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- PDB-8rlv: TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 L6I... -

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Basic information

Entry
Database: PDB / ID: 8rlv
TitleTCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 L6I peptide
Components
  • (T cell receptor ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain E
  • Large envelope protein
KeywordsIMMUNE SYSTEM / TCR-MHC / TCR / HLA-E / HBV / affinity matured / pHLA
Function / homology
Function and homology information


detection of tumor cell / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction ...detection of tumor cell / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / caveolin-mediated endocytosis of virus by host cell / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / alpha-beta T cell receptor complex / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / 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 / positive regulation of interleukin-4 production / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / negative regulation of receptor binding / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / 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 / response to bacterium / 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 / sensory perception of smell / 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 T cell mediated cytotoxicity / positive regulation of cellular senescence / 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 / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / antibacterial humoral response / late endosome membrane / signaling receptor activity / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium
Similarity search - Function
Large envelope protein S / Major surface antigen from hepadnavirus / : / : / : / 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 alpha chain, alpha1 alpha2 domains ...Large envelope protein S / Major surface antigen from hepadnavirus / : / : / : / 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 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
T cell receptor alpha variable 12-2 / T cell receptor beta variable 6-5 / T cell receptor alpha chain MC.7.G5 / T cell receptor beta chain MC.7.G5 / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin / Large envelope protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.609 Å
AuthorsPengelly, R.J. / Godinho, L.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: To Be Published
Title: TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 L6I peptide
Authors: Pengelly, R.J. / Godinho, L.F.
History
DepositionJan 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 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, alpha chain E
B: Beta-2-microglobulin
C: Large envelope protein
D: T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5
E: T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5
F: HLA class I histocompatibility antigen, alpha chain E
G: Beta-2-microglobulin
H: Large envelope protein
I: T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5
J: T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5


Theoretical massNumber of molelcules
Total (without water)188,19310
Polymers188,19310
Non-polymers00
Water2,342130
1
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
C: Large envelope protein
D: T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5
E: T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5


Theoretical massNumber of molelcules
Total (without water)94,0975
Polymers94,0975
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, alpha chain E
G: Beta-2-microglobulin
H: Large envelope protein
I: T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5
J: T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5


Theoretical massNumber of molelcules
Total (without water)94,0975
Polymers94,0975
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.185, 153.813, 93.400
Angle α, β, γ (deg.)90.000, 96.628, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A

NCS domain segments:

Refine code: 1 / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPRO1 - 2761 - 276
211GLYGLYPROPRO1 - 2761 - 276
322GLYGLYHISHIS1 - 991 - 99
422GLYGLYHISHIS1 - 991 - 99
533SERSERTHRTHR2 - 1902 - 190
633SERSERTHRTHR2 - 1902 - 190
744HISHISASPASP3 - 2383 - 238
844HISHISASPASP3 - 2383 - 238

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8

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Components

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Protein , 2 types, 4 molecules AFBG

#1: Protein HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


Mass: 31824.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / 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

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T cell receptor ... , 2 types, 4 molecules DIEJ

#4: Protein T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 / MC.7.G5 TRA / TR alpha chain TRAV38-2DV8*01J31*01C*01


Mass: 21944.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV12-2, TRA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A075B6T6, UniProt: P0DTU3
#5: Protein T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 / TR beta chain TRBV25-1*01J2S3*01C2*01 / MC.7.G5 TRB


Mass: 27436.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV6-5, TRB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0K1A5, UniProt: P0DTU4

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Protein/peptide / Non-polymers , 2 types, 132 molecules CH

#3: Protein/peptide Large envelope protein / L glycoprotein / L-HBsAg / LHB / Large S protein / Large surface protein / Major surface antigen


Mass: 1012.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Hepatitis B virus / References: UniProt: Q67953
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Collection Temp: 100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.609→79.65 Å / Num. obs: 67783 / % possible obs: 99.2 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.057 / Net I/σ(I): 0.142
Reflection shellResolution: 2.609→2.65 Å / Rmerge(I) obs: 3.246 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 3323 / CC1/2: 0.313 / Rpim(I) all: 1.345

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
DIALS3.8.2data reduction
DIALS3.8.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.609→79.65 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 20.743 / SU ML: 0.36 / Cross valid method: FREE R-VALUE / ESU R: 0.544 / ESU R Free: 0.3
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2506 3360 4.961 %
Rwork0.1976 64366 -
all0.2 --
obs-67726 99.097 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 94.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.208 Å20 Å24.013 Å2
2--2.416 Å2-0 Å2
3----3.464 Å2
Refinement stepCycle: LAST / Resolution: 2.609→79.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12910 0 0 130 13040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01213270
X-RAY DIFFRACTIONr_bond_other_d0.0020.01611887
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.65618036
X-RAY DIFFRACTIONr_angle_other_deg0.5471.57527417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4351597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.812591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.556102134
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.02410675
X-RAY DIFFRACTIONr_chiral_restr0.0670.21901
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023223
X-RAY DIFFRACTIONr_nbd_refined0.210.22570
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.211666
X-RAY DIFFRACTIONr_nbtor_refined0.1840.26214
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.27302
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2394
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.020.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1050.211
X-RAY DIFFRACTIONr_nbd_other0.1890.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.23
X-RAY DIFFRACTIONr_mcbond_it8.6989.5366430
X-RAY DIFFRACTIONr_mcbond_other8.6889.5366429
X-RAY DIFFRACTIONr_mcangle_it12.5917.1148013
X-RAY DIFFRACTIONr_mcangle_other12.58917.1148014
X-RAY DIFFRACTIONr_scbond_it8.5649.776840
X-RAY DIFFRACTIONr_scbond_other8.5639.776841
X-RAY DIFFRACTIONr_scangle_it12.67317.79510023
X-RAY DIFFRACTIONr_scangle_other12.67217.79510024
X-RAY DIFFRACTIONr_lrange_it15.95889.14314400
X-RAY DIFFRACTIONr_lrange_other15.95789.14714399
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.058849
X-RAY DIFFRACTIONr_ncsr_local_group_20.0930.053126
X-RAY DIFFRACTIONr_ncsr_local_group_30.1130.055112
X-RAY DIFFRACTIONr_ncsr_local_group_40.1230.057132
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.091370.05009
12AX-RAY DIFFRACTIONLocal ncs0.091370.05009
23AX-RAY DIFFRACTIONLocal ncs0.092880.05009
24AX-RAY DIFFRACTIONLocal ncs0.092880.05009
35AX-RAY DIFFRACTIONLocal ncs0.11260.05009
36AX-RAY DIFFRACTIONLocal ncs0.11260.05009
47AX-RAY DIFFRACTIONLocal ncs0.123110.05008
48AX-RAY DIFFRACTIONLocal ncs0.123110.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.609-2.6770.4352260.4084705X-RAY DIFFRACTION97.3352
2.677-2.750.3942480.3784632X-RAY DIFFRACTION98.9858
2.75-2.830.3842210.3694458X-RAY DIFFRACTION98.7756
2.83-2.9170.3492160.3484357X-RAY DIFFRACTION98.7689
2.917-3.0120.3262100.3154224X-RAY DIFFRACTION98.8849
3.012-3.1180.3082090.2924087X-RAY DIFFRACTION99.009
3.118-3.2350.3372230.2623937X-RAY DIFFRACTION99.0712
3.235-3.3670.2951700.2343834X-RAY DIFFRACTION99.1826
3.367-3.5160.2851860.2243679X-RAY DIFFRACTION99.2808
3.516-3.6880.3021860.2143493X-RAY DIFFRACTION99.3519
3.688-3.8870.2061920.1693313X-RAY DIFFRACTION99.4044
3.887-4.1220.2151820.1533135X-RAY DIFFRACTION99.4305
4.122-4.4060.2021620.1272969X-RAY DIFFRACTION99.4284
4.406-4.7570.1651520.1162756X-RAY DIFFRACTION99.4868
4.757-5.210.1741320.1172564X-RAY DIFFRACTION99.741
5.21-5.8210.231190.1632324X-RAY DIFFRACTION99.633
5.821-6.7160.2651200.182052X-RAY DIFFRACTION99.8162
6.716-8.2110.2281010.1541699X-RAY DIFFRACTION99.8336
8.211-11.5510.207700.1421371X-RAY DIFFRACTION99.7922
11.551-79.650.337350.279777X-RAY DIFFRACTION100

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