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基本情報
登録情報 | データベース: PDB / ID: 3j0g | ||||||
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タイトル | Homology model of E3 protein of Venezuelan Equine Encephalitis Virus TC-83 strain fitted with a cryo-EM map | ||||||
![]() | E3 protein | ||||||
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機能・相同性 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Zhang, R. / Hryc, C.F. / Chiu, W. | ||||||
![]() | ![]() タイトル: 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. 著者: Rui Zhang / Corey F Hryc / Yao Cong / Xiangan Liu / Joanita Jakana / Rodion Gorchakov / Matthew L Baker / Scott C Weaver / Wah Chiu / ![]() 要旨: Venezuelan equine encephalitis virus (VEEV), a member of the membrane-containing Alphavirus genus, is a human and equine pathogen, and has been developed as a biological weapon. Using electron cryo- ...Venezuelan equine encephalitis virus (VEEV), a member of the membrane-containing Alphavirus genus, is a human and equine pathogen, and has been developed as a biological weapon. Using electron cryo-microscopy (cryo-EM), we determined the structure of an attenuated vaccine strain, TC-83, of VEEV to 4.4 Å resolution. Our density map clearly resolves regions (including E1, E2 transmembrane helices and cytoplasmic tails) that were missing in the crystal structures of domains of alphavirus subunits. These new features are implicated in the fusion, assembly and budding processes of alphaviruses. Furthermore, our map reveals the unexpected E3 protein, which is cleaved and generally thought to be absent in the mature VEEV. Our structural results suggest a mechanism for the initial stage of nucleocapsid core formation, and shed light on the virulence attenuation, host recognition and neutralizing activities of VEEV and other alphavirus pathogens. | ||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 48.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 37.9 KB | 表示 | ![]() |
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その他 | ![]() |
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アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
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対称性 | 点対称性: (シェーンフリース記号![]() ![]() |
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要素
#1: タンパク質 | 分子量: 6488.601 Da / 分子数: 4 / 断片: UNP residues 276-334 / 由来タイプ: 天然 詳細: purified from infected Baby hamster kidney (BHK) cells 由来: (天然) ![]() ![]() 株: TC-83 / 参照: UniProt: P05674 |
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-実験情報
-実験
実験 | 手法: ![]() |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: ![]() |
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試料調製
構成要素 | 名称: Venezuelan Equine Encephalitis Virus TC83 strain E3 protein that is cleaved from p62 protein タイプ: VIRUS 詳細: The virus contains 240 copies of E1, E2, E3 and capsid proteins |
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ウイルスについての詳細 | 中空か: NO / エンベロープを持つか: YES / ホストのカテゴリ: VERTEBRATES / 単離: STRAIN / タイプ: VIRION |
天然宿主 | 生物種: Cricetinae / 株: Baby Hamster Kidney cells |
緩衝液 | 名称: TEN buffer / pH: 7.4 / 詳細: TEN buffer |
試料 | 包埋: NO / シャドウイング: NO / 染色![]() ![]() |
試料支持 | 詳細: two of the eight grids used for imaging contained continuous carbon film underneath the samples |
急速凍結![]() | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / Temp: 89.34 K / 湿度: 100 % / 詳細: vitrification carried out in Chiu lab, Houston, TX 手法: 2 blots, each blot 2 second before plunging, offset = 0 |
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電子顕微鏡撮影
顕微鏡 | モデル: JEOL 3200FSC / 日付: 2008年4月9日 / 詳細: omega energy filter |
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電子銃 | 電子線源![]() ![]() |
電子レンズ | モード: BRIGHT FIELD![]() ![]() 非点収差 ![]() |
試料ホルダ | 試料ホルダーモデル: JEOL 3200FSC CRYOHOLDER / 資料ホルダタイプ: Eucentric / 温度: 96 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 18 e/Å2 フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) |
電子光学装置 | エネルギーフィルター名称![]() |
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解析
EMソフトウェア |
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CTF補正![]() | 詳細: CTF parameters were determined from particles within each CCD image | ||||||||||||
対称性 | 点対称性![]() ![]() | ||||||||||||
3次元再構成![]() | 手法: projection matching / 解像度: 4.8 Å / 粒子像の数: 37000 / ピクセルサイズ(公称値): 1.07 Å 詳細: After each iteration, the non-icosahedral parts (which included the lipids and the RNA) in the reconstruction were removed by a soft-edged mask derived from an icosahedrally organized, ...詳細: After each iteration, the non-icosahedral parts (which included the lipids and the RNA) in the reconstruction were removed by a soft-edged mask derived from an icosahedrally organized, protein-only map that was low-pass filtered to 30 Angstroms. This map then served as the reference model for the next iteration. クラス平均像の数: 3328 / 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL 詳細: METHOD--rigid-body fitting DETAILS--The E3 homology model was not further refined against the cryo-EM density map due to its less-resolved quality | ||||||||||||
原子モデル構築 | PDB-ID: 3N40 | ||||||||||||
精密化ステップ | サイクル: LAST
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