+Open data
-Basic information
Entry | Database: PDB / ID: 2n29 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution-state NMR structure of Vpu cytoplasmic domain | ||||||
Components | Protein Vpu | ||||||
Keywords | VIRAL PROTEIN / alpha helix | ||||||
Function / homology | Function and homology information nuclear transport / uncoating of virus / RNA-templated DNA biosynthetic process / receptor catabolic process / Synthesis and processing of ENV and VPU / CD4 receptor binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis ...nuclear transport / uncoating of virus / RNA-templated DNA biosynthetic process / receptor catabolic process / Synthesis and processing of ENV and VPU / CD4 receptor binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / virion assembly / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / host cell membrane / viral release from host cell / Binding and entry of HIV virion / monoatomic cation channel activity / viral life cycle / Vpu mediated degradation of CD4 / Assembly Of The HIV Virion / Budding and maturation of HIV virion / establishment of integrated proviral latency / suppression by virus of host tetherin activity / membrane => GO:0016020 / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / fusion of virus membrane with host plasma membrane / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Zhang, H. / Lin, E.C. / Tian, Y. / Das, B.B. / Opella, S.J. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2015 Title: Structural determination of virus protein U from HIV-1 by NMR in membrane environments. Authors: Zhang, H. / Lin, E.C. / Das, B.B. / Tian, Y. / Opella, S.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2n29.cif.gz | 26.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2n29.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 2n29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2n29_validation.pdf.gz | 389 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2n29_full_validation.pdf.gz | 391.4 KB | Display | |
Data in XML | 2n29_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 2n29_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/2n29 ftp://data.pdbj.org/pub/pdb/validation_reports/n2/2n29 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 6265.957 Da / Num. of mol.: 1 / Fragment: cytoplasmic domain (UNP residues 28-81) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: vpu / Plasmid: pET31b+ / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P69700, UniProt: P05919*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 0.5 mM [U-100% 15N] Vpu Cytoplasmic domain, 0.5 mM [U-100% 13C; U-100% 15N] Vpu Cytoplasmic domain, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||
Sample conditions | Ionic strength: 5 / pH: 4 / Pressure: 1 atm / Temperature: 323 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
---|
-Processing
NMR software | Name: CNS / Developer: Brunger, A.T. et.al. / Classification: refinement |
---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE ANI COORDINATES HAVE BEEN INCLUDED IN THE RESTRAINT FILE. THE ANI Z AXIS SPECIFIES THE DIRECTION OF THE NORMAL TO THE PLANE OF THE LIPID BILAYER MEMBRANE. |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 1 |