+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3dik | ||||||
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タイトル | Pseudo-atomic model of the HIV-1 CA hexameric lattice | ||||||
要素 | Capsid protein p24 | ||||||
キーワード | VIRAL PROTEIN / MATURE RETROVIRAL CAPSID / FULLERENE CONE / HEXAMER / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Hydrolase / Lipoprotein / Magnesium / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc-finger | ||||||
機能・相同性 | 機能・相同性情報 HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / 転移酵素; リンを含む基を移すもの; 核酸を移すもの / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / 加水分解酵素; エステル加水分解酵素 / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane 類似検索 - 分子機能 | ||||||
生物種 | Human immunodeficiency virus type 1 (ヒト免疫不全ウイルス) | ||||||
手法 | 電子線結晶学 / クライオ電子顕微鏡法 / 解像度: 9 Å | ||||||
データ登録者 | Ganser-Pornillos, B.K. / Cheng, A. / Yeager, M. | ||||||
引用 | ジャーナル: Cell / 年: 2007 タイトル: Structure of full-length HIV-1 CA: a model for the mature capsid lattice. 著者: Barbie K Ganser-Pornillos / Anchi Cheng / Mark Yeager / 要旨: The capsids of mature retroviruses perform the essential function of organizing the viral genome for efficient replication. These capsids are modeled as fullerene structures composed of closed ...The capsids of mature retroviruses perform the essential function of organizing the viral genome for efficient replication. These capsids are modeled as fullerene structures composed of closed hexameric arrays of the viral CA protein, but a high-resolution structure of the lattice has remained elusive. A three-dimensional map of two-dimensional crystals of the R18L mutant of HIV-1 CA was derived by electron cryocrystallography. The docking of high-resolution domain structures into the map yielded the first unambiguous model for full-length HIV-1 CA. Three important protein-protein assembly interfaces are required for capsid formation. Each CA hexamer is composed of an inner ring of six N-terminal domains and an outer ring of C-terminal domains that form dimeric linkers connecting neighboring hexamers. Interactions between the two domains of CA further stabilize the hexamer and provide a structural explanation for the mechanism of action of known HIV-1 assembly inhibitors. | ||||||
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 | 3dik.cif.gz | 18 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3dik.ent.gz | 7.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3dik.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 | 3dik_validation.pdf.gz | 765.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3dik_full_validation.pdf.gz | 765.3 KB | 表示 | |
XML形式データ | 3dik_validation.xml.gz | 8.9 KB | 表示 | |
CIF形式データ | 3dik_validation.cif.gz | 11.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/di/3dik ftp://data.pdbj.org/pub/pdb/validation_reports/di/3dik | 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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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 24498.084 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Human immunodeficiency virus type 1 (ヒト免疫不全ウイルス) 遺伝子: gag-pol / プラスミド: pET11a / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P12497 |
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-実験情報
-実験
実験 | 手法: 電子線結晶学 |
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EM実験 | 試料の集合状態: 2D ARRAY / 3次元再構成法: 電子線結晶学 |
-試料調製
構成要素 |
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緩衝液 | 名称: 17.5%(w/v) PEG 20,000, 50mM Na Cacodylate, 100mM Calcium Acetate pH: 6.5 詳細: 17.5%(w/v) PEG 20,000, 50mM Na Cacodylate, 100mM Calcium Acetate | ||||||||||||||||||||
試料 | 濃度: 32 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: Carbon coated molybdenum grids | ||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE 詳細: Washed with 0.1M KCl, blotted briefly, and plunged into liquid ethane |
-データ収集
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F20 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 120 kV / 照射モード: OTHER |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 52000 X / 最大 デフォーカス(公称値): 1500 nm / 最小 デフォーカス(公称値): 400 nm / Cs: 2 mm |
試料ホルダ | 温度: 90 K / 傾斜角・最大: 40.3 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 10 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: electron |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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3次元再構成 | 手法: 2D crystallography / 解像度: 9 Å 詳細: THIS MODDEL CONTAINS CA ATOMS ONLY. THE TWO DOMAINS UNP RESIDUES 133-280 AND UNP RESIDUES 281-351 WERE ALLOWED TO MOVE INDEPENDENTLY. THAT IS WHY THE CONNECTIVITY BETWEEN THEM IS NOT WELL- ...詳細: THIS MODDEL CONTAINS CA ATOMS ONLY. THE TWO DOMAINS UNP RESIDUES 133-280 AND UNP RESIDUES 281-351 WERE ALLOWED TO MOVE INDEPENDENTLY. THAT IS WHY THE CONNECTIVITY BETWEEN THEM IS NOT WELL-PRESERVED. MRC AND CCP4 PROGRAMS WERE USED. 対称性のタイプ: 2D CRYSTAL | |||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / 詳細: REFINEMENT PROTOCOL--RIGID BODY | |||||||||||||||||||||
原子モデル構築 |
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精密化ステップ | サイクル: LAST
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