3FUS

Improved Structure of the Unliganded Simian Immunodeficiency Virus gp120 Core

Summary for 3FUS

• Entry DOI: 10.2210/pdb3fus/pdb
• Descriptor: EXTERIOR MEMBRANE GLYCOPROTEIN GP120, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (12 entities in total)
• Functional Keywords: siv, aids, gp120, structural refinement, normal mode, apoptosis, cell membrane, envelope protein, fusion protein, host-virus interaction, membrane, transmembrane, virion, viral protein
• Biological source: Simian immunodeficiency virus (SIV-cpz); More
• Total number of polymer chains: 1
• Total formula weight: 46858.91

Authors

Chen, X.,Poon, B.,Wang, Q.,Ma, J. (deposition date: 2009-01-14, release date: 2009-06-30, Last modification date: 2024-10-16)

Primary citation

Chen, X.,Lu, M.,Poon, B.K.,Wang, Q.,Ma, J.
Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement.
Acta Crystallogr.,Sect.D, 65:339-347, 2009

PubMed Abstract: The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous difficulties in the pursuit of high-resolution structural investigation of some of its conformational states. An unliganded and fully glycosylated gp120 core structure was recently determined to 4.0 A resolution. The rather low data-to-parameter ratio limited refinement efforts in the original structure determination. In this work, refinement of this gp120 core structure was carried out using a normal-mode-based refinement method that has been shown in previous studies to be effective in improving models of a supramolecular complex at 3.42 A resolution and of a membrane protein at 3.2 A resolution. By using only the first four nonzero lowest-frequency normal modes to construct the anisotropic thermal parameters, combined with manual adjustments and standard positional refinement using REFMAC5, the structural model of the gp120 core was significantly improved in many aspects, including substantial decreases in R factors, better fitting of several flexible regions in electron-density maps, the addition of five new sugar rings at four glycan chains and an excellent correlation of the B-factor distribution with known structural flexibility. These results further underscore the effectiveness of this normal-mode-based method in improving models of protein and nonprotein components in low-resolution X-ray structures.

PubMed: 19307715
DOI: 10.1107/S0907444909003539

Experimental method

X-RAY DIFFRACTION (4 Å)