Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.27 kDa 
• Atom Count: 441 
• Modelled Residue Count: 54 
• Deposited Residue Count: 54 
• Unique protein chains: 1

2N29

Solution-state NMR structure of Vpu cytoplasmic domain

• PDB DOI: 10.2210/pdb2N29/pdb
• BMRB: 25592

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-01 Released: 2015-09-30 
• Deposition Author(s): Zhang, H., Lin, E.C., Tian, Y., Das, B.B., Opella, S.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 

Literature

Structural determination of virus protein U from HIV-1 by NMR in membrane environments.

Zhang, H., Lin, E.C., Das, B.B., Tian, Y., Opella, S.J.

(2015) Biochim Biophys Acta 1848: 3007-3018

• PubMed: 26362058 
• DOI: 10.1016/j.bbamem.2015.09.008
• Primary Citation of Related Structures:  
  2N28, 2N29


• PubMed Abstract: 
  

Virus protein U (Vpu) from HIV-1, a small membrane protein composed of a transmembrane helical domain and two α-helices in an amphipathic cytoplasmic domain, down modulates several cellular proteins, including CD4, BST-2/CD317/tetherin, NTB-A, and CCR7. The interactions of Vpu with these proteins interfere with the immune system and enhance the release of newly synthesized virus particles. It is essential to characterize the structure and dynamics of Vpu in order to understand the mechanisms of the protein-protein interactions, and potentially to discover antiviral drugs. In this article, we describe investigations of the cytoplasmic domain of Vpu as well as full-length Vpu by NMR spectroscopy. These studies are complementary to earlier analysis of the transmembrane domain of Vpu. The results suggest that the two helices in the cytoplasmic domain form a U-shape. The length of the inter-helical loop in the cytoplasmic domain and the orientation of the third helix vary with the lipid composition, which demonstrate that the C-terminal helix is relatively flexible, providing accessibility for interaction partners.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Vpu	A	54	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: vpu
UniProt
Find proteins for P05919 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P05919  Go to UniProtKB:  P05919

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2N29 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-05-01 
• Released Date: 2015-09-30 
Deposition Author(s): Zhang, H., Lin, E.C., Tian, Y., Das, B.B., Opella, S.J.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Database references