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- PDB-3h9s: The complex between TCR A6 and human Class I MHC HLA-A2 with the ... -

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Basic information

Entry
Database: PDB / ID: 3h9s
TitleThe complex between TCR A6 and human Class I MHC HLA-A2 with the bound Tel1p peptide
Components
  • A6 TCR alpha chain
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • TRBV6-5 protein
  • Tel1p peptide
KeywordsIMMUNE SYSTEM / Tel1p peptide / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Pexophagy / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Pexophagy / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 / telomeric DNA binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / signal transduction in response to DNA damage / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / negative regulation of TORC1 signaling / telomere maintenance / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / DNA damage checkpoint signaling / 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 / 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 / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / double-strand break repair / 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 / chromatin organization / 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 / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / chromosome, telomeric region / learning or memory / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / protein kinase activity / immune response / Amyloid fiber formation
Similarity search - Function
Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. ...Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic 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 / Protein kinase-like domain superfamily / 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 / Serine/threonine-protein kinase TEL1 / Beta-2-microglobulin / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: Immunity / Year: 2009
Title: T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
Authors: Borbulevych, O.Y. / Piepenbrink, K.H. / Gloor, B.E. / Scott, D.R. / Sommese, R.F. / Cole, D.K. / Sewell, A.K. / Baker, B.M.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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

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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: Tel1p peptide
D: A6 TCR alpha chain
E: TRBV6-5 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,90811
Polymers94,3555
Non-polymers5536
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-57 kcal/mol
Surface area38360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.106, 48.308, 92.482
Angle α, β, γ (deg.)90.000, 90.970, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-207-

GOL

21E-248-

HOH

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Components

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Protein , 4 types, 4 molecules ABDE

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


Mass: 31854.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein A6 TCR alpha chain


Mass: 22088.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#5: Protein TRBV6-5 protein


Mass: 27361.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV6-5 / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2YDB4

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Tel1p peptide


Mass: 1172.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: P38110*PLUS

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Non-polymers , 2 types, 46 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000 15%, TRIS 0.1M, MgCl2 0.2M, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98494 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 29, 2007
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98494 Å / Relative weight: 1
ReflectionResolution: 2.68→20 Å / Num. all: 28088 / Num. obs: 27920 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 64.1 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.013 / Net I/σ(I): 15.186
Reflection shellResolution: 2.68→2.78 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 1.98 / Num. unique all: 2695 / Χ2: 0.664 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å20.02 Å
Translation3.5 Å20.02 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GJ6

2gj6


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.779 / SU B: 34.783 / SU ML: 0.332 / SU Rfree: 0.405 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.404 / Stereochemistry target values: Engh & Huber
Details: Residue numbering for the chains D,E (A6 TCR) has been chosen to match with previously published TCR A6 structures (PDB Entries e.g. 1AO7,1QSE, 1QRN, 2GJ6)
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1387 5.1 %RANDOM
Rwork0.217 ---
all0.221 27538 --
obs0.221 27378 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.55 Å2 / Biso mean: 62.787 Å2 / Biso min: 28.97 Å2
Baniso -1Baniso -2Baniso -3
1--7.15 Å20 Å20.74 Å2
2--8.76 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6647 0 36 40 6723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216861
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.9349317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5655824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22723.886350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.199151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6611548
X-RAY DIFFRACTIONr_chiral_restr0.1190.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025368
X-RAY DIFFRACTIONr_nbd_refined0.1310.082606
X-RAY DIFFRACTIONr_nbtor_refined0.3230.54456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.5367
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.0868
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.57
X-RAY DIFFRACTIONr_mcbond_it0.924222
X-RAY DIFFRACTIONr_mcangle_it1.48136678
X-RAY DIFFRACTIONr_scbond_it0.8123042
X-RAY DIFFRACTIONr_scangle_it1.2232639
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 96 -
Rwork0.303 1842 -
all-1938 -
obs--98.23 %
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)
14.3732-1.64181.21582.5193-0.97714.63920.01430.4777-0.4378-0.0245-0.14650.17460.1491-0.68390.1322-0.26590.01320.051-0.3339-0.1319-0.145737.2694-9.3057-4.0764
29.4818-1.96270.072811.02682.85198.77940.26272.0655-2.3769-1.2591-0.42330.01221.6134-0.26620.16060.41250.03350.04590.3735-0.52630.372249.9612-25.1787-33.3395
35.9081.5095-1.41283.9833-0.87176.05290.02610.8673-0.0515-0.46290.0267-0.1775-0.07070.3733-0.0528-0.19220.08280.0313-0.4037-0.0477-0.248159.3373-9.4576-19.8165
412.4698-1.5513-1.47571.08941.24233.43130.12680.4483-0.1434-0.1767-0.25620.2129-0.0788-1.18330.1294-0.2880.0157-0.0430.0241-0.1027-0.17299.3391.53976.3082
511.75432.59222.762515.19823.224511.5412-0.00720.25321.26140.0574-0.49380.5652-1.1275-1.25680.501-0.25280.27120.00010.91210.0189-0.0535-13.302817.668224.6076
67.8392-2.6574-2.3516.20551.75645.05560.1843-0.01510.18610.2495-0.08870.0488-0.2152-0.0842-0.0957-0.2751-0.09520.0033-0.42270.0289-0.304325.983110.903119.9141
711.2693.7279-1.3674.44320.32265.86090.2245-0.29820.59850.0242-0.12330.0315-0.2345-1.2177-0.1012-0.12860.12380.04160.1052-0.0675-0.3142-0.569415.440335.5796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A183 - 275
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 116
6X-RAY DIFFRACTION5D117 - 200
7X-RAY DIFFRACTION6E1 - 116
8X-RAY DIFFRACTION7E117 - 245

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