EMDB-7453: Structure of the HIV-Nef dileucine mutant bound AP-1:Arf1 dimer m...

基本情報

• エントリ情報: データベース: EMDB / ID: 7453
• タイトル: Structure of the HIV-Nef dileucine mutant bound AP-1:Arf1 dimer monomeric subunit
• マップデータ: AP-1:Arf1:Tetherin-Nef dileucine mutant dimer monomeric subunit
• 試料: Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant:
• 機能・相同性: Adaptin C-terminal domain / HIV negative factor Nef / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / TBP domain superfamily / Synthesis of PIPs at the plasma membrane / Longin-like domain superfamily / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Gamma-adaptin ear (GAE) domain / Lysosome Vesicle Biogenesis / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Small GTPase superfamily, ARF/SAR type / Clathrin derived vesicle budding / Small GTP-binding protein domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Clathrin adaptor, mu subunit / Beta-adaptin appendage, C-terminal subdomain / Clathrin adaptor complex, small chain / アルマジロ / MHC class II antigen presentation / Nef Mediated CD4 Down-regulation / Synthesis of PIPs at the Golgi membrane / Bone marrow stromal antigen 2 / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor complexes medium chain signature 2. / Gamma-adaptin ear (GAE) domain profile. / Mu homology domain (MHD) profile. / small GTPase Arf family profile. / Nef mediated downregulation of MHC class I complex cell surface expression / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Armadillo-like helical / Armadillo-type fold / Mu homology domain / Neutrophil degranulation / Adaptin N terminal region / Golgi Associated Vesicle Biogenesis / Clathrin adaptor complex small chain / Lysosome Vesicle Biogenesis / Adaptor complexes medium subunit family / Negative factor, (F-Protein) or Nef / MHC class II antigen presentation / Interferon alpha/beta signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / AP-1/2/4 complex subunit beta / ADP-ribosylation factor family / AP-2 complex subunit mu, C-terminal superfamily / Beta2-adaptin appendage, C-terminal sub-domain / HIV-1 Nef protein, core domain superfamily / AP complex subunit beta / HIV-1 Nef protein, anchor domain superfamily / Adaptor protein complex, sigma subunit / COPI-dependent Golgi-to-ER retrograde traffic / Adaptor protein complex AP-1, gamma subunit / COPI-mediated anterograde transport / Neutrophil degranulation / P-loop containing nucleoside triphosphate hydrolase / Clathrin adaptor, mu subunit, conserved site / Golgi Associated Vesicle Biogenesis / AP complex, mu/sigma subunit / Intra-Golgi traffic / Bone marrow stromal antigen 2 / clathrin adaptor complex / Golgi to transport vesicle transport / synaptic vesicle budding / lysosomal membrane organization / negative regulation of intracellular transport of viral material / negative regulation of plasmacytoid dendritic cell cytokine production / positive regulation of late endosome to lysosome transport / phospholipase D activator activity / regulation of phospholipid metabolic process / positive regulation of natural killer cell degranulation / negative regulation by symbiont of host T-cell mediated immune response / negative regulation of CD4 biosynthetic process / regulation of Arp2/3 complex-mediated actin nucleation / mitotic cleavage furrow ingression / AP-1 adaptor complex / endosome to melanosome transport / positive regulation of ER to Golgi vesicle-mediated transport / Golgi to lysosome transport / response to interferon-beta / very-low-density lipoprotein particle assembly / melanosome organization / regulation of receptor internalization / postsynaptic actin cytoskeleton organization / suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I / COPI-coated vesicle / response to interferon-alpha / dendritic spine organization / GTP-dependent protein binding / membrane coat / suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host adaptive immune response / metalloendopeptidase inhibitor activity / positive regulation of calcium ion-dependent exocytosis / suppression by virus of host autophagy / positive regulation of natural killer cell mediated cytotoxicity / long-term synaptic depression / Golgi to plasma membrane transport / determination of left/right symmetry / regulation of calcium-mediated signaling
• 由来: Homo sapiens (ヒト)
• 実験手法: 単粒子再構成法 / クライオ電子顕微鏡法 / 4.27Å分解能
• データ登録者: Buffalo CZ / Morris KL / Hurley JH
• 引用: ジャーナル: Cell / 年: 2018; タイトル: HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation.; 著者: Kyle L Morris / Cosmo Z Buffalo / Christina M Stürzel / Elena Heusinger / Frank Kirchhoff / Xuefeng Ren / James H Hurley; 要旨: The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 Å structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates.
• 構造検証レポート: PDB-ID: 6d83; ; 簡易版詳細版構造検証レポートについて
• 日付: 登録: 2018年2月2日 / ヘッダ(付随情報) 公開: 2018年3月14日 / マップ公開: 2018年7月25日 / 最新の更新: 2018年8月8日

マップデータ

• ファイル: emd_7453.map.gz (map file in CCP4 format, 67109 KB)
• ボクセルのサイズ: X=Y=Z: 1.067 Å

密度

表面のレベル:	0.0303 (by author), 0.0303 (ムービー #1)
最小 - 最大	-0.056176327 - 0.096912995
平均 (標準偏差)	0.00032869034 (0.0033635767)

詳細

EMDB XML:

空間群番号	1
マップ形状	Axis order X Y Z Dimensions 256 256 256 Origin 0. 0. 0. Limit 255. 255. 255. Spacing 256 256 256
セル	A=B=C: 273.152 Å α=β=γ: 90.0 deg.

CCP4マップヘッダ:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.067	1.067	1.067
M x/y/z	256	256	256
origin x/y/z	0.000	0.000	0.000
length x/y/z	273.152	273.152	273.152
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	256	256	256
D min/max/mean	-0.063	0.102	0.000

添付データ

試料の構成要素

全体 Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant

• 全体: 名称: Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant / 構成要素数: 1

構成要素 #1: タンパク質, Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant

• タンパク質: 名称: Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant / 組換発現: No
• 分子量: 理論値: 230 kDa
• 由来: 生物種: Homo sapiens (ヒト)
• 由来(合成): 発現系: Escherichia coli (大腸菌)

実験情報

試料調製

• 試料: 試料の状態: 粒子 / 実験手法: クライオ電子顕微鏡法
• 試料溶液: 試料濃度: 0.7 mg/ml; 緩衝液: 20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP; pH: 8
• 急速凍結: 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 温度: 294 K / 湿度: 100 %

電子顕微鏡撮影

• 実験機器: モデル: Titan Krios / 画像提供: FEI Company
• 撮影: 顕微鏡: FEI TITAN KRIOS
• 電子銃: 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射量: 39.7 e/Ų / 照射モード: FLOOD BEAM
• レンズ: 倍率: 22500. X (公称値), 46849. X (実測値) / Cs: 2.6 mm / 撮影モード: BRIGHT FIELD / デフォーカス: 750.0 - 2500.0 nm
• 試料ホルダ: モデル: FEI TITAN KRIOS AUTOGRID HOLDER
• カメラ: ディテクター: GATAN K2 SUMMIT (4k x 4k)

画像取得

• 画像取得: デジタル画像の数: 1989

画像解析

• 解析: 実験手法: 単粒子再構成法 / 想定した対称性: C1 (非対称) / 投影像の数: 85529
• 3次元再構成: 分解能: 4.27 Å / 分解能の算定法: FSC 0.143 CUT-OFF

原子モデル構築

得られたモデル

6d83