+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7o24 | ||||||
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タイトル | Structure of the foamy viral protease-reverse transcriptase in complex with dsDNA. | ||||||
要素 |
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キーワード | VIRAL PROTEIN / reverse trancscriptase / complex with dsDNA | ||||||
機能・相同性 | 機能・相同性情報 virion component / DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / nucleic acid binding / aspartic-type endopeptidase activity ...virion component / DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / nucleic acid binding / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / proteolysis / metal ion binding / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | White-tufted-ear marmoset simian foamy virus (ウイルス) synthetic construct (人工物) | ||||||
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: 4.8 Å | ||||||
データ登録者 | Nowotny, M. / Czarnocki-Cieciura, M. | ||||||
資金援助 | ポーランド, 1件
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引用 | ジャーナル: J Virol / 年: 2021 タイトル: Structures of Substrate Complexes of Foamy Viral Protease-Reverse Transcriptase. 著者: Marzena Nowacka / Elżbieta Nowak / Mariusz Czarnocki-Cieciura / Justyna Jackiewicz / Krzysztof Skowronek / Roman H Szczepanowski / Birgitta M Wöhrl / Marcin Nowotny / 要旨: Reverse transcriptases (RTs) use their DNA polymerase and RNase H activities to catalyze the conversion of single-stranded RNA to double-stranded DNA (dsDNA), a crucial process for the replication of ...Reverse transcriptases (RTs) use their DNA polymerase and RNase H activities to catalyze the conversion of single-stranded RNA to double-stranded DNA (dsDNA), a crucial process for the replication of retroviruses. Foamy viruses (FVs) possess a unique RT, which is a fusion with the protease (PR) domain. The mechanism of substrate binding by this enzyme has been unknown. Here, we report a crystal structure of monomeric full-length marmoset FV (MFV) PR-RT in complex with an RNA/DNA hybrid substrate. We also describe a structure of MFV PR-RT with an RNase H deletion in complex with a dsDNA substrate in which the enzyme forms an asymmetric homodimer. Cryo-electron microscopy reconstruction of the full-length MFV PR-RT-dsDNA complex confirmed the dimeric architecture. These findings represent the first structural description of nucleic acid binding by a foamy viral RT and demonstrate its ability to change its oligomeric state depending on the type of bound nucleic acid. Reverse transcriptases (RTs) are intriguing enzymes converting single-stranded RNA to dsDNA. Their activity is essential for retroviruses, which are divided into two subfamilies differing significantly in their life cycles: and . The latter family is much more ancient and comprises five genera. A unique feature of foamy viral RTs is that they contain N-terminal protease (PR) domains, which are not present in orthoretroviral enzymes. So far, no structural information for full-length foamy viral PR-RT interacting with nucleic substrates has been reported. Here, we present crystal and cryo-electron microscopy structures of marmoset foamy virus (MFV) PR-RT. These structures revealed the mode of binding of RNA/DNA and dsDNA substrates. Moreover, unexpectedly, the structures and biochemical data showed that foamy viral PR-RT can adopt both a monomeric configuration, which is observed in our structures in the presence of an RNA/DNA hybrid, and an asymmetric dimer arrangement, which we observed in the presence of dsDNA. | ||||||
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 | 7o24.cif.gz | 235.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7o24.ent.gz | 175.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7o24.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
文書・要旨 | 7o24_validation.pdf.gz | 1.5 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7o24_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 7o24_validation.xml.gz | 50.9 KB | 表示 | |
CIF形式データ | 7o24_validation.cif.gz | 74.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/o2/7o24 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/7o24 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 85467.289 Da / 分子数: 3 / 由来タイプ: 組換発現 / 詳細: foamy virus 由来: (組換発現) White-tufted-ear marmoset simian foamy virus (ウイルス) 遺伝子: pol 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: D5JWV1, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H #2: DNA鎖 | | 分子量: 7347.770 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) #3: DNA鎖 | | 分子量: 6783.375 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
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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 |
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分子量 | 値: 0.19 MDa / 実験値: YES | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7 | ||||||||||||||||||||||||
試料 | 濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/1 | ||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 95 % / 凍結前の試料温度: 277 K |
-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 |
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 FIELD |
撮影 | 電子線照射量: 40 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19_4092: / 分類: 精密化 | |||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 344421 | |||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 20071 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | |||||||||||||||||||||||||||||||||||
拘束条件 |
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