+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9205 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Red Clover Necrotic Mosaic Virus | |||||||||
マップデータ | Red clover necrotic mosaic virus | |||||||||
試料 |
| |||||||||
キーワード | RCNMV / virus | |||||||||
機能・相同性 | Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / RNA binding / Capsid protein 機能・相同性情報 | |||||||||
生物種 | Red clover necrotic mosaic virus (ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.9 Å | |||||||||
データ登録者 | Sherman MB / Smith TJ | |||||||||
引用 | ジャーナル: J Virol / 年: 2020 タイトル: Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes. 著者: Michael B Sherman / Richard Guenther / Ron Reade / D'Ann Rochon / Tim Sit / Thomas J Smith / 要旨: Members of the family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the family have single-stranded ...Members of the family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the family have single-stranded RNA (ssRNA) genomes with T=3 icosahedral protein shells with a maximum diameter of ∼340 Å. Each capsid protein is comprised of three domains: R (RNA binding), S (shell), and P (protruding). Between the R domain and S domain is the "arm" region that studies have shown to play a critical role in assembly. To better understand how the details of structural differences and similarities influence the viral life cycles, the structures of cucumber leaf spot virus (CLSV; genus ) and red clover necrotic mosaic virus (RCNMV; genus ) were determined to resolutions of 3.2 Å and 2.9 Å, respectively, with cryo-electron microscopy and image reconstruction methods. While the shell domains had homologous structures, the stabilizing interactions at the icosahedral 3-fold axes and the R domains differed greatly. The heterogeneity in the R domains among the members of the family is likely correlated with differences in the sizes and characteristics of the corresponding genomes. We propose that the changes in the R domain/RNA interactions evolved different arm domain interactions at the β-annuli. For example, RCNMV has the largest genome and it appears to have created the necessary space in the capsid by evolving the shortest R domain. The resulting loss in RNA/R domain interactions may have been compensated for by increased intersubunit β-strand interactions at the icosahedral 3-fold axes. Therefore, the R and arm domains may have coevolved to package different genomes within the conserved and rigid shell. Members of the family have nearly identical shells, and yet they package genomes that range from 4.6 kb (monopartite) to 5.3 kb (bipartite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high-resolution cryo-electron microscopy (cryo-EM) structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the "arm," seems to have also coevolved with the R domain to allow particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_9205.map.gz | 476.4 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-9205-v30.xml emd-9205.xml | 9.1 KB 9.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9205.png | 261.4 KB | ||
Filedesc metadata | emd-9205.cif.gz | 5.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9205 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9205 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9205_validation.pdf.gz | 698.6 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_9205_full_validation.pdf.gz | 698.2 KB | 表示 | |
XML形式データ | emd_9205_validation.xml.gz | 8.7 KB | 表示 | |
CIF形式データ | emd_9205_validation.cif.gz | 10 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9205 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9205 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_9205.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Red clover necrotic mosaic virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.0556 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
-全体 : Red clover necrotic mosaic virus
全体 | 名称: Red clover necrotic mosaic virus (ウイルス) |
---|---|
要素 |
|
-超分子 #1: Red clover necrotic mosaic virus
超分子 | 名称: Red clover necrotic mosaic virus / タイプ: virus / ID: 1 / 親要素: 0 / 含まれる分子: #1 / NCBI-ID: 12267 / 生物種: Red clover necrotic mosaic virus / ウイルスタイプ: VIRION / ウイルス・単離状態: STRAIN / ウイルス・エンベロープ: No / ウイルス・中空状態: No |
---|
-分子 #1: Capsid protein
分子 | 名称: Capsid protein / タイプ: protein_or_peptide / ID: 1 / コピー数: 3 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Red clover necrotic mosaic virus (ウイルス) |
分子量 | 理論値: 36.617473 KDa |
配列 | 文字列: MSSKAPKKSK QRSQPRNRTP NTSVKTVAIP FAKTQIIKTV NPPPKPARGI LHTQLVMSVV GSVQMRTNNG KSNQRFRLNP SNPALFPTL AYEAANYDMY RLKKLTLRYV PLVTVQNSGR VAMIWDPDSQ DSAPQSRQEI SAYSRSVSTA VYEKCSLTIP A DNQWRFVA ...文字列: MSSKAPKKSK QRSQPRNRTP NTSVKTVAIP FAKTQIIKTV NPPPKPARGI LHTQLVMSVV GSVQMRTNNG KSNQRFRLNP SNPALFPTL AYEAANYDMY RLKKLTLRYV PLVTVQNSGR VAMIWDPDSQ DSAPQSRQEI SAYSRSVSTA VYEKCSLTIP A DNQWRFVA DNTTVDRKLV DFGQLLFVTH SGSDGIETGD IFLDCEVEFK GPQPTASIVQ KTVIDLGGTL TSFEGPSYLM PP DAFITSS SFGLFVDVAG TYLLTLVVTC STTGSVTVGG NSTLVGDGRA AYGSSNYIAS IVFTSSGVLS TTPSVQFSGS SGV SRVQMN ICRCKQGNTF ILG UniProtKB: Capsid protein |
-分子 #2: CALCIUM ION
分子 | 名称: CALCIUM ION / タイプ: ligand / ID: 2 / コピー数: 3 / 式: CA |
---|---|
分子量 | 理論値: 40.078 Da |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7 |
---|---|
グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: DIRECT ELECTRON DE-64 (8k x 8k) 平均電子線量: 54.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: NONE |
---|---|
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 1236 |
初期 角度割当 | タイプ: COMMON LINE |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |