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- PDB-1im3: Crystal Structure of the human cytomegalovirus protein US2 bound ... -

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Basic information

Entry
Database: PDB / ID: 1im3
TitleCrystal Structure of the human cytomegalovirus protein US2 bound to the MHC class I molecule HLA-A2/tax
Components
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
  • Human T-cell lymphotropic virus type 1 Tax peptide
  • beta-2-microglobulinBeta-2 microglobulin
  • cytomegalovirus protein US2
KeywordsViral protein/Immune system / Beta sheet / Beta sandwhich / Immunoglobulin (Ig) fold / immunoglobulin (IG)-like domain / protein complex / alpha helix / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / virus-mediated perturbation of host defense response => GO:0019049 / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / virus-mediated perturbation of host defense response => GO:0019049 / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / detection of bacterium / T cell receptor binding / regulation of mRNA stability / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 / 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 / ER to Golgi transport vesicle membrane / 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 / SH3 domain binding / 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 / recycling endosome membrane / specific granule lumen / 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 / 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 / positive regulation of type II interferon production / Interferon alpha/beta signaling / 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 / T cell differentiation in thymus / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / cellular response to lipopolysaccharide / host cell cytoplasm / amyloid fibril formation / membrane => GO:0016020 / learning or memory / host cell endoplasmic reticulum membrane / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane
Similarity search - Function
Immunoglobulin-like - #1200 / Herpesvirus US2/US3 / : / Cytomegalovirus US3 protein / HTLV Tax / HTLV Tax / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...Immunoglobulin-like - #1200 / Herpesvirus US2/US3 / : / Cytomegalovirus US3 protein / HTLV Tax / HTLV Tax / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 E-set / 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
: / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Unique short US2 glycoprotein / Protein Tax-1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGewurz, B.E. / Gaudet, R. / Tortorella, D. / Wang, E.W. / Ploegh, H.L. / Wiley, D.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Antigen presentation subverted: Structure of the human cytomegalovirus protein US2 bound to the class I molecule HLA-A2.
Authors: Gewurz, B.E. / Gaudet, R. / Tortorella, D. / Wang, E.W. / Ploegh, H.L. / Wiley, D.C.
#1: Journal: J.Virol. / Year: 2001
Title: Human cytomegalovirus US2 endoplasmic reticulum-lumenal domain dictates association with major histocompatibility complex class I in a locus-specific manner
Authors: Gewurz, B.E. / Wang, E.W. / Tortorella, D. / Schust, D.S. / Ploegh, H.L.
#2: Journal: J.Immunol. / Year: 2000
Title: The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site
Authors: Khan, A.R. / Baker, B.M. / Ghosh, B. / E Biddison, W. / Wiley, D.C.
#3: Journal: Nature / Year: 1996
Title: Sec61-mediated transfer of a membrane protein from the endoplasmic reticulum to the proteasome for destruction
Authors: Wiertz, E.J. / Tortorella, D. / Bogyo, M. / Rapoport, T.A. / Ploegh, H.L.
History
DepositionMay 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: beta-2-microglobulin
C: Human T-cell lymphotropic virus type 1 Tax peptide
D: cytomegalovirus protein US2
E: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
F: beta-2-microglobulin
G: Human T-cell lymphotropic virus type 1 Tax peptide
H: cytomegalovirus protein US2
I: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
J: beta-2-microglobulin
K: Human T-cell lymphotropic virus type 1 Tax peptide
L: cytomegalovirus protein US2
M: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
N: beta-2-microglobulin
O: Human T-cell lymphotropic virus type 1 Tax peptide
P: cytomegalovirus protein US2


Theoretical massNumber of molelcules
Total (without water)222,81316
Polymers222,81316
Non-polymers00
Water26,0501446
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: beta-2-microglobulin
C: Human T-cell lymphotropic virus type 1 Tax peptide
D: cytomegalovirus protein US2


Theoretical massNumber of molelcules
Total (without water)55,7034
Polymers55,7034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
F: beta-2-microglobulin
G: Human T-cell lymphotropic virus type 1 Tax peptide
H: cytomegalovirus protein US2


Theoretical massNumber of molelcules
Total (without water)55,7034
Polymers55,7034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
J: beta-2-microglobulin
K: Human T-cell lymphotropic virus type 1 Tax peptide
L: cytomegalovirus protein US2


Theoretical massNumber of molelcules
Total (without water)55,7034
Polymers55,7034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
N: beta-2-microglobulin
O: Human T-cell lymphotropic virus type 1 Tax peptide
P: cytomegalovirus protein US2


Theoretical massNumber of molelcules
Total (without water)55,7034
Polymers55,7034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.480, 96.700, 99.540
Angle α, β, γ (deg.)109.02, 109.46, 107.93
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN


Mass: 31854.203 Da / Num. of mol.: 4 / Fragment: extracellular domain, heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A2 / Plasmid: pET27 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein
beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: recombinant residues 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Beta 2-microglobulin / Plasmid: Plm-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide
Human T-cell lymphotropic virus type 1 Tax peptide


Mass: 1070.280 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: HTLV Tax peptide (LLFGYPVYV) was produced by FMOC solid phase peptide synthesis
References: GenBank: 699503, UniProt: P14079*PLUS
#4: Protein
cytomegalovirus protein US2 /


Mass: 10899.435 Da / Num. of mol.: 4 / Fragment: recombinant ER-lumenal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Gene: US2 / Plasmid: pET27d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09713
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1446 / 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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: PEG 6000, MPD, Tris, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris1drop
3150 mM1dropNaCl
412-14 %PEG60001reservoir
57 %MPD1reservoir
6100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 139486 / Num. obs: 139486 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.3 / Num. unique all: 13849 / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Num. obs: 13849 / Num. measured all: 139486
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 97.1 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1DUZ

1duz


Resolution: 2.2→38.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 387634.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2713 2 %RANDOM
Rwork0.206 ---
all0.222 134391 --
obs0.206 134391 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.11 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å23.97 Å23.94 Å2
2---0.88 Å24.56 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15716 0 0 1446 17162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 419 2 %
Rwork0.3 20366 -
obs-20366 87.4 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 2 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.348 / % reflection Rfree: 2 % / Rfactor Rwork: 0.3 / Rfactor obs: 0.3

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