+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20645 | |||||||||||||||
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タイトル | MicroED structure of a FIB-milled CypA Crystal | |||||||||||||||
マップデータ | 2mFo-DFc at 1.5 sigma | |||||||||||||||
試料 |
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キーワード | Peptidyl-prolyl / cis-trans / isomerase / cyclophilin | |||||||||||||||
機能・相同性 | 機能・相同性情報 negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) | |||||||||||||||
手法 | 電子線結晶学 / クライオ電子顕微鏡法 / 解像度: 2.5 Å | |||||||||||||||
データ登録者 | Wolff AM / Martynowycz MW / Zhao W / Gonen T / Fraser JS / Thompson MC | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: IUCrJ / 年: 2020 タイトル: Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. 著者: Alexander M Wolff / Iris D Young / Raymond G Sierra / Aaron S Brewster / Michael W Martynowycz / Eriko Nango / Michihiro Sugahara / Takanori Nakane / Kazutaka Ito / Andrew Aquila / Asmit ...著者: Alexander M Wolff / Iris D Young / Raymond G Sierra / Aaron S Brewster / Michael W Martynowycz / Eriko Nango / Michihiro Sugahara / Takanori Nakane / Kazutaka Ito / Andrew Aquila / Asmit Bhowmick / Justin T Biel / Sergio Carbajo / Aina E Cohen / Saul Cortez / Ana Gonzalez / Tomoya Hino / Dohyun Im / Jake D Koralek / Minoru Kubo / Tomas S Lazarou / Takashi Nomura / Shigeki Owada / Avi J Samelson / Tomoyuki Tanaka / Rie Tanaka / Erin M Thompson / Henry van den Bedem / Rahel A Woldeyes / Fumiaki Yumoto / Wei Zhao / Kensuke Tono / Sebastien Boutet / So Iwata / Tamir Gonen / Nicholas K Sauter / James S Fraser / Michael C Thompson / 要旨: Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal ...Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme. | |||||||||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_20645.map.gz | 2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20645-v30.xml emd-20645.xml | 16.2 KB 16.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_20645.png | 92.9 KB | ||
Filedesc metadata | emd-20645.cif.gz | 6.2 KB | ||
Filedesc structureFactors | emd_20645_sf.cif.gz | 117.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20645 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20645 | HTTPS FTP |
-関連構造データ
関連構造データ | 6u5gMC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_20645.map.gz / 形式: CCP4 / 大きさ: 2.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | 2mFo-DFc at 1.5 sigma | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X: 0.58889 Å / Y: 0.59333 Å / Z: 0.60944 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : Peptidyl-prolyl cis-trans isomerase A
全体 | 名称: Peptidyl-prolyl cis-trans isomerase A |
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要素 |
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-超分子 #1: Peptidyl-prolyl cis-trans isomerase A
超分子 | 名称: Peptidyl-prolyl cis-trans isomerase A / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 / 詳細: monomer |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Peptidyl-prolyl cis-trans isomerase A
分子 | 名称: Peptidyl-prolyl cis-trans isomerase A / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO / EC番号: peptidylprolyl isomerase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 18.036504 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: MVNPTVFFDI AVDGEPLGRV SFELFADKVP KTAENFRALS TGEKGFGYKG SCFHRIIPGF MCQGGDFTRH NGTGGKSIYG EKFEDENFI LKHTGPGILS MANAGPNTNG SQFFICTAKT EWLDGKHVVF GKVKEGMNIV EAMERFGSRN GKTSKKITIA D CGQLE UniProtKB: Peptidyl-prolyl cis-trans isomerase A |
-分子 #2: water
分子 | 名称: water / タイプ: ligand / ID: 2 / コピー数: 32 / 式: HOH |
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分子量 | 理論値: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 電子線結晶学 |
試料の集合状態 | 3D array |
-試料調製
緩衝液 | pH: 7.5 |
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グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
結晶化 | 温度: 296.0 K 詳細: 600 uL of protein at 60 mg/mL was combined with 400 uL of 50 percent PEG 3350 in a glass vial and stirred with an Octagon stir bar at 500 RPM |
-電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
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撮影 | フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) 撮影したグリッド数: 1 / 平均電子線量: 0.06 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: DIFFRACTION / カメラ長: 2055 mm |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.5 Å / 解像度の算出法: DIFFRACTION PATTERN/LAYERLINES / ソフトウェア - 名称: PHENIX (ver. dev2880) | ||||||||||||||||||||||||||||
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Molecular replacement | ソフトウェア - 名称: PHENIX (ver. dev2880) / ソフトウェア - 詳細: PHASER | ||||||||||||||||||||||||||||
Crystallography statistics | Number intensities measured: 22370 / Number structure factors: 6236 / Fourier space coverage: 86 / R sym: 0.217 / R merge: 0.217 / Overall phase error: 23.06 / Overall phase residual: 23.06 / Phase error rejection criteria: 0 / High resolution: 2.5 Å 殻:
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