAY DIFFRACTION100
2.4206-2.57150.26111370.2262583X-RAY DIFFRACTION100
2.5715-2.76890.29491260.22992597X-RAY DIFFRACTION100
2.7689-3.04540.26181260.21342620X-RAY DIFFRACTION100
3.0454-3.48110.25261490.18972623X-RAY DIFFRACTION100
3.4811-4.36750.21231310.15242664X-RAY DIFFRACTION100
4.3675-14.90040.18031500.15442655X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.83760.0955-0.4610.8821-0.08963.05270.1086-0.1934-0.07280.1313-0.0382-0.0847-0.14820.4597-0.07510.1879-0.0119-0.00150.23040.00490.25584.368624.917416.3326
21.45150.0760.18882.32810.32961.56910.302-0.12940.49910.02990.0164-0.2429-1.49880.1677-0.08640.9357-0.17770.19230.2687-0.07540.36779.020541.150424.5384
34.56725.8024-1.7597.376-2.19180.8208-0.45740.459-0.341-0.25310.5167-0.00150.395-0.2221-0.10770.2459-0.02080.02190.2398-0.00230.276373.845418.24242.1102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:279)
2X-RAY DIFFRACTION2(chain B and resseq 1:98)
3X-RAY DIFFRACTION3(chain C and resseq 1:8)

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