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- PDB-6ile: CRYSTAL STRUCTURE OF A MUTANT PTAL-N*01:01 FOR 2.9 ANGSTROM, 52M ... -

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Basic information

Entry
Database: PDB / ID: 6ile
TitleCRYSTAL STRUCTURE OF A MUTANT PTAL-N*01:01 FOR 2.9 ANGSTROM, 52M 53D 54L DELETED
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 / external side of plasma membrane ...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 / external side of plasma membrane / signaling receptor binding / 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 / Immunoglobulins / Immunoglobulin-like fold / 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: 2.9 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-1


Theoretical massNumber of molelcules
Total (without water)44,3853
Polymers44,3853
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-17 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.343, 80.198, 129.539
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: 31986.039 Da / Num. of mol.: 1 / Fragment: UNP residues 25-303 / Mutation: 52M, 53D, 54L deleted
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
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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dehydrate pH 5.6 and 30%(w/v) polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.97934 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 3, 2018
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→64.78 Å / Num. obs: 9390 / % possible obs: 99.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.431 / Net I/σ(I): 5.8
Reflection shellResolution: 2.7→2.84 Å / Rmerge(I) obs: 0.845 / Num. unique obs: 1306

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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: 2.9→64.769 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.73
RfactorNum. reflection% reflection
Rfree0.2932 375 4.3 %
Rwork0.2129 --
obs0.2164 8730 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→64.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 0 0 3136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023251
X-RAY DIFFRACTIONf_angle_d0.5214433
X-RAY DIFFRACTIONf_dihedral_angle_d9.8592440
X-RAY DIFFRACTIONf_chiral_restr0.039440
X-RAY DIFFRACTIONf_plane_restr0.004594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.31970.38951170.27682735X-RAY DIFFRACTION99
3.3197-4.18240.27111330.20122767X-RAY DIFFRACTION100
4.1824-64.78560.26031250.18742853X-RAY DIFFRACTION99

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