+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8fvi | ||||||
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タイトル | Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5 | ||||||
要素 |
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キーワード | ANTIVIRAL PROTEIN / virus-host protein complex | ||||||
機能・相同性 | 機能・相同性情報 RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / mRNA Editing: C to U Conversion / Formation of the Editosome / 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 ...RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / mRNA Editing: C to U Conversion / Formation of the Editosome / 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 / single-stranded DNA cytosine deaminase / negative regulation of CD4-positive, alpha-beta T cell differentiation / DNA cytosine deamination / negative regulation by host of viral genome replication / : / lymphocyte differentiation / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / retrotransposon silencing / cullin-RING ubiquitin ligase complex / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / target-directed miRNA degradation / RUNX3 Regulates Immune Response and Cell Migration / elongin complex / VCB complex / definitive hemopoiesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / 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 / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RUNX3 regulates p14-ARF / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cell maturation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / viral life cycle / transcription corepressor binding / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation of granulopoiesis / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of RUNX3 expression and activity / P-body / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / virion component / osteoblast differentiation / protein polyubiquitination / Regulation of RUNX2 expression and activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / sequence-specific DNA binding / defense response to virus / Estrogen-dependent gene expression / transcription coactivator activity / host cell cytoplasm / transcription by RNA polymerase II / protein ubiquitination / innate immune response / ubiquitin protein ligase binding / 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 / nucleoplasm / membrane / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) Escherichia coli (大腸菌) | ||||||
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: 3.24 Å | ||||||
データ登録者 | Ito, F. / Alvarez-Cabrera, A.L. / Zhou, Z.H. / Chen, X.S. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Structural basis of HIV-1 Vif-mediated E3 ligase targeting of host APOBEC3H. 著者: Fumiaki Ito / Ana L Alvarez-Cabrera / Kyumin Kim / Z Hong Zhou / Xiaojiang S Chen / 要旨: Human APOBEC3 (A3) cytidine deaminases are antiviral factors that are particularly potent against retroviruses. As a countermeasure, HIV-1 uses a viral infectivity factor (Vif) to target specific ...Human APOBEC3 (A3) cytidine deaminases are antiviral factors that are particularly potent against retroviruses. As a countermeasure, HIV-1 uses a viral infectivity factor (Vif) to target specific human A3s for proteasomal degradation. Vif recruits cellular transcription cofactor CBF-β and Cullin-5 (CUL5) RING E3 ubiquitin ligase to bind different A3s distinctively, but how this is accomplished remains unclear in the absence of the atomic structure of the complex. Here, we present the cryo-EM structures of HIV-1 Vif in complex with human A3H, CBF-β and components of CUL5 ubiquitin ligase (CUL5, ELOB, and ELOC). Vif nucleates the entire complex by directly binding four human proteins, A3H, CBF-β, CUL5, and ELOC. The structures reveal a large interface area between A3H and Vif, primarily mediated by an α-helical side of A3H and a five-stranded β-sheet of Vif. This A3H-Vif interface unveils the basis for sensitivity-modulating polymorphism of both proteins, including a previously reported gain-of-function mutation in Vif isolated from HIV/AIDS patients. Our structural and functional results provide insights into the remarkable interplay between HIV and humans and would inform development efforts for anti-HIV therapeutics. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8fvi.cif.gz | 189.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8fvi.ent.gz | 141.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8fvi.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 | 8fvi_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8fvi_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 8fvi_validation.xml.gz | 55.4 KB | 表示 | |
CIF形式データ | 8fvi_validation.cif.gz | 79.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fv/8fvi ftp://data.pdbj.org/pub/pdb/validation_reports/fv/8fvi | 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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-要素
-タンパク質 , 6種, 6分子 01Axyz
#1: タンパク質 | 分子量: 18643.814 Da / 分子数: 1 / 断片: UNP residues 1-157 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CBFB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q13951 |
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#2: タンパク質 | 分子量: 21160.451 Da / 分子数: 1 / 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) 株: pNL4-3 / 遺伝子: vif / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P12504 |
#3: タンパク質 | 分子量: 22103.410 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APOBEC3H / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: Q6NTF7, single-stranded DNA cytosine deaminase |
#6: タンパク質 | 分子量: 36613.980 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CUL5 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A2K5ZN28 |
#7: タンパク質 | 分子量: 11488.030 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ELOB, TCEB2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15370 |
#8: タンパク質 | 分子量: 10843.420 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ELOC, TCEB1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15369 |
-RNA鎖 , 2種, 2分子 BC
#4: RNA鎖 | 分子量: 3039.740 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) |
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#5: RNA鎖 | 分子量: 2917.895 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) |
-非ポリマー , 2種, 3分子
#9: 化合物 | #10: 水 | ChemComp-HOH / | |
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-詳細
研究の焦点であるリガンドがあるか | N |
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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: Hetero-hexameric complex of HIV-1 Vif and human APOBEC3H, CBF-beta, ELOB, ELOC, and CUL5 タイプ: COMPLEX / Entity ID: #1-#8 / 由来: MULTIPLE SOURCES | ||||||||||||||||
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分子量 | 値: 0.12 MDa / 実験値: NO | ||||||||||||||||
由来(天然) |
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由来(組換発現) | 生物種: Escherichia coli (大腸菌) | ||||||||||||||||
緩衝液 | pH: 7.5 | ||||||||||||||||
試料 | 濃度: 0.15 mg/ml / 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 IV / 凍結剤: ETHANE / 湿度: 100 % / 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 / 倍率(公称値): 165000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm |
撮影 | 平均露光時間: 3.5 sec. / 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 14725 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 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: 3637921 | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.24 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 89986 / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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