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- PDB-8i5d: Crystal structure of a TCR in complex with HLA-A*11:01 bound to K... -

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Basic information

Entry
Database: PDB / ID: 8i5d
TitleCrystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVGAVGVGK)
Components
  • Beta-2-microglobulin
  • MHC class I antigen (Fragment)
  • TCR alpha chain
  • TCR beta chain
  • peptide KRAS-G12V-9
KeywordsIMMUNE SYSTEM / KRAS / TCR
Function / homology
Function and homology information


: / : / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 / 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-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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLu, D. / Chen, Y. / Jiang, M. / Tan, S.G. / Chai, Y. / Gao, G.F.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2022YFC2302900 China
National Natural Science Foundation of China (NSFC)2021YFC2301400 China
National Natural Science Foundation of China (NSFC)92169208 China
National Natural Science Foundation of China (NSFC)32222031 China
CitationJournal: Nat Commun / Year: 2023
Title: Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVGAVGVGK)
Authors: Lu, D. / Chen, Y. / Jiang, M. / Tan, S.G. / Chai, Y. / Gao, G.F.
History
DepositionJan 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.2Oct 16, 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: TCR alpha chain
B: TCR beta chain
H: MHC class I antigen (Fragment)
L: Beta-2-microglobulin
P: peptide KRAS-G12V-9


Theoretical massNumber of molelcules
Total (without water)92,9955
Polymers92,9955
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.819, 117.819, 314.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein TCR alpha chain


Mass: 21426.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein TCR beta chain


Mass: 27281.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein MHC class I antigen (Fragment)


Mass: 31753.006 Da / Num. of mol.: 1 / Mutation: A245V,E253Q
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: U5YJJ6
#4: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#5: Protein/peptide peptide KRAS-G12V-9


Mass: 785.951 Da / Num. of mol.: 1 / Mutation: G12V / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 10% w/v PEG 8000/ 8% v/v Ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 20334 / % possible obs: 99.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 74.5 Å2 / Rmerge(I) obs: 0.263 / Net I/σ(I): 8.333
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 1.2 / Num. unique obs: 1975

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.18.2_3874refinement
Cootmodel building
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UON, 6DFV, 6OVN, 7Z50

6uon

6dfv

6ovn

7z50


Resolution: 3.3→46.65 Å / SU ML: 0.443 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2557 867 5.04 %
Rwork0.2357 16326 -
obs0.2367 17193 84.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.79 Å2
Refinement stepCycle: LAST / Resolution: 3.3→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6543 0 0 0 6543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036708
X-RAY DIFFRACTIONf_angle_d0.6479110
X-RAY DIFFRACTIONf_chiral_restr0.0484965
X-RAY DIFFRACTIONf_plane_restr0.00431196
X-RAY DIFFRACTIONf_dihedral_angle_d15.56922453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.50.4181800.32491318X-RAY DIFFRACTION42.52
3.5-3.780.33431030.30642066X-RAY DIFFRACTION65.43
3.78-4.150.28651530.2773106X-RAY DIFFRACTION97.99
4.16-4.760.24271790.22583168X-RAY DIFFRACTION99.85
4.76-5.990.24381480.21563255X-RAY DIFFRACTION99.42
5.99-46.650.21862040.20213413X-RAY DIFFRACTION99.18

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