+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4d1k | ||||||
---|---|---|---|---|---|---|---|
タイトル | Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. | ||||||
要素 | GAG PROTEIN | ||||||
キーワード | VIRAL PROTEIN / CAPSID / SP1 / HELICAL RECONSTRUCTION | ||||||
機能・相同性 | : / gag protein p24 N-terminal domain / viral process / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / viral capsid / Retrovirus capsid, N-terminal / Gag protein 機能・相同性情報 | ||||||
生物種 | HUMAN IMMUNODEFICIENCY VIRUS 1 (ヒト免疫不全ウイルス) | ||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 9.4 Å | ||||||
データ登録者 | Bharat, T.A.M. / Castillo-Menendez, L.R. / Hagen, W.J.H. / Lux, V. / Igonet, S. / Schorb, M. / Schur, F.K.M. / Krauesslich, H.G. / Briggs, J.A.G. | ||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2014 タイトル: Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. 著者: Tanmay A M Bharat / Luis R Castillo Menendez / Wim J H Hagen / Vanda Lux / Sebastien Igonet / Martin Schorb / Florian K M Schur / Hans-Georg Kräusslich / John A G Briggs / 要旨: The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and ...The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position. | ||||||
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 | 4d1k.cif.gz | 149.2 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb4d1k.ent.gz | 77.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4d1k.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 | 4d1k_validation.pdf.gz | 987.3 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 4d1k_full_validation.pdf.gz | 989.8 KB | 表示 | |
XML形式データ | 4d1k_validation.xml.gz | 30.6 KB | 表示 | |
CIF形式データ | 4d1k_validation.cif.gz | 52 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/d1/4d1k ftp://data.pdbj.org/pub/pdb/validation_reports/d1/4d1k | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
#1: タンパク質 | 分子量: 24421.988 Da / 分子数: 6 / 断片: CAPSID, RESIDUES 1-219 / 変異: YES / 由来タイプ: 組換発現 詳細: 10NM PROTEIN-A CONJUGATED GOLD PARTICLES WERE ADDED TO THE SAMPLE. PROTEIN CONSTRUCT CONSISTS OF CA TO NC DOMAINS WITH MUTATION IN POSITION Y169. 由来: (組換発現) HUMAN IMMUNODEFICIENCY VIRUS 1 (ヒト免疫不全ウイルス) 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q5D0H3 配列の詳細 | THE PROTEIN DEPOSITED IS A MUTANT AT POSITION Y169. | |
---|
-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: HELICAL ARRAY / 3次元再構成法: らせん対称体再構成法 |
-試料調製
構成要素 | 名称: HIV-1 CANC Y169 MUTANT PROTEIN ASSEMBLED WITH 73MER DNA INTO TUBULAR PARTICLES タイプ: COMPLEX |
---|---|
緩衝液 | 名称: 30 MM MES, 1 MM EDTA, 1 MM DTT, 0.5 M NACL / pH: 6 / 詳細: 30 MM MES, 1 MM EDTA, 1 MM DTT, 0.5 M NACL |
試料 | 濃度: 2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE 詳細: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- HOMEMADE PLUNGER, |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2012年12月25日 |
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 / 最大 デフォーカス(公称値): 4500 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm |
撮影 | 電子線照射量: 23 e/Å2 / 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: 82 |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3次元再構成 | 解像度: 9.4 Å / ピクセルサイズ(公称値): 1.5 Å / ピクセルサイズ(実測値): 1.53 Å 詳細: ATOMIC MODELS WERE FITTED USING MOLECULAR MOLECULAR DYNAMICS FLEXIBLE FITTING (MDFF). THE CA-NTD ATOMIC MODEL PDB ID 2JPR AND THE CA-CTD ATOMIC MODEL PDB ID 4COP WERE USED AS STARTING MODELS. ...詳細: ATOMIC MODELS WERE FITTED USING MOLECULAR MOLECULAR DYNAMICS FLEXIBLE FITTING (MDFF). THE CA-NTD ATOMIC MODEL PDB ID 2JPR AND THE CA-CTD ATOMIC MODEL PDB ID 4COP WERE USED AS STARTING MODELS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2638. (DEPOSITION ID: 12470). 対称性のタイプ: HELICAL | |||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL / 詳細: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY | |||||||||||||||
原子モデル構築 | PDB-ID: 4COP Accession code: 4COP / Source name: PDB / タイプ: experimental model | |||||||||||||||
精密化 | 最高解像度: 9.4 Å | |||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 9.4 Å
|