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基本情報
登録情報 | ![]() | |||||||||
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タイトル | Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2 | |||||||||
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![]() | Viral protein / RNA binding protein / Complex / Ubiquitin E3 ligase / VIRAL PROTEIN-IMMUNE SYSTEM-RNA complex | |||||||||
機能・相同性 | ![]() RUNX3 regulates RUNX1-mediated transcription / apolipoprotein B mRNA editing enzyme complex / RUNX1 regulates transcription of genes involved in BCR signaling / dCTP deaminase activity / cytidine deamination / 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 ...RUNX3 regulates RUNX1-mediated transcription / apolipoprotein B mRNA editing enzyme complex / RUNX1 regulates transcription of genes involved in BCR signaling / dCTP deaminase activity / cytidine deamination / 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 / single-stranded DNA cytosine deaminase / negative regulation of CD4-positive, alpha-beta T cell differentiation / DNA cytosine deamination / : / lymphocyte differentiation / cytidine to uridine editing / cytidine deaminase activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / negative regulation of viral process / 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 / 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 / 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 / APOBEC3G mediated resistance to HIV-1 infection / 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 / 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 / cell maturation / positive regulation of defense response to virus by host / viral life cycle / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / virion component / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / Transcriptional regulation of granulopoiesis / osteoblast differentiation / protein polyubiquitination / Regulation of RUNX2 expression and activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / defense response to virus / Estrogen-dependent gene expression / sequence-specific DNA binding / host cell cytoplasm / transcription by RNA polymerase II / transcription coactivator activity / protein ubiquitination / ribonucleoprotein complex / 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 / identical protein binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.2 Å | |||||||||
![]() | Li Y / Langley C / Azumaya CM / Echeverria I / Chesarino NM / Emerman M / Cheng Y / Gross JD | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: The structural basis for HIV-1 Vif antagonism of human APOBEC3G. 著者: Yen-Li Li / Caroline A Langley / Caleigh M Azumaya / Ignacia Echeverria / Nicholas M Chesarino / Michael Emerman / Yifan Cheng / John D Gross / ![]() 要旨: The APOBEC3 (A3) proteins are host antiviral cellular proteins that hypermutate the viral genome of diverse viral families. In retroviruses, this process requires A3 packaging into viral particles. ...The APOBEC3 (A3) proteins are host antiviral cellular proteins that hypermutate the viral genome of diverse viral families. In retroviruses, this process requires A3 packaging into viral particles. The lentiviruses encode a protein, Vif, that antagonizes A3 family members by targeting them for degradation. Diversification of A3 allows host escape from Vif whereas adaptations in Vif enable cross-species transmission of primate lentiviruses. How this 'molecular arms race' plays out at the structural level is unknown. Here, we report the cryogenic electron microscopy structure of human APOBEC3G (A3G) bound to HIV-1 Vif, and the hijacked cellular proteins that promote ubiquitin-mediated proteolysis. A small surface explains the molecular arms race, including a cross-species transmission event that led to the birth of HIV-1. Unexpectedly, we find that RNA is a molecular glue for the Vif-A3G interaction, enabling Vif to repress A3G by ubiquitin-dependent and -independent mechanisms. Our results suggest a model in which Vif antagonizes A3G by intercepting it in its most dangerous form for the virus-when bound to RNA and on the pathway to packaging-to prevent viral restriction. By engaging essential surfaces required for restriction, Vif exploits a vulnerability in A3G, suggesting a general mechanism by which RNA binding helps to position key residues necessary for viral antagonism of a host antiviral gene. | |||||||||
履歴 |
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構造の表示
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 83.2 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 26.3 KB 26.3 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 12.5 KB | 表示 | ![]() |
画像 | ![]() | 48.4 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
その他 | ![]() ![]() ![]() ![]() | 143.6 MB 22.6 MB 154.5 MB 154.5 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 957.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 957.3 KB | 表示 | |
XML形式データ | ![]() | 20.2 KB | 表示 | |
CIF形式データ | ![]() | 26.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 8cx2MC ![]() 8cx0C ![]() 8cx1C C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.835 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: Primary map sharpened with DeepEMhancer
ファイル | emd_27034_additional_1.map | ||||||||||||
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注釈 | Primary map sharpened with DeepEMhancer | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Density modified map
ファイル | emd_27034_additional_2.map | ||||||||||||
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注釈 | Density modified map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_27034_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_27034_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : HIV-1 Vif-E3 ligase substrate receptor (VCBC) in complex with hum...
全体 | 名称: HIV-1 Vif-E3 ligase substrate receptor (VCBC) in complex with human APOBEC3G and RNA |
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要素 |
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-超分子 #1: HIV-1 Vif-E3 ligase substrate receptor (VCBC) in complex with hum...
超分子 | 名称: HIV-1 Vif-E3 ligase substrate receptor (VCBC) in complex with human APOBEC3G and RNA タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#7 |
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由来(天然) | 生物種: ![]() |
-分子 #1: DNA dC->dU-editing enzyme APOBEC-3G
分子 | 名称: DNA dC->dU-editing enzyme APOBEC-3G / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO / EC番号: single-stranded DNA cytosine deaminase |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 50.034598 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MKPHFRNTVE RMYRDTFSYN FYNRPILSRR NTVWLCYEVK TKGPSRPPLD AKIFRGQVYS ELKYHPEMRF FHWFSKWRKL HRDQEYEVT WYISWSPCTK CTRDMATFLA EDPKVTLTIF VARLYYFWDP DYQEALRSLC QKRDGPRATM KIMNYDEFQH C WSKFVYSQ ...文字列: MKPHFRNTVE RMYRDTFSYN FYNRPILSRR NTVWLCYEVK TKGPSRPPLD AKIFRGQVYS ELKYHPEMRF FHWFSKWRKL HRDQEYEVT WYISWSPCTK CTRDMATFLA EDPKVTLTIF VARLYYFWDP DYQEALRSLC QKRDGPRATM KIMNYDEFQH C WSKFVYSQ RELFEPWNNL PKYYILLHIM LGEILRHSMD PPTFTFNFNN EPWVRGRHET YLCYEVERMH NDTWVLLNQR RG FLCNQAP HKHGFLEGRH AELCFLDVIP FWKLDLDQDY RVTCFTSWSP CFSCAQEMAK FISKNKHVSL CIFTARIYDD QGR CQEGLR TLAEAGAKIS IMTYSEFKHC WDTFVDHQGC PFQPWDGLDE HSQDLSGRLR AILQNQENGS SLEGGGGWSH PQFE KGGGS GGGSGGGSWS HPQFEK UniProtKB: DNA dC->dU-editing enzyme APOBEC-3G |
-分子 #2: Virion infectivity factor
分子 | 名称: Virion infectivity factor / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 22.556002 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MENRWQVMIV WQVDRMRIRT WKSLVKHHMY VSGKARGWFY RHHYESPHPR ISSEVHIPLG DARLVITTYW GLHTGERDWH LGQGVSIEW RKKRYSTQVD PELADQLIHL YYFDCFSDSA IRKALLGHIV SPRCEYQAGH NKVGSLQYLA LAALITPKKI K PPLPSVTK ...文字列: MENRWQVMIV WQVDRMRIRT WKSLVKHHMY VSGKARGWFY RHHYESPHPR ISSEVHIPLG DARLVITTYW GLHTGERDWH LGQGVSIEW RKKRYSTQVD PELADQLIHL YYFDCFSDSA IRKALLGHIV SPRCEYQAGH NKVGSLQYLA LAALITPKKI K PPLPSVTK LTEDRWNKPQ KTKGHRGSHT MNGH UniProtKB: Virion infectivity factor |
-分子 #3: Core-binding factor subunit beta
分子 | 名称: Core-binding factor subunit beta / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 21.542188 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MPRVVPDQRS KFENEEFFRK LSRECEIKYT GFRDRPHEER QARFQNACRD GRSEIAFVAT GTNLSLQFFP ASWQGEQRQT PSREYVDLE REAGKVYLKA PMILNGVCVI WKGWIDLQRL DGMGCLEFDE ERAQQEDALA QQAFEEARRR TREFEDRDRS H REEMEVRV SQLLAVTGKK TTRP UniProtKB: Core-binding factor subunit beta |
-分子 #4: Elongin-B
分子 | 名称: Elongin-B / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 13.147781 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ UniProtKB: Elongin-B |
-分子 #5: Elongin-C
分子 | 名称: Elongin-C / タイプ: protein_or_peptide / ID: 5 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 12.485135 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC UniProtKB: Elongin-C |
-分子 #6: RNA (5'-R(P*AP*AP*UP*AP*AP*AP*AP*AP*U)-3')
分子 | 名称: RNA (5'-R(P*AP*AP*UP*AP*AP*AP*AP*AP*U)-3') / タイプ: rna / ID: 6 / コピー数: 1 |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 2.871814 KDa |
配列 | 文字列: AAUAAAAAU |
-分子 #7: RNA (5'-R(P*UP*UP*UP*AP*AP*AP*AP*AP*U)-3')
分子 | 名称: RNA (5'-R(P*UP*UP*UP*AP*AP*AP*AP*AP*U)-3') / タイプ: rna / ID: 7 / コピー数: 1 |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 2.825735 KDa |
配列 | 文字列: UUUAAAAAU |
-分子 #8: ZINC ION
分子 | 名称: ZINC ION / タイプ: ligand / ID: 8 / コピー数: 6 / 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.46 mg/mL |
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緩衝液 | pH: 7 |
凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 68.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.8 µm / 倍率(公称値): 105000 |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |