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- PDB-1inq: Structure of Minor Histocompatibility Antigen peptide, H13a, comp... -

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Basic information

Entry
Database: PDB / ID: 1inq
TitleStructure of Minor Histocompatibility Antigen peptide, H13a, complexed to H2-Db
Components
  • BETA-2 MICROGLOBULIN
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
  • MHC Class I H13a minor histocompatibility peptide
KeywordsIMMUNE SYSTEM / minor histocompatibility antigen / MHC complex
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 / 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 ...Regulation of HMOX1 expression and activity / membrane protein proteolysis involved in retrograde protein transport, ER to cytosol / aspartic endopeptidase activity, intramembrane cleaving / 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 / cellular defense response / rough endoplasmic reticulum / 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 / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / peptidase activity / negative regulation of neuron projection development / protein refolding / protein homotetramerization / in utero embryonic development / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / external side of plasma membrane / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / 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 / Immunoglobulin-like fold / Immunoglobulins / 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 / Signal peptide peptidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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. / 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
DepositionMay 14, 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 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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: MHC Class I H13a minor histocompatibility peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7824
Polymers44,7043
Non-polymers781
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-19 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.64, 109.42, 57.56
Angle α, β, γ (deg.)90.00, 120.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN / H2-Db


Mass: 31990.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Db / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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: B2M / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01887
#3: Protein/peptide MHC Class I H13a minor histocompatibility peptide


Mass: 1009.156 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus.
References: UniProt: Q9D8V0
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 56.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG 4000, 0.1 M Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 %PEG40001drop
20.1 MHEPES1droppH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 25365 / Num. obs: 25365 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.4
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.075 / Num. unique all: 1077 / % possible all: 83.4
Reflection
*PLUS
Num. measured all: 109562
Reflection shell
*PLUS
% possible obs: 83.4 % / Mean I/σ(I) obs: 19.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.74 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1803 7.4 %Random
Rwork0.208 ---
all0.212 24897 --
obs0.212 24403 --
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 4 132 3298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.289 282 -
Rwork0.238 --
obs-3570 92.2 %
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.209 / Rfactor Rfree: 0.261
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor obs: 0.238

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