+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7ptu | ||||||||||||
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タイトル | Structure of pentameric S-layer protein from Halofaerax volcanii | ||||||||||||
要素 | Cell surface glycoprotein | ||||||||||||
キーワード | STRUCTURAL PROTEIN / S-layer csg | ||||||||||||
機能・相同性 | 機能・相同性情報 | ||||||||||||
生物種 | Haloferax volcanii DS2 (古細菌) | ||||||||||||
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: 3.87 Å | ||||||||||||
データ登録者 | von Kuegelgen, A. / Bharat, T.A.M. | ||||||||||||
資金援助 | 英国, 3件
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引用 | ジャーナル: Cell Rep / 年: 2021 タイトル: Complete atomic structure of a native archaeal cell surface. 著者: Andriko von Kügelgen / Vikram Alva / Tanmay A M Bharat / 要旨: Many prokaryotic cells are covered by an ordered, proteinaceous, sheet-like structure called a surface layer (S-layer). S-layer proteins (SLPs) are usually the highest copy number macromolecules in ...Many prokaryotic cells are covered by an ordered, proteinaceous, sheet-like structure called a surface layer (S-layer). S-layer proteins (SLPs) are usually the highest copy number macromolecules in prokaryotes, playing critical roles in cellular physiology such as blocking predators, scaffolding membranes, and facilitating environmental interactions. Using electron cryomicroscopy of two-dimensional sheets, we report the atomic structure of the S-layer from the archaeal model organism Haloferax volcanii. This S-layer consists of a hexagonal array of tightly interacting immunoglobulin-like domains, which are also found in SLPs across several classes of archaea. Cellular tomography reveal that the S-layer is nearly continuous on the cell surface, completed by pentameric defects in the hexagonal lattice. We further report the atomic structure of the SLP pentamer, which shows markedly different relative arrangements of SLP domains needed to complete the S-layer. Our structural data provide a framework for understanding cell surfaces of archaea at the atomic level. | ||||||||||||
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 | 7ptu.cif.gz | 390.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7ptu.ent.gz | 321.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7ptu.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 | 7ptu_validation.pdf.gz | 786.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7ptu_full_validation.pdf.gz | 806.8 KB | 表示 | |
XML形式データ | 7ptu_validation.xml.gz | 62.7 KB | 表示 | |
CIF形式データ | 7ptu_validation.cif.gz | 87.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/pt/7ptu ftp://data.pdbj.org/pub/pdb/validation_reports/pt/7ptu | 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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-要素
#1: タンパク質 | 分子量: 81755.602 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Haloferax volcanii DS2 (古細菌) / Plasmid details: Allers et al 2004 / 参照: UniProt: P25062 #2: 糖 | ChemComp-BGC / 研究の焦点であるリガンドがあるか | Y | |
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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: 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: Structure of pentameric S-layer protein csg / タイプ: COMPLEX / 詳細: Structure of pentameric S-layer protein csg / Entity ID: #1 / 由来: NATURAL | |||||||||||||||||||||||||
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分子量 | 実験値: NO | |||||||||||||||||||||||||
由来(天然) | 生物種: Haloferax volcanii DS2 (古細菌) / 細胞内の位置: Cell surface | |||||||||||||||||||||||||
緩衝液 | pH: 7.5 詳細: Buffer solutions were prepared fresh from sterile filtered concentrated stocksolutions. Solutions were filtered through a 0.22 um filter to avoid microbial contamination and degassed using a ...詳細: Buffer solutions were prepared fresh from sterile filtered concentrated stocksolutions. Solutions were filtered through a 0.22 um filter to avoid microbial contamination and degassed using a vacuum fold pump. The pH of the HEPES stock solution was adjusted with sodium hydroxide at 4 deg C. 1.75 mM holmium chloride was added 2 hours before vitrification. | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 2.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: Purified csg protein mixed with 1.75 mM HoCl3 after 2 hour incubation. | |||||||||||||||||||||||||
試料支持 | 詳細: 20 seconds, 15 mA / グリッドの材料: COPPER/RHODIUM / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/2 | |||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 283.15 K 詳細: Vitrobot options: Blot time 5 seconds, Blot force -10,1, Wait time 10 seconds, Drain time 0.5 seconds |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS 詳細: EPU software with faster acquisition mode AFIS (Aberration Free Image Shift). |
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 / 倍率(公称値): 81000 X / 倍率(補正後): 81000 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 1000 nm / Calibrated defocus min: 1000 nm / 最大 デフォーカス(補正後): 4000 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: ZEMLIN TABLEAU |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER 最高温度: 70 K / 最低温度: 70 K |
撮影 | 平均露光時間: 3.6 sec. / 電子線照射量: 53.9 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 2 / 実像数: 11871 詳細: Images were collected in two sessions in movie-mode and subjected to 3.6 seconds of exposure where a total dose of 53.45 or 53.9 e-/A2 was applied, and 40 frames were recorded per movie. A ...詳細: Images were collected in two sessions in movie-mode and subjected to 3.6 seconds of exposure where a total dose of 53.45 or 53.9 e-/A2 was applied, and 40 frames were recorded per movie. A total of 11871 movies were collected in two sessions with the same microscope and settings. |
電子光学装置 | エネルギーフィルター名称: GIF Quantum LS / エネルギーフィルタースリット幅: 20 eV |
画像スキャン | 横: 5760 / 縦: 4092 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19_4092: / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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画像処理 | 詳細: Imported movies were motion-corrected, dose weighted, and Fourier cropped (2x) with MotionCor2 (Zheng et al., 2017) implemented in RELION3.1 (Zivanov et al., 2018). Contrast transfer ...詳細: Imported movies were motion-corrected, dose weighted, and Fourier cropped (2x) with MotionCor2 (Zheng et al., 2017) implemented in RELION3.1 (Zivanov et al., 2018). Contrast transfer functions (CTFs) of the resulting motion-corrected micrographs were estimated using CTFFIND4 (Rohou and Grigorieff, 2015). | ||||||||||||||||||||||||||||||||||||||||||||||||||
CTF補正 | 詳細: RELION refinement with in-built CTF correction. The function is similar to a Wiener filter, so amplitude correction included. タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 1773652 詳細: Particles were initially picking using the Laplacian-of gaussian algorithm implemented in RELION3.0 (Zivanov et al., 2018). Particles were extracted in 8x down-sampled in 50x50 pixel boxes ...詳細: Particles were initially picking using the Laplacian-of gaussian algorithm implemented in RELION3.0 (Zivanov et al., 2018). Particles were extracted in 8x down-sampled in 50x50 pixel boxes and classified using reference-free 2D classification inside RELION3.0. | ||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C5 (5回回転対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.87 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 382105 / アルゴリズム: FOURIER SPACE 詳細: The final map (RELION3.1) was obtained from 382,105 particles and post-processed using a soft mask focused on the entire pentameric map yielding a global resolution of 3.87 angstrom with ...詳細: The final map (RELION3.1) was obtained from 382,105 particles and post-processed using a soft mask focused on the entire pentameric map yielding a global resolution of 3.87 angstrom with resolution anisotropy from 3.49-8.11 angstrom from the central C5 axis near domains D1-D3 (well resolved) to the more flexible domains D4 (partially resolved) and D5-D6 (not resolved). クラス平均像の数: 3 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 179.68 / プロトコル: AB INITIO MODEL / 空間: REAL / Target criteria: Best Fit 詳細: The initial manual build of D1-D2 was performed independently using the csg pentameric cryo-EM map, which served as an additional validation of the manual building performed in the csg ...詳細: The initial manual build of D1-D2 was performed independently using the csg pentameric cryo-EM map, which served as an additional validation of the manual building performed in the csg hexamer in the related deposition. The manual building exercise yielded a nearly identical result to the hexamer; thus, the final refined hexameric structures of D1-D2, along with D3-D4 were taken and fitted into the pentameric map (~3.87 angstrom resolution in D1-D3, lower in D4 which is partially resolved). Five copies of these D1-D4 were used for refinement and model building as for the hexamer, except D3 and D4 was restrained in position, due to steadily deteriorating resolution in this part of the map. D5-D6 were not resolved in the pentameric structure and were thus not included in the refinements. Model validation was performed in PHENIX and CCP-EM. |