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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-MICROGLOBULINBeta-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 / Viral mRNA Translation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / 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 / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / T cell receptor binding / viral budding from plasma 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 / ER to Golgi transport vesicle membrane / 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 / 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 / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / 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 / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen
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 / Immunoglobulins / Immunoglobulin-like fold / 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
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 / 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 / Water


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

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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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