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- PDB-3mq9: Crystal Structure of Ectodomain Mutant of BST-2/Tetherin/CD317 Fu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mq9 | ||||||
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Title | Crystal Structure of Ectodomain Mutant of BST-2/Tetherin/CD317 Fused to MBP | ||||||
![]() | Bone marrow stromal antigen 2 fused to Maltose-binding periplasmic protein | ||||||
![]() | ANTIVIRAL PROTEIN / HIV | ||||||
Function / homology | ![]() 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 / detection of maltose stimulus / 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 / detection of maltose stimulus / B cell activation / maltose transport complex / response to type II interferon / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / side of membrane / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / multivesicular body / negative regulation of cell migration / cell chemotaxis / 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 / outer membrane-bounded periplasmic space / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / periplasmic space / membrane raft / apical plasma membrane / intracellular membrane-bounded organelle / innate immune response / DNA damage 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiong, Y. / Yang, H. / Wang, J. / Meng, W. | ||||||
![]() | ![]() Title: Structural insight into the mechanisms of enveloped virus tethering by tetherin. Authors: Yang, H. / Wang, J. / Jia, X. / McNatt, M.W. / Zang, T. / Pan, B. / Meng, W. / Wang, H.W. / Bieniasz, P.D. / Xiong, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 684.3 KB | Display | ![]() |
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PDB format | ![]() | 572.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 506.3 KB | Display | ![]() |
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Full document | ![]() | 586.3 KB | Display | |
Data in XML | ![]() | 122.3 KB | Display | |
Data in CIF | ![]() | 166.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mq7C ![]() 3mqbC ![]() 3mqcC ![]() 1pebS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Details | 1 |
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Components
#1: Protein | Mass: 52193.426 Da / Num. of mol.: 8 Fragment: MBP residues 27-395 fused to BST-2 residues 66-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994, BST2 / Plasmid: pMAT9s / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.95 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 5 Details: Crystals were grown at 25C by using microbatch under oil by mixing protein with crystallization buffer containing 100 mM sodium acetate (pH 5.0), 200 mM NaCl, 20% PEG 6000. Micro batch under ...Details: Crystals were grown at 25C by using microbatch under oil by mixing protein with crystallization buffer containing 100 mM sodium acetate (pH 5.0), 200 mM NaCl, 20% PEG 6000. Micro batch under oil, pH 5.0, EVAPORATION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0091 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→42.47 Å / Num. obs: 94908 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1 / Rsym value: 1 / % possible all: 90.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Code:1PEB Resolution: 2.8→42.47 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 48.185 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.576 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→42.47 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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