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- PDB-2av7: Crystal structure of HTLV-1 TAX peptide Bound to Human Class I MH... -

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Basic information

Entry
Database: PDB / ID: 2av7
TitleCrystal structure of HTLV-1 TAX peptide Bound to Human Class I MHC HLA-A2 with the K66A mutation in the heavy chain.
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Trans-activating transcriptional regulatory peptide
KeywordsIMMUNE SYSTEM / TAX peptide / MHC / mutated HLA-A2 / K66A.
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 ...symbiont-mediated perturbation of host exit from mitosis / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / regulation of mRNA stability / detection of bacterium / T cell receptor binding / 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 / 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 / SH3 domain binding / 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 / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / negative regulation of gene expression / signaling receptor binding
Similarity search - Function
HTLV Tax / HTLV Tax / 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 ...HTLV Tax / HTLV Tax / 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 / HLA class I histocompatibility antigen, A alpha chain / Protein Tax-1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human T-cell leukemia virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Unraveling a Hotspot for TCR Recognition on HLA-A2: Evidence Against the Existence of Peptide-independent TCR Binding Determinants.
Authors: Gagnon, S.J. / Borbulevych, O.Y. / Davis-Harrison, R.L. / Baxter, T.K. / Clemens, J.R. / Armstrong, K.M. / Turner, R.V. / Damirjian, M. / Biddison, W.E. / Baker, B.M.
History
DepositionAug 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Mar 13, 2013Group: Other
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Trans-activating transcriptional regulatory peptide
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Trans-activating transcriptional regulatory peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,33326
Polymers89,4916
Non-polymers1,84220
Water12,520695
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Trans-activating transcriptional regulatory peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,03517
Polymers44,7463
Non-polymers1,28914
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-25 kcal/mol
Surface area18670 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Trans-activating transcriptional regulatory peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2989
Polymers44,7463
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-26 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.320, 62.532, 74.801
Angle α, β, γ (deg.)82.13, 76.57, 78.06
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: 31796.098 Da / Num. of mol.: 2 / Mutation: K66A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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) / Gene: B2M / Plasmid: pHN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide Trans-activating transcriptional regulatory peptide / X-LOR protein / PX protein


Mass: 1070.280 Da / Num. of mol.: 2 / Fragment: HTLV-1 TAX peptide / Source method: obtained synthetically / Details: Commercial synthesis
Source: (synth.) Human T-cell leukemia virus 1 (isolate Caribbea HS-35 subtype A)
References: UniProt: P14079
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.5 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350 24%, MES 0.025M., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97925 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 21, 2004
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 56534 / Num. obs: 53990 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.34 / Num. unique all: 4763 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1DUZ

1duz


Resolution: 2.05→10 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.077 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.214 / ESU R Free: 0.189 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23408 2612 5.1 %RANDOM
Rwork0.17149 ---
all0.17472 53796 --
obs0.17472 49005 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.881 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20.32 Å20.36 Å2
2---0.78 Å20.19 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6314 0 120 695 7129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0216607
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.938930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635762
X-RAY DIFFRACTIONr_chiral_restr0.1430.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025141
X-RAY DIFFRACTIONr_nbd_refined0.1570.082916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.51003
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.0872
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.546
X-RAY DIFFRACTIONr_mcbond_it0.9621.53826
X-RAY DIFFRACTIONr_mcangle_it1.69526160
X-RAY DIFFRACTIONr_scbond_it2.93932781
X-RAY DIFFRACTIONr_scangle_it4.3524.52770
LS refinement shellResolution: 2.05→2.101 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 175
Rwork0.215 3140
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)
11.29060.13380.10811.6517-0.28872.5216-0.0849-0.0250.12960.02370.00150.0137-0.15760.05220.08340.1211-0.0082-0.01370.0995-0.02120.12712.58213.53116.8435
21.9097-1.8966-1.48954.31662.20213.07410.04860.1474-0.0898-0.223-0.01160.02190.14060.0574-0.0370.1492-0.0147-0.01080.1091-0.00210.13126.6161-19.4264-6.16
32.17782.1205-0.51934.619-0.73171.6702-0.06950.1209-0.0135-0.13960.07190.25250.0874-0.1614-0.00240.11010.0035-0.01050.13920.00580.1329-10.9561-4.9198-6.7121
40.7093-0.0228-0.83075.5722-5.33338.8032-0.0786-0.46090.45361.03750.11030.147-1.38810.0953-0.03170.26440.0312-0.04480.2578-0.00450.17243.333721.543910.2466
51.1942-0.34390.00162.29250.46222.1362-0.04920.04860.08150.03250.0043-0.0744-0.04910.0360.04490.10760.00110.01930.11830.02580.11942.469647.511626.8793
64.85631.8683-3.21122.2027-1.02692.92320.05380.029-0.1003-0.0401-0.0909-0.01040.0585-0.13430.0370.0630.0234-0.00560.1153-0.00040.113425.567618.954339.5314
71.0286-0.72240.05355.38350.77242.4102-0.0136-0.0609-0.06030.05850.0524-0.17020.0926-0.0351-0.03890.0025-0.00830.0140.130.00080.098247.302225.20440.1338
81.71990.32992.5683.531-0.4844.4729-0.50520.48210.4632-0.9155-0.13540.0805-1.22240.27370.64070.1392-0.0107-0.02340.18920.0480.207144.729555.323523.5303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1821 - 182
2X-RAY DIFFRACTION2AA183 - 275183 - 275
3X-RAY DIFFRACTION3BB0 - 991 - 100
4X-RAY DIFFRACTION4CC1 - 91 - 9
5X-RAY DIFFRACTION5DD1 - 1821 - 182
6X-RAY DIFFRACTION6DD183 - 275183 - 275
7X-RAY DIFFRACTION7EE0 - 991 - 100
8X-RAY DIFFRACTION8FF1 - 91 - 9

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