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Yorodumi- PDB-2xg7: Crystal Structure of BST2-Tetherin Ectodomain expressed in HEK293... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xg7 | ||||||
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Title | Crystal Structure of BST2-Tetherin Ectodomain expressed in HEK293T cells | ||||||
Components | BONE MARROW STROMAL ANTIGEN 2 | ||||||
Keywords | ANTIVIRAL PROTEIN / INNATE IMMUNE FACTOR | ||||||
Function / homology | Function and homology information negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / response to interferon-alpha / metalloendopeptidase inhibitor activity / positive regulation of leukocyte proliferation / azurophil granule membrane / negative regulation of viral genome replication / response to type II interferon / B cell activation ...negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / response to interferon-alpha / metalloendopeptidase inhibitor activity / positive regulation of leukocyte proliferation / azurophil granule membrane / negative regulation of viral genome replication / response to type II interferon / B cell activation / side of membrane / multivesicular body / negative regulation of cell migration / regulation of actin cytoskeleton organization / response to virus / negative regulation of cell growth / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / apical plasma membrane / membrane raft / intracellular membrane-bounded organelle / innate immune response / Neutrophil degranulation / Golgi apparatus / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å | ||||||
Authors | Steiner, R.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural and Functional Studies on the Extracellular Domain of Bst2/Tetherin in Reduced and Oxidized Conformations. Authors: Schubert, H.L. / Zhai, Q. / Sandrin, V. / Eckert, D.M. / Garcia-Maya, M. / Saul, L. / Sundquist, W.I. / Steiner, R.A. / Hill, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xg7.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xg7.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xg7_validation.pdf.gz | 456.7 KB | Display | wwPDB validaton report |
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Full document | 2xg7_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 2xg7_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 2xg7_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xg7 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xg7 | HTTPS FTP |
-Related structure data
Related structure data | 3nwhC 3mkx S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11463.895 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 51-151 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell (production host): HUMAN EMBRYONIC KIDNEY CELLS / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q10589 #2: Sugar | 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: 4.2 Å3/Da / Density % sol: 70 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 8% PEG8000, 0.1M TRIS-HCL PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 30, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→38.95 Å / Num. obs: 5576 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3.45→3.64 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MKX 3mkx Resolution: 3.45→77.89 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.929 / SU B: 62.942 / SU ML: 0.417 / Cross valid method: THROUGHOUT / ESU R: 1.768 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE-CHAINS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.784 Å2
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Refinement step | Cycle: LAST / Resolution: 3.45→77.89 Å
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