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- PDB-8ryq: Structure of S8-9F3 TCR in complex with HLA-A*11:01 bound to ELFS... -

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Basic information

Entry
Database: PDB / ID: 8ryq
TitleStructure of S8-9F3 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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / 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 / multicellular organismal-level iron ion homeostasis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / phagocytic vesicle membrane / recycling endosome 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 / positive regulation of T cell activation / Modulation by Mtb of host immune system / 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 / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / Golgi 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: 2.49 Å
AuthorsKaruppiah, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: To Be Published
Title: Structure of S8-9F3 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

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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
F: MHC class I antigen
G: Beta-2-microglobulin
H: ELFSYLIEK peptide
I: TCR alpha
J: TCR beta


Theoretical massNumber of molelcules
Total (without water)188,64710
Polymers188,64710
Non-polymers00
Water39622
1
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)94,3245
Polymers94,3245
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: ELFSYLIEK peptide
I: TCR alpha
J: TCR beta


Theoretical massNumber of molelcules
Total (without water)94,3245
Polymers94,3245
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.020, 88.890, 121.860
Angle α, β, γ (deg.)90.90, 98.54, 97.72
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22G
13D
23I
14E
24J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUAA1 - 2751 - 275
21GLYGLYGLUGLUFF1 - 2751 - 275
12ILEILEMETMETBB1 - 992 - 100
22ILEILEMETMETGG1 - 992 - 100
13LYSLYSCYSCYSDD2 - 1872 - 187
23LYSLYSCYSCYSII2 - 1872 - 187
14GLYGLYTRPTRPEE4 - 2404 - 240
24GLYGLYTRPTRPJJ4 - 2404 - 240

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

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


Mass: 31952.164 Da / Num. of mol.: 2
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.: 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
#4: Protein TCR alpha


Mass: 21891.350 Da / Num. of mol.: 2
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.: 2
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, 24 molecules CH

#3: Protein/peptide ELFSYLIEK peptide


Mass: 1142.321 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 150 mM Magnesium acetate, 20 mM MOPS pH 7.2, 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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→45.07 Å / Num. obs: 65184 / % possible obs: 98.43 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.044 / Rrim(I) all: 0.089 / Net I/σ(I): 9.3
Reflection shellResolution: 2.49→2.53 Å / Redundancy: 4 % / Rmerge(I) obs: 1.734 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3303 / CC1/2: 0.279 / Rpim(I) all: 0.987 / Rrim(I) all: 2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→45.07 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.927 / SU B: 40.89 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R: 0.711 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28286 3169 4.9 %RANDOM
Rwork0.2447 ---
obs0.24651 62015 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.397 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å2-3.9 Å21.48 Å2
2--1.77 Å2-0.21 Å2
3----4.4 Å2
Refinement stepCycle: 1 / Resolution: 2.49→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12978 0 0 22 13000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01313320
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711999
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.64818088
X-RAY DIFFRACTIONr_angle_other_deg1.0421.58427660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22451611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16522.316790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.848152176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.771599
X-RAY DIFFRACTIONr_chiral_restr0.0340.21672
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023259
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_it0.5093.5036471
X-RAY DIFFRACTIONr_mcbond_other0.513.5036469
X-RAY DIFFRACTIONr_mcangle_it0.9295.2538067
X-RAY DIFFRACTIONr_mcangle_other0.9295.2538067
X-RAY DIFFRACTIONr_scbond_it0.3743.5276849
X-RAY DIFFRACTIONr_scbond_other0.3743.5276850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6935.27510020
X-RAY DIFFRACTIONr_long_range_B_refined1.69837.92613385
X-RAY DIFFRACTIONr_long_range_B_other1.69837.92513385
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88160.06
12F88160.06
21B30560.06
22G30560.06
31D49200.09
32I49200.09
41E72450.07
42J72450.07
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 279 -
Rwork0.371 4553 -
obs--97.95 %
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)
11.6866-0.4587-0.65531.76390.572.9640.13150.23070.0604-0.3445-0.1128-0.0016-0.25260.0581-0.01870.103-0.0039-0.10660.35910.06990.4196-1.88720.3896-64.3529
23.4024-0.4677-2.57893.25811.52985.18230.0780.121-0.5054-0.2104-0.15990.09270.35610.1550.08190.12790.056-0.14990.41760.03550.36331.74353.077-72.4852
30.44071.63060.37246.89612.18921.21860.2028-0.0440.14960.3076-0.18880.3912-0.23260.1677-0.01390.2667-0.08850.04020.46080.06620.4901-4.868322.4308-44.7219
41.49390.3637-0.84512.19011.87854.17930.2557-0.51170.48540.3853-0.12670.3792-0.9756-0.232-0.12890.9640.14310.11380.6444-0.00190.7914-2.974938.5823-11.5862
51.2480.07-0.98040.3771-0.14374.06090.0596-0.4350.20560.40490.06550.1434-0.17550.2696-0.12510.4898-0.01170.01330.51970.04560.5216-1.263120.3532-6.2334
61.186-0.1186-0.67120.3895-0.12554.4146-0.0061-0.1625-0.0569-0.06090.13060.14550.5086-0.4309-0.12450.4831-0.0582-0.02010.54090.03940.5124-21.5932-15.918-0.9226
73.2569-0.22251.51541.8086-0.73446.54680.1191-0.18650.3521-0.0496-0.0611-0.2147-0.16850.0632-0.0580.42550.02450.09090.4881-0.0330.3817-11.2529-2.68479.0329
80.7182-1.83332.48156.629-6.20828.6999-0.0596-0.1229-0.0630.02710.2707-0.05030.073-0.4334-0.21120.6171-0.03360.0170.54010.06020.5334-20.5986-17.7655-20.5396
92.08230.5588-0.03532.3462-0.04145.6786-0.1350.4432-0.1835-0.42590.17-0.05720.0622-0.0155-0.0350.3192-0.0486-0.07560.3616-0.01690.5629-18.7359-35.2044-54.0072
101.53940.5331-0.23641.6765-0.02044.1822-0.16780.4559-0.0095-0.36580.1262-0.13650.18370.06270.04160.464-0.0893-0.05070.40780.03150.4776-6.778-20.4257-56.5544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION2B1 - 99
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4D2 - 188
5X-RAY DIFFRACTION5E4 - 244
6X-RAY DIFFRACTION6F1 - 275
7X-RAY DIFFRACTION7G1 - 99
8X-RAY DIFFRACTION8H1 - 9
9X-RAY DIFFRACTION9I2 - 193
10X-RAY DIFFRACTION10J3 - 241

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