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Yorodumi- PDB-4p6z: Crystal structure of the human BST2 cytoplasmic domain and the HI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p6z | |||||||||||||||
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Title | Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic domain bound to the clathrin adaptor protein complex 1 (AP1) core | |||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / BST2 / tetherin / Vpu / HIV / clathrin / AP1 / antiviral / restriction factor / antagonism | |||||||||||||||
Function / homology | Function and homology information virus-mediated perturbation of host defense response => GO:0019049 / negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / basolateral protein secretion / AP-1 adaptor complex / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization ...virus-mediated perturbation of host defense response => GO:0019049 / negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / basolateral protein secretion / AP-1 adaptor complex / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / response to interferon-alpha / melanosome assembly / Golgi to lysosome transport / Golgi to vacuole transport / metalloendopeptidase inhibitor activity / Golgi Associated Vesicle Biogenesis / receptor catabolic process / melanosome organization / GTP-dependent protein binding / clathrin adaptor activity / positive regulation of leukocyte proliferation / MHC class II antigen presentation / CD4 receptor binding / retrograde transport, endosome to Golgi / determination of left/right symmetry / clathrin-coated vesicle / azurophil granule membrane / Lysosome Vesicle Biogenesis / clathrin binding / negative regulation of viral genome replication / Golgi Associated Vesicle Biogenesis / B cell activation / positive regulation of natural killer cell mediated cytotoxicity / response to type II interferon / kinesin binding / host cell membrane / viral release from host cell / side of membrane / monoatomic cation channel activity / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / receptor-mediated endocytosis / Neutrophil degranulation / multivesicular body / kidney development / negative regulation of cell migration / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / regulation of actin cytoskeleton organization / intracellular protein transport / response to virus / trans-Golgi network / cytoplasmic vesicle membrane / terminal bouton / recycling endosome / small GTPase binding / negative regulation of cell growth / SARS-CoV-1 activates/modulates innate immune responses / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon alpha/beta signaling / heart development / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / suppression by virus of host tetherin activity / early endosome / apical plasma membrane / membrane raft / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) Human immunodeficiency virus type 1 group M subtype B | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | |||||||||||||||
Authors | Jia, X. / Xiong, Y. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Elife / Year: 2014 Title: Structural basis of HIV-1 Vpu-mediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1. Authors: Jia, X. / Weber, E. / Tokarev, A. / Lewinski, M. / Rizk, M. / Suarez, M. / Guatelli, J. / Xiong, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p6z.cif.gz | 688.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p6z.ent.gz | 572.9 KB | Display | PDB format |
PDBx/mmJSON format | 4p6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/4p6z ftp://data.pdbj.org/pub/pdb/validation_reports/p6/4p6z | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-AP-1 complex subunit ... , 4 types, 4 molecules GSMB
#1: Protein | Mass: 70944.023 Da / Num. of mol.: 1 Fragment: BST2/tetheirn cytoplasmic domain, UNP residues 1-613 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1g1, Adtg, Clapg1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22892 |
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#2: Protein | Mass: 18787.059 Da / Num. of mol.: 1 / Fragment: HIV-1 Vpu cytoplasmic domain / Mutation: Q11R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP1S1, AP19, CLAPS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61966 |
#3: Protein | Mass: 48606.730 Da / Num. of mol.: 1 Fragment: Clathrin adaptor protein complex 1 (AP1) core, UNP residues 1-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1m1, Cltnm / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35585 |
#4: Protein | Mass: 67770.258 Da / Num. of mol.: 1 / Fragment: UNP residues 1-584 / Mutation: T431A, E476K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP1B1, ADTB1, BAM22, CLAPB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q10567 |
-Protein / Protein/peptide / Non-polymers , 3 types, 16 molecules VT
#5: Protein | Mass: 7123.607 Da / Num. of mol.: 1 / Fragment: UNP residues 21-81 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B Strain: isolate SF162 / Gene: vpu / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19554 |
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#6: Protein/peptide | Mass: 2822.180 Da / Num. of mol.: 1 / Fragment: UNP residues 1-21 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q10589 |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.29 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 / Details: Peg 6000, NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 59937 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 67.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1 / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 30.036 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.988 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 261.61 Å2 / Biso mean: 107.107 Å2 / Biso min: 36.27 Å2
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Refinement step | Cycle: final / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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