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- PDB-8jhw: The first crystal structure of a H-2Kb-restricted decapeptide fro... -

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Basic information

Entry
Database: PDB / ID: 8jhw
TitleThe first crystal structure of a H-2Kb-restricted decapeptide from Cryptosporidium parvum
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL
KeywordsIMMUNE SYSTEM / Cryptosporidium parvum / MHC I / T cell epitope / cell-mediated immunity
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Cryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsFan, S. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31702232 China
CitationJournal: To Be Published
Title: The first crystal structure of a H-2Kb-restricted decapeptide from Cryptosporidium parvum
Authors: Fan, S. / Wang, Y.
History
DepositionMay 25, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0067
Polymers44,7573
Non-polymers2484
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, none
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-8 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.940, 86.940, 293.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2K(B)


Mass: 31777.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11791.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL


Mass: 1188.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Production host: Synthecium (invertebrata)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.58 Å3/Da / Density % sol: 65.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20%(w/v) Polyethylene glycol 3350; 0.2M Lithium acetate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.12→46.38 Å / Num. obs: 12577 / % possible obs: 100 % / Redundancy: 15.93 % / CC1/2: 0.999 / Net I/σ(I): 15
Reflection shellResolution: 3.12→3.34 Å / Num. unique obs: 2207 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→46.359 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.892 / SU B: 0.8 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.401 / ESU R Free: 0.472
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2879 644 5.15 %
Rwork0.2447 11860 -
all0.247 --
obs-12504 99.936 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.351 Å20.175 Å20 Å2
2--0.351 Å2-0 Å2
3----1.138 Å2
Refinement stepCycle: LAST / Resolution: 3.12→46.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 16 2 3159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.2010.424420.364852X-RAY DIFFRACTION100
3.201-3.2890.45400.361821X-RAY DIFFRACTION100
3.289-3.3840.317290.317818X-RAY DIFFRACTION100
3.384-3.4880.321460.298792X-RAY DIFFRACTION100
3.488-3.6020.294490.266747X-RAY DIFFRACTION100
3.602-3.7280.24350.24733X-RAY DIFFRACTION100
3.728-3.8680.303470.222711X-RAY DIFFRACTION100
3.868-4.0260.333370.217695X-RAY DIFFRACTION100
4.026-4.2040.251430.233656X-RAY DIFFRACTION100
4.204-4.4090.219390.183638X-RAY DIFFRACTION100
4.409-4.6460.292340.169600X-RAY DIFFRACTION99.8426
4.646-4.9270.194300.194588X-RAY DIFFRACTION100
4.927-5.2660.303320.2543X-RAY DIFFRACTION100
5.266-5.6850.313240.236527X-RAY DIFFRACTION100
5.685-6.2240.407250.263494X-RAY DIFFRACTION100
6.224-6.9530.345230.269431X-RAY DIFFRACTION100
6.953-7.0170.233210.233401X-RAY DIFFRACTION100
7.017-8.0210.290.232345X-RAY DIFFRACTION100
8.021-8.7910.29140.232345X-RAY DIFFRACTION100
8.791-9.7310.417100.416183X-RAY DIFFRACTION96.9849

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