2K7Y | pdb_00002k7y

Solution fold of HIV-1 Virus protein U cytoplasmic domain in the presence of DPC micelles

• PDB DOI: https://doi.org/10.2210/pdb2K7Y/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 (SF162 ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2008-08-28 Released: 2009-11-10 
• Deposition Author(s): Wittlich, M., Koenig, B.W., Willbold, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

NMR structural characterization of HIV-1 virus protein U cytoplasmic domain in the presence of dodecylphosphatidylcholine micelles

Wittlich, M., Koenig, B.W., Stoldt, M., Schmidt, H., Willbold, D.

(2009) FEBS J 276: 6560-6575

• PubMed: 19804408 
• DOI: https://doi.org/10.1111/j.1742-4658.2009.07363.x
• Primary Citation Related Structures: 
  2K7Y


• PubMed Abstract: 
  

  The HIV-1 encoded virus protein U (VpU) is required for efficient viral release from human host cells and for induction of CD4 degradation in the endoplasmic reticulum. The cytoplasmic domain of the membrane protein VpU (VpUcyt) is essential for the latter activity. The structure and dynamics of VpUcyt were characterized in the presence of membrane simulating dodecylphosphatidylcholine (DPC) micelles by high-resolution liquid state NMR. VpUcyt is unstructured in aqueous buffer. The addition of DPC micelles induces a well-defined membrane proximal alpha-helix (residues I39-E48) and an additional helical segment (residues L64-R70). A tight loop (L73-V78) is observed close to the C-terminus, whereas the interhelical linker (R49-E63) remains highly flexible. A 3D structure of VpUcyt in the presence of DPC micelles was calculated from a large set of proton-proton distance constraints. The topology of micelle-associated VpUcyt was derived from paramagnetic relaxation enhancement of protein nuclear spins after the introduction of paramagnetic probes into the interior of the micelle or the aqueous buffer. Qualitative analysis of secondary chemical shift and paramagnetic relaxation enhancement data in conjunction with dynamic information from heteronuclear NOEs and structural insight from homonuclear NOE-based distance constraints indicated that micelle-associated VpUcyt retains a substantial degree of structural flexibility.

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Organizational Affiliation: 
• Institut für Strukturbiologie und Biophysik (ISB-3), Forschungszentrum Jülich, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.01 kDa 
• Atom Count: 351 
• Modeled Residue Count: 45 
• Deposited Residue Count: 45 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Vpu	A	45	Human immunodeficiency virus type 1 (SF162 ISOLATE)	Mutation(s): 0  Gene Names: vpu Membrane Entity: Yes
UniProt
Find proteins for P19554 (Human immunodeficiency virus type 1 group M subtype B (isolate SF162)) Explore P19554  Go to UniProtKB:  P19554

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Wittlich, M., Koenig, B.W., Willbold, D.

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Database references, Derived calculations
• Version 1.3: 2024-05-22
  Changes: Data collection