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- PDB-2av1: Crystal structure of HTLV-1 TAX peptide Bound to Human Class I MH... -

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Basic information

Entry
Database: PDB / ID: 2av1
TitleCrystal structure of HTLV-1 TAX peptide Bound to Human Class I MHC HLA-A2 with the E63Q and K66A mutations in the heavy chain.
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Trans-activating transcriptional regulatory peptide
KeywordsIMMUNE SYSTEM / TAX peptide / MHC / mutated HLA-A2 / E63Q / 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 / antigen processing and presentation of peptide antigen via MHC class I / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / antigen processing and presentation of peptide antigen via MHC class I / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 exogenous peptide antigen via MHC class I / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / regulation of mRNA stability / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / SH3 domain binding / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / negative regulation of gene expression / innate immune response
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
THIOCYANATE ION / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Protein Tax-1 / Beta-2-microglobulin / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human T-cell leukemia virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)91,66630
Polymers89,4896
Non-polymers2,17624
Water13,529751
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)46,00017
Polymers44,7453
Non-polymers1,25514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-25 kcal/mol
Surface area18840 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)45,66613
Polymers44,7453
Non-polymers92110
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-29 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.328, 62.536, 74.747
Angle α, β, γ (deg.)82.10, 76.39, 78.10
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31795.113 Da / Num. of mol.: 2 / Mutation: E63Q, 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


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: P61770, UniProt: P61769*PLUS

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Protein/peptide , 1 types, 2 molecules CF

#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

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Non-polymers , 3 types, 775 molecules

#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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 20%, MES 0.025M, NaSCN 0.1M, 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: 0.97951 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 17, 2004
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 63772 / Num. obs: 61476 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 17.73 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.29
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.22 / Num. unique all: 5799 / % possible all: 91.2

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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: 1.95→10 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.169 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.176 / ESU R Free: 0.164 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23059 3050 5.1 %RANDOM
Rwork0.17441 ---
all0.17724 62423 --
obs0.17724 57226 96.56 %-
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: 12.902 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0.06 Å20.44 Å2
2---0.79 Å20.45 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6314 0 141 751 7206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0216619
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.9318940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575762
X-RAY DIFFRACTIONr_chiral_restr0.1420.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025136
X-RAY DIFFRACTIONr_nbd_refined0.1650.083045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.51062
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.0886
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.560
X-RAY DIFFRACTIONr_mcbond_it1.0531.53828
X-RAY DIFFRACTIONr_mcangle_it1.76626161
X-RAY DIFFRACTIONr_scbond_it3.11332791
X-RAY DIFFRACTIONr_scangle_it4.624.52779
LS refinement shellResolution: 1.95→1.999 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 220
Rwork0.212 3838
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)
11.14360.04890.01661.6957-0.33932.2598-0.0689-0.0090.10070.02730.02120.0143-0.11270.02870.04770.0897-0.0026-0.01790.0806-0.02030.09412.549413.51146.8765
21.7836-1.8397-1.35513.79851.93042.66050.03680.0866-0.092-0.2082-0.0176-0.01970.11970.107-0.01920.1263-0.0059-0.01010.1048-0.01150.09856.6076-19.4127-6.1365
32.00981.9291-0.63343.9198-0.8671.5114-0.03340.11030.0226-0.14590.07020.25860.0709-0.1218-0.03680.08350.005-0.01380.11820.01060.1091-10.9254-4.915-6.6779
40.4703-0.7960.40367.4197-2.96475.42670.0273-0.14480.44620.8154-0.2314-0.0569-0.96340.69810.20410.245-0.0191-0.02520.2684-0.00630.2213.17821.729810.287
51.1636-0.19120.02092.22260.48322.1199-0.05130.03650.09020.04770.007-0.0702-0.06460.03360.04430.10140.00750.00850.09210.01790.08842.546347.488626.7563
64.38681.5841-2.96882.359-0.97763.20350.05050.0164-0.0721-0.0116-0.0962-0.04190.0421-0.16060.04570.04510.0111-0.00740.08850.00150.082625.676718.955839.4812
70.8477-0.39840.22354.55650.42022.1624-0.0234-0.0397-0.0530.05740.0765-0.17980.0861-0.0212-0.0530.0013-0.00070.01040.1111-0.00840.079847.411925.234940.058
81.1031-0.04192.31351.33050.6496.7383-0.44010.32970.3659-0.73010.03070.0032-1.11620.18070.40940.22650.0166-0.00990.25820.04850.262144.889255.340423.2801
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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