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

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Basic information

Entry
Database: PDB / ID: 8yiv
TitleN17.1.2 recognition of NRAS neoantigens
Components
  • Beta-2-microglobulin
  • ILE-LEU-ASP-THR-ALA-GLY-LYS-GLU-GLU-TYR
  • MHC class I antigen
  • TCR ALPHA
  • TCR beta
KeywordsIMMUNE SYSTEM / T cell receptor / p-MHC
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 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: 2.101 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: MHC class I antigen
C: ILE-LEU-ASP-THR-ALA-GLY-LYS-GLU-GLU-TYR
B: Beta-2-microglobulin
D: TCR ALPHA
E: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,03815
Polymers96,1775
Non-polymers86110
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13960 Å2
ΔGint-39 kcal/mol
Surface area37590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.144, 133.223, 222.468
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-518-

HOH

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein MHC class I 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
#3: 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 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)
#5: 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 , 1 types, 1 molecules C

#2: Protein/peptide ILE-LEU-ASP-THR-ALA-GLY-LYS-GLU-GLU-TYR


Mass: 1139.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 557 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10mg/ml, 8% TacsimateTM pH7.0, 20% PEG4K

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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: 2.1→42.7 Å / Num. obs: 387710 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.992 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.18 Å / CC1/2: 0.857

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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: 2.101→42.692 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 3116 5.05 %
Rwork0.1907 --
obs0.1925 61738 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.101→42.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6683 0 56 547 7286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116919
X-RAY DIFFRACTIONf_angle_d1.1319374
X-RAY DIFFRACTIONf_dihedral_angle_d7.8674124
X-RAY DIFFRACTIONf_chiral_restr0.061985
X-RAY DIFFRACTIONf_plane_restr0.0081223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1012-2.1340.27061450.22042576X-RAY DIFFRACTION99
2.134-2.1690.31481340.23162636X-RAY DIFFRACTION99
2.169-2.20640.31541380.22832609X-RAY DIFFRACTION100
2.2064-2.24650.29421540.22932634X-RAY DIFFRACTION100
2.2465-2.28970.29531470.23222672X-RAY DIFFRACTION100
2.2897-2.33640.27991370.22482610X-RAY DIFFRACTION100
2.3364-2.38720.23591370.22142635X-RAY DIFFRACTION100
2.3872-2.44280.27051420.2172679X-RAY DIFFRACTION100
2.4428-2.50390.31141340.21362648X-RAY DIFFRACTION100
2.5039-2.57150.29291450.22342642X-RAY DIFFRACTION100
2.5715-2.64720.26731360.20872636X-RAY DIFFRACTION100
2.6472-2.73260.22411280.21252691X-RAY DIFFRACTION100
2.7326-2.83030.26981330.21072658X-RAY DIFFRACTION100
2.8303-2.94360.2761200.21542674X-RAY DIFFRACTION100
2.9436-3.07750.25531400.21432678X-RAY DIFFRACTION100
3.0775-3.23970.23551500.20222669X-RAY DIFFRACTION100
3.2397-3.44260.21491480.18832680X-RAY DIFFRACTION100
3.4426-3.70830.19641610.1812659X-RAY DIFFRACTION100
3.7083-4.08120.21141570.16632652X-RAY DIFFRACTION100
4.0812-4.67110.16221390.14292735X-RAY DIFFRACTION100
4.6711-5.88270.16471520.15352728X-RAY DIFFRACTION100
5.8827-42.6920.21731390.1932821X-RAY DIFFRACTION98

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