3FUS

Improved Structure of the Unliganded Simian Immunodeficiency Virus gp120 Core

3FUS の概要

• エントリーDOI: 10.2210/pdb3fus/pdb
• 分子名称: 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)
• 機能のキーワード: siv, aids, gp120, structural refinement, normal mode, apoptosis, cell membrane, envelope protein, fusion protein, host-virus interaction, membrane, transmembrane, virion, viral protein
• 由来する生物種: Simian immunodeficiency virus (SIV-cpz); 詳細
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 46858.91

構造登録者

Chen, X.,Poon, B.,Wang, Q.,Ma, J. (登録日: 2009-01-14, 公開日: 2009-06-30, 最終更新日: 2024-10-16)

主引用文献

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

実験手法

X-RAY DIFFRACTION (4 Å)