+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1x1l | ||||||
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タイトル | Interaction of ERA,a GTPase protein, with the 3'minor domain of the 16S rRNA within the THERMUS THERMOPHILUS 30S subunit. | ||||||
要素 |
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キーワード | STRUCTURAL PROTEIN/RNA / Interaction of Era protein with the 3'minor domain of 16S rRNA / STRUCTURAL PROTEIN-RNA COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 guanosine tetraphosphate binding / ribosomal small subunit binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA binding / protein phosphorylation / GTPase activity / GTP binding / RNA binding ...guanosine tetraphosphate binding / ribosomal small subunit binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA binding / protein phosphorylation / GTPase activity / GTP binding / RNA binding / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Thermus thermophilus (バクテリア) Escherichia coli (大腸菌) | ||||||
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: 13.5 Å | ||||||
データ登録者 | Sharma, M.R. / Barat, C. / Agrawal, R.K. | ||||||
引用 | ジャーナル: Mol Cell / 年: 2005 タイトル: Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly. 著者: Manjuli R Sharma / Chandana Barat / Daniel N Wilson / Timothy M Booth / Masahito Kawazoe / Chie Hori-Takemoto / Mikako Shirouzu / Shigeyuki Yokoyama / Paola Fucini / Rajendra K Agrawal / 要旨: Era (E. coliRas-like protein) is a highly conserved and essential GTPase in bacteria. It binds to the 16S ribosomal RNA (rRNA) of the small (30S) ribosomal subunit, and its depletion leads to ...Era (E. coliRas-like protein) is a highly conserved and essential GTPase in bacteria. It binds to the 16S ribosomal RNA (rRNA) of the small (30S) ribosomal subunit, and its depletion leads to accumulation of an unprocessed precursor of the 16S rRNA. We have obtained a three-dimensional cryo-electron microscopic map of the Thermus thermophilus 30S-Era complex. Era binds in the cleft between the head and platform of the 30S subunit and locks the subunit in a conformation that is not favorable for association with the large (50S) ribosomal subunit. The RNA binding KH motif present within the C-terminal domain of Era interacts with the conserved nucleotides in the 3' region of the 16S rRNA. Furthermore, Era makes contact with several assembly elements of the 30S subunit. These observations suggest a direct involvement of Era in the assembly and maturation of the 30S subunit. #1: ジャーナル: Nature / 年: 2000 タイトル: Molecular biology. Small subunit, big science. #2: ジャーナル: Proc Natl Acad Sci U S A / 年: 1999 タイトル: Crystal structure of ERA: a GTPase-dependent cell cycle regulator containing an RNA binding motif. 著者: X Chen / D L Court / X Ji / 要旨: ERA forms a unique family of GTPase. It is widely conserved and essential in bacteria. ERA functions in cell cycle control by coupling cell division with growth rate. ERA homologues also are found in ...ERA forms a unique family of GTPase. It is widely conserved and essential in bacteria. ERA functions in cell cycle control by coupling cell division with growth rate. ERA homologues also are found in eukaryotes. Here we report the crystal structure of ERA from Escherichia coli. The structure has been determined at 2.4-A resolution. It reveals a two-domain arrangement of the molecule: an N-terminal domain that resembles p21 Ras and a C-terminal domain that is unique. Structure-based topological search of the C domain fails to reveal any meaningful match, although sequence analysis suggests that it contains a KH domain. KH domains are RNA binding motifs that usually occur in tandem repeats and exhibit low sequence similarity except for the well-conserved segment VIGxxGxxIK. We have identified a betaalphaalphabeta fold that contains the VIGxxGxxIK sequence and is shared by the C domain of ERA and the KH domain. We propose that this betaalphaalphabeta fold is the RNA binding motif, the minimum structural requirement for RNA binding. ERA dimerizes in crystal. The dimer formation involves a significantly distorted switch II region, which may shed light on how ERA protein regulates downstream events. #3: ジャーナル: To be Published タイトル: Crystal structure of Era from Thermus thermophilus 著者: Kawazoe, M. / Takemoto, C. / Kaminishi, T. / Sekine, S. / Shirouzu, M. / Fucini, P. / Agrawal, R.K. / Yokoyama, S. | ||||||
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 | 1x1l.cif.gz | 29.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1x1l.ent.gz | 13.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1x1l.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 | 1x1l_validation.pdf.gz | 309.5 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1x1l_full_validation.pdf.gz | 309 KB | 表示 | |
XML形式データ | 1x1l_validation.xml.gz | 944 B | 表示 | |
CIF形式データ | 1x1l_validation.cif.gz | 4.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/x1/1x1l ftp://data.pdbj.org/pub/pdb/validation_reports/x1/1x1l | 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: RNA鎖 | 分子量: 42303.242 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) |
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#2: タンパク質 | 分子量: 33858.078 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 参照: UniProt: P06616 |
-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: THERMUS THERMOPHILUS 30S ribosomal subunit complexed with Era タイプ: RIBOSOME / 詳細: Era was bound to a S1-depleted 30S subunit |
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緩衝液 | 名称: Hepes-KOH / pH: 7.5 / 詳細: Hepes-KOH |
試料 | 濃度: 0.032 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: Quantifoil holley-carbon film GRIDS |
急速凍結 | 詳細: Rapid-freezing in liquid ethane |
-電子顕微鏡撮影
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 / 日付: 2003年3月25日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 50000 X / 倍率(補正後): 49696 X / 最大 デフォーカス(公称値): 3940 nm / 最小 デフォーカス(公称値): 1180 nm / Cs: 2 mm |
試料ホルダ | 温度: 93 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
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 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: CTF correction of 3D-maps by wiener filtration | |||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||
3次元再構成 | 手法: reference based alignment / 解像度: 13.5 Å / ピクセルサイズ(実測値): 2.82 Å / 倍率補正: TMV 詳細: projection matching using spider package. The coordinates for only the alpha carbons in protein and phosphoruses in rRNA are present in the structure. The number of missing atoms was so much ...詳細: projection matching using spider package. The coordinates for only the alpha carbons in protein and phosphoruses in rRNA are present in the structure. The number of missing atoms was so much that remark 470 for the missing atoms list were removed. 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL Target criteria: X-ray coordinates of the 30S ribosomal subunit and ERA were fitted into the 13.5 angstroms resolution CRYO-EM map of the T. Thermophilus 30S subunit-ERA complex. the atomic structure ...Target criteria: X-ray coordinates of the 30S ribosomal subunit and ERA were fitted into the 13.5 angstroms resolution CRYO-EM map of the T. Thermophilus 30S subunit-ERA complex. the atomic structure of ERA was fitted as 3 rigid bodies, N-terminal domain, C-terminal domain and C-terminal helix within the C-terminal domain. The resultant ERA structure was then energy minimized. The X-ray coordinates of T. Thermophilus 30S subunit was fitted as 4 rigid bodies, head, body, platform and 16S rRNA 3' minor domains. Only the coordinates of the 16S rRNA 3' minor domain and ERA are included HERE. The KH domain of ERA makes direct contact with the 3' terminus of the 16S rRNA. 詳細: METHOD--cross-correlation based manual fitting in O REFINEMENT PROTOCOL--MULTIPLE RIGID BODY | |||||||||||||||||||||
原子モデル構築 |
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精密化ステップ | サイクル: LAST
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