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- PDB-7wcy: Crystal Structure of H-2Kb with Cryptosporidium parvum gp40/15 epitope -

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Basic information

Entry
Database: PDB / ID: 7wcy
TitleCrystal Structure of H-2Kb with Cryptosporidium parvum gp40/15 epitope
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • SER-VAL-PHE-ALA-ILE-PHE-ALA-ALA-LEU
KeywordsIMMUNE SYSTEM / MHC I / peptide epitope / T cell immunity
Function / homology
Function and homology information


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / inner ear development / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation
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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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
NICKEL (II) ION / 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: 2.36 Å
AuthorsWang, Y.L. / Gao, M.H. / Zhang, L.X. / Fan, S.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31702232, 32172882 China
CitationJournal: Mbio / Year: 2023
Title: Structural Analyses of a Dominant Cryptosporidium parvum Epitope Presented by H-2K b Offer New Options To Combat Cryptosporidiosis.
Authors: Wang, Y. / Gao, M. / Li, X. / Zhu, W. / Zhao, M. / Li, J. / Liu, X. / Cao, L. / Li, S. / Zhang, S. / Zhang, L. / Fan, S.
History
DepositionDec 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: SER-VAL-PHE-ALA-ILE-PHE-ALA-ALA-LEU
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: SER-VAL-PHE-ALA-ILE-PHE-ALA-ALA-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,22114
Polymers88,7526
Non-polymers4708
Water1,08160
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: SER-VAL-PHE-ALA-ILE-PHE-ALA-ALA-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5526
Polymers44,3763
Non-polymers1763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-42 kcal/mol
Surface area19460 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: SER-VAL-PHE-ALA-ILE-PHE-ALA-ALA-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6698
Polymers44,3763
Non-polymers2935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-41 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.920, 84.770, 95.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Beta-2 microglobulin


Mass: 11660.350 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 SER-VAL-PHE-ALA-ILE-PHE-ALA-ALA-LEU


Mass: 938.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Cryptosporidium parvum (eukaryote)
#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12%(w/v) Polyethylene glycol 3350, 0.005M Cobalt(II) chloride hexahydrate; 0.005M Nickel(II) chloride hexahydrate; 0.005M Cadmium chloride hydrate; 0.1M HEPES (PH7.5)

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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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / 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: 2.36→49.47 Å / Num. obs: 40181 / % possible obs: 97.98 % / Redundancy: 2.5 % / CC1/2: 0.999 / Net I/σ(I): 15.259
Reflection shellResolution: 2.36→2.45 Å / Num. unique obs: 4091 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vac

1vac


Resolution: 2.36→49.47 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.222 / ESU R Free: 0.254
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2584 2079 5.215 %
Rwork0.2258 37789 -
all0.228 --
obs-39868 99.715 %
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: 68.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.141 Å20 Å2-0.071 Å2
2---0.19 Å2-0 Å2
3---0.049 Å2
Refinement stepCycle: LAST / Resolution: 2.36→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 8 60 6316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.4210.3481320.282791X-RAY DIFFRACTION99.659
2.421-2.4870.3181470.2642681X-RAY DIFFRACTION99.6476
2.487-2.560.3281420.2582656X-RAY DIFFRACTION99.8572
2.56-2.6380.3191410.2432573X-RAY DIFFRACTION99.9632
2.638-2.7250.2911550.2062463X-RAY DIFFRACTION100
2.725-2.820.3331230.2352439X-RAY DIFFRACTION99.922
2.82-2.9270.271430.2232271X-RAY DIFFRACTION99.7521
2.927-3.0460.2851300.2592251X-RAY DIFFRACTION99.7486
3.046-3.1810.331210.2662129X-RAY DIFFRACTION99.7783
3.181-3.3360.3351100.2742065X-RAY DIFFRACTION100
3.336-3.5170.2621190.2451948X-RAY DIFFRACTION99.8551
3.517-3.730.267850.2391850X-RAY DIFFRACTION99.8452
3.73-3.9870.2371040.2241719X-RAY DIFFRACTION99.2919
3.987-4.3050.228920.2091641X-RAY DIFFRACTION99.7123
4.305-4.7150.214950.1961492X-RAY DIFFRACTION99.7486
4.715-5.270.223670.1691344X-RAY DIFFRACTION99.7173
5.27-6.0830.267470.2141233X-RAY DIFFRACTION99.1479
6.083-7.4420.229641009X-RAY DIFFRACTION99.7212
7.442-100.311250.189803X-RAY DIFFRACTION99.1617

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