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- PDB-2fwo: MHC Class I H-2Kd heavy chain in complex with beta-2microglobulin... -

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Basic information

Entry
Database: PDB / ID: 2fwo
TitleMHC Class I H-2Kd heavy chain in complex with beta-2microglobulin and peptide derived from influenza nucleoprotein
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-D alpha chain
  • TYQRTRALV peptide from Nucleoprotein
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / MHC / Antigens/Peptides/Epitopes / Antigen Processing/Presentation / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX
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 exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...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 exogenous peptide antigen via MHC class I / inner ear development / 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 Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / 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 / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / viral penetration into host nucleus / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / host cell / 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 / defense response to bacterium / immune response / symbiont entry into host cell / ribonucleoprotein complex / 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 / cytosol
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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, K-D alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMitaksov, V. / Fremont, D.H.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Definition of the H-2Kd Peptide-binding Motif.
Authors: Mitaksov, V. / Fremont, D.H.
History
DepositionFeb 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, K-D alpha chain
B: Beta-2-microglobulin
P: TYQRTRALV peptide from Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)45,8553
Polymers45,8553
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-13 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.200, 85.300, 42.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein H-2 class I histocompatibility antigen, K-D alpha chain / H-2KD


Mass: 32910.566 Da / Num. of mol.: 1 / Fragment: Extracellular domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(DE3)RIL / References: UniProt: P01902
#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: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(DE3)RIL / References: UniProt: P01887
#3: Protein/peptide TYQRTRALV peptide from Nucleoprotein


Mass: 1109.279 Da / Num. of mol.: 1 / Fragment: Residues 147-155 / Source method: obtained synthetically
Details: Peptide derived from Influenza Virus A/PR/8/34 nucleoprotein residues 147-155
References: UniProt: Q701N7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM HEPES, 12% (w:v) PEG2000, 5% (w:v) MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 30, 2004 / Details: Yale Mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 7.3 / Number: 72826 / Rmerge(I) obs: 0.138 / Χ2: 1.06 / D res high: 2.6 Å / D res low: 20 Å / Num. obs: 12405 / % possible obs: 89.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squared
5.1720183197.810.0791.063
4.125.17147183.210.0871.071
3.64.12143483.310.1231.109
3.273.6148486.110.1951.089
3.043.2715008810.3121.085
2.863.04154190.110.4931.05
2.722.8615549110.7171.011
2.62.72159092.910.9411.005
ReflectionResolution: 2.6→20 Å / Num. all: 13969 / Num. obs: 12405 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Χ2: 1.059 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.72 Å / % possible obs: 92.9 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.66 / Num. unique obs: 1590 / Rsym value: 0.615 / Χ2: 1.005 / % possible all: 92.9

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Phasing

Phasing MRRfactor: 0.494 / Cor.coef. Fo:Fc: 0.331 / Cor.coef. Io to Ic: 0.365
Highest resolutionLowest resolution
Rotation4 Å15 Å
Translation4 Å8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VAC

1vac


Resolution: 2.6→20 Å / FOM work R set: 0.808 / Isotropic thermal model: Anisotropic, restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 592 4.3 %Random
Rwork0.218 ---
all0.252 11808 --
obs0.252 11652 85.1 %-
Solvent computationBsol: 45.049 Å2
Displacement parametersBiso mean: 52.628 Å2
Baniso -1Baniso -2Baniso -3
1--23.064 Å20 Å20 Å2
2--17.182 Å20 Å2
3---5.882 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 0 114 3284
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.6-2.680.345400.353946986
2.68-2.780.373580.332937995
2.78-2.890.313660.3129601026
2.89-3.020.359510.2869971048
3.02-3.180.345390.26910041043
3.18-3.380.277400.23710041044
3.38-3.640.301580.2329611019
3.64-40.221560.1719611017
4-4.570.246480.1719741022
4.57-5.740.242550.19310721127
5.74-200.244810.19412441325
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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