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- PDB-2bst: Crystal structures and KIR3DL1 recognition of three immunodominan... -

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Basic information

Entry
Database: PDB / ID: 2bst
TitleCrystal structures and KIR3DL1 recognition of three immunodominant viral peptides complexed to HLA-B2705
Components
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-27 ALPHA CHAIN PRECURSOR
  • INFLUENZA NUCLEOPROTEIN
KeywordsIMMUNE SYSTEM/PEPTIDE / IMMUNE SYSTEM-PEPTIDE COMPLEX / MHC / HLA-B27 / HUMAN EBV / HIV / FLU / GLYCOPROTEIN / MHC I / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / PYRROLIDONE CARBOXYLIC ACID / COMPLEX (ANTIGEN-PEPTIDE) / VIRAL NUCLEOPROTEIN
Function / homology
Function and homology information


cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus ...cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / regulation of interleukin-12 production / regulation of dendritic cell differentiation / NEP/NS2 Interacts with the Cellular Export Machinery / regulation of T cell anergy / regulation of interleukin-6 production / Viral Messenger RNA Synthesis / vRNP Assembly / helical viral capsid / Viral mRNA Translation / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / viral penetration into host nucleus / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / ribonucleoprotein complex / symbiont entry into host cell / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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
HLA class I histocompatibility antigen, B alpha chain / Nucleoprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Nucleoprotein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
INFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsStewart-Jones, G.B.E. / diGleria, K. / Kollnberger, S. / McMichael, A.J. / Bowness, P. / Jones, E.Y.
CitationJournal: Eur.J.Immunol. / Year: 2005
Title: Crystal Structures and Kir3Dl1 Recognition of Three Immunodominant Viral Peptides Complexed to Hla-B2705
Authors: Stewart-Jones, G.B.E. / Di Gleria, K. / Kollnberger, S. / Mcmichael, A.J. / Jones, E.Y. / Bowness, P.
History
DepositionMay 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 27, 2015Group: Database references / Source and taxonomy / Structure summary
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-27 ALPHA CHAIN PRECURSOR
B: BETA-2-MICROGLOBULIN
C: INFLUENZA NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)45,0193
Polymers45,0193
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-15.6 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.200, 81.900, 108.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-27 ALPHA CHAIN PRECURSOR / HLA-B2705 / MHC CLASS I ANTIGEN B*27


Mass: 31928.160 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P03989, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P61769
#3: Protein/peptide INFLUENZA NUCLEOPROTEIN


Mass: 1211.397 Da / Num. of mol.: 1 / Fragment: RESIDUES 15-23 / Source method: obtained synthetically / Details: SEQUENCE FROM UNIDENTIFIED INFLUENZA VIRUS / Source: (synth.) INFLUENZA A VIRUS / References: UniProt: Q8B2U6, UniProt: P03466*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM

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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: 2.45 Å3/Da / Density % sol: 49.44 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 27436 / % possible obs: 99.7 % / Observed criterion σ(I): 0.9 / Redundancy: 15 % / Rmerge(I) obs: 0.11

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.234 --
obs0.234 27436 99.7 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 148 3323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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