+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4v19 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Structure of the large subunit of the mammalian mitoribosome, part 1 of 2 | |||||||||
要素 |
| |||||||||
キーワード | RIBOSOME / TRANSLATION / LARGE RIBOSOMAL SUBUNIT / MITORIBOSOME / MAMMALIAN MITOCHONDRIAL RIBOSOME / CRYO-EM | |||||||||
機能・相同性 | 機能・相同性情報 Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / organelle membrane / mitochondrial translation / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit ...Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / organelle membrane / mitochondrial translation / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / mitochondrion / RNA binding / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | SUS SCROFA (ブタ) | |||||||||
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: 3.4 Å | |||||||||
データ登録者 | Greber, B.J. / Boehringer, D. / Leibundgut, M. / Bieri, P. / Leitner, A. / Schmitz, N. / Aebersold, R. / Ban, N. | |||||||||
引用 | ジャーナル: Nature / 年: 2014 タイトル: The complete structure of the large subunit of the mammalian mitochondrial ribosome. 著者: Basil J Greber / Daniel Boehringer / Marc Leibundgut / Philipp Bieri / Alexander Leitner / Nikolaus Schmitz / Ruedi Aebersold / Nenad Ban / 要旨: Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy ...Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy conversion and ATP production inside mitochondria. Mammalian mitoribosomes, which comprise 39S and 28S subunits, have diverged markedly from the bacterial ribosomes from which they are derived, rendering them unique compared to bacterial, eukaryotic cytosolic and fungal mitochondrial ribosomes. We have previously determined at 4.9 Å resolution the architecture of the porcine (Sus scrofa) 39S subunit, which is highly homologous to the human mitoribosomal large subunit. Here we present the complete atomic structure of the porcine 39S large mitoribosomal subunit determined in the context of a stalled translating mitoribosome at 3.4 Å resolution by cryo-electron microscopy and chemical crosslinking/mass spectrometry. The structure reveals the locations and the detailed folds of 50 mitoribosomal proteins, shows the highly conserved mitoribosomal peptidyl transferase active site in complex with its substrate transfer RNAs, and defines the path of the nascent chain in mammalian mitoribosomes along their idiosyncratic exit tunnel. Furthermore, we present evidence that a mitochondrial tRNA has become an integral component of the central protuberance of the 39S subunit where it architecturally substitutes for the absence of the 5S ribosomal RNA, a ubiquitous component of all cytoplasmic ribosomes. | |||||||||
履歴 |
| |||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -6-STRANDED BARREL THIS IS REPRESENTED BY A -5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-構造の表示
ムービー |
ムービービューア |
---|---|
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 | 4v19.cif.gz | 1.7 MB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb4v19.ent.gz | 1.4 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4v19.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 | 4v19_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 4v19_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 4v19_validation.xml.gz | 148.7 KB | 表示 | |
CIF形式データ | 4v19_validation.cif.gz | 244 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/v1/4v19 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/4v19 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
+MITORIBOSOMAL ... , 30種, 30分子 0123456789ABDEFIJKNOPQRSTUVWXY
-RNA鎖 , 1種, 2分子 CZ
#13: RNA鎖 | 分子量: 894.612 Da / 分子数: 2 / Fragment: CCA-3' END / 由来タイプ: 天然 / 詳細: CHAIN C IS P-SITE TRNA AND CHAIN Z IS A-SITE TRNA / 由来: (天然) SUS SCROFA (ブタ) / 器官: LIVER |
---|
-非ポリマー , 3種, 375分子
#32: 化合物 | #33: 化合物 | ChemComp-MG / #34: 水 | ChemComp-HOH / | |
---|
-詳細
非ポリマーの詳細 | ZINC ION (ZN): ZN IONS COORDINATED BY ZINC FINGER PROTEINS PYRIMIDINE RIBOSIDE-5'-MONOPHOSPHATE ...ZINC ION (ZN): ZN IONS COORDINATE |
---|---|
配列の詳細 | A-SITE TRNA, UNIVERSALLY CONSERVED CCA-3' END P-SITE TRNA, UNIVERSALLY CONSERVED CCA-3' END ...A-SITE TRNA, UNIVERSALL |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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: SUS SCROFA 55S MITOCHONDRIAL RIBOSOME / タイプ: RIBOSOME 詳細: QUANTIFOIL HOLEY CARBON GRIDS WERE COATED WITH A THIN CARBON FILM |
---|---|
緩衝液 | 名称: 20 MM HEPES-KOH, 50 MM KCL, 40 MM MGCL2, 1 MM DTT / pH: 7.4 / 詳細: 20 MM HEPES-KOH, 50 MM KCL, 40 MM MGCL2, 1 MM DTT |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: CARBON |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE-PROPANE / 詳細: MIXTURE OF LIQUID ETHANE AND PROPANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2014年5月30日 詳細: IMAGES WERE ACQUIRED IN 2 SESSIONS ON A FEI TITAN KRIOS IN MAY 2014 |
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): 59000 X / 倍率(補正後): 100000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 800 nm / Cs: 2.7 mm |
試料ホルダ | 温度: 85 K |
撮影 | 電子線照射量: 20 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | 詳細: PER DETECTOR FRAME | ||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||
3次元再構成 | 手法: MAXIMUM LIKELIHOOD BASED REFINEMENT IMPLEMENTED IN RELION 解像度: 3.4 Å / 粒子像の数: 141675 / ピクセルサイズ(実測値): 1.4 Å 詳細: FOR VISUALIZATION PURPOSES THE FINAL MAP WAS FILTERED AND AMPLITUDE CORRECTED IN RELION SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2787. (DEPOSITION ID: 12830). THE COMBINED ...詳細: FOR VISUALIZATION PURPOSES THE FINAL MAP WAS FILTERED AND AMPLITUDE CORRECTED IN RELION SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2787. (DEPOSITION ID: 12830). THE COMBINED COORDINATES (SPLIT ENTRIES 4V19 AND 4V1A) WERE REFINED IN RECIPROCAL SPACE USING PHENIX.REFINE AGAINST THE MLHL TARGET. FOR THIS, THE CRYO-EM MAPS (EMD-2787) WERE CONVERTED TO RECIPROCAL SPACE STRUCTURE FACTORS. 対称性のタイプ: POINT | ||||||||||||||||||||||||||||
原子モデル構築 | 空間: REAL | ||||||||||||||||||||||||||||
精密化 | 最高解像度: 3.4 Å | ||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 3.4 Å
|