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- PDB-8yj2: N17.1.2 recognition of NRAS neoantigens -

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Basic information

Entry
Database: PDB / ID: 8yj2
TitleN17.1.2 recognition of NRAS neoantigens
Components
  • Beta-2-microglobulin
  • ILE-LEU-ASP-THR-ALA-GLY-ARG-GLU-GLU-TYR
  • human leukocyte antigen
  • tcr alpha
  • tcr beta
KeywordsIMMUNE SYSTEM / T cell receptor / p-MHC
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma 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 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. ...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: 2.261 Å
AuthorsWu, D.C. / Mariuzza, R.A.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270995 China
National Natural Science Foundation of China (NSFC)32100985 China
CitationJournal: Sci Adv / Year: 2024
Title: Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens.
Authors: Wu, D. / Yin, R. / Chen, G. / Ribeiro-Filho, H.V. / Cheung, M. / Robbins, P.F. / Mariuzza, R.A. / Pierce, B.G.
History
DepositionFeb 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 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: human leukocyte antigen
B: Beta-2-microglobulin
C: ILE-LEU-ASP-THR-ALA-GLY-ARG-GLU-GLU-TYR
E: tcr beta
D: tcr alpha


Theoretical massNumber of molelcules
Total (without water)96,2055
Polymers96,2055
Non-polymers00
Water7,674426
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11510 Å2
ΔGint-36 kcal/mol
Surface area37860 Å2
Unit cell
Length a, b, c (Å)71.524, 134.158, 222.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-327-

HOH

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Components

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Protein , 3 types, 3 molecules ABE

#1: Protein human leukocyte antigen


Mass: 31897.266 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: F6IQR9
#2: Protein Beta-2-microglobulin


Mass: 11879.356 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
#4: Protein tcr beta


Mass: 28186.664 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 / Antibody / Non-polymers , 3 types, 428 molecules CD

#3: Protein/peptide ILE-LEU-ASP-THR-ALA-GLY-ARG-GLU-GLU-TYR


Mass: 1167.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Antibody tcr alpha


Mass: 23074.811 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)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10mg/ml, 0.2 M NH4 citrate tribasic, 16% PEG3350, pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.26→42.8 Å / Num. obs: 464104 / % possible obs: 98.5 % / Redundancy: 9.3 % / CC1/2: 0.985 / Net I/σ(I): 13.5
Reflection shellResolution: 2.26→2.34 Å / CC1/2: 0.883

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.261→42.776 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 2476 4.99 %
Rwork0.189 --
obs0.1909 49611 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.261→42.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6680 0 0 426 7106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086860
X-RAY DIFFRACTIONf_angle_d0.9299316
X-RAY DIFFRACTIONf_dihedral_angle_d7.6714099
X-RAY DIFFRACTIONf_chiral_restr0.054983
X-RAY DIFFRACTIONf_plane_restr0.0061223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2613-2.30480.26011280.22742333X-RAY DIFFRACTION88
2.3048-2.35180.28831250.2282472X-RAY DIFFRACTION96
2.3518-2.40290.25471450.21952624X-RAY DIFFRACTION99
2.4029-2.45880.29181590.22012596X-RAY DIFFRACTION100
2.4588-2.52030.26711490.21312597X-RAY DIFFRACTION100
2.5203-2.58850.2661700.21522613X-RAY DIFFRACTION100
2.5885-2.66460.25481240.21362611X-RAY DIFFRACTION100
2.6646-2.75060.24831530.20692623X-RAY DIFFRACTION99
2.7506-2.84890.28341120.21412639X-RAY DIFFRACTION100
2.8489-2.96290.25421120.21352669X-RAY DIFFRACTION100
2.9629-3.09770.24391250.21122614X-RAY DIFFRACTION98
3.0977-3.2610.25651210.20372671X-RAY DIFFRACTION100
3.261-3.46520.23321190.18752665X-RAY DIFFRACTION100
3.4652-3.73260.23061560.18722640X-RAY DIFFRACTION100
3.7326-4.1080.21931270.17352657X-RAY DIFFRACTION99
4.108-4.70180.17751500.14622652X-RAY DIFFRACTION98
4.7018-5.92130.19031700.15352689X-RAY DIFFRACTION100
5.9213-42.7760.20161310.18462770X-RAY DIFFRACTION97

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