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基本情報
登録情報 | データベース: PDB / ID: 5k2e | |||||||||||||||||||||
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タイトル | Structure of NNQQNY from yeast prion Sup35 with zinc acetate determined by MicroED | |||||||||||||||||||||
![]() | Eukaryotic peptide chain release factor GTP-binding subunit | |||||||||||||||||||||
![]() | PROTEIN FIBRIL / ![]() ![]() | |||||||||||||||||||||
機能・相同性 | ![]() Eukaryotic Translation Termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 類似検索 - 分子機能 | |||||||||||||||||||||
生物種 | ![]() ![]() ![]() | |||||||||||||||||||||
手法 | ![]() ![]() | |||||||||||||||||||||
![]() | Rodriguez, J.A. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.S. | |||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED. 著者: Michael R Sawaya / Jose Rodriguez / Duilio Cascio / Michael J Collazo / Dan Shi / Francis E Reyes / Johan Hattne / Tamir Gonen / David S Eisenberg / ![]() 要旨: Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This ...Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods. | |||||||||||||||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 18.3 KB | 表示 | ![]() |
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PDB形式 | ![]() | 8.3 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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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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詳細 | The biological unit is an extended pair of beta sheets comprising peptides at positions X,Y,Z and -X,Y+1/2,-Z extended ad infinitum along the b crystal axis. |
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要素
#1: タンパク質・ペプチド | 分子量: 779.755 Da / 分子数: 1 / 断片: UNP residues 8-13 / 由来タイプ: 合成 / 由来: (合成) ![]() ![]() ![]() |
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#2: 化合物 | ChemComp-ZN / |
#3: 化合物 | ChemComp-ACY / ![]() |
#4: 水 | ChemComp-HOH / ![]() |
-実験情報
-実験
実験 | 手法: ![]() |
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EM実験 | 試料の集合状態: 3D ARRAY / 3次元再構成法: ![]() |
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試料調製
構成要素 | 名称: Prion fibril composed of a 6-residue segment of Sup35 and zinc タイプ: COMPLEX / Entity ID: #1 / 由来: MULTIPLE SOURCES | ||||||||||||||||||||
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分子量 | 値: 3.25 kDa/nm / 実験値: NO | ||||||||||||||||||||
由来(天然) | 生物種: ![]() ![]() ![]() | ||||||||||||||||||||
EM crystal formation | 装置: 24-well plate Atmosphere: in air, in sealed chamber, in equilibrium with reservoir solution 詳細: Crystals were grown by hanging-drop vapor diffusion at ~20 degrees C. The reservoir solution contained 100 mM HEPES, pH 7.0, and 1 M sodium acetate (pH not adjusted). Drops were prepared by ...詳細: Crystals were grown by hanging-drop vapor diffusion at ~20 degrees C. The reservoir solution contained 100 mM HEPES, pH 7.0, and 1 M sodium acetate (pH not adjusted). Drops were prepared by pipetting 5 microliters of 30 mg/mL aqueous peptide solution, 4 microliters of reservoir solution, and 1 microliter of 0.1 M zinc sulfate onto a glass coverslip. Crystals grew within a day. Lipid mixture: none / 温度: 298 K / Time: 1 DAY | ||||||||||||||||||||
緩衝液 | pH: 7 | ||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 30 mg/ml / 包埋: NO / シャドウイング: NO / 染色![]() ![]() | ||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 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 / 詳細: Plunged into liquid ethane (FEI VITROBOT MARK IV) | ||||||||||||||||||||
結晶化![]() | 温度: 273 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 詳細: 1.0 M sodium acetate, 0.1 M HEPES, pH 7.0, 0.01 M zinc sulfate |
-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![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
電子レンズ | モード: DIFFRACTION![]() | ||||||||||||||||||||||||||||||||||||||||||
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER 最高温度: 100 K / 最低温度: 100 K | ||||||||||||||||||||||||||||||||||||||||||
撮影 | 平均露光時間: 2 sec. / 電子線照射量: 0.01 e/Å2 フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) Num. of diffraction images: 879 / 撮影したグリッド数: 2 詳細: The detector was operated in rolling shutter mode with 2x2 pixel binning. | ||||||||||||||||||||||||||||||||||||||||||
画像スキャン | サンプリングサイズ: 15.6 µm / 横: 4096 / 縦: 4096 | ||||||||||||||||||||||||||||||||||||||||||
EM回折 | カメラ長: 1350 mm | ||||||||||||||||||||||||||||||||||||||||||
EM回折 シェル |
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EM回折 統計 | 詳細: Phase statistics are not applicable. No imaging was used. The phases were obtained by a crystallographic direct methods program, SHELXD. フーリエ空間範囲: 82.7 % / 再高解像度: 1 Å / 測定した強度の数: 16753 / 構造因子数: 2399 / 位相誤差: 0.1 ° / 位相残差: 0.1 ° / 位相誤差の除外基準: 0 / Rmerge: 15.1 / Rsym: 15.1 | ||||||||||||||||||||||||||||||||||||||||||
回折 | 平均測定温度: 100 K | ||||||||||||||||||||||||||||||||||||||||||
放射光源 | 由来: ELECTRON MICROSCOPE / タイプ: TECNAI F20 TEM / 波長: 0.0251 Å | ||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: TVIPS F416 CMOS CAMERA / 検出器: CMOS / 日付: 2016年2月3日 | ||||||||||||||||||||||||||||||||||||||||||
放射波長 | 波長![]() | ||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1→90 Å / Num. obs: 2712 / % possible obs: 85.8 % / 冗長度: 4.9 % / Rmerge(I) obs: 0.211 / Χ2: 1.051 / Net I/av σ(I): 5.767 / Net I/σ(I): 4.1 / Num. measured all: 13199 | ||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1 / Rejects: 0
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解析
ソフトウェア |
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EMソフトウェア |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 104 ° / ∠γ: 90 ° / A: 21.5 Å / B: 4.9 Å / C: 23.9 Å / 空間群名: P1211 / 空間群番号: 4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF補正![]() | タイプ: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成![]() | 解像度の算出法: DIFFRACTION PATTERN/LAYERLINES 詳細: The density map was obtained using measured diffraction intensities and phases acquired from crystallographic direct methods program SHELXD. 対称性のタイプ: 3D CRYSTAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 4.4 / プロトコル: OTHER / 空間: RECIPROCAL / Target criteria: maximum likelihood | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | 解像度: 1→23.17 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.912 / SU B: 1.746 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0353 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.038 / 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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原子変位パラメータ | Biso max: 23.95 Å2 / Biso mean: 4.445 Å2 / Biso min: 2.99 Å2
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精密化ステップ | サイクル: final / 解像度: 1→23.17 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 0.997→1.023 Å / Total num. of bins used: 20
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