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- PDB-2vll: The Structural Dynamics and Energetics of an Immunodominant T-cel... -

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Basic information

Entry
Database: PDB / ID: 2vll
TitleThe Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain
Components
  • BETA-2-MICROGLOBULIN
  • FLU MATRIX PEPTIDE
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / TRANSMEMBRANE / UBL CONJUGATION / IMMUNE SYSTEM-RECEPTOR-COMPLEX / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / IMMUNE RESPONSE / IMMUNODOMINANCE / DISEASE MUTATION / MEMBRANE / SECRETED / RECEPTOR / GLYCATION / POLYMORPHISM / TCR / FLU / MHC / MHC I / T-CELL / COMPLEX
Function / homology
Function and homology information


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 / NEP/NS2 Interacts with the Cellular Export Machinery ...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 / NEP/NS2 Interacts with the Cellular Export Machinery / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / TAP binding / endoplasmic reticulum exit site / detection of bacterium / 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 / Viral mRNA Translation / beta-2-microglobulin binding / T cell receptor binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / positive regulation of T cell mediated cytotoxicity / DAP12 interactions / viral budding from plasma membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / positive regulation of type II interferon production / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / T cell receptor signaling pathway / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / E3 ubiquitin ligases ubiquitinate target proteins / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / structural constituent of virion / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / focal adhesion / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / host cell nucleus
Similarity search - Function
Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / MHC class I, alpha chain, C-terminal ...Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / 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
HLA class I histocompatibility antigen, A alpha chain / Matrix protein 1 / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
UNIDENTIFIED INFLUENZA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsIshizuka, J. / Stewart-Jones, G. / Van Der Merwe, A. / Bell, J. / Mcmichael, A. / Jones, Y.
CitationJournal: Immunity / Year: 2008
Title: The Structural Dynamics and Energetics of an Immunodominant T-Cell Receptor are Programmed by its Vbeta Domain
Authors: Ishizuka, J. / Stewart-Jones, G. / Van Der Merwe, A. / Bell, J. / Mcmichael, A. / Jones, Y.
History
DepositionJan 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: FLU MATRIX PEPTIDE
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: FLU MATRIX PEPTIDE


Theoretical massNumber of molelcules
Total (without water)89,5946
Polymers89,5946
Non-polymers00
Water21,7621208
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: FLU MATRIX PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,7973
Polymers44,7973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-29.5 kcal/mol
Surface area21690 Å2
MethodPQS
2
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: FLU MATRIX PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,7973
Polymers44,7973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-30.7 kcal/mol
Surface area21690 Å2
MethodPQS
Unit cell
Length a, b, c (Å)49.615, 62.335, 74.521
Angle α, β, γ (deg.)82.33, 76.44, 78.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN / MHC CLASS I ANTIGEN A*2


Mass: 31951.316 Da / Num. of mol.: 2 / Fragment: HLA-A2, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769
#3: Protein/peptide FLU MATRIX PEPTIDE


Mass: 966.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) UNIDENTIFIED INFLUENZA VIRUS / References: UniProt: P03485*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1208 / 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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 49.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→3 Å / Num. obs: 100261 / % possible obs: 89.7 % / Observed criterion σ(I): 1.9 / Redundancy: 6.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.9 / % possible all: 62.4

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.6→72.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.986 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 5029 5 %RANDOM
Rwork0.192 ---
obs0.194 95226 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.48 Å20.96 Å2
2--0.28 Å20.09 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.6→72.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6212 0 0 1208 7420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216394
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9238674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0435762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92122.952332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.682151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8991554
X-RAY DIFFRACTIONr_chiral_restr0.0980.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.23364
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24376
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.21070
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9541.53878
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53826104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.34232919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5544.52570
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 239
Rwork0.253 4725

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