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- PDB-3p9l: Crystal Structure of H2-Kb in complex with the chicken ovalbumin ... -

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Basic information

Entry
Database: PDB / ID: 3p9l
TitleCrystal Structure of H2-Kb in complex with the chicken ovalbumin epitope OVA
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Ovalbumin epitope, SIINFEKL
KeywordsIMMUNE SYSTEM / H2Kb / OVA / APL / altered peptide ligands / ovalbumin / TCR / T cell
Function / homology
Function and homology information


intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / embryo development ending in birth or egg hatching / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / response to steroid hormone ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / embryo development ending in birth or egg hatching / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / response to steroid hormone / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to corticosterone / 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 / phagocytic vesicle / monoatomic ion transport / Neutrophil degranulation / response to progesterone / early endosome lumen / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading 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 / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / response to estrogen / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protease binding / protein homotetramerization / vesicle / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytosol
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / MHC class I, alpha chain, C-terminal ...Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ovalbumin / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWesselingh, R. / Gras, S. / Guillonneau, C. / Turner, S.J. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2011
Title: Affinity thresholds for naive CD8+ CTL activation by peptides and engineered influenza A viruses
Authors: Denton, A.E. / Wesselingh, R. / Gras, S. / Guillonneau, C. / Olson, M.R. / Mintern, J.D. / Zeng, W. / Jackson, D.C. / Rossjohn, J. / Hodgkin, P.D. / Doherty, P.C. / Turner, S.J.
History
DepositionOct 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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: Ovalbumin epitope, SIINFEKL
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: Ovalbumin epitope, SIINFEKL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5959
Polymers89,4756
Non-polymers1203
Water16,718928
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
F: Ovalbumin epitope, SIINFEKL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7774
Polymers44,7373
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-18 kcal/mol
Surface area19880 Å2
MethodPISA
2
C: Ovalbumin epitope, SIINFEKL
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8175
Polymers44,7373
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-17 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.990, 90.410, 89.740
Angle α, β, γ (deg.)90.000, 111.710, 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: 32068.777 Da / Num. of mol.: 2 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide Ovalbumin epitope, SIINFEKL / Allergen Gal d II / Egg albumin / Plakalbumin


Mass: 964.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P01012
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M calcium acetate, 15% PEG 8K, 0.1M Na-cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 65977 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.362 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.10.30.2535.736459913388710.29197.1
2.1-2.20.2540.201730287753073340.23197.4
2.2-2.30.2050.1619.624015630059410.18594.3
2.3-2.40.1420.11811.121379525051570.13698.2
2.4-2.50.1020.08913.718400450444370.10398.5
2.5-2.60.0840.07615.715570379837530.08798.8
2.6-2.70.0680.06517.913294323732010.07598.9
2.7-2.80.0590.05819.511704284928170.06698.9
2.8-2.90.0460.04722.710167246224430.05599.2
2.9-30.040.04325.18719211320980.0599.3
3-40.030.03431.84739611544114380.03999.1
4-60.0180.02640.224865599059700.0399.7
6-100.0170.02439.88343200720030.02799.8
100.0150.02142.819495675140.02590.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
PHENIX1.6.1_357refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vac

1vac


Resolution: 2→31.042 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8151 / SU ML: 0.29 / σ(F): 0.01 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 3084 5.02 %
Rwork0.1861 --
obs0.189 61416 91.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.897 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 96.88 Å2 / Biso mean: 26.2578 Å2 / Biso min: 6.61 Å2
Baniso -1Baniso -2Baniso -3
1--2.2094 Å20 Å2-0.8132 Å2
2--8.0957 Å20 Å2
3----5.8863 Å2
Refinement stepCycle: LAST / Resolution: 2→31.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6301 0 3 928 7232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076674
X-RAY DIFFRACTIONf_angle_d1.0429080
X-RAY DIFFRACTIONf_chiral_restr0.073927
X-RAY DIFFRACTIONf_plane_restr0.0041196
X-RAY DIFFRACTIONf_dihedral_angle_d13.4722518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07150.30312830.22315233551683
2.0715-2.15440.27323020.20315494579686
2.1544-2.25240.32182300.2475163539381
2.2524-2.37110.2652750.19725301557683
2.3711-2.51960.26783270.18415896622393
2.5196-2.71410.22993110.17936078638995
2.7141-2.9870.25713190.19046199651897
2.987-3.41870.24833410.17926276661798
3.4187-4.30540.20243450.15856260660598
4.3054-31.0460.20533510.16026432678399

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