+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9380 | |||||||||
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タイトル | cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Human antiviral restriction factor / HIV viral protein / ANTIVIRAL PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 RUNX3 regulates RUNX1-mediated transcription / apolipoprotein B mRNA editing enzyme complex / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / base conversion or substitution editing ...RUNX3 regulates RUNX1-mediated transcription / apolipoprotein B mRNA editing enzyme complex / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / base conversion or substitution editing / 活性化誘導シチジンデアミナーゼ / negative regulation of CD4-positive, alpha-beta T cell differentiation / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / lymphocyte differentiation / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / negative regulation of viral process / RUNX2 regulates genes involved in cell migration / virion component => GO:0044423 / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / retrotransposon silencing / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / definitive hemopoiesis / DNA demethylation / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / negative regulation of viral genome replication / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX2 regulates osteoblast differentiation / RUNX3 regulates p14-ARF / cell maturation / positive regulation of defense response to virus by host / ウイルスのライフサイクル / virion component / P-body / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / osteoblast differentiation / protein polyubiquitination / Transcriptional regulation of granulopoiesis / Regulation of RUNX2 expression and activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / defense response to virus / Estrogen-dependent gene expression / host cell cytoplasm / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity / ribonucleoprotein complex / 自然免疫系 / regulation of transcription by RNA polymerase II / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / 核質 / 生体膜 / identical protein binding / 細胞核 / 細胞膜 / 細胞質 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 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Hu Y / Xiong Y | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2019 タイトル: Structural basis of antagonism of human APOBEC3F by HIV-1 Vif. 著者: Yingxia Hu / Belete A Desimmie / Henry C Nguyen / Samantha J Ziegler / Tat Cheung Cheng / John Chen / Jia Wang / Hongwei Wang / Kai Zhang / Vinay K Pathak / Yong Xiong / 要旨: HIV-1 virion infectivity factor (Vif) promotes degradation of the antiviral APOBEC3 (A3) proteins through the host ubiquitin-proteasome pathway to enable viral immune evasion. Disrupting Vif-A3 ...HIV-1 virion infectivity factor (Vif) promotes degradation of the antiviral APOBEC3 (A3) proteins through the host ubiquitin-proteasome pathway to enable viral immune evasion. Disrupting Vif-A3 interactions to reinstate the A3-catalyzed suppression of human immunodeficiency virus type 1 (HIV-1) replication is a potential approach for antiviral therapeutics. However, the molecular mechanisms by which Vif recognizes A3 proteins remain elusive. Here we report a cryo-EM structure of the Vif-targeted C-terminal domain of human A3F in complex with HIV-1 Vif and the cellular cofactor core-binding factor beta (CBFβ) at 3.9-Å resolution. The structure shows that Vif and CBFβ form a platform to recruit A3F, revealing a direct A3F-recruiting role of CBFβ beyond Vif stabilization, and captures multiple independent A3F-Vif interfaces. Together with our biochemical and cellular studies, our structural findings establish the molecular determinants that are critical for Vif-mediated neutralization of A3F and provide a comprehensive framework of how HIV-1 Vif hijacks the host protein degradation machinery to counteract viral restriction by A3F. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_9380.map.gz | 4.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9380-v30.xml emd-9380.xml | 14.2 KB 14.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9380.png | 135.3 KB | ||
Filedesc metadata | emd-9380.cif.gz | 6.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9380 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9380 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_9380.map.gz / 形式: CCP4 / 大きさ: 42.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : truncated Vif/CBFbeta/A3Fctd complex
全体 | 名称: truncated Vif/CBFbeta/A3Fctd complex |
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要素 |
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-超分子 #1: truncated Vif/CBFbeta/A3Fctd complex
超分子 | 名称: truncated Vif/CBFbeta/A3Fctd complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3 |
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由来(天然) | 生物種: Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) |
分子量 | 理論値: 17 KDa |
-超分子 #2: 6xHis tagged hA3Fctd-40aa-hCBFbeta fusion
超分子 | 名称: 6xHis tagged hA3Fctd-40aa-hCBFbeta fusion / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1-#2 詳細: The N-terminus of human CBFbeta is fused to human A3Fctd through a 40 amino acid linker:GVDGSDEASELACPTPKEDGLAQQQTQLNLRSQATGSGSG |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-超分子 #3: alpha domain truncated HIV-1 Vif
超分子 | 名称: alpha domain truncated HIV-1 Vif / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #3 |
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由来(天然) | 生物種: Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) |
-分子 #1: DNA dC->dU-editing enzyme APOBEC-3F
分子 | 名称: DNA dC->dU-editing enzyme APOBEC-3F / タイプ: protein_or_peptide / ID: 1 / コピー数: 4 / 光学異性体: LEVO / EC番号: 活性化誘導シチジンデアミナーゼ |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 24.433271 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MGSSHHHHHH SQDPNSMGKE ILRNPMEAMD PHIFYFHFKN LRKAYGRNES WLCFTMEVVK HHSPVSWKRG VFRNQVDPET GRHAERCFL SWFCDDILSP NTNYEVTWYT SWSPCPECAG EVAEFLARHS NVNLTIKTAR LYYFKDTDAA EGLRSLSQEG A SVEIMGYK ...文字列: MGSSHHHHHH SQDPNSMGKE ILRNPMEAMD PHIFYFHFKN LRKAYGRNES WLCFTMEVVK HHSPVSWKRG VFRNQVDPET GRHAERCFL SWFCDDILSP NTNYEVTWYT SWSPCPECAG EVAEFLARHS NVNLTIKTAR LYYFKDTDAA EGLRSLSQEG A SVEIMGYK DFKYCWENFV YNDDEPFKPW DGLDYNFLDL DSKLQEILE UniProtKB: DNA dC->dU-editing enzyme APOBEC-3F |
-分子 #2: Core-binding factor subunit beta
分子 | 名称: Core-binding factor subunit beta / タイプ: protein_or_peptide / ID: 2 / コピー数: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 17.851043 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MPRVVPDQRS KFENEEFFRK LSRECEIKYT GFRDRPHEER QARFQNACRD GRSEIAFVAT GTNLSLQFFP ASWQGEQRQT PSREYVDLE REAGKVYLKA PMILNGVCVI WKGWIDLQRL DGMGCLEFDE ERAQQEDALA QQAFEEARRR TR UniProtKB: Core-binding factor subunit beta |
-分子 #3: Virion infectivity factor
分子 | 名称: Virion infectivity factor / タイプ: protein_or_peptide / ID: 3 詳細: Residues 114-157 was replaced with a 6 amino acid linker (EASEGS). The C-terminal residues 177-192 were deleted. コピー数: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) |
分子量 | 理論値: 16.736102 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MENRWQVMIV WQVDRMRINT WKRLVKHHMY ISRKAKDWFY RHHYESTNPK ISSEVHIPLG DAKLVITTYW GLHTGERDWH LGQGVSIEW RKKRYSTQVD PDLADQLIHL HYFDEASEGS QIKPPLPSVR KLTEDRWNK UniProtKB: Virion infectivity factor, Virion infectivity factor |
-分子 #4: ZINC ION
分子 | 名称: ZINC ION / タイプ: ligand / ID: 4 / コピー数: 4 / 式: ZN |
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分子量 | 理論値: 65.409 Da |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 8 |
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グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 56.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: INSILICO MODEL |
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初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |
最終 再構成 | 想定した対称性 - 点群: D2 (2回x2回 2面回転対称) 解像度のタイプ: BY AUTHOR / 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 337256 |