+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5fjb | ||||||
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タイトル | Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non- canonical Binding Site | ||||||
要素 |
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キーワード | ISOMERASE | ||||||
機能・相同性 | 機能・相同性情報 host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / Membrane binding and targetting of GAG proteins / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / platelet aggregation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / host multivesicular body / platelet activation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / Platelet degranulation / protein folding / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / viral nucleocapsid / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / viral translational frameshifting / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / host cell nucleus / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / protein-containing complex / RNA binding / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | HUMAN IMMUNODEFICIENCY VIRUS 1 (ヒト免疫不全ウイルス) HOMO SAPIENS (ヒト) | ||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 9 Å | ||||||
データ登録者 | Liu, C. / Perilla, J.R. / Ning, J. / Lu, M. / Hou, G. / Ramalhu, R. / Bedwell, G.J. / Ahn, J. / Shi, J. / Gronenborn, A.M. ...Liu, C. / Perilla, J.R. / Ning, J. / Lu, M. / Hou, G. / Ramalhu, R. / Bedwell, G.J. / Ahn, J. / Shi, J. / Gronenborn, A.M. / Prevelige Jr, P.E. / Rousso, I. / Aiken, C. / Polenova, T. / Schulten, K. / Zhang, P. | ||||||
引用 | ジャーナル: Nat Commun / 年: 2016 タイトル: Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site. 著者: Chuang Liu / Juan R Perilla / Jiying Ning / Manman Lu / Guangjin Hou / Ruben Ramalho / Benjamin A Himes / Gongpu Zhao / Gregory J Bedwell / In-Ja Byeon / Jinwoo Ahn / Angela M Gronenborn / ...著者: Chuang Liu / Juan R Perilla / Jiying Ning / Manman Lu / Guangjin Hou / Ruben Ramalho / Benjamin A Himes / Gongpu Zhao / Gregory J Bedwell / In-Ja Byeon / Jinwoo Ahn / Angela M Gronenborn / Peter E Prevelige / Itay Rousso / Christopher Aiken / Tatyana Polenova / Klaus Schulten / Peijun Zhang / 要旨: The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the ...The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection. | ||||||
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 | 5fjb.cif.gz | 108 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5fjb.ent.gz | 85 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5fjb.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 | 5fjb_validation.pdf.gz | 745.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5fjb_full_validation.pdf.gz | 759.2 KB | 表示 | |
XML形式データ | 5fjb_validation.xml.gz | 23.5 KB | 表示 | |
CIF形式データ | 5fjb_validation.cif.gz | 34.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fjb ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fjb | 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: 24345.912 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) HUMAN IMMUNODEFICIENCY VIRUS 1 (ヒト免疫不全ウイルス) 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P03347, UniProt: P04591*PLUS #2: タンパク質 | | 分子量: 17905.307 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P62937, peptidylprolyl isomerase 配列の詳細 | HX2B CAPSID PROTEIN HUMAN CYCLOPHILI | |
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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: HELICAL ARRAY / 3次元再構成法: らせん対称体再構成法 |
-試料調製
構成要素 | 名称: Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A タイプ: COMPLEX |
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緩衝液 | pH: 8 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: OTHER |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F30 / 日付: 2013年6月20日 |
電子銃 | 電子線源: OTHER / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: OTHER / 倍率(公称値): 59000 X / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 15 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
-解析
EMソフトウェア |
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3次元再構成 | 解像度: 9 Å 詳細: MOLECULAR DYNAMICS FLEXIBLE FITTING (MDFF) DERIVED MODEL. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3076. (DEPOSITION ID: 13564). 対称性のタイプ: HELICAL | ||||||||||||
原子モデル構築 | PDB-ID: 3J4F | ||||||||||||
精密化 | 最高解像度: 9 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 9 Å
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