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- PDB-3p9m: Crystal Structure of H2-Kb in complex with a mutant of the chicke... -

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Basic information

Entry
Database: PDB / ID: 3p9m
TitleCrystal Structure of H2-Kb in complex with a mutant of the chicken ovalbumin epitope OVA-G4
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Ovalbumin epitope, SIIGFEKL
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 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, SIIGFEKL
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: Ovalbumin epitope, SIIGFEKL


Theoretical massNumber of molelcules
Total (without water)89,1666
Polymers89,1666
Non-polymers00
Water16,177898
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
F: Ovalbumin epitope, SIIGFEKL


Theoretical massNumber of molelcules
Total (without water)44,5833
Polymers44,5833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-15 kcal/mol
Surface area19650 Å2
MethodPISA
2
C: Ovalbumin epitope, SIIGFEKL
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)44,5833
Polymers44,5833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-15 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.979, 85.694, 89.290
Angle α, β, γ (deg.)90.000, 111.500, 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: 31971.664 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, SIIGFEKL / Allergen Gal d II / Egg albumin / Plakalbumin


Mass: 907.086 Da / Num. of mol.: 2 / Mutation: N4G / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P01012
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M calcium acetate, 15% PEG 8K, 0.1M Na-malonate, pH 6, 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: Jun 20, 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: 60157 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.539 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.75
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
2-2.10.1710.203728927862578130.23890.6
2.1-2.20.1320.168.325780711166360.18593.3
2.2-2.30.1450.1429.720496596255410.16792.9
2.3-2.40.0970.10911.618199496046880.12694.5
2.4-2.50.0840.09313.615479422039820.10894.4
2.5-30.0610.06218.85028313705130730.07295.4
3-40.030.03133.93975610919105360.03796.5
4-60.0160.0247.421235566955340.02397.6
6-100.0180.02145.66963188918480.02597.8
100.0130.01851.817285445060.02193

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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→41.54 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8376 / SU ML: 0.28 / σ(F): 0.08 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 3031 5.06 %
Rwork0.1797 --
obs0.1829 59862 94.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.991 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 95.02 Å2 / Biso mean: 22.7481 Å2 / Biso min: 4.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.8953 Å20 Å21.6296 Å2
2--5.6281 Å20 Å2
3----3.7328 Å2
Refinement stepCycle: LAST / Resolution: 2→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6278 0 0 898 7176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076542
X-RAY DIFFRACTIONf_angle_d1.0698890
X-RAY DIFFRACTIONf_chiral_restr0.075917
X-RAY DIFFRACTIONf_plane_restr0.0051162
X-RAY DIFFRACTIONf_dihedral_angle_d13.5932440
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 (%)
2-2.07150.2932850.22515368565390
2.0715-2.15440.29133140.215525583992
2.1544-2.25250.30762910.20995532582391
2.2525-2.37120.29943090.19625555586493
2.3712-2.51980.27573030.18175688599195
2.5198-2.71430.25082990.17265713601295
2.7143-2.98730.24043130.17245765607896
2.9873-3.41940.23182890.17065846613596
3.4194-4.30740.20123300.15155837616797
4.3074-41.54860.19172980.15526002630097

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