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- PDB-1u58: Crystal structure of the murine cytomegalovirus MHC-I homolog m144 -

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Basic information

Entry
Database: PDB / ID: 1u58
TitleCrystal structure of the murine cytomegalovirus MHC-I homolog m144
Components
  • MHC-I homolog m144
  • beta-2-microglobulin
KeywordsIMMUNE SYSTEM / MCMV / MHC-I homolog / m144 / beta-2m
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 / negative regulation of forebrain neuron differentiation ...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 / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / 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 / : / 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 ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / : / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Immunoevasin / Beta-2-microglobulin
Similarity search - Component
Biological speciesMurid herpesvirus 1 (Murine cytomegalovirus)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNatarajan, K. / Hicks, A. / Robinson, H. / Guan, R. / Margulies, D.H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of the murine cytomegalovirus MHC-I homolog m144.
Authors: Natarajan, K. / Hicks, A. / Mans, J. / Robinson, H. / Guan, R. / Mariuzza, R.A. / Margulies, D.H.
History
DepositionJul 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE AMINO ACID SEQUENCE OF CHAIN A IS TRANSLATED FROM THE M144 OPEN READING FRAME AS FOUND ...SEQUENCE THE AMINO ACID SEQUENCE OF CHAIN A IS TRANSLATED FROM THE M144 OPEN READING FRAME AS FOUND IN MCMV GENOME, ACCESSION NUMBER NC_004065.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC-I homolog m144
B: beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)40,0122
Polymers40,0122
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-10 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.400, 51.200, 71.700
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC-I homolog m144


Mass: 28351.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 1 (Murine cytomegalovirus)
Genus: Muromegalovirus / Gene: m144 / Plasmid: pET21-b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2Q6L5*PLUS
#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) / Plasmid: pET21-b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 31981890, UniProt: P01887*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.96 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 20K, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 39025 / Num. obs: 36627 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.11
Reflection shellResolution: 1.87→1.94 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.8 / % possible all: 95.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A6Z

1a6z


Resolution: 1.9→41.14 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.229 3518 RANDOM
Rwork0.211 --
all-35397 -
obs-35397 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.66 Å20 Å2-3.97 Å2
2--1.39 Å20 Å2
3---1.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 0 290 2857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.027
X-RAY DIFFRACTIONc_angle_deg2
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.274 553 -
Rwork0.272 --
obs-4972 90.6 %

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