- PDB-2vgq: Crystal Structure of Human IPS-1 CARD -
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基本情報
登録情報
データベース: PDB / ID: 2vgq
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 / IPS1/MAVS/VISA/CARDIF / CASPASE ACTIVATION / CASPASE RECRUITMENT DOMAIN / INNATE IMMUNITY / FUSION PROTEIN / SUGAR TRANSPORT / TRANSPORT / IMMUNE SYSTEM / CHIMERA / IMMUNE SYSTEM-TRANSPORT complex
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 / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / detection of maltose stimulus / maltose transport complex / cellular response to exogenous dsRNA / carbohydrate transport / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / positive regulation of type I interferon production / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / signaling adaptor activity / ubiquitin ligase complex / antiviral innate immune response / 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 / cell chemotaxis / molecular condensate scaffold activity / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / Evasion by RSV of host interferon responses / positive regulation of DNA-binding transcription factor activity / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / outer membrane-bounded periplasmic space / TRAF3-dependent IRF activation pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / mitochondrial outer membrane / periplasmic space / molecular adaptor activity / defense response to bacterium / positive regulation of protein phosphorylation / innate immune response / DNA damage response / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / identical protein binding / membrane 類似検索 - 分子機能
: / IPS1, CARD domain / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / Caspase recruitment domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein ...: / IPS1, CARD domain / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / Caspase recruitment domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Death-like domain superfamily / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
alpha-maltotetraose / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein / Mitochondrial antiviral-signaling protein 類似検索 - 構成要素
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.
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.
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
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.2.0019
精密化
PHASER
位相決定
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.
Rfactor
反射数
%反射
Selection details
Rfree
0.22
2404
5 %
RANDOM
Rwork
0.181
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obs
0.183
45853
99.7 %
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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