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- PDB-3nwm: Crystal structure of a single chain construct composed of MHC cla... -

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Basic information

Entry
Database: PDB / ID: 3nwm
TitleCrystal structure of a single chain construct composed of MHC class I H-2Kd, beta-2microglobulin and a peptide which is an autoantigen for type 1 diabetes
ComponentsPeptide/beta-2microglobulin/MHC class I H-2Kd chimeric protein
KeywordsIMMUNE SYSTEM / MHC class I / H-2Kd / peptide-MHC complex / Immunoglobulin fold
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 / cellular defense response / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, 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 / cellular defense response / Neutrophil degranulation / 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 / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / membrane => GO:0016020 / learning or memory / lysosomal membrane / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
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. ...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 / MHC class I heavy chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2FWO / Resolution: 2.7 Å
AuthorsRamagopal, U.A. / Samanta, D. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural and functional characterization of a single-chain peptide-MHC molecule that modulates both naive and activated CD8+ T cells.
Authors: Samanta, D. / Mukherjee, G. / Ramagopal, U.A. / Chaparro, R.J. / Nathenson, S.G. / DiLorenzo, T.P. / Almo, S.C.
History
DepositionJul 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Database references
Revision 1.3Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide/beta-2microglobulin/MHC class I H-2Kd chimeric protein


Theoretical massNumber of molelcules
Total (without water)49,6591
Polymers49,6591
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.347, 88.527, 61.203
Angle α, β, γ (deg.)90.000, 102.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptide/beta-2microglobulin/MHC class I H-2Kd chimeric protein


Mass: 49659.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q91XJ8, UniProt: Q5KTQ2, UniProt: P01887*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 8K, TrisHCl pH 8.5, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 11893 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.099 / Rsym value: 0.077 / Χ2: 1.32 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.754.10.5365941.349199.8
2.75-2.84.10.445951.3611100
2.8-2.854.20.3815771.3281100
2.85-2.914.20.3915951.3271100
2.91-2.974.10.3025871.3851100
2.97-3.044.10.3065901.7521100
3.04-3.124.20.2485851.481199.8
3.12-3.24.20.1925971.311100
3.2-3.34.20.1525851.3511100
3.3-3.44.10.1416141.3791100
3.4-3.524.20.1115761.322199.8
3.52-3.664.20.16021.3811100
3.66-3.834.10.0926001.3121100
3.83-4.034.10.0785821.3431100
4.03-4.294.10.0735951.2911100
4.29-4.624.10.066081.1951100
4.62-5.084.10.066011.1941100
5.08-5.8140.0555891.0851100
5.81-7.324.10.0615991.1221100
7.32-504.10.0496221.114199

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: 2FWO / Resolution: 2.7→59.65 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.26 / WRfactor Rwork: 0.1913 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7827 / SU ML: 0.31 / SU Rfree: 0.4143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 564 4.8 %RANDOM
Rwork0.2024 ---
all0.2064 11853 --
obs0.2064 11853 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 79.64 Å2 / Biso mean: 43.0386 Å2 / Biso min: 19.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20.93 Å2
2---3.87 Å20 Å2
3---5.61 Å2
Refinement stepCycle: LAST / Resolution: 2.7→59.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 0 14 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223259
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.934432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34423.118170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69415521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9031527
X-RAY DIFFRACTIONr_chiral_restr0.0760.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212559
X-RAY DIFFRACTIONr_mcbond_it0.88421918
X-RAY DIFFRACTIONr_mcangle_it1.59733100
X-RAY DIFFRACTIONr_scbond_it0.69321341
X-RAY DIFFRACTIONr_scangle_it1.13831331
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 31 -
Rwork0.332 846 -
all-877 -
obs--96.91 %

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