+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13245 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | E. faecalis 70S ribosome with P-tRNA, state IV | |||||||||
マップデータ | 70S ribosome from E. faecalis with P-tRNA, state IV. From RELION Refine3D. | |||||||||
試料 |
| |||||||||
キーワード | Ribosome / Enterococcus faecalis / P-tRNA | |||||||||
機能・相同性 | 機能・相同性情報 large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Enterococcus faecalis (乳酸球菌) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.1 Å | |||||||||
データ登録者 | Crowe-McAuliffe C / Wilson DN | |||||||||
資金援助 | ドイツ, スウェーデン, 2件
| |||||||||
引用 | ジャーナル: mSphere / 年: 2018 タイトル: The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci. 著者: A Sivertsen / J Janice / T Pedersen / T M Wagner / J Hegstad / K Hegstad / 要旨: has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of ... has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of staphylococcus cassette chromosome elements SCC This novel element termed the enterococcus cassette chromosome (ECC) element was located in the 3' region of and encoded large serine recombinases similar to SCC Horizontal transfer of an ECC element termed ECC:: containing a knock-in chloramphenicol resistance determinant occurred in the presence of a conjugative plasmid. We determined the ECC:: insertion site in the 3' region of in the recipient by long-read sequencing. ECC:: also mobilized by homologous recombination through sequence identity between flanking insertion sequence (IS) elements in ECC:: and the conjugative plasmid. The genes were found in 69 of 516 genomes in GenBank. Full-length ECC elements were retrieved from 32 of these genomes. ECCs were flanked by and sites of approximately 50 bp. The sequences were found by PCR and sequencing of circularized ECCs in three strains. The genes in ECCs contained an amalgam of common and rare genes. Taken together, our data imply that ECC elements act as hot spots for genetic exchange and contribute to the large variation of accessory genes found in is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental adaptation. Identifying mobile genetic elements causing sequence variation is important to understand how genetic content variation occurs. Here, a novel genetic island, the enterococcus cassette chromosome, is shown to contain a wealth of genes, which may aid in adapting to new environments. The transmission mechanism involves the only two conserved genes within ECC, , large serine recombinases that insert ECC into the host genome similarly to SCC elements found in staphylococci. #1: ジャーナル: Biorxiv / 年: 2021 タイトル: Structural basis for PoxtA-mediated resistance to Phenicol and Oxazolidinone antibiotics 著者: Crowe-McAuliffe C / Murina V / Kasari M / Takada H / Turnbull KJ / Sundsfjord A / Hegstad K / Atkinson GC / Wilson DN / Hauryliuk V | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_13245.map.gz | 253 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-13245-v30.xml emd-13245.xml | 74.9 KB 74.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_13245_fsc.xml | 14.9 KB | 表示 | FSCデータファイル |
画像 | emd_13245.png | 113.2 KB | ||
マスクデータ | emd_13245_msk_1.map | 282.6 MB | マスクマップ | |
Filedesc metadata | emd-13245.cif.gz | 14 KB | ||
その他 | emd_13245_additional_1.map.gz emd_13245_half_map_1.map.gz emd_13245_half_map_2.map.gz | 41.4 MB 254.6 MB 254.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13245 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13245 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_13245_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_13245_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_13245_validation.xml.gz | 22.7 KB | 表示 | |
CIF形式データ | emd_13245_validation.cif.gz | 29.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13245 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13245 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_13245.map.gz / 形式: CCP4 / 大きさ: 282.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | 70S ribosome from E. faecalis with P-tRNA, state IV. From RELION Refine3D. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-マスク #1
ファイル | emd_13245_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-追加マップ: 70S ribosome from E. faecalis with P-tRNA, state IV. Sharpened map.
ファイル | emd_13245_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | 70S ribosome from E. faecalis with P-tRNA, state IV. Sharpened map. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: 70S ribosome from E. faecalis with P-tRNA, state IV. Half map.
ファイル | emd_13245_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | 70S ribosome from E. faecalis with P-tRNA, state IV. Half map. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: 70S ribosome from E. faecalis with P-tRNA, state IV. Half map.
ファイル | emd_13245_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | 70S ribosome from E. faecalis with P-tRNA, state IV. Half map. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : 70S ribosome from E. faecalis with P-tRNA (initiation complex), s...
+超分子 #1: 70S ribosome from E. faecalis with P-tRNA (initiation complex), s...
+分子 #1: 50S ribosomal protein L29
+分子 #2: 50S ribosomal protein L30
+分子 #3: 50S ribosomal protein L31 type B
+分子 #4: 50S ribosomal protein L32
+分子 #5: 50S ribosomal protein L33
+分子 #6: 50S ribosomal protein L34
+分子 #7: 50S ribosomal protein L35
+分子 #8: 50S ribosomal protein L36
+分子 #12: 50S ribosomal protein L2
+分子 #13: 50S ribosomal protein L3
+分子 #14: 50S ribosomal protein L4
+分子 #15: 50S ribosomal protein L5
+分子 #16: 50S ribosomal protein L6
+分子 #17: 50S ribosomal protein L13
+分子 #18: 50S ribosomal protein L14
+分子 #19: 50S ribosomal protein L15
+分子 #20: 50S ribosomal protein L16
+分子 #21: 50S ribosomal protein L17
+分子 #22: 50S ribosomal protein L18
+分子 #23: 50S ribosomal protein L19
+分子 #24: 50S ribosomal protein L20
+分子 #25: 50S ribosomal protein L21
+分子 #26: 50S ribosomal protein L22
+分子 #27: 50S ribosomal protein L23
+分子 #28: 50S ribosomal protein L24
+分子 #29: 50S ribosomal protein L27
+分子 #30: 50S ribosomal protein L28
+分子 #33: 30S ribosomal protein S2
+分子 #34: 30S ribosomal protein S3
+分子 #35: 30S ribosomal protein S4
+分子 #36: 30S ribosomal protein S5
+分子 #37: 30S ribosomal protein S6
+分子 #38: 30S ribosomal protein S7
+分子 #39: 30S ribosomal protein S8
+分子 #40: 30S ribosomal protein S9
+分子 #41: 30S ribosomal protein S10
+分子 #42: 30S ribosomal protein S11
+分子 #43: 30S ribosomal protein S12
+分子 #44: 30S ribosomal protein S13
+分子 #45: 30S ribosomal protein S14 type Z
+分子 #46: 30S ribosomal protein S15
+分子 #47: 30S ribosomal protein S16
+分子 #48: 30S ribosomal protein S17
+分子 #49: 30S ribosomal protein S18
+分子 #50: 30S ribosomal protein S19
+分子 #51: 30S ribosomal protein S20
+分子 #9: 23S rRNA
+分子 #10: 5S rRNA
+分子 #11: tRNA-fMet
+分子 #31: 16S rRNA
+分子 #32: mRNA
+分子 #52: ZINC ION
+分子 #53: POTASSIUM ION
+分子 #54: MAGNESIUM ION
+分子 #55: 1,4-DIAMINOBUTANE
+分子 #56: SPECTINOMYCIN
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 9 |
---|---|
グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 2 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 278 K / 装置: FEI VITROBOT MARK II |
詳細 | Grid was prepared by four applications of elution fraction from affinity purification. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) デジタル化 - サイズ - 横: 3838 pixel / デジタル化 - サイズ - 縦: 3710 pixel / デジタル化 - 画像ごとのフレーム数: 1-40 / 撮影したグリッド数: 1 / 実像数: 3639 / 平均露光時間: 5.0 sec. / 平均電子線量: 30.255 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.5 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 165000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |