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Yorodumi- PDB-2cwb: Solution Structure of the Ubiquitin-Associated Domain of Human BM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cwb | ||||||
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Title | Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin | ||||||
Components | Immunoglobulin G-binding protein G,Ubiquitin-like protein 7 | ||||||
Keywords | PROTEIN BINDING / HELICAL BUNDLE | ||||||
Function / homology | Function and homology information IgG binding / polyubiquitin modification-dependent protein binding / ubiquitin-dependent protein catabolic process / defense response to virus / molecular adaptor activity / innate immune response / extracellular region / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus sp. group G (bacteria) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Chang, Y.G. / Song, A.X. / Gao, Y.G. / Shi, Y.H. / Lin, X.J. / Cao, X.T. / Lin, D.H. / Hu, H.Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Solution structure of the ubiquitin-associated domain of human BMSC-UbP and its complex with ubiquitin. Authors: Chang, Y.G. / Song, A.X. / Gao, Y.G. / Shi, Y.H. / Lin, X.J. / Cao, X.T. / Lin, D.H. / Hu, H.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cwb.cif.gz | 152.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cwb.ent.gz | 129.2 KB | Display | PDB format |
PDBx/mmJSON format | 2cwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/2cwb ftp://data.pdbj.org/pub/pdb/validation_reports/cw/2cwb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 11908.023 Da / Num. of mol.: 1 / Fragment: C-TERMINAL UBA DOMAIN,C-TERMINAL UBA DOMAIN / Mutation: I12A Source method: isolated from a genetically manipulated source Details: A solubility-enhancement tag (SET) GB1, immunoglobulin G binding domain 1 of Streptococcal protein G, was used to enhance the solubility of the UBA domain of BMSC-UbP. The sequence of the ...Details: A solubility-enhancement tag (SET) GB1, immunoglobulin G binding domain 1 of Streptococcal protein G, was used to enhance the solubility of the UBA domain of BMSC-UbP. The sequence of the chimerical HGB1-UBA is as follows:MHHHHHHQYKLALNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSQWQPQLQQLRDMGIQDDELSLRALQATGGDIQAALELIFAGGAP.,A solubility-enhancement tag (SET) GB1, immunoglobulin G binding domain 1 of Streptococcal protein G, was used to enhance the solubility of the UBA domain of BMSC-UbP. The sequence of the chimerical HGB1-UBA is as follows:MHHHHHHQYKLALNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSQWQPQLQQLRDMGIQDDELSLRALQATGGDIQAALELIFAGGAP. Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Homo sapiens (human) Genus: Streptococcus, Homo / Species: , / Gene: spg, UBL7, BMSCUBP, SB132 / Plasmid: pHGB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06654, UniProt: Q96S82 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1mM HGB1-UBA U-15N,13C; 20mM phosphate buffer; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |