- PDB-4uf1: Deerpox virus DPV022 in complex with Bak BH3 -
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基本情報
登録情報
データベース: PDB / ID: 4uf1
タイトル
Deerpox virus DPV022 in complex with Bak BH3
要素
Antiapoptotic membrane protein
Bcl-2 homologous antagonist/killer
キーワード
VIRAL PROTEIN / DEERPOX VIRUS / APOPTOSIS / BCL-2 / BAK BH3
機能・相同性
機能・相同性情報
Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / pore complex / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / B cell homeostasis / host cell mitochondrion / host cell membrane / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / Pyroptosis / animal organ regeneration / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / regulation of apoptotic process / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane / metal ion binding / cytosol 類似検索 - 分子機能
Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. ...Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha 類似検索 - ドメイン・相同性
ジャーナル: Acta Crystallogr D Biol Crystallogr / 年: 2015 タイトル: Structural basis of Deerpox virus-mediated inhibition of apoptosis. 著者: Denis R Burton / Sofia Caria / Bevan Marshall / Michele Barry / Marc Kvansakul / 要旨: Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use ...Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use of Bcl-2 proteins, to ensure their own survival. Here, it is reported that the Deerpox virus inhibitor of apoptosis, DPV022, only engages a highly restricted set of death-inducing Bcl-2 proteins, including Bim, Bax and Bak, with modest affinities. Structural analysis reveals that DPV022 adopts a Bcl-2 fold with a dimeric domain-swapped topology and binds pro-death Bcl-2 proteins via two conserved ligand-binding grooves found on opposite sides of the dimer. Structures of DPV022 bound to Bim, Bak and Bax BH3 domains reveal that a partial obstruction of the binding groove is likely to be responsible for the modest affinities of DPV022 for BH3 domains. These findings reveal that domain-swapped dimeric Bcl-2 folds are not unusual and may be found more widely in viruses. Furthermore, the modest affinities of DPV022 for pro-death Bcl-2 proteins suggest that two distinct classes of anti-apoptotic viral Bcl-2 proteins exist: those that are monomeric and tightly bind a range of death-inducing Bcl-2 proteins, and others such as DPV022 that are dimeric and only bind a very limited number of death-inducing Bcl-2 proteins with modest affinities.
履歴
登録
2014年12月23日
登録サイト: PDBE / 処理サイト: PDBE
改定 1.0
2015年8月5日
Provider: repository / タイプ: Initial release
改定 1.1
2015年8月12日
Group: Database references
改定 1.2
2015年8月19日
Group: Database references
改定 2.0
2019年10月23日
Group: Atomic model / Data collection / Other / カテゴリ: atom_site / pdbx_database_status Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
モノクロメーター: DOUBLE CRYSTAL MONOCHROMATOR (SI111) プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.9537 Å / 相対比: 1
反射
解像度: 2.3→41.71 Å / Num. obs: 9129 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / 冗長度: 5.7 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.9
反射 シェル
解像度: 2.3→2.39 Å / 冗長度: 5.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.1 / % possible all: 99
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解析
ソフトウェア
名称
バージョン
分類
PHENIX
(PHENIX.REFINE)
精密化
iMOSFLM
データ削減
Aimless
データスケーリング
PHASER
位相決定
精密化
構造決定の手法: 分子置換 開始モデル: DPV022_BIM 解像度: 2.3→41.707 Å / SU ML: 0.24 / σ(F): 1.36 / 位相誤差: 22.37 / 立体化学のターゲット値: ML 詳細: RESIDUES FROM 1 AND 2 AND FROM 138 TO 155 ARE MISSING IN DPV022. IN BAK,THE RESIDUES 67 AND 68 AS WELL AS 91 AND 92
Rfactor
反射数
%反射
Rfree
0.2059
446
4.9 %
Rwork
0.1782
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obs
0.1796
9109
96.99 %
溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL