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- PDB-1jpg: Crystal Structure Of The LCMV Peptidic Epitope Np396 In Complex W... -

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Basic information

Entry
Database: PDB / ID: 1jpg
TitleCrystal Structure Of The LCMV Peptidic Epitope Np396 In Complex With The Murine Class I Mhc Molecule H-2Db
Components
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
  • LCMV peptidic epitope np396
KeywordsIMMUNE SYSTEM / Ig fold
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 / regulation of membrane depolarization / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / beta-2-microglobulin binding ...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 / regulation of membrane depolarization / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / beta-2-microglobulin binding / 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 / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / 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 classes I/II-like antigen recognition protein ...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: 2.2 Å
AuthorsCiatto, C. / Tissot, A.C. / Tschopp, M. / Capitani, G. / Pecorari, F. / Pluckthun, A. / Grutter, M.G.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Zooming in on the hydrophobic ridge of H-2D(b): implications for the conformational variability of bound peptides.
Authors: Ciatto, C. / Tissot, A.C. / Tschopp, M. / Capitani, G. / Pecorari, F. / Pluckthun, A. / Grutter, M.G.
History
DepositionAug 2, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / 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: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: LCMV peptidic epitope np396


Theoretical massNumber of molelcules
Total (without water)45,5153
Polymers45,5153
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-18 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.122, 109.952, 57.744
Angle α, β, γ (deg.)90.00, 122.88, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a ternary complex consisting of H-2Db, beta-2 microglobulin, and the peptidic epitope

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Components

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


Mass: 32601.303 Da / Num. of mol.: 1 / Fragment: extracellular domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin


Mass: 11835.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide LCMV peptidic epitope np396


Mass: 1078.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid-phase peptide synthesis
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Ammonium phosphate, PEG8000, Tris-HCl, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.1 mg/mlprotein1drop
20.2 Mammonium phosphate1reservoir
325 %PEG80001reservoir
40.1 MTris-HCl1reservoir
50.02 %(w/v)sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 8, 1998
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 23164 / Num. obs: 23164 / % possible obs: 95.6 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.25 Å / % possible all: 79.7
Reflection
*PLUS
Redundancy: 3.2 % / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 79.7 % / Redundancy: 2.4 % / Num. unique obs: 1278 / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.288 2285 RANDOM
Rwork0.228 --
all-23164 -
obs-23164 -
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 0 33 3191
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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