+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2vgq | |||||||||
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タイトル | Crystal Structure of Human IPS-1 CARD | |||||||||
要素 | Sugar ABC transporter substrate-binding protein,Mitochondrial antiviral-signaling protein | |||||||||
キーワード | IMMUNE SYSTEM/TRANSPORT (免疫系) / IPS1/MAVS/VISA/CARDIF / CASPASE ACTIVATION / CASPASE RECRUITMENT DOMAIN / INNATE IMMUNITY (自然免疫系) / FUSION PROTEIN (融合タンパク質) / SUGAR TRANSPORT / TRANSPORT / IMMUNE SYSTEM (免疫系) / CHIMERA / IMMUNE SYSTEM-TRANSPORT complex (免疫系) | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of response to cytokine stimulus / positive regulation of type I interferon-mediated signaling pathway ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of response to cytokine stimulus / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of viral genome replication / detection of maltose stimulus / maltose binding / type I interferon-mediated signaling pathway / maltose transport complex / maltose transport / cellular response to exogenous dsRNA / maltodextrin transmembrane transport / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / positive regulation of type I interferon production / ubiquitin ligase complex / signaling adaptor activity / positive regulation of defense response to virus by host / activation of innate immune response / positive regulation of interferon-beta production / ATP-binding cassette (ABC) transporter complex / molecular condensate scaffold activity / cell chemotaxis / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / ミトコンドリア / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / positive regulation of tumor necrosis factor production / outer membrane-bounded periplasmic space / TRAF3-dependent IRF activation pathway / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / ペリプラズム / molecular adaptor activity / defense response to bacterium / positive regulation of protein phosphorylation / 自然免疫系 / DNA damage response / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / シグナル伝達 / positive regulation of transcription by RNA polymerase II / ミトコンドリア / 生体膜 / identical protein binding 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (大腸菌) Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.1 Å | |||||||||
データ登録者 | Potter, J.A. / Randall, R.E. / Taylor, G.L. | |||||||||
引用 | ジャーナル: BMC Struct Biol / 年: 2008 タイトル: Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain. 著者: Jane A Potter / Richard E Randall / Garry L Taylor / 要旨: BACKGROUND: IPS-1/MAVS/VISA/Cardif is an adaptor protein that plays a crucial role in the induction of interferons in response to viral infection. In the initial stage of the intracellular antiviral ...BACKGROUND: IPS-1/MAVS/VISA/Cardif is an adaptor protein that plays a crucial role in the induction of interferons in response to viral infection. In the initial stage of the intracellular antiviral response two RNA helicases, retinoic acid inducible gene-I (RIG-I) and melanoma differentiation-association gene 5 (MDA5), are independently able to bind viral RNA in the cytoplasm. The 62 kDa protein IPS-1/MAVS/VISA/Cardif contains an N-terminal caspase activation and recruitment (CARD) domain that associates with the CARD regions of RIG-I and MDA5, ultimately leading to the induction of type I interferons. As a first step towards understanding the molecular basis of this important adaptor protein we have undertaken structural studies of the IPS-1 MAVS/VISA/Cardif CARD region. RESULTS: The crystal structure of human IPS-1/MAVS/VISA/Cardif CARD has been determined to 2.1A resolution. The protein was expressed and crystallized as a maltose-binding protein (MBP) fusion ...RESULTS: The crystal structure of human IPS-1/MAVS/VISA/Cardif CARD has been determined to 2.1A resolution. The protein was expressed and crystallized as a maltose-binding protein (MBP) fusion protein. The MBP and IPS-1 components each form a distinct domain within the structure. IPS-1/MAVS/VISA/Cardif CARD adopts a characteristic six-helix bundle with a Greek-key topology and, in common with a number of other known CARD structures, contains two major polar surfaces on opposite sides of the molecule. One face has a surface-exposed, disordered tryptophan residue that may explain the poor solubility of untagged expression constructs. CONCLUSION: The IPS-1/MAVS/VISA/Cardif CARD domain adopts the classic CARD fold with an asymmetric surface charge distribution that is typical of CARD domains involved in homotypic protein-protein ...CONCLUSION: The IPS-1/MAVS/VISA/Cardif CARD domain adopts the classic CARD fold with an asymmetric surface charge distribution that is typical of CARD domains involved in homotypic protein-protein interactions. The location of the two polar areas on IPS-1/MAVS/VISA/Cardif CARD suggest possible types of associations that this domain makes with the two CARD domains of MDA5 or RIG-I. The N-terminal CARD domains of RIG-I and MDA5 share greatest sequence similarity with IPS-1/MAVS/VISA/Cardif CARD and this has allowed modelling of their structures. These models show a very different charge profile for the equivalent surfaces compared to IPS-1/MAVS/VISA/Cardif CARD. | |||||||||
履歴 |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-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 | 2vgq.cif.gz | 110.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2vgq.ent.gz | 84.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2vgq.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/vg/2vgq ftp://data.pdbj.org/pub/pdb/validation_reports/vg/2vgq | HTTPS FTP |
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-関連構造データ
関連構造データ | |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 53411.324 Da / 分子数: 1 断片: MMBP RESIDUES 27-392, CARD DOMAIN RESIDUES 3-93,MMBP RESIDUES 27-392, CARD DOMAIN RESIDUES 3-93 由来タイプ: 組換発現 詳細: THE CONSTRUCT IS A FUSION OF E. COLI MBP (RESIDUES 2-366) AND HUMAN IPS-1 CARD (RESIDUES 1 TO 93) 由来: (組換発現) Escherichia coli (大腸菌), (組換発現) Homo sapiens (ヒト) 遺伝子: malE, PU06_05845, MAVS, IPS1, KIAA1271, VISA / 発現宿主: ESCHERICHIA COLI (大腸菌) 参照: UniProt: A0A0B1N7A9, UniProt: Q7Z434, UniProt: P0AEX9*PLUS | ||
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#2: 多糖 | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose | ||
#3: 化合物 | ChemComp-SO4 / #4: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 3.6 Å3/Da / 溶媒含有率: 66 % / 解説: NONE |
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-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: ESRF / ビームライン: ID14-2 / 波長: 0.934 |
検出器 | タイプ: ADSC CCD / 検出器: CCD |
放射 | 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: 0.934 Å / 相対比: 1 |
反射 | 解像度: 2.1→32.7 Å / Num. obs: 48262 / % possible obs: 99.8 % / Observed criterion σ(I): 4.4 / 冗長度: 7.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.1 |
反射 シェル | 解像度: 2.1→2.21 Å / 冗長度: 7.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.4 / % possible all: 99.9 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.1→32.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.449 / SU ML: 0.09 / 交差検証法: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.138 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 21.55 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.1→32.24 Å
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拘束条件 |
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