[English] 日本語
![](img/lk-miru.gif)
- PDB-4p6z: Crystal structure of the human BST2 cytoplasmic domain and the HI... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4p6z | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||||||||||
![]() |
| |||||||||||||||
![]() | PROTEIN TRANSPORT / BST2 / tetherin / Vpu / HIV / clathrin / AP1 / antiviral / restriction factor / antagonism | |||||||||||||||
Function / homology | ![]() 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 / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / response to interferon-alpha ...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 / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / response to interferon-alpha / melanosome assembly / metalloendopeptidase inhibitor activity / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / receptor catabolic process / clathrin adaptor activity / MHC class II antigen presentation / positive regulation of leukocyte proliferation / 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 / response to type II interferon / viral release from host cell / host cell membrane / monoatomic cation channel activity / side of membrane / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / Neutrophil degranulation / multivesicular body / negative regulation of cell migration / receptor-mediated endocytosis / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / regulation of actin cytoskeleton organization / intracellular protein transport / response to virus / cytoplasmic vesicle membrane / trans-Golgi network / terminal bouton / 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 / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / suppression by virus of host tetherin activity / early endosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / membrane raft / apical plasma membrane / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / lipid binding / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||
![]() | Jia, X. / Xiong, Y. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 688.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 572.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 509.4 KB | Display | |
Data in XML | ![]() | 59.7 KB | Display | |
Data in CIF | ![]() | 82.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() ![]() |
---|---|
#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.) ![]() ![]() ![]() |
#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.) ![]() ![]() ![]() ![]() |
#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.) ![]() ![]() ![]() |
-Protein / Protein/peptide / Non-polymers , 3 types, 16 molecules VT![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#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.) ![]() Strain: isolate SF162 / Gene: vpu / Production host: ![]() ![]() |
---|---|
#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.) ![]() ![]() ![]() |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.29 % |
---|---|
Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 / Details: Peg 6000, NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|