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- PDB-6ilf: CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.7 ANGSTROM -

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Basic information

Entry
Database: PDB / ID: 6ilf
TitleCRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.7 ANGSTROM
Components
  • Beta-2-microglobulin
  • HEV-2
  • 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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 23, 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-2


Theoretical massNumber of molelcules
Total (without water)44,8683
Polymers44,8683
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-15 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.126, 87.871, 133.992
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 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-2


Mass: 1048.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hendra virus / References: UniProt: O89342*PLUS
Has protein modificationY
Sequence detailsNCBI 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH 6.5, 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: 0.97892 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 13, 2018
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 12065 / % possible obs: 75.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.213 / Net I/σ(I): 2.6
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 0.614 / Num. unique obs: 1349

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Processing

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

3vfn


Resolution: 2.7→28.713 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.48
RfactorNum. reflection% reflection
Rfree0.2925 584 4.96 %
Rwork0.2153 --
obs0.219 11786 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 0 0 3164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033275
X-RAY DIFFRACTIONf_angle_d0.6464465
X-RAY DIFFRACTIONf_dihedral_angle_d10.0132464
X-RAY DIFFRACTIONf_chiral_restr0.044446
X-RAY DIFFRACTIONf_plane_restr0.005596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.97160.36261250.27942634X-RAY DIFFRACTION93
2.9716-3.4010.31981510.22922806X-RAY DIFFRACTION100
3.401-4.28260.29741360.1932851X-RAY DIFFRACTION100
4.2826-28.7150.25721720.20482911X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 82.1999 Å / Origin y: 28.9961 Å / Origin z: 17.776 Å
111213212223313233
T0.1887 Å2-0.0344 Å20.0086 Å2-0.2106 Å2-0.014 Å2--0.1918 Å2
L0.6496 °20.1856 °2-0.4464 °2--0.1383 °2-0.1903 °2--0.7715 °2
S0.0681 Å °-0.0932 Å °-0.1116 Å °-0.0078 Å °-0.016 Å °-0.026 Å °-0.1309 Å °0.18 Å °0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:279 ) OR ( CHAIN C AND RESID 1:9 ) OR ( CHAIN B AND RESID 1:98 )A1 - 279
2X-RAY DIFFRACTION1( CHAIN A AND RESID 1:279 ) OR ( CHAIN C AND RESID 1:9 ) OR ( CHAIN B AND RESID 1:98 )C1 - 9
3X-RAY DIFFRACTION1( CHAIN A AND RESID 1:279 ) OR ( CHAIN C AND RESID 1:9 ) OR ( CHAIN B AND RESID 1:98 )B1 - 98

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