+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1jew | ||||||
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タイトル | CRYO-EM STRUCTURE OF COXSACKIEVIRUS B3(M STRAIN) WITH ITS CELLULAR RECEPTOR, COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR (CAR). | ||||||
要素 |
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キーワード | Virus/Receptor / COXSACKIEVIRUS B3 / CVB3 / CAR / CRYO-EM STRUCTURE / Icosahedral virus / Virus-Receptor COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / germ cell migration / apicolateral plasma membrane / transepithelial transport ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / germ cell migration / apicolateral plasma membrane / transepithelial transport / cell-cell junction organization / connexin binding / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / intercalated disc / bicellular tight junction / cell adhesion molecule binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / neutrophil chemotaxis / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / acrosomal vesicle / mitochondrion organization / T=pseudo3 icosahedral viral capsid / filopodium / PDZ domain binding / Cell surface interactions at the vascular wall / adherens junction / host cell cytoplasmic vesicle membrane / neuromuscular junction / endocytosis involved in viral entry into host cell / beta-catenin binding / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell junction / cell-cell junction / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / heart development / basolateral plasma membrane / cell body / growth cone / actin cytoskeleton organization / DNA replication / defense response to virus / RNA helicase activity / neuron projection / membrane raft / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / signaling receptor binding / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / protein-containing complex / proteolysis / RNA binding / extracellular space / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Coxsackievirus B3 (コクサッキーウイルス) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 22 Å | ||||||
データ登録者 | Rossmann, M.G. / He, Y. | ||||||
引用 | ジャーナル: Nat Struct Biol / 年: 2001 タイトル: Interaction of coxsackievirus B3 with the full length coxsackievirus-adenovirus receptor. 著者: Y He / P R Chipman / J Howitt / C M Bator / M A Whitt / T S Baker / R J Kuhn / C W Anderson / P Freimuth / M G Rossmann / 要旨: Group B coxsackieviruses (CVB) utilize the coxsackievirus-adenovirus receptor (CAR) to recognize host cells. CAR is a membrane protein with two Ig-like extracellular domains (D1 and D2), a ...Group B coxsackieviruses (CVB) utilize the coxsackievirus-adenovirus receptor (CAR) to recognize host cells. CAR is a membrane protein with two Ig-like extracellular domains (D1 and D2), a transmembrane domain and a cytoplasmic domain. The three-dimensional structure of coxsackievirus B3 (CVB3) in complex with full length human CAR and also with the D1D2 fragment of CAR were determined to approximately 22 A resolution using cryo-electron microscopy (cryo-EM). Pairs of transmembrane domains of CAR associate with each other in a detergent cloud that mimics a cellular plasma membrane. This is the first view of a virus-receptor interaction at this resolution that includes the transmembrane and cytoplasmic portion of the receptor. CAR binds with the distal end of domain D1 in the canyon of CVB3, similar to how other receptor molecules bind to entero- and rhinoviruses. The previously described interface of CAR with the adenovirus knob protein utilizes a side surface of D1. #1: ジャーナル: Science / 年: 1997 タイトル: ISOLATION OF A COMMON RECEPTOR FOR COXSACKIE B VIRUSES AND ADENOVIRUSES 2 AND 5 著者: Bergelson, J.M. / Cunningham, J.A. / Droguett, G. / Kurt-Jones, E.A. / Krithivas, A. / Hong, J.S. / Horwitz, M.S. / Crowell, R.L. / Finberg, R.W. #2: ジャーナル: Science / 年: 1999 タイトル: STRUCTURAL ANALYSIS OF THE MECHANISM OF ADENOVIRUS BINDING TO ITS HUMAN CELLULAR RECEPTOR CAR 著者: Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M. #3: ジャーナル: Structure / 年: 1995 タイトル: THE STRUCTURE OF COXSACKIEVIRUS B3 AT 3.5A RESOLUTION 著者: Muckelbauer, J.K. / Kremer, M. / Minor, I. / Diana, G. / Dutko, F.J. / Groarke, J. / Pevear, D.C. / Rossman, M.G. | ||||||
履歴 |
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Remark 999 | SEQUENCE THE COXSACKIEVIRUS B3 USED IN THE EM EXPERIMENT IS M STRAIN, WHICH MIGHT BE DIFFERENT ...SEQUENCE THE COXSACKIEVIRUS B3 USED IN THE EM EXPERIMENT IS M STRAIN, WHICH MIGHT BE DIFFERENT SLIGHTLY WITH OTHER ISOLATES GIVING ARISE TO THE CONFLICTS. |
-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 | 1jew.cif.gz | 46.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1jew.ent.gz | 24.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1jew.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 | 1jew_validation.pdf.gz | 330.6 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1jew_full_validation.pdf.gz | 330.3 KB | 表示 | |
XML形式データ | 1jew_validation.xml.gz | 1 KB | 表示 | |
CIF形式データ | 1jew_validation.cif.gz | 9.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/je/1jew ftp://data.pdbj.org/pub/pdb/validation_reports/je/1jew | HTTPS FTP |
-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
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対称性 | 点対称性: (ヘルマン・モーガン記号: 532 / 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: 13358.203 Da / 分子数: 1 / 断片: Residues 21-140 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CAR / 細胞株 (発現宿主): A9 CELLS / 発現宿主: Mus musculus (ハツカネズミ) / 参照: UniProt: P78310 |
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#2: タンパク質 | 分子量: 31380.068 Da / 分子数: 1 / 断片: Residues 571-851 / 由来タイプ: 組換発現 由来: (組換発現) Coxsackievirus B3 (strain Woodruff) (コクサッキーウイルス) 属: Enterovirus / 生物種: Human enterovirus B / 株: Woodruff / 解説: COXSACKIEVIRUS B3 / 細胞株 (発現宿主): HELA CELLS / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q66282 |
#3: タンパク質 | 分子量: 28877.592 Da / 分子数: 1 / 断片: Residues 70-332 / 由来タイプ: 組換発現 由来: (組換発現) Coxsackievirus B3 (strain Woodruff) (コクサッキーウイルス) 属: Enterovirus / 生物種: Human enterovirus B / 株: Woodruff / 解説: COXSACKIEVIRUS B3 / 細胞株 (発現宿主): HELA CELLS / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q66282 |
#4: タンパク質 | 分子量: 26198.684 Da / 分子数: 1 / 断片: Residues 333-570 / 由来タイプ: 組換発現 由来: (組換発現) Coxsackievirus B3 (strain Woodruff) (コクサッキーウイルス) 属: Enterovirus / 生物種: Human enterovirus B / 株: Woodruff / 解説: COXSACKIEVIRUS B3 / 細胞株 (発現宿主): HELA CELLS / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q66282 |
#5: タンパク質 | 分子量: 7379.065 Da / 分子数: 1 / 断片: Residues 2-69 / 由来タイプ: 組換発現 由来: (組換発現) Coxsackievirus B3 (strain Woodruff) (コクサッキーウイルス) 属: Enterovirus / 生物種: Human enterovirus B / 株: Woodruff / 解説: COXSACKIEVIRUS B3 / 細胞株 (発現宿主): HELA CELLS / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q66282 |
-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: COXSACKIEVIRUS B3(M STRAIN) WITH ITS CELLULAR RECEPTOR タイプ: VIRUS | ||||||||||||
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.5 | ||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||
急速凍結 | 詳細: CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, ...詳細: CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. | ||||||||||||
結晶化 | 温度: 298 K / pH: 7.5 詳細: WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K | ||||||||||||
結晶化 | *PLUS 手法: 電子顕微鏡法 |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM300FEG/T / 日付: 2000年6月1日 |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 61000 X / 最大 デフォーカス(公称値): 4600 nm / 最小 デフォーカス(公称値): 1500 nm |
試料ホルダ | 温度: 120 K |
撮影 | 電子線照射量: 20 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
-解析
EMソフトウェア | 名称: PURDUE PROGRAMS / カテゴリ: 3次元再構成 | ||||||||||||
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対称性 | 点対称性: I (正20面体型対称) | ||||||||||||
3次元再構成 | 手法: COMMON-LINES AND POLAR-FOURIER-TRANSFORM FULLER ET AL. 1996, J.STRUC.BIOL.c 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130 解像度: 22 Å / 解像度の算出法: OTHER / 粒子像の数: 635 / ピクセルサイズ(実測値): 2.3 Å 倍率補正: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS B3. DENSITIES WERE COMPARED BY CROSS- ...倍率補正: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS B3. DENSITIES WERE COMPARED BY CROSS-CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 110 ANGSTROMS AND EXTERNAL RADIUS OF 145 ANGSTROMS. 詳細: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 22 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND COMPARING STRUCTURE FACTORS ...詳細: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 22 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND COMPARING STRUCTURE FACTORS OBTAINED FROM SEPARATE RECONSTRUCTIONS (BAKER ET AL. 1991, BIOPHYS.J. 60, 1445-1456). THE EIGENVALUE SPECTRUM GAVE AN INDICATION OF THE RANDOMNESS OF THE DATA THAT WAS INCLUDED IN THE RECONSTRUCTION. THE COMPLETENESS OF THE DATA WAS VERIFIED IN THAT ALL EIGENVALUES EXCEEDED 1.0. 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL 詳細: METHOD--Acta Cryst. D56, 1341 REFINEMENT PROTOCOL--EMFIT DETAILS--THE DIFFERENCE MAP BETWEEN CVB3-CAR COMPLEX AND NATIVE CVB WAS CALCULATED AND THEN FITTED WITH THE N-TERMINAL DOMAIN OF CAR ...詳細: METHOD--Acta Cryst. D56, 1341 REFINEMENT PROTOCOL--EMFIT DETAILS--THE DIFFERENCE MAP BETWEEN CVB3-CAR COMPLEX AND NATIVE CVB WAS CALCULATED AND THEN FITTED WITH THE N-TERMINAL DOMAIN OF CAR (1KAC, B-CHAIN). THE AUTOMATIC FITTING WAS DONE USI PROGRAM EMFIT DESCRIBED IN ACTA CRYST. D56, 1341-1349. THE CRYSTAL STRUCTURE OF POLIOVIRUS WAS PLACED INTO THE | ||||||||||||
精密化ステップ | サイクル: LAST
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