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- PDB-5sws: Crystal Structure of NP2-B17 TCR-H2Db-NP complex -

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Basic information

Entry
Database: PDB / ID: 5sws
TitleCrystal Structure of NP2-B17 TCR-H2Db-NP complex
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • NP1-B17 TCR alpha chain
  • NP1-B17 TCR beta chain
  • influenza NP366 epitope
KeywordsIMMUNE SYSTEM / H2Db / influenza / NP366 / reversed docking / naive T cell / NP1-B17 TCR / TCR / T cell
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / 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 / viral penetration into host nucleus / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / host cell / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / ribonucleoprotein complex / symbiont entry into host cell / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / host cell nucleus / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / 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-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 ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.86 Å
AuthorsGras, S. / Del Campo, C.M. / Farenc, C. / Josephs, T.M. / Rossjohn, J.
CitationJournal: Immunity / Year: 2016
Title: Reversed T Cell Receptor Docking on a Major Histocompatibility Class I Complex Limits Involvement in the Immune Response.
Authors: Gras, S. / Chadderton, J. / Del Campo, C.M. / Farenc, C. / Wiede, F. / Josephs, T.M. / Sng, X.Y. / Mirams, M. / Watson, K.A. / Tiganis, T. / Quinn, K.M. / Rossjohn, J. / La Gruta, N.L.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: influenza NP366 epitope
D: NP1-B17 TCR alpha chain
E: NP1-B17 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)95,9505
Polymers95,9505
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-49 kcal/mol
Surface area39900 Å2
Unit cell
Length a, b, c (Å)48.017, 126.942, 80.479
Angle α, β, γ (deg.)90.000, 105.660, 90.000
Int Tables number4
Space group name H-MP1211

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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: 32470.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#4: Protein NP1-B17 TCR alpha chain


Mass: 23172.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein NP1-B17 TCR beta chain


Mass: 27621.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Protein/peptide / Non-polymers , 2 types, 140 molecules C

#3: Protein/peptide influenza NP366 epitope


Mass: 1026.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) unidentified influenza virus / References: UniProt: Q9Q0U8*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.46 Å3/Da / Density % sol: 50.03 % / Mosaicity: 0.08 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 17% 3350, 0.2 KNaTartrate, 0.1 BTP 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.86→49.1 Å / Num. all: 21354 / Num. obs: 21354 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 64.49 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.081 / Rrim(I) all: 0.169 / Rsym value: 0.124 / Net I/σ(I): 10.6 / Num. measured all: 90916
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.86-3.014.20.5791301730880.7730.0220.0430.0292.397.2
9.04-49.13.90.02926966920.9980.0350.0730.05338.697.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHASERphasing
BUSTER-TNT2.10.1refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HUU, 1KGC

4huu

1kgc


Resolution: 2.86→30.48 Å / Cor.coef. Fo:Fc: 0.8685 / Cor.coef. Fo:Fc free: 0.8198 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.428
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 1102 5.18 %RANDOM
Rwork0.2307 ---
obs0.2329 21281 99.06 %-
Displacement parametersBiso max: 139.53 Å2 / Biso mean: 47.82 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.0562 Å20 Å2-7.273 Å2
2--11.5034 Å20 Å2
3----11.4472 Å2
Refine analyzeLuzzati coordinate error obs: 0.474 Å
Refinement stepCycle: final / Resolution: 2.86→30.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6591 0 0 143 6734
Biso mean---28.08 -
Num. residues----816
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2319SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes187HARMONIC2
X-RAY DIFFRACTIONt_gen_planes973HARMONIC5
X-RAY DIFFRACTIONt_it6808HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion851SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6975SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6808HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg9248HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion1.61
X-RAY DIFFRACTIONt_other_torsion21.3
LS refinement shellResolution: 2.86→3 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3416 132 4.69 %
Rwork0.2643 2681 -
all0.2678 2813 -
obs--99.06 %
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)
10.3987-0.00170.25362.512-0.80670.3762-0.00770.0143-0.01230.0129-0.0016-0.08550.00980.00770.0093-0.09610.06910.0712-0.0376-0.03680.0445107.996932.9699-17.5433
21.32440.6249-0.73280.7672-0.40190.28950.0067-0.0065-0.01660.01250.00760.02320.0178-0.0472-0.0143-0.0279-0.00930.0320.01530.0290.042393.403821.1548-9.7616
30.73750.3456-0.20971.565-0.1579-0.17550.02350.0238-0.01930.00420.00920.0001-0.09560.0018-0.0327-0.0590.0784-0.00720.0007-0.09320.044377.515388.9953-23.6397
40.4888-0.3775-0.11743.2796-0.2470.01130.02630.0071-0.0081-0.0083-0.0222-0.0264-0.0310.0254-0.0041-0.00050.00860.001-0.05640.0151-0.005797.103488.6546-26.0407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 277
2X-RAY DIFFRACTION2{ B|* }B3 - 99
3X-RAY DIFFRACTION3{ D|* }D1 - 214
4X-RAY DIFFRACTION4{ E|* }E3 - 254

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