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

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Basic information

Entry
Database: PDB / ID: 8jhv
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 / cellular defense response ...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 / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / 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: 3.47 Å
AuthorsFan, S. / Wang, Y. / Zhao, J.
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
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL


Theoretical massNumber of molelcules
Total (without water)89,5156
Polymers89,5156
Non-polymers00
Water00
1
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


Theoretical massNumber of molelcules
Total (without water)44,7573
Polymers44,7573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-15 kcal/mol
Surface area20090 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL


Theoretical massNumber of molelcules
Total (without water)44,7573
Polymers44,7573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-15 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.380, 89.380, 296.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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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.: 2
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.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Production host: Synthecium (invertebrata)
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: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal growTemperature: 291 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: 3.47→47.16 Å / Num. obs: 18018 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 11.3
Reflection shellResolution: 3.47→3.8 Å / Num. unique obs: 4242 / CC1/2: 0.875

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.47→47.105 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.854 / SU B: 1.7 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.529 / ESU R Free: 0.659
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.29678 894 4.975 %
Rwork0.23039 17075 -
all0.25 --
obs-17969 99.889 %
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: 42.986 Å2
Baniso -1Baniso -2Baniso -3
1-0.135 Å20.067 Å2-0 Å2
2--0.135 Å20 Å2
3----0.438 Å2
Refinement stepCycle: LAST / Resolution: 3.47→47.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 0 0 6282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.47-3.560.32660.3141249X-RAY DIFFRACTION99.3953
3.56-3.6570.329410.3261220X-RAY DIFFRACTION100
3.657-3.7630.417550.3431203X-RAY DIFFRACTION100
3.763-3.8790.263550.251174X-RAY DIFFRACTION100
3.879-4.0060.241650.2021072X-RAY DIFFRACTION99.9121
4.006-4.1460.211580.1891090X-RAY DIFFRACTION99.8261
4.146-4.3020.205650.2041039X-RAY DIFFRACTION100
4.302-4.4780.214460.2121013X-RAY DIFFRACTION100
4.478-4.6770.215550.201961X-RAY DIFFRACTION100
4.677-4.9040.218640.213899X-RAY DIFFRACTION100
4.904-5.1690.31500.23879X-RAY DIFFRACTION100
5.169-5.4810.419480.254822X-RAY DIFFRACTION100
5.481-5.8590.503280.292798X-RAY DIFFRACTION100
5.859-6.3260.432350.298754X-RAY DIFFRACTION100
6.326-6.9270.348520.258661X-RAY DIFFRACTION100
6.927-7.740.32190.246636X-RAY DIFFRACTION100
7.74-7.9280.315320.21553X-RAY DIFFRACTION100
7.928-8.9280.238220.198466X-RAY DIFFRACTION100
7.991-9.8860.365180.221379X-RAY DIFFRACTION100
8-100.48200.478207X-RAY DIFFRACTION96.1864

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