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- PDB-1juf: Structure of Minor Histocompatibility Antigen peptide, H13b, comp... -

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Basic information

Entry
Database: PDB / ID: 1juf
TitleStructure of Minor Histocompatibility Antigen peptide, H13b, complexed to H2-Db
Components
  • Beta-2-microglobulin
  • H13b peptide
  • H2-Db major histocompatibility antigen
KeywordsIMMUNE SYSTEM / MHC Class-I / H2-Db / H13 / Minor histocompatibility antigens
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / membrane protein proteolysis involved in retrograde protein transport, ER to cytosol / aspartic endopeptidase activity, intramembrane cleaving / signal peptide processing / membrane protein proteolysis / Derlin-1 retrotranslocation complex / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...Regulation of HMOX1 expression and activity / membrane protein proteolysis involved in retrograde protein transport, ER to cytosol / aspartic endopeptidase activity, intramembrane cleaving / signal peptide processing / membrane protein proteolysis / Derlin-1 retrotranslocation complex / 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 / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / cytoplasmic side of endoplasmic reticulum membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / rough endoplasmic reticulum / Neutrophil degranulation / 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 / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / peptidase activity / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / in utero embryonic development / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
Peptidase A22B, signal peptide peptidase / Signal peptide peptidase / Presenilin/signal peptide peptidase / Presenilin, signal peptide peptidase, family / 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 ...Peptidase A22B, signal peptide peptidase / Signal peptide peptidase / Presenilin/signal peptide peptidase / Presenilin, signal peptide peptidase, family / 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 / Minor histocompatibility antigen H13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsOstrov, D.A. / Roden, M.M. / Shi, W. / Palmieri, E. / Christianson, G.J. / Mendoza, L. / Villaflor, G. / Tilley, D. / Shastri, N. / Grey, H. ...Ostrov, D.A. / Roden, M.M. / Shi, W. / Palmieri, E. / Christianson, G.J. / Mendoza, L. / Villaflor, G. / Tilley, D. / Shastri, N. / Grey, H. / Almo, S.C. / Roopenian, D.C. / Nathenson, S.G.
CitationJournal: J.Immunol. / Year: 2002
Title: How H13 histocompatibility peptides differing by a single methyl group and lacking conventional MHC binding anchor motifs determine self-nonself discrimination.
Authors: Ostrov, D.A. / Roden, M.M. / Shi, W. / Palmieri, E. / Christianson, G.J. / Mendoza, L. / Villaflor, G. / Tilley, D. / Shastri, N. / Grey, H. / Almo, S.C. / Roopenian, D. / Nathenson, S.G.
History
DepositionAug 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 25, 2016Group: Database references / Source and taxonomy
Revision 1.4Aug 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H2-Db major histocompatibility antigen
B: Beta-2-microglobulin
C: H13b peptide


Theoretical massNumber of molelcules
Total (without water)44,8753
Polymers44,8753
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-21 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.997, 109.707, 57.654
Angle α, β, γ (deg.)90.00, 120.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H2-Db major histocompatibility antigen


Mass: 32147.785 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D / Plasmid: Novagen pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: beta-2-microglobulin / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide H13b peptide


Mass: 1023.183 Da / Num. of mol.: 1 / Fragment: H13b nonamer peptide epitope / Source method: obtained synthetically / Details: Peptide generated by solid-phase fmoc chemistry / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9D8V0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Sodium Acetates, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 18, 2000
RadiationMonochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 33573 / Num. obs: 32587 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Net I/σ(I): 47.6
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 15.8 / % possible all: 75.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1INQ

1inq


Resolution: 2→19.81 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 421264.35 / Data cutoff high rms absF: 421264.35 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3251 10 %RANDOM
Rwork0.205 ---
all0.205 32581 --
obs0.205 32581 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8994 Å2 / ksol: 0.349821 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.22 Å20 Å26.62 Å2
2---2.51 Å20 Å2
3----1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 0 279 3442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 521 10 %
Rwork0.237 4711 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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