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- PDB-1pqz: MURINE CYTOMEGALOVIRUS IMMUNOMODULATORY PROTEIN M144 -

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Basic information

Entry
Database: PDB / ID: 1pqz
TitleMURINE CYTOMEGALOVIRUS IMMUNOMODULATORY PROTEIN M144
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MCMV M144
KeywordsViral protein/Immune system / Virus / immune evasion / MCMV / MHC / IG domain / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Viral protein-Immune system 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 / regulation of membrane depolarization / cellular defense response / Neutrophil degranulation / cellular response to iron(III) ion ...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 / regulation of membrane depolarization / 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 / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / 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 ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / 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
Similarity search - Component
Biological speciesMurid herpesvirus 1 (Murine cytomegalovirus)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsMiley, M.J. / Fremont, D.H. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: MURINE CYTOMEGALOVIRUS IMMUNOMODULATORY PROTEIN M144
Authors: Miley, M.J. / Fremont, D.H.
History
DepositionJun 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE The complete MCMV genome can be found at NCBI accession NC_004065

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MCMV M144
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)38,1892
Polymers38,1892
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-8 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.800, 50.600, 71.200
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MCMV M144


Mass: 26484.465 Da / Num. of mol.: 1 / Fragment: Mature m144 EctoDomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 1 (Murine cytomegalovirus)
Genus: Muromegalovirus / Gene: m144 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(DE3)RIL
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: Mature Beta-2-Microglobulin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(DE3)RIL / References: UniProt: P01887
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 16% PEG 8k 100mM cacodylate pH 5.8, .02% Ethyl Acetate, 150mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 117 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 18, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 27229 / % possible obs: 95.9 % / Redundancy: 2.57 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 18.61
Reflection shellResolution: 2.05→2.14 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.16 / % possible all: 95.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→19.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 844514.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1161 4.9 %RANDOM
Rwork0.245 ---
obs0.245 23529 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.2 Å2 / ksol: 0.324161 e/Å3
Displacement parametersBiso mean: 55.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.12 Å20 Å2-12.97 Å2
2---6.34 Å20 Å2
3----5.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 0 172 2853
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 183 5.1 %
Rwork0.389 3382 -
obs--82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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