+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j2v | ||||||
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タイトル | CryoEM structure of HBV core | ||||||
要素 | PreC/core protein | ||||||
キーワード | VIRUS (ウイルス) / Hepatitis B virus core antigen (HBc) / no Cys61 intermolecular disulfide bond | ||||||
機能・相同性 | 機能・相同性情報 virus-mediated perturbation of host defense response => GO:0019049 / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / : / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / extracellular region 類似検索 - 分子機能 | ||||||
生物種 | Hepatitis B virus (B 型肝炎ウイルス) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | ||||||
データ登録者 | Yu, X. / Jin, L. / Jih, J. / Shih, C. / Zhou, Z.H. | ||||||
引用 | ジャーナル: PLoS One / 年: 2013 タイトル: 3.5Å cryoEM structure of hepatitis B virus core assembled from full-length core protein. 著者: Xuekui Yu / Lei Jin / Jonathan Jih / Chiaho Shih / Z Hong Zhou / 要旨: The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was ...The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was determined previously by X-ray crystallography. In an attempt to obtain atomic structural information of HBV core in a near native, non-crystalline environment, we reconstructed a 3.5Å-resolution structure of a recombinant core assembled from full-length HBc by cryo electron microscopy (cryoEM) and derived an atomic model. The structure shows that the 240 molecules of full-length HBc form a core with two layers. The outer layer, composed of the N-terminal assembly domain, is similar to the crystal structure of the truncated HBc, but has three differences. First, unlike the crystal structure, our cryoEM structure shows no disulfide bond between the Cys61 residues of the two subunits within the dimer building block, indicating such bond is not required for core formation. Second, our cryoEM structure reveals up to four more residues in the linker region (amino acids 140-149). Third, the loops in the cryoEM structures containing this linker region in subunits B and C are oriented differently (~30° and ~90°) from their counterparts in the crystal structure. The inner layer, composed of the C-terminal arginine-rich domain (ARD) and the ARD-bound RNAs, is partially-ordered and connected with the outer layer through linkers positioned around the two-fold axes. Weak densities emanate from the rims of positively charged channels through the icosahedral three-fold and local three-fold axes. We attribute these densities to the exposed portions of some ARDs, thus explaining ARD's accessibility by proteases and antibodies. Our data supports a role of ARD in mediating communication between inside and outside of the core during HBV maturation and envelopment. | ||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3j2v.cif.gz | 125.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j2v.ent.gz | 99.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j2v.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j2/3j2v ftp://data.pdbj.org/pub/pdb/validation_reports/j2/3j2v | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
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対称性 | 点対称性: (シェーンフリース記号: I (正20面体型対称)) |
-要素
#1: タンパク質 | 分子量: 21398.465 Da / 分子数: 4 / 断片: UNP residues 30-214 / 由来タイプ: 組換発現 由来: (組換発現) Hepatitis B virus (B 型肝炎ウイルス) 遺伝子: C, PreC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q765F0, UniProt: P03149*PLUS |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Hepatitis B virus core / タイプ: VIRUS |
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試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: NITROGEN |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2009年1月1日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 75000 X |
撮影 | 電子線照射量: 25 e/Å2 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
-解析
対称性 | 点対称性: I (正20面体型対称) | ||||||||||||
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3次元再構成 | 解像度: 3.5 Å / 粒子像の数: 8093 / 対称性のタイプ: POINT | ||||||||||||
精密化ステップ | サイクル: LAST
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