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- PDB-8frt: X-ray crystal structure of the N-terminal region from HCMV US11 b... -

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Basic information

Entry
Database: PDB / ID: 8frt
TitleX-ray crystal structure of the N-terminal region from HCMV US11 binding to HLA-A*02:01
ComponentsUnique short US11 glycoprotein, Beta-2-microglobulin, MHC class I HLA-A fusion
KeywordsIMMUNE SYSTEM / immunoevasin / molecular mimicry
Function / homology
Function and homology information


: / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding ...: / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / host cell endoplasmic reticulum membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Cytomegalovirus US glycoprotein / CMV US / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...Cytomegalovirus US glycoprotein / CMV US / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I HLA-A / Unique short US11 glycoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHuman cytomegalovirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWatson, G.M. / Berry, R. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Diverse cytomegalovirus US11 antagonism and MHC-A evasion strategies reveal a tit-for-tat coevolutionary arms race in hominids.
Authors: Zimmermann, C. / Watson, G.M. / Bauersfeld, L. / Berry, R. / Ciblis, B. / Lan, H. / Gerke, C. / Oberhardt, V. / Fuchs, J. / Hofmann, M. / Freund, C. / Rossjohn, J. / Momburg, F. / Hengel, H. / Halenius, A.
History
DepositionJan 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Unique short US11 glycoprotein, Beta-2-microglobulin, MHC class I HLA-A fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7493
Polymers49,5651
Non-polymers1842
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.386, 80.503, 56.082
Angle α, β, γ (deg.)90.00, 113.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Unique short US11 glycoprotein, Beta-2-microglobulin, MHC class I HLA-A fusion / Protein HXLF1 / gpUS11


Mass: 49564.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain AD169), (gene. exp.) Homo sapiens (human)
Gene: US11, B2M, CDABP0092, HDCMA22P, MHC class I HLA-A / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P09727, UniProt: P61769, UniProt: O78126
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% (w/v) PEG3350, 0.1 M DL-malic acid pH 7.0, 83 mM cesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.8→48.04 Å / Num. obs: 39611 / % possible obs: 100 % / Redundancy: 3.5 % / CC1/2: 0.996 / Net I/σ(I): 6.8
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 2325 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIXv1.20.1refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.04 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2389 1875 -
Rwork0.2061 --
obs-39591 99.9 %
Refinement stepCycle: LAST / Resolution: 1.8→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 12 239 3382

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