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- PDB-8ryp: Structure of S8 TCR in complex with HLA-A*03:01 bound to ELFSYLIE... -

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Basic information

Entry
Database: PDB / ID: 8ryp
TitleStructure of S8 TCR in complex with HLA-A*03:01 bound to ELFSYLIEK peptide
Components
  • Beta-2-microglobulin
  • ELFSYLIEK peptide
  • HLA class I histocompatibility antigen, A alpha chain
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / TCR / HLA
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / endoplasmic reticulum exit site ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / 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 / 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 / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / 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 / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum
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
HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKaruppiah, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: To Be Published
Title: Structure of S8 TCR in complex with HLA-A*03:01 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

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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 alpha chain
B: Beta-2-microglobulin
C: ELFSYLIEK peptide
D: TCR alpha
E: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2756
Polymers94,2125
Non-polymers621
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint-33 kcal/mol
Surface area37750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.120, 45.710, 121.680
Angle α, β, γ (deg.)90.00, 94.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


Mass: 31855.066 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: P04439
#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: 21877.305 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: 27458.391 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 , 1 types, 1 molecules C

#3: Protein/peptide ELFSYLIEK peptide


Mass: 1142.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 355 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM Magnesium acetate, 20 mM MOPS pH 7.2, 50 mM Sodium chloride, 12 % 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: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.81→121.23 Å / Num. obs: 104807 / % possible obs: 99.93 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.024 / Rrim(I) all: 0.066 / Net I/σ(I): 14.6
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 6 % / Rmerge(I) obs: 1.182 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5220 / CC1/2: 0.604 / Rpim(I) all: 0.526 / Rrim(I) all: 1.297 / % possible all: 99.98

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→121.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.699 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24099 5073 4.8 %RANDOM
Rwork0.22088 ---
obs0.22186 99734 99.93 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.154 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-1.31 Å2
2--1.87 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 1.81→121.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6498 0 4 354 6856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136683
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176042
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.6499070
X-RAY DIFFRACTIONr_angle_other_deg1.0831.58413926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2655810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36922.273396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.961151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5911550
X-RAY DIFFRACTIONr_chiral_restr0.0380.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027691
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021637
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_it0.7160.9963246
X-RAY DIFFRACTIONr_mcbond_other0.7150.9953245
X-RAY DIFFRACTIONr_mcangle_it1.2381.4864045
X-RAY DIFFRACTIONr_mcangle_other1.2381.4874046
X-RAY DIFFRACTIONr_scbond_it0.9241.0853437
X-RAY DIFFRACTIONr_scbond_other0.9241.0833435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4661.5945022
X-RAY DIFFRACTIONr_long_range_B_refined6.31212.0856938
X-RAY DIFFRACTIONr_long_range_B_other6.28811.4596858
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 383 -
Rwork0.366 7309 -
obs--99.97 %
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)
11.54930.00620.72221.12090.09282.38090.0238-0.40080.10410.1550.03580.22960.0556-0.3889-0.05960.4965-0.01360.06310.12840.01890.323-26.553-1.4560.824
23.5047-0.04411.67851.5573-0.22523.4059-0.0463-0.35350.19560.16340.0271-0.019-0.03130.07370.01920.43380.01180.06440.0661-0.0320.2445-10.4895.5128.746
32.2941-1.06550.81613.96980.48492.91330.02670.1521-0.1301-0.0508-0.00330.26670.12440.0968-0.02340.389-0.0394-0.01570.04690.0520.3297-28.588-3.856-19.393
41.00160.45561.84370.97570.45075.32960.09910.1767-0.0599-0.0399-0.073-0.05660.3993-0.7634-0.02610.5481-0.00290.01730.8496-0.05850.3093-37.423-17.66-53.108
50.55350.27711.1220.54140.62586.48020.03180.6376-0.041-0.06570.1133-0.22220.0970.856-0.14510.55890.08720.03980.87950.03380.3653-20.117-11.08-56.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 276
2X-RAY DIFFRACTION2B0 - 101
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4D1 - 192
5X-RAY DIFFRACTION5E4 - 244

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