+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3jc1 | ||||||
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タイトル | Electron cryo-microscopy of the IST1-CHMP1B ESCRT-III copolymer | ||||||
要素 |
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キーワード | LIPID BINDING PROTEIN / ESCRT-III / IST1 / CHMP1B / membrane tubulation / helical filament | ||||||
機能・相同性 | 機能・相同性情報 viral capsid secondary envelopment / MIT domain binding / abscission / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule ...viral capsid secondary envelopment / MIT domain binding / abscission / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / cytoskeleton-dependent cytokinesis / regulation of centrosome duplication / collateral sprouting / nuclear membrane reassembly / positive regulation of collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body sorting pathway / membrane coat / plasma membrane repair / membrane fission / late endosome to vacuole transport / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / Flemming body / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / positive regulation of proteolysis / autophagosome maturation / endoplasmic reticulum-Golgi intermediate compartment / viral release from host cell / nuclear pore / multivesicular body / viral budding from plasma membrane / establishment of protein localization / kinetochore / autophagy / nuclear envelope / azurophil granule lumen / protein localization / protein transport / midbody / endosome membrane / cadherin binding / protein domain specific binding / cell division / lysosomal membrane / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / chromatin / protein-containing complex binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
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: 4 Å | ||||||
データ登録者 | McCullough, J. / Clippinger, A.K. / Talledge, N. / Skowyra, M.L. / Saunders, M.G. / Naismith, T.V. / Colf, L.A. / Afonine, P. / Arthur, C. / Sundquist, W.I. ...McCullough, J. / Clippinger, A.K. / Talledge, N. / Skowyra, M.L. / Saunders, M.G. / Naismith, T.V. / Colf, L.A. / Afonine, P. / Arthur, C. / Sundquist, W.I. / Hanson, P.I. / Frost, A. | ||||||
引用 | ジャーナル: Science / 年: 2015 タイトル: Structure and membrane remodeling activity of ESCRT-III helical polymers. 著者: John McCullough / Amy K Clippinger / Nathaniel Talledge / Michael L Skowyra / Marissa G Saunders / Teresa V Naismith / Leremy A Colf / Pavel Afonine / Christopher Arthur / Wesley I Sundquist ...著者: John McCullough / Amy K Clippinger / Nathaniel Talledge / Michael L Skowyra / Marissa G Saunders / Teresa V Naismith / Leremy A Colf / Pavel Afonine / Christopher Arthur / Wesley I Sundquist / Phyllis I Hanson / Adam Frost / 要旨: The endosomal sorting complexes required for transport (ESCRT) proteins mediate fundamental membrane remodeling events that require stabilizing negative membrane curvature. These include endosomal ...The endosomal sorting complexes required for transport (ESCRT) proteins mediate fundamental membrane remodeling events that require stabilizing negative membrane curvature. These include endosomal intralumenal vesicle formation, HIV budding, nuclear envelope closure, and cytokinetic abscission. ESCRT-III subunits perform key roles in these processes by changing conformation and polymerizing into membrane-remodeling filaments. Here, we report the 4 angstrom resolution cryogenic electron microscopy reconstruction of a one-start, double-stranded helical copolymer composed of two different human ESCRT-III subunits, charged multivesicular body protein 1B (CHMP1B) and increased sodium tolerance 1 (IST1). The inner strand comprises "open" CHMP1B subunits that interlock in an elaborate domain-swapped architecture and is encircled by an outer strand of "closed" IST1 subunits. Unlike other ESCRT-III proteins, CHMP1B and IST1 polymers form external coats on positively curved membranes in vitro and in vivo. Our analysis suggests how common ESCRT-III filament architectures could stabilize different degrees and directions of membrane curvature. | ||||||
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 | 3jc1.cif.gz | 1.8 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3jc1.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 3jc1.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 | 3jc1_validation.pdf.gz | 1.6 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3jc1_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 3jc1_validation.xml.gz | 241.2 KB | 表示 | |
CIF形式データ | 3jc1_validation.cif.gz | 358 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/jc/3jc1 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/3jc1 | 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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対称性 | らせん対称: (回転対称性: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 34 / Rise per n subunits: 2.96 Å / Rotation per n subunits: 21.06 °) |
-要素
#1: タンパク質 | 分子量: 20934.514 Da / 分子数: 34 / 断片: N-terminal domain (UNP residues 6-187) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IST1, KIAA0174 / プラスミド: PGEX-2T-TEV / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) RIPL / 参照: UniProt: P53990 #2: タンパク質 | 分子量: 17937.719 Da / 分子数: 34 / 断片: UNP residues 4-163 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: C18orf2, CHMP1B / プラスミド: PGEX-2T-TEV / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) RIPL / 参照: UniProt: Q7LBR1 |
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-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: FILAMENT / 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 |
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緩衝液 | 名称: 25 mM Tris, pH 8.0, 25 mM sodium chloride / pH: 8 / 詳細: 25 mM Tris, pH 8.0, 25 mM sodium chloride | ||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||
試料支持 | 詳細: Quantifoil R2/2 200 Mesh (glow-discharged) holey carbon grids | ||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 298 K 詳細: Deposited 3.5 uL sample, blotted 3-6 seconds (0 mm offset), and plunged into liquid ethane (VITROBOT MARK III). 手法: Deposited 3.5 uL sample, blotted 3-6 seconds (0 mm offset) |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company / モデル: Tecnai F20 / 画像提供: FEI Company | ||||||||||||||||||||||||
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EM imaging | 日付: 2013年6月1日 / 電子線源: FIELD EMISSION GUN / 照射モード: FLOOD BEAM / モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 600 nm / Specimen-ID: 1
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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 |
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CTF補正 | 詳細: CTFFIND3 | ||||||||||||||||||||||||||||||||||||||||||||
らせん対称 | 回転角度/サブユニット: 21.06 ° / 軸方向距離/サブユニット: 2.96 Å / らせん対称軸の対称性: C1 | ||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 手法: Iterative Helical Real Space Reconstruction (IHRSR) / 解像度: 4 Å / 粒子像の数: 188713 / ピクセルサイズ(公称値): 1.22 Å / ピクセルサイズ(実測値): 1.22 Å 詳細: Modified version of IHRSR algorithms as implemented in SPIDER was used to determine the helical symmetry. 3D reconstructions were performed using RELION. 対称性のタイプ: HELICAL | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 空間: REAL / Target criteria: Molprobity validation, cross-correlation 詳細: DETAILS--IST1 starting model (3FRR) was idealized in Rosetta, then relaxed while the structure was constrained. Iterative loop building was used. | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 3FRR Accession code: 3FRR / Source name: PDB / タイプ: experimental model | ||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST
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