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- PDB-7jwi: Crystal structure of B17.R2 TCR in complex with H2D-b-NP366 -

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Basic information

Entry
Database: PDB / ID: 7jwi
TitleCrystal structure of B17.R2 TCR in complex with H2D-b-NP366
Components
  • B17.R2 TCR alpha chain
  • B17.R2 TCR beta chain
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / TCR / MHC
Function / homology
Function and homology information


helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 ...helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / lumenal side of endoplasmic reticulum membrane / 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 / viral penetration into host nucleus / 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 / host cell / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / ribonucleoprotein complex / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / symbiont entry into host cell / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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
H-2 class I histocompatibility antigen, D-B alpha chain / Beta-2-microglobulin / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsFarenc, C. / Rossjohn, J.
CitationJournal: Science / Year: 2021
Title: Canonical T cell receptor docking on peptide-MHC is essential for T cell signaling.
Authors: Zareie, P. / Szeto, C. / Farenc, C. / Gunasinghe, S.D. / Kolawole, E.M. / Nguyen, A. / Blyth, C. / Sng, X.Y.X. / Li, J. / Jones, C.M. / Fulcher, A.J. / Jacobs, J.R. / Wei, Q. / Wojciech, L. ...Authors: Zareie, P. / Szeto, C. / Farenc, C. / Gunasinghe, S.D. / Kolawole, E.M. / Nguyen, A. / Blyth, C. / Sng, X.Y.X. / Li, J. / Jones, C.M. / Fulcher, A.J. / Jacobs, J.R. / Wei, Q. / Wojciech, L. / Petersen, J. / Gascoigne, N.R.J. / Evavold, B.D. / Gaus, K. / Gras, S. / Rossjohn, J. / La Gruta, N.L.
History
DepositionAug 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Nucleoprotein
D: B17.R2 TCR alpha chain
E: B17.R2 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8386
Polymers104,7765
Non-polymers621
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-47 kcal/mol
Surface area38820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.668, 140.997, 217.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 40885.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01899
#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, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#4: Protein B17.R2 TCR alpha chain


Mass: 23117.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein B17.R2 TCR beta chain


Mass: 27868.260 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)

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 1026.099 Da / Num. of mol.: 1 / Fragment: NP-366 epitope (UNP residues 366-374) / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q9Q0U8

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Non-polymers , 2 types, 91 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG3350, 0.2 M potassium/sodium tartrate, 0.1 M Bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.02→44.27 Å / Num. obs: 28123 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.99 / Net I/σ(I): 11.53
Reflection shellResolution: 3.02→3.13 Å / Mean I/σ(I) obs: 1.82 / Num. unique obs: 2781 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XFITdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5SWZ

5swz


Resolution: 3.02→44.27 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1412 5.02 %RANDOM
Rwork0.239 ---
obs-28123 100 %-
Displacement parametersBiso mean: 63.18 Å2
Baniso -1Baniso -2Baniso -3
1-27.6662 Å20 Å20 Å2
2---32.6788 Å20 Å2
3---5.0126 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: 1 / Resolution: 3.02→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6707 0 4 92 6803
LS refinement shellResolution: 3.02→3.04 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3139 33 5.86 %
Rwork0.2964 530 -
obs--100 %

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