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- PDB-3ftg: Crystal Structure of H2Db in complex with NP366-N3A variant pepti... -

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Basic information

Entry
Database: PDB / ID: 3ftg
TitleCrystal Structure of H2Db in complex with NP366-N3A variant peptide from influenza
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • NP366-N3A variant peptide from influenza virus
KeywordsIMMUNE SYSTEM / H2Db / mouse MHC / influenza / immunology / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain / Secreted
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 / 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 ...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 / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / 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 / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGras, S. / Guillonneau, C. / Rossjohn, J.
CitationJournal: Plos Pathog. / Year: 2010
Title: Protective efficacy of cross-reactive CD8+ T cells recognising mutant viral epitopes depends on peptide-MHC-I structural interactions and T cell activation threshold.
Authors: Valkenburg, S.A. / Gras, S. / Guillonneau, C. / La Gruta, N.L. / Thomas, P.G. / Purcell, A.W. / Rossjohn, J. / Doherty, P.C. / Turner, S.J. / Kedzierska, K.
History
DepositionJan 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: NP366-N3A variant peptide from influenza virus


Theoretical massNumber of molelcules
Total (without water)45,4203
Polymers45,4203
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-16 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.640, 94.980, 132.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 32601.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide NP366-N3A variant peptide from influenza virus


Mass: 983.074 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M lithium sulfate, 28% PEG 3350, 0.1M sodium citrate, pH 5.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 14, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 18264 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.22 % / Biso Wilson estimate: 47.68 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.55
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 6.93 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 6.4 / Num. measured obs: 13218 / Num. unique all: 1905 / Num. unique obs: 1905 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CPL

3cpl


Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.839 / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.814 / SU B: 22.366 / SU ML: 0.248 / SU R Cruickshank DPI: 0.52 / SU Rfree: 0.355 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.526 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1857 10.2 %RANDOM
Rwork0.221 ---
obs0.229 18178 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.26 Å2 / Biso mean: 40.807 Å2 / Biso min: 9.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 0 46 2982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213138
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9334268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0485372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41323.333168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70115525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.51528
X-RAY DIFFRACTIONr_chiral_restr0.0990.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022497
X-RAY DIFFRACTIONr_nbd_refined0.2320.21412
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.22
X-RAY DIFFRACTIONr_mcbond_it0.6861.51892
X-RAY DIFFRACTIONr_mcangle_it1.21622980
X-RAY DIFFRACTIONr_scbond_it1.34631467
X-RAY DIFFRACTIONr_scangle_it2.0374.51288
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 132 -
Rwork0.275 1130 -
all-1262 -
obs--97.23 %
Refinement TLS params.Method: refined / Origin x: -25.9475 Å / Origin y: 2.5776 Å / Origin z: 21.4264 Å
111213212223313233
T0.0057 Å2-0.028 Å20.0076 Å2--0.0135 Å20.005 Å2---0.0667 Å2
L0.467 °2-0.3306 °20.0957 °2-0.5904 °20.1539 °2--0.4579 °2
S0.0244 Å °-0.0483 Å °0.0004 Å °-0.0703 Å °-0.0058 Å °0.0479 Å °-0.0227 Å °-0.0397 Å °-0.0186 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1A181 - 275
3X-RAY DIFFRACTION1B1 - 99

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