4BIP

Homology model of coxsackievirus A7 (CAV7) full capsid proteins.

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4BIP の概要

• エントリーDOI: 10.2210/pdb4bip/pdb
• 関連するPDBエントリー: 4BIQ
• EMDBエントリー: 2028
• 分子名称: VP1, VP2, VP3 (3 entities in total)
• 機能のキーワード: virus, picornavirus, enterovirus, hev-a
• 由来する生物種: HUMAN COXSACKIEVIRUS A7 (CAV7); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 73298.15

構造登録者

Seitsonen, J.J.T.,Shakeel, S.,Susi, P.,Pandurangan, A.P.,Sinkovits, R.S.,Hyvonen, H.,Laurinmaki, P.,Yla-Pelto, J.,Topf, M.,Hyypia, T.,Butcher, S.J. (登録日: 2013-04-12, 公開日: 2013-10-02, 最終更新日: 2024-05-08)

主引用文献

Pandurangan, A.P.,Shakeel, S.,Butcher, S.J.,Topf, M.
Combined Approaches to Flexible Fitting and Assessment in Virus Capsids Undergoing Conformational Change.
J.Struct.Biol., 185:427-, 2014

PubMed Abstract: Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to be agreed upon among the experts in the field. Here, we created and tested a protocol that highlights important issues related to homology modelling, density map segmentation, rigid and flexible fitting, as well as the assessment of fits. As part of it, we use two different flexible fitting methods (Flex-EM and iMODfit) and demonstrate how combining the analysis of multiple fits and model assessment could result in an improved model. The protocol is applied to the case of the mature and empty capsids of Coxsackievirus A7 (CAV7) by flexibly fitting homology models into the corresponding cryoEM density maps at 8.2 and 6.1Å resolution. As a result, and due to the improved homology models (derived from recently solved crystal structures of a close homolog - EV71 capsid - in mature and empty forms), the final models present an improvement over previously published models. In close agreement with the capsid expansion observed in the EV71 structures, the new CAV7 models reveal that the expansion is accompanied by ∼5° counterclockwise rotation of the asymmetric unit, predominantly contributed by the capsid protein VP1. The protocol could be applied not only to viral capsids but also to many other complexes characterised by a combination of atomic structure modelling and cryoEM density fitting.

PubMed: 24333899
DOI: 10.1016/J.JSB.2013.12.003

実験手法

ELECTRON MICROSCOPY (8.23 Å)