+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2c8i | ||||||
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タイトル | Complex Of Echovirus Type 12 With Domains 1, 2, 3 and 4 Of Its Receptor Decay Accelerating Factor (Cd55) By Cryo Electron Microscopy At 16 A | ||||||
要素 |
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キーワード | VIRUS/RECEPTOR / PICORNAVIRUS / DAF / VIRUS-RECEPTOR COMPLEX / ANTIGEN / BLOOD GROUP ANTIGEN / COMPLEMENT PATHWAY / GPI-ANCHOR / IMMUNE RESPONSE / INNATE IMMUNITY / LIPOPROTEIN / PLASMA / SUSHI | ||||||
機能・相同性 | 機能・相同性情報 regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / transport vesicle / complement activation, classical pathway / picornain 2A / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / secretory granule membrane / T=pseudo3 icosahedral viral capsid / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / channel activity / endocytosis involved in viral entry into host cell / positive regulation of T cell cytokine production / monoatomic ion transmembrane transport / nucleoside-triphosphate phosphatase / virus receptor activity / positive regulation of cytosolic calcium ion concentration / DNA replication / RNA helicase activity / induction by virus of host autophagy / membrane raft / RNA-directed RNA polymerase / Golgi membrane / viral RNA genome replication / cysteine-type endopeptidase activity / innate immune response / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / Neutrophil degranulation / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) HUMAN ECHOVIRUS 11 (ウイルス) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / クライオ電子顕微鏡法 / 解像度: 14 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D, E | ||||||
データ登録者 | Pettigrew, D.M. / Williams, D.T. / Kerrigan, D. / Evans, D.J. / Lea, S.M. / Bhella, D. | ||||||
引用 | ジャーナル: J Biol Chem / 年: 2006 タイトル: Structural and functional insights into the interaction of echoviruses and decay-accelerating factor. 著者: David M Pettigrew / David T Williams / David Kerrigan / David J Evans / Susan M Lea / David Bhella / 要旨: Many enteroviruses bind to the complement control protein decay-accelerating factor (DAF) to facilitate cell entry. We present here a structure for echovirus (EV) type 12 bound to DAF using cryo- ...Many enteroviruses bind to the complement control protein decay-accelerating factor (DAF) to facilitate cell entry. We present here a structure for echovirus (EV) type 12 bound to DAF using cryo-negative stain transmission electron microscopy and three-dimensional image reconstruction to 16-A resolution, which we interpreted using the atomic structures of EV11 and DAF. DAF binds to a hypervariable region of the capsid close to the 2-fold symmetry axes in an interaction that involves mostly the short consensus repeat 3 domain of DAF and the capsid protein VP2. A bulge in the density for the short consensus repeat 3 domain suggests that a loop at residues 174-180 rearranges to prevent steric collision between closely packed molecules at the 2-fold symmetry axes. Detailed analysis of receptor interactions between a variety of echoviruses and DAF using surface plasmon resonance and comparison of this structure (and our previous work; Bhella, D., Goodfellow, I. G., Roversi, P., Pettigrew, D., Chaudhry, Y., Evans, D. J., and Lea, S. M. (2004) J. Biol. Chem. 279, 8325-8332) with reconstructions published for EV7 bound to DAF support major differences in receptor recognition among these viruses. However, comparison of the electron density for the two virus.receptor complexes (rather than comparisons of the pseudo-atomic models derived from fitting the coordinates into these densities) suggests that the dramatic differences in interaction affinities/specificities may arise from relatively subtle structural differences rather than from large-scale repositioning of the receptor with respect to the virus surface. #1: ジャーナル: J Biol Chem / 年: 2004 タイトル: The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55). 著者: David Bhella / Ian G Goodfellow / Pietro Roversi / David Pettigrew / Yasmin Chaudhry / David J Evans / Susan M Lea / 要旨: Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three- ...Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses. | ||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 2c8i.cif.gz | 53.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2c8i.ent.gz | 27.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2c8i.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
文書・要旨 | 2c8i_validation.pdf.gz | 798.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2c8i_full_validation.pdf.gz | 798 KB | 表示 | |
XML形式データ | 2c8i_validation.xml.gz | 20.1 KB | 表示 | |
CIF形式データ | 2c8i_validation.cif.gz | 29.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/c8/2c8i ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c8i | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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対称性 | 点対称性: (シェーンフリース記号: I (正20面体型対称)) |
-要素
#1: タンパク質 | 分子量: 32447.342 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) HUMAN ECHOVIRUS 11 (ウイルス) / 株: GREGORY / 参照: UniProt: P29813 |
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#2: タンパク質 | 分子量: 27996.480 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) HUMAN ECHOVIRUS 11 (ウイルス) / 株: GREGORY / 参照: UniProt: P29813 |
#3: タンパク質 | 分子量: 25897.391 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) HUMAN ECHOVIRUS 11 (ウイルス) / 株: GREGORY / 参照: UniProt: P29813 |
#4: タンパク質 | 分子量: 6620.287 Da / 分子数: 1 / 由来タイプ: 天然 詳細: STRUCTURE OF ECHOVIRUS TYPE 11 FITTED INTO CRYO-EM ELECTRON DENSITY FOR ECHOVIRUS TYPE 12. THE EM DENSITY HAS BEEN DEPOSITED IN THE EMDB, WITH ACCESSION CODE 1057 由来: (天然) HUMAN ECHOVIRUS 11 (ウイルス) / 株: GREGORY / 参照: UniProt: P29813 |
#5: タンパク質 | 分子量: 35034.164 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P08174 |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: ECHOVIRUS TYPE 12 BOUND TO DECAY ACCELERATING FACTOR タイプ: VIRUS / 詳細: CRYO-NEGATIVE STAIN IMAGES. 96 FOCAL PAIRS. |
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緩衝液 | 名称: PHOSPHATE BUFFERED SALINE / pH: 7.4 / 詳細: PHOSPHATE BUFFERED SALINE |
試料 | 濃度: 0.2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: YES |
染色 | タイプ: NEGATIVE / 染色剤: Ammonium Molybdate |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 凍結剤: ETHANE 詳細: STAINED WITH AMMONIUM MOLYBDATE PH 7.2. VITRIFIED IN LIQUID ETHANE (CRYO-NEGATIVE STAIN) |
-電子顕微鏡撮影
顕微鏡 | モデル: JEOL 1200 / 日付: 2004年9月1日 |
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電子銃 | 電子線源: LAB6 / 加速電圧: 120 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 30000 X / 倍率(補正後): 29100 X / 最大 デフォーカス(公称値): 2800 nm / 最小 デフォーカス(公称値): 600 nm / Cs: 3.4 mm |
試料ホルダ | 温度: 100 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | フィルム・検出器のモデル: KODAK SO-163 FILM |
画像スキャン | デジタル画像の数: 192 |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: DEFOCUS PAIR IMAGES OF INDIVIDUAL PARTICLES | ||||||||||||
対称性 | 点対称性: I (正20面体型対称) | ||||||||||||
3次元再構成 | 手法: POLAR FOURIER TRANSFORM METHOD / 解像度: 14 Å / 粒子像の数: 1501 / ピクセルサイズ(公称値): 2.18 Å / ピクセルサイズ(実測値): 2.18 Å 詳細: THE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL / Target criteria: OPTIMAL CORRELATION 詳細: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--LOCAL CORRELATION | ||||||||||||
原子モデル構築 | PDB-ID: 1H8T Accession code: 1H8T / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化 | 最高解像度: 14 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 14 Å
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