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

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Entry
Database: PDB / ID: 2vlr
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
  • JM22 TCR ALPHA CHAIN
  • JM22 TCR BETA CHAIN
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / TRANSMEMBRANE / IMMUNE SYSTEM-RECEPTOR-COMPLEX / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / IMMUNE RESPONSE / IMMUNODOMINANCE / DISEASE MUTATION / MEMBRANE / SECRETED / RECEPTOR / GLYCATION / 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 / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / viral budding from plasma membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / T cell mediated cytotoxicity / lumenal side of endoplasmic reticulum membrane / negative regulation of iron ion transport / 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 / regulation of iron ion transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / transferrin transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / 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 neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of type II interferon production / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / structural constituent of virion / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 18, 2019Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.3Oct 23, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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

Downloads & links

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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: JM22 TCR ALPHA CHAIN
E: JM22 TCR BETA CHAIN
F: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
G: BETA-2-MICROGLOBULIN
H: FLU MATRIX PEPTIDE
I: JM22 TCR ALPHA CHAIN
J: JM22 TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)189,18210
Polymers189,18210
Non-polymers00
Water10,503583
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: FLU MATRIX PEPTIDE
D: JM22 TCR ALPHA CHAIN
E: JM22 TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)94,5915
Polymers94,5915
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-71 kcal/mol
Surface area48780 Å2
MethodPQS
2
F: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
G: BETA-2-MICROGLOBULIN
H: FLU MATRIX PEPTIDE
I: JM22 TCR ALPHA CHAIN
J: JM22 TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)94,5915
Polymers94,5915
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-72.2 kcal/mol
Surface area48370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)48.622, 95.523, 122.045
Angle α, β, γ (deg.)110.29, 98.64, 93.59
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769
#4: Protein JM22 TCR ALPHA CHAIN


Mass: 22040.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#5: Protein JM22 TCR BETA CHAIN


Mass: 27753.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)

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Protein/peptide / Non-polymers , 2 types, 585 molecules CH

#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.02 % / 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: 2.3→30 Å / Num. obs: 1032287 / % possible obs: 97.5 % / Observed criterion σ(I): 1.9 / Redundancy: 11.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.75 / % possible all: 96.1

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→112.51 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / SU B: 15.774 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 4402 5 %RANDOM
Rwork0.219 ---
obs0.222 83095 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-1.28 Å2-0.47 Å2
2---0.85 Å2-2.84 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→112.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13236 0 0 583 13819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02213592
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.93218450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24951638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46623.948694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.58152206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4641592
X-RAY DIFFRACTIONr_chiral_restr0.110.21932
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210604
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.24263
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.290.28463
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2525
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4420.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4550.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7161.58587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19213244
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86535996
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.94.55206
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 336
Rwork0.284 5993
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83290.1333-0.15351.79960.15641.00670.0525-0.0398-0.0358-0.0970.0236-0.06770.13310.0252-0.0761-0.01150.00150.0086-0.07360.0267-0.081926.2278.36952.4817
24.5941-2.5794-1.81667.9722.06826.46440.0630.222-0.1712-0.08330.4316-1.3531.37971.0592-0.49460.16190.3176-0.15750.0152-0.20730.249739.7222-23.7598-4.9445
32.29240.74940.14482.9969-0.28011.92810.160.1985-0.2453-0.2130.0034-0.12980.3141-0.0692-0.16330.09290.039-0.0132-0.1088-0.0194-0.077124.0594-11.339-16.1251
40.5783-0.5935-0.39353.2043.47443.90110.1673-0.07720.07190.1351-0.03930.0946-0.01140.1311-0.128-0.03350.027-0.0458-0.0218-0.0027-0.034325.286516.37385.0794
50.68020.18120.11661.78290.05841.14690.02490.06110.06540.06930.0021-0.0083-0.17980.053-0.027-0.0109-0.00490.0031-0.04360.0182-0.095626.579762.449374.6635
64.88241.2797-1.0995.15051.44218.98930.3796-0.79750.73450.08270.1313-0.563-2.2461.8396-0.5110.5667-0.61790.22630.1337-0.10610.079939.498396.119681.4455
72.571-0.4483-0.29334.12250.73192.0220.2237-0.25110.37860.0662-0.10130.0188-0.37360.0191-0.12240.1119-0.07560.0803-0.0844-0.0336-0.074124.664582.313993.2634
81.66361.34880.80253.94492.92292.1980.27330.1792-0.10190.2341-0.19380.14690.03210.045-0.07950.03680.00270.0457-0.0106-0.0089-0.070125.457454.475372.1408
90.17890.0146-0.06250.80080.65581.9424-0.062-0.0805-0.00360.03450.0988-0.0158-0.0490.109-0.0368-0.02880.0026-0.0175-0.009-0.018-0.042727.554734.767927.0984
103.7846-0.1421.50192.47731.00934.2412-0.076-0.3510.09180.3348-0.10940.22960.0016-0.54030.18540.0519-0.01110.0279-0.10450.0453-0.08819.630561.601639.2382
112.0893-0.8058-0.24141.32310.80470.8750.03690.03260.0379-0.0498-0.06740.0494-0.0394-0.07860.0306-0.0509-0.00570.0051-0.00970.0219-0.051411.427234.20459.0861
121.55371.35260.93082.54481.07441.4435-0.08090.14510.19620.0476-0.08730.1687-0.2499-0.03180.16820.02120.0058-0.0359-0.11320.0773-0.00767.311963.170121.9288
130.4189-0.1851-0.46380.99650.22091.9894-0.06340.0304-0.0617-0.09690.0434-0.02040.10220.01450.02-0.03530.00970.0314-0.0188-0.0213-0.030627.520335.574550.5099
147.05371.6065-1.34335.57252.49689.0097-0.28070.5811-0.7298-1.25470.2496-0.4799-0.0707-0.49050.03110.0484-0.27220.2358-0.1021-0.3035-0.10759.6787.937339.502
151.95571.08370.41441.51180.6630.78880.0637-0.16680.01530.0393-0.12330.0860.056-0.15080.0596-0.06940.01310.00980.04710.0082-0.062111.134536.636468.4211
163.7488-0.862-1.46654.82092.51063.1129-0.1353-0.0244-0.799-0.18020.0989-0.24540.1223-0.05620.0364-0.1208-0.06670.0513-0.17980.01950.12726.47627.269156.9435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION2A182 - 275
3X-RAY DIFFRACTION3B0 - 99
4X-RAY DIFFRACTION4C1 - 9
5X-RAY DIFFRACTION5F1 - 181
6X-RAY DIFFRACTION6F182 - 275
7X-RAY DIFFRACTION7G0 - 99
8X-RAY DIFFRACTION8H1 - 9
9X-RAY DIFFRACTION9D3 - 115
10X-RAY DIFFRACTION10D116 - 201
11X-RAY DIFFRACTION11E5 - 115
12X-RAY DIFFRACTION12E116 - 244
13X-RAY DIFFRACTION13I3 - 115
14X-RAY DIFFRACTION14I116 - 201
15X-RAY DIFFRACTION15J5 - 115
16X-RAY DIFFRACTION16J116 - 244

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