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- PDB-4iho: Crystal structure of H-2Db Y159F in complex with chimeric gp100 -

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Basic information

Entry
Database: PDB / ID: 4iho
TitleCrystal structure of H-2Db Y159F in complex with chimeric gp100
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • NONAMERIC PEPTIDE CHIMERIC GP100
KeywordsIMMUNE SYSTEM / MHC / H-2DB / GLYCOPROTEIN / IMMUNE RESPONSE / MHC I / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / DISEASE MUTATION / MELANOMA / TUMOR ASSOCIATED ANTIGEN / ALTERED PEPTIDE LIGAND / T CELL RECEPTOR
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 endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation ...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 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / 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 / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
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 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsUchtenhagen, H. / Stahl, E. / Achour, A.
CitationJournal: Eur.J.Immunol. / Year: 2013
Title: Proline substitution independently enhances H-2D(b) complex stabilization and TCR recognition of melanoma-associated peptides
Authors: Uchtenhagen, H. / Abualrous, E.T. / Stahl, E. / Allerbring, E.B. / Sluijter, M. / Zacharias, M. / Sandalova, T. / van Hall, T. / Springer, S. / Nygren, P.A. / Achour, A.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: NONAMERIC PEPTIDE CHIMERIC GP100
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: NONAMERIC PEPTIDE CHIMERIC GP100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,15510
Polymers89,7826
Non-polymers3724
Water1,910106
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: NONAMERIC PEPTIDE CHIMERIC GP100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2647
Polymers44,8913
Non-polymers3724
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-18 kcal/mol
Surface area19910 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: NONAMERIC PEPTIDE CHIMERIC GP100


Theoretical massNumber of molelcules
Total (without water)44,8913
Polymers44,8913
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-12 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.661, 146.011, 187.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.355836, 0.291955, 0.887774), (-0.178342, -0.953706, 0.242155), (0.917374, -0.07216, 0.391431)-61.10905, -91.97601, 21.08749

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Components

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Protein , 2 types, 4 molecules ADBE

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


Mass: 32071.703 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-300 / Mutation: Y159F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide NONAMERIC PEPTIDE CHIMERIC GP100


Mass: 1115.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide

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Non-polymers , 3 types, 110 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsASP 85 IS NATURAL VARIANT, ALLELE A.

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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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6-1.8M NH4SO4, 100mM Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2010
RadiationMonochromator: channel-cut double-crystal silicon [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.8→42.1 Å / Num. all: 30269 / Num. obs: 30269 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.85 Å / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CH1

3ch1


Resolution: 2.8→42.1 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.855 / SU B: 19.931 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R: 0.956 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30541 1537 5.1 %RANDOM
Rwork0.24935 ---
all0.25222 28732 --
obs0.25222 28732 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.554 Å2
Baniso -1Baniso -2Baniso -3
1--4.77 Å2-0 Å20 Å2
2--10.08 Å20 Å2
3----5.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6251 0 23 106 6380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196377
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.948656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63723.415328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.492151019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4061550
X-RAY DIFFRACTIONr_chiral_restr0.0960.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215030
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 109 -
Rwork0.388 2132 -
obs--98.68 %

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