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Yorodumi- PDB-3d2u: Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a ... -
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-Basic information
Entry | Database: PDB / ID: 3d2u | ||||||
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Title | Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class I homolog / Disease mutation / Glycation / Glycoprotein / Immune response / Immunoglobulin domain / MHC I / Pyrrolidone carboxylic acid / Secreted / Membrane / Phosphoprotein / Receptor / Transmembrane | ||||||
Function / homology | Function and homology information evasion by virus of host natural killer cell activity / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding ...evasion by virus of host natural killer cell activity / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / MHC class Ib receptor activity / negative regulation of T cell mediated cytotoxicity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / MHC class I receptor activity / immune response-regulating signaling pathway / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of transforming growth factor beta production / regulation of transepithelial transport / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / morphogenesis of a polarized epithelium / negative regulation of serotonin secretion / negative regulation of natural killer cell mediated cytotoxicity / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / protein localization to adherens junction / nBAF complex / brahma complex / dendritic cell differentiation / Tat protein binding / postsynaptic actin cytoskeleton / interleukin-10-mediated signaling pathway / negative regulation of mononuclear cell proliferation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / structural constituent of postsynaptic actin cytoskeleton / protein phosphatase 1 binding / GBAF complex / negative regulation of osteoclast development / Formation of annular gap junctions / regulation of G0 to G1 transition / Gap junction degradation / dense body / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / negative regulation of interleukin-12 production / negative regulation of endocytosis / apical protein localization / regulation of double-strand break repair / negative regulation of dendritic cell apoptotic process / negative regulation of interferon-beta production / adherens junction assembly / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / tight junction / antigen processing and presentation of peptide antigen via MHC class I / Interaction between L1 and Ankyrins / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / regulation of norepinephrine uptake / positive regulation of macrophage cytokine production / regulation of synaptic vesicle endocytosis / positive regulation of double-strand break repair / apical junction complex / positive regulation of T cell differentiation / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of interleukin-10 production / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / cortical cytoskeleton / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / Regulation of MITF-M-dependent genes involved in pigmentation / MHC class I protein binding / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / brush border / negative regulation of calcium ion transport / kinesin binding / negative regulation of cell differentiation / negative regulation of type II interferon production / calyx of Held / negative regulation of cell cycle / negative regulation of tumor necrosis factor production / EPH-ephrin mediated repulsion of cells / host cell membrane / regulation of protein localization to plasma membrane / RHO GTPases Activate WASPs and WAVEs / T cell proliferation involved in immune response / positive regulation of myoblast differentiation / positive regulation of double-strand break repair via homologous recombination / RHO GTPases activate IQGAPs / negative regulation of T cell proliferation Similarity search - Function | ||||||
Biological species | Human herpesvirus 5 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å | ||||||
Authors | Yang, Z. / Bjorkman, P.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor Authors: Yang, Z. / Bjorkman, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d2u.cif.gz | 251.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d2u.ent.gz | 201 KB | Display | PDB format |
PDBx/mmJSON format | 3d2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d2u_validation.pdf.gz | 557.4 KB | Display | wwPDB validaton report |
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Full document | 3d2u_full_validation.pdf.gz | 607.1 KB | Display | |
Data in XML | 3d2u_validation.xml.gz | 52.2 KB | Display | |
Data in CIF | 3d2u_validation.cif.gz | 71.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d2u ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d2u | HTTPS FTP |
-Related structure data
Related structure data | 1p7qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules BFDH
#2: Protein | Mass: 11748.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: beta2m / Source: (natural) Homo sapiens (human) / References: UniProt: P61769 #3: Protein | Mass: 22055.697 Da / Num. of mol.: 2 / Fragment: Ig-like C2-type 1 and C2-type 2 domains / Source method: isolated from a natural source / Details: LIR-1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NHL6 |
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-Antibody / Protein/peptide / Non-polymers , 3 types, 366 molecules AEGC
#1: Antibody | Mass: 31664.994 Da / Num. of mol.: 2 / Fragment: sequence database residues 21-301 / Source method: isolated from a natural source / Details: gene UL18 / Source: (natural) Human herpesvirus 5 / Strain: AD169 / References: UniProt: Q4A1U8, UniProt: P08560*PLUS #4: Protein/peptide | Mass: 1005.257 Da / Num. of mol.: 2 / Fragment: sequence database residues 170-178 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60709 #9: Water | ChemComp-HOH / | |
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-Sugars , 4 types, 16 molecules
#5: Sugar | ChemComp-NAG / #6: Sugar | ChemComp-MAN / | #7: Sugar | ChemComp-BMA / | #8: Sugar | ChemComp-FUC / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. obs: 85873 / % possible obs: 98.6 % / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 2.21→2.29 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 6.6 / Num. unique all: 7747 / % possible all: 89.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1P7Q Resolution: 2.21→47.46 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42.508 Å2 | ||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.031 Å | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→47.46 Å
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Refine LS restraints |
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