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- PDB-6q3s: Engineered Human HLA_A2 MHC Class I molecule in complex with TCR ... -

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Basic information

Entry
Database: PDB / ID: 6q3s
TitleEngineered Human HLA_A2 MHC Class I molecule in complex with TCR and SV9 peptide
Components
  • (T cell receptor ...T-cell receptor) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • SER-LEU-LEU-MET-TRP-ILE-THR-GLN-VAL
KeywordsIMMUNE SYSTEM / MHC molecule / engineered disulphide bond / TCR
Function / homology
Function and homology information


T cell receptor complex / 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 ...T cell receptor complex / 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 / 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 / response to bacterium / 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 / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / 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 / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
ACETATE ION / T cell receptor alpha variable 21 / T cell receptor beta variable 6-5 / Human nkt tcr beta chain / T-cell receptor, sp3.4 alpha chain / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsMeijers, R. / Anjanappa, R. / Springer, S. / Garcia-Alai, M.
Funding support1items
OrganizationGrant numberCountry
European Commission653706
CitationJournal: Sci Immunol / Year: 2019
Title: High-throughput peptide-MHC complex generation and kinetic screenings of TCRs with peptide-receptive HLA-A*02:01 molecules.
Authors: Moritz, A. / Anjanappa, R. / Wagner, C. / Bunk, S. / Hofmann, M. / Pszolla, G. / Saikia, A. / Garcia-Alai, M. / Meijers, R. / Rammensee, H.G. / Springer, S. / Maurer, D.
History
DepositionDec 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: SER-LEU-LEU-MET-TRP-ILE-THR-GLN-VAL
D: T cell receptor alpha variable 21,T-cell receptor, sp3.4 alpha chain
E: T cell receptor beta variable 6-5,Human nkt tcr beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6227
Polymers94,4715
Non-polymers1512
Water23413
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: SER-LEU-LEU-MET-TRP-ILE-THR-GLN-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0445
Polymers44,8933
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-18 kcal/mol
Surface area19160 Å2
MethodPISA
2
D: T cell receptor alpha variable 21,T-cell receptor, sp3.4 alpha chain
E: T cell receptor beta variable 6-5,Human nkt tcr beta chain


Theoretical massNumber of molelcules
Total (without water)49,5782
Polymers49,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-22 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.445, 53.669, 121.741
Angle α, β, γ (deg.)90.00, 98.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 31923.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide SER-LEU-LEU-MET-TRP-ILE-THR-GLN-VAL


Mass: 1090.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)

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T cell receptor ... , 2 types, 2 molecules DE

#4: Protein T cell receptor alpha variable 21,T-cell receptor, sp3.4 alpha chain / T-cell receptor / sp3.4 beta chain


Mass: 22571.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV21 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J279, UniProt: K7N5N2
#5: Protein T cell receptor beta variable 6-5,Human nkt tcr beta chain


Mass: 27005.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV6-5, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0K1A5, UniProt: K7N5M4

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Non-polymers , 3 types, 15 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate; 0.1 M bis-tris pH 5.5, 17 %(w/v) PEG 10.000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→65 Å / Num. obs: 33552 / % possible obs: 99.3 % / Redundancy: 4.8 % / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.6 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.5→29.936 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.64
RfactorNum. reflection% reflection
Rfree0.2733 1654 4.93 %
Rwork0.2287 --
obs0.2311 33552 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 10 13 6627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026795
X-RAY DIFFRACTIONf_angle_d0.4719236
X-RAY DIFFRACTIONf_dihedral_angle_d13.1644045
X-RAY DIFFRACTIONf_chiral_restr0.04977
X-RAY DIFFRACTIONf_plane_restr0.0031209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4997-2.57330.41861210.40592662X-RAY DIFFRACTION99
2.5733-2.65630.45221380.39852624X-RAY DIFFRACTION99
2.6563-2.75110.41411240.3752619X-RAY DIFFRACTION99
2.7511-2.86120.37371390.34282656X-RAY DIFFRACTION99
2.8612-2.99130.3641370.33062651X-RAY DIFFRACTION99
2.9913-3.14890.38691290.31742643X-RAY DIFFRACTION99
3.1489-3.34590.3611430.30992641X-RAY DIFFRACTION99
3.3459-3.60380.32261380.27282650X-RAY DIFFRACTION99
3.6038-3.96580.29371520.2412641X-RAY DIFFRACTION99
3.9658-4.53790.25961270.18872686X-RAY DIFFRACTION99
4.5379-5.71080.20551510.17772673X-RAY DIFFRACTION99
5.7108-29.93850.22251550.1772752X-RAY DIFFRACTION99
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)
14.11910.2668-0.43541.77080.05655.0715-0.0107-0.2234-0.40020.1313-0.17540.05560.4183-0.0001-0.00030.6213-0.1270.0310.489-0.08280.74322.6097-10.3585-40.4501
23.8482-0.7586-1.51713.0551-2.00363.42030.17240.8052-0.0488-0.6793-0.17770.60450.3179-0.00130.00010.82320.0499-0.2230.8738-0.05170.708725.1892-15.9693-75.751
31.2742-1.37860.95522.4812-0.1331.1239-0.2261-0.25470.0111-0.04330.01920.20750.6663-0.0796-0.00040.73310.08920.07970.7142-0.07790.758132.7148-25.4461-62.216
42.4044-0.28810.70424.3723-0.32371.90240.05180.1734-0.33860.6601-0.30690.1750.49470.4396-00.77510.00010.03320.689-0.00990.716933.8827-29.2176-57.518
50.27-0.2530.0410.1988-0.09040.14030.0637-0.17740.3522-0.2916-0.1253-0.039-0.15950.1205-0.00010.6302-0.16390.00910.6362-0.04320.734820.7391-7.3704-32.489
62.0307-1.52670.41011.9295-0.20223.4562-0.6843-0.30920.66730.11330.8293-0.1621-1.875-0.0892-0.02591.12720.0451-0.02360.8006-0.10150.803513.05198.7004-12.0252
71.85790.7213-0.93031.6803-2.03442.0034-0.3468-0.8410.71890.97520.5547-0.0792-1.2113-0.6285-0.00011.76020.6066-0.0991.4986-0.30811.358814.47711.366520.6748
82.2942-0.75010.61520.7359-0.99034.2135-0.3943-0.4044-0.3079-0.0470.3681-0.25020.35141.256200.75670.06450.0851.1084-0.0430.79929.3109-9.0343-11.5798
93.4012-0.63580.75662.3123-1.0454.6843-0.1256-0.54320.0190.42750.3990.0737-0.3178-0.24720.00150.89250.3816-0.00371.13330.05120.701918.8695-4.887217.2172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:180)
2X-RAY DIFFRACTION2(chain A and resid 181:274)
3X-RAY DIFFRACTION3(chain B and resid 0:21)
4X-RAY DIFFRACTION4(chain B and resid 22:99)
5X-RAY DIFFRACTION5(chain C and resid 1:9)
6X-RAY DIFFRACTION6(chain D and resid 2:123)
7X-RAY DIFFRACTION7(chain D and resid 124:204)
8X-RAY DIFFRACTION8(chain E and resid 2:104)
9X-RAY DIFFRACTION9(chain E and resid 105:242)

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