+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6crj | ||||||
---|---|---|---|---|---|---|---|
タイトル | Mouse norovirus model using the crystal structure of MNV P domain and the Norwalkvirus shell domain | ||||||
要素 | Norwalk virus, MNV-1 capsid protein chimeraノロウイルス | ||||||
キーワード | VIRUS (ウイルス) / norovirus (ノロウイルス) / mouse | ||||||
機能・相同性 | 機能・相同性情報 T=3 icosahedral viral capsid / virus-mediated perturbation of host defense response / host cell cytoplasm / identical protein binding 類似検索 - 分子機能 | ||||||
生物種 | Norwalk virus (ノロウイルス) Murine norovirus 1 (マウスノロウイルス 1) | ||||||
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: 8 Å | ||||||
データ登録者 | Smith, T.J. | ||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2018 タイトル: Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor. 著者: Christopher A Nelson / Craig B Wilen / Ya-Nan Dai / Robert C Orchard / Arthur S Kim / Roderick A Stegeman / Leon L Hsieh / Thomas J Smith / Herbert W Virgin / Daved H Fremont / 要旨: Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric ...Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric MNoV VP1 protruding (P) domain in complex with its cellular receptor CD300lf. CD300lf binds the P domain with a 2:2 stoichiometry, engaging a cleft between the AB and DE loops of the P2 subdomain at a site that overlaps the epitopes of neutralizing antibodies. We also identify that bile acids are cofactors enhancing MNoV cell-binding and infectivity. Structures of CD300lf-P domain in complex with glycochenodeoxycholic acid (GCDCA) and lithocholic acid (LCA) reveal two bile acid binding sites at the P domain dimer interface distant from receptor binding sites. The structural determinants for receptor and bile acid binding are supported by numerous biophysical assays utilizing interface residue mutations. We find that the monomeric affinity of CD300lf for the P domain is low and is divalent cation dependent. We have also determined the crystal structure of CD300lf in complex with phosphocholine, revealing that MNoV engages its receptor in a manner mimicking host ligands including similar metal coordination. Docking of the cocomplex structures onto a cryo-EM-derived model of MNoV suggests that each virion can make multiple CD300lf engagements, and thus, infection may be driven by the avidity of cell surface clustered CD300lf. These studies identify multiple potential modulators of norovirus infection that may act to regulate the interaction between the viral capsid P domain and its cognate cellular receptor. #1: ジャーナル: J Virol / 年: 2010 タイトル: High-resolution cryo-electron microscopy structures of murine norovirus 1 and rabbit hemorrhagic disease virus reveal marked flexibility in the receptor binding domains. 著者: Umesh Katpally / Neil R Voss / Tommaso Cavazza / Stefan Taube / John R Rubin / Vivienne L Young / Jeanne Stuckey / Vernon K Ward / Herbert W Virgin / Christiane E Wobus / Thomas J Smith / 要旨: Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. ...Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. Here, the three-dimensional (3D) reconstructions of recombinant rabbit hemorrhagic disease virus (rRHDV) virus-like particles (VLPs) and intact MNV-1 were determined to approximately 8-A resolution. rRHDV also has a raised P domain, and therefore, this conformation is independent of infectivity and genus. The atomic structure of the MNV-1 P domain was used to interpret the MNV-1 reconstruction. Connections between the P and shell domains and between the floating P domains were modeled. This observed P-domain flexibility likely facilitates virus-host receptor interactions. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6crj.cif.gz | 293.7 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6crj.ent.gz | 238.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6crj.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/cr/6crj ftp://data.pdbj.org/pub/pdb/validation_reports/cr/6crj | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
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: 57127.523 Da / 分子数: 3 断片: Norwalk shell domain (UNP residues 10-221), MNV-1 P domain (UNP residues 228-540) 由来タイプ: 組換発現 由来: (組換発現) Norwalk virus (ノロウイルス), (組換発現) Murine norovirus 1 (マウスノロウイルス 1) 遺伝子: ORF2 / 発現宿主: Mus abbotti (ハツカネズミ) / 参照: UniProt: Q83884, UniProt: Q2V8W4 |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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: mouse norovirus model / タイプ: VIRUS 詳細: chimera of Norwalk virus shell domain and MNV P domain Entity ID: all / 由来: RECOMBINANT |
---|---|
由来(天然) | 生物種: Murine norovirus 1 (マウスノロウイルス 1) |
由来(組換発現) | 生物種: Mus abbotti (ハツカネズミ) |
ウイルスについての詳細 | 中空か: NO / エンベロープを持つか: NO / 単離: STRAIN / タイプ: VIRION |
天然宿主 | 生物種: Mus |
緩衝液 | pH: 7.2 / 詳細: PBS |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TECNAI F20 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy |
撮影 | 電子線照射量: 10 e/Å2 / フィルム・検出器のモデル: FEI EAGLE (2k x 2k) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3次元再構成 | 解像度: 8 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 粒子像の数: 20425 / 対称性のタイプ: POINT |
原子モデル構築 | プロトコル: RIGID BODY FIT |