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- PDB-8ryn: Structure of S2 TCR in complex with HLA-A*11:01 bound to ELFSYLIE... -

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Basic information

Entry
Database: PDB / ID: 8ryn
TitleStructure of S2 TCR in complex with HLA-A*11:01 bound to ELFSYLIEK peptide
Components
  • Beta-2-microglobulin
  • ELFSYLIEK peptide
  • MHC class I antigen
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / TCR / HLA
Function / homology
Function and homology information


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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion ...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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKaruppiah, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: To Be Published
Title: Structure of S2 TCR in complex with HLA-A*11:01 bound to ELFSYLIEK peptide
Authors: Karuppiah, V.
History
DepositionFeb 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: ELFSYLIEK peptide
D: TCR alpha
E: TCR beta


Theoretical massNumber of molelcules
Total (without water)94,0775
Polymers94,0775
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-41 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.750, 48.690, 115.300
Angle α, β, γ (deg.)90.00, 106.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein MHC class I antigen / HLA-A11


Mass: 31952.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A583ZB34
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
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
#4: Protein TCR alpha


Mass: 21546.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein TCR beta


Mass: 27556.705 Da / Num. of mol.: 1
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, 302 molecules C

#3: Protein/peptide ELFSYLIEK peptide


Mass: 1142.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Amino acids (0.02 M Sodium Glutamate; 0.02 M Alanine; 0.02 M Glycine; 0.02 M Lysine hydrochloride; 0.02 M Serine), 0.1 M Buffer system 1 (Imidazole; MES monohydrate) pH 6.5, 50 % ...Details: 0.1 M Amino acids (0.02 M Sodium Glutamate; 0.02 M Alanine; 0.02 M Glycine; 0.02 M Lysine hydrochloride; 0.02 M Serine), 0.1 M Buffer system 1 (Imidazole; MES monohydrate) pH 6.5, 50 % Precipitant mix 2 (20% v/v Ethylene glycol; 10 % w/v PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.97→77.9 Å / Num. obs: 65906 / % possible obs: 99.94 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.039 / Rrim(I) all: 0.105 / Net I/σ(I): 13.3
Reflection shellResolution: 1.97→2 Å / Redundancy: 6 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3267 / CC1/2: 0.633 / Rpim(I) all: 0.545 / Rrim(I) all: 1.34 / % possible all: 99.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→77.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.492 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25052 3242 4.9 %RANDOM
Rwork0.22019 ---
obs0.22166 62652 99.92 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.49 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å2-1.2 Å2
2--2.91 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.97→77.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 0 301 6767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136633
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185955
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.6529008
X-RAY DIFFRACTIONr_angle_other_deg1.0861.58413723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83322.194392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.503151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.521550
X-RAY DIFFRACTIONr_chiral_restr0.0380.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021625
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2581.6993229
X-RAY DIFFRACTIONr_mcbond_other1.241.6973228
X-RAY DIFFRACTIONr_mcangle_it2.0312.5384024
X-RAY DIFFRACTIONr_mcangle_other2.0332.5394025
X-RAY DIFFRACTIONr_scbond_it1.641.8883404
X-RAY DIFFRACTIONr_scbond_other1.641.8863402
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6412.7594984
X-RAY DIFFRACTIONr_long_range_B_refined5.18619.1636824
X-RAY DIFFRACTIONr_long_range_B_other5.16718.9746794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 248 -
Rwork0.305 4639 -
obs--99.94 %
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)
12.48320.0006-1.89022.618-0.38466.41840.04010.1793-0.0638-0.0365-0.0288-0.12970.1650.1749-0.01130.32210.00620.05990.0327-0.00990.0216-19.117-3.261-13.895
20.9205-0.04530.45040.89090.09283.30250.02050.01170.0391-0.0803-0.13320.145-0.0632-0.32980.11260.3911-0.01560.10120.056-0.03940.0624-27.9669.12-2.006
30.51742.0377-0.06789.7279-3.98938.32940.0063-0.01380.0096-0.0159-0.03010.0189-0.03470.14890.02380.2587-0.02410.08680.1872-0.01190.0295-23.19710.84517.116
41.07681.08472.27591.58142.01494.9736-0.2117-0.30510.3035-0.1621-0.4960.207-0.4187-0.53710.70760.44930.04250.06640.3151-0.14360.2074-5.64528.22647.08
50.44570.23520.84690.59841.04573.15080.0748-0.0237-0.06810.06710.0807-0.11250.26090.1736-0.15550.43140.01020.10440.0676-0.00130.06013.13911.51747.63
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 98
2X-RAY DIFFRACTION2A1 - 275
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4D2 - 192
5X-RAY DIFFRACTION5E4 - 245

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