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- EMDB-2239: Cryo-electron microscopy structure of the Trypanosoma brucei 80S ... -

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基本情報

登録情報
データベース: EMDB / ID: EMD-2239
タイトルCryo-electron microscopy structure of the Trypanosoma brucei 80S ribosome
マップデータTrypanosoma Brucei 80S Ribosome cryo-em reconstruction filtered according to the local FSC at 0.5
試料
  • 試料: Trypanosoma Brucei 80S Ribosome
  • 複合体: 80S Ribosome
キーワードTrypanosoma / brucei / 80S / ribosome / eukaryotic / kinetoplastids / expansion segments / high-resolution
機能・相同性
機能・相同性情報


organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / mitochondrial large ribosomal subunit / nuclear lumen / phosphate ion binding / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / mitochondrial large ribosomal subunit / nuclear lumen / phosphate ion binding / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / translation regulator activity / rescue of stalled ribosome / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein kinase C binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / regulation of cell growth / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosome biogenesis / regulation of cell population proliferation / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Ribosomal protein L14, KOW motif / Ribosomal protein L28e / Ribosomal protein L23 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e ...Ribosomal protein L14, KOW motif / Ribosomal protein L28e / Ribosomal protein L23 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4 C-terminus / : / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein L27e superfamily / Ribosomal protein S19e / Ribosomal L27e protein family / Ribosomal protein S8e signature. / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein L30e, conserved site / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S7e / Ribosomal protein L39e, conserved site / Ribosomal protein S7e / Ribosomal protein L39e signature. / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S19A/S15e / : / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e
類似検索 - ドメイン・相同性
60S ribosomal protein L44 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL14 / 60S ribosomal protein L27, putative / 60S ribosomal protein L18a / 40S ribosomal protein S17, putative / Guanine nucleotide-binding protein beta subunit-like protein / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL22 ...60S ribosomal protein L44 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL14 / 60S ribosomal protein L27, putative / 60S ribosomal protein L18a / 40S ribosomal protein S17, putative / Guanine nucleotide-binding protein beta subunit-like protein / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL22 / 60S ribosomal protein L29 / 60S ribosomal protein L34, putative / 40S ribosomal protein S27, putative / Ribosomal protein / 40S ribosomal protein S26 / 40S ribosomal protein S21, putative / 40S ribosomal protein S5, putative / 60S ribosomal protein L28, putative / 60S ribosomal protein L17, putative / 40S ribosomal protein S12 / 40S ribosomal protein S4 / Ribosomal protein L37 / Small ribosomal subunit protein uS5 / 40S ribosomal protein S3 / 60S ribosomal protein L6, putative / 40S ribosomal protein S24 / 60S ribosomal protein L37a, putative / 60S ribosomal protein L24, putative / 40S ribosomal protein S10, putative / 40S ribosomal protein S18, putative / 60S ribosomal protein L30 / Small ribosomal subunit protein eS1 / 60S ribosomal protein L9, putative / 40S ribosomal protein S23, putative / 40S ribosomal proteins S11, putative / 60S ribosomal protein L32, putative / 40S ribosomal protein S6 / Ribosomal protein L36, putative / Ribosomal protein L15 / 60S ribosomal protein L5, putative / 60S ribosomal protein L26, putative / 60S ribosomal subunit protein L31, putative / 60S ribosomal protein L27a / 60S ribosomal protein L23, putative / 60S ribosomal protein L10, putative / 60S ribosomal protein L11, putative / 40S ribosomal protein S7 / 60S ribosomal protein L38, putative / 60S ribosomal protein L35, putative / 60S ribosomal protein L21E, putative / 40S ribosomal protein S14 / 40S ribosomal protein S33, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L7, putative / 60S ribosomal protein L13 / 60S ribosomal protein L7a / 40S ribosomal protein S9, putative / 40S ribosomal protein S16, putative / 60S ribosomal protein L2, putative / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S15, putative / 40S ribosomal protein S25 / 60S ribosomal protein L12, putative / 40S ribosomal protein S8 / 60S ribosomal protein L23a / 60S ribosomal protein L19, putative / 40S ribosomal protein S15a, putative / Ribosomal protein L3, mitochondrial, putative / 60S ribosomal protein L4 / Ribosomal protein S19, putative / 60S ribosomal protein L35A, putative / 40S ribosomal protein S30 / 60S ribosomal protein L13a, putative / 40S ribosomal protein S13, putative
類似検索 - 構成要素
生物種Trypanosoma brucei (トリパノソーマ)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.57 Å
データ登録者Hashem Y / des Georges A / Fu J / Buss SN / Jossinet F / Jobe A / Zhang Q / Liao HY / Grassucci B / Bajaj C ...Hashem Y / des Georges A / Fu J / Buss SN / Jossinet F / Jobe A / Zhang Q / Liao HY / Grassucci B / Bajaj C / Westhof E / Madison-Antenucci S / Frank J
引用ジャーナル: Nature / 年: 2013
タイトル: High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome.
著者: Yaser Hashem / Amedee des Georges / Jie Fu / Sarah N Buss / Fabrice Jossinet / Amy Jobe / Qin Zhang / Hstau Y Liao / Robert A Grassucci / Chandrajit Bajaj / Eric Westhof / Susan Madison- ...著者: Yaser Hashem / Amedee des Georges / Jie Fu / Sarah N Buss / Fabrice Jossinet / Amy Jobe / Qin Zhang / Hstau Y Liao / Robert A Grassucci / Chandrajit Bajaj / Eric Westhof / Susan Madison-Antenucci / Joachim Frank /
要旨: Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and ...Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and maintenance. The few available structures of the eukaryotic ribosome reveal that it is more complex than its prokaryotic counterpart, owing mainly to the presence of eukaryote-specific ribosomal proteins and additional ribosomal RNA insertions, called expansion segments. The structures also differ among species, partly in the size and arrangement of these expansion segments. Such differences are extreme in kinetoplastids, unicellular eukaryotic parasites often infectious to humans. Here we present a high-resolution cryo-electron microscopy structure of the ribosome of Trypanosoma brucei, the parasite that is transmitted by the tsetse fly and that causes African sleeping sickness. The atomic model reveals the unique features of this ribosome, characterized mainly by the presence of unusually large expansion segments and ribosomal-protein extensions leading to the formation of four additional inter-subunit bridges. We also find additional rRNA insertions, including one large rRNA domain that is not found in other eukaryotes. Furthermore, the structure reveals the five cleavage sites of the kinetoplastid large ribosomal subunit (LSU) rRNA chain, which is known to be cleaved uniquely into six pieces, and suggests that the cleavage is important for the maintenance of the T. brucei ribosome in the observed structure. We discuss several possible implications of the large rRNA expansion segments for the translation-regulation process. The structure could serve as a basis for future experiments aimed at understanding the functional importance of these kinetoplastid-specific ribosomal features in protein-translation regulation, an essential step towards finding effective and safe kinetoplastid-specific drugs.
履歴
登録2012年12月6日-
ヘッダ(付随情報) 公開2012年12月26日-
マップ公開2013年2月13日-
更新2013年2月27日-
現状2013年2月27日処理サイト: PDBe / 状態: 公開

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構造の表示

ムービー
  • 表面図（断面を密度値に従い着色）
  • 表面レベル: 108000
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（高さに従い着色）
  • 表面レベル: 108000
  • UCSF Chimeraによる作画
  • ダウンロード
  • あてはめたモデルとの重ね合わせ
  • 原子モデル: PDB-4v8m
  • 表面レベル: 108000
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューアEMマップ:
SurfViewMolmilJmol/JSmol
添付画像

emd_2239.jpg

ダウンロードとリンク

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マップ

ファイルダウンロード / ファイル: emd_2239.map.gz / 形式: CCP4 / 大きさ: 172.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Trypanosoma Brucei 80S Ribosome cryo-em reconstruction filtered according to the local FSC at 0.5
投影像・断面図

画像のコントロール

大きさ
明度
コントラスト
その他
軸Z (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 359 pix.
= 391.31 Å		1.09 Å/pix.
x 359 pix.
= 391.31 Å		1.09 Å/pix.
x 359 pix.
= 391.31 Å

表面

投影像

断面 (1/3)

断面 (1/2)

断面 (2/3)

画像は Spider により作成

ボクセルのサイズX=Y=Z: 1.09 Å
密度

ヒストグラム

ヒストグラム (対数)
表面レベル登録者による: 108000.0 / ムービー #1: 108000
最小 - 最大-202702.703125 - 483783.78125
平均 (標準偏差)7679.428710940000201 (±33729.66015625)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin-179-179-179
サイズ359359359
Spacing359359359
セルA=B=C: 391.31 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z359359359
origin x/y/z0.0000.0000.000
length x/y/z391.310391.310391.310
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS-179-179-179
NC/NR/NS359359359
D min/max/mean-202702.703483783.7817679.429

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添付データ

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試料の構成要素

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全体 : Trypanosoma Brucei 80S Ribosome

全体名称: Trypanosoma Brucei 80S Ribosome
要素
  • 試料: Trypanosoma Brucei 80S Ribosome
  • 複合体: 80S Ribosome

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超分子 #1000: Trypanosoma Brucei 80S Ribosome

超分子名称: Trypanosoma Brucei 80S Ribosome / タイプ: sample / ID: 1000 / 集合状態: monomer / Number unique components: 1
分子量理論値: 3.305 MDa
手法: Molecular weight estimated form the protein and RNA sequence.

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超分子 #1: 80S Ribosome

超分子名称: 80S Ribosome / タイプ: complex / ID: 1 / 組換発現: No / Ribosome-details: ribosome-eukaryote: ALL
由来(天然)生物種: Trypanosoma brucei (トリパノソーマ) / 株: TREU 667 / 細胞中の位置: Cytoplasm
分子量理論値: 3.3 MDa

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実験情報

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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

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試料調製

濃度0.105 mg/mL
緩衝液pH: 7.2
詳細: 20 mM Tris pH 7.2, 100mM MgCl2, 500 mM KCl, 5 mM beta-mercaptoethanol
グリッド詳細: 300 mesh Copper/Molbydenum holey carbon-coated Quantifoil 2/4 grid (Quantifoil Micro Tools GmbH) containing an additional continuous thin layer of carbon
凍結凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 100 K / 装置: FEI VITROBOT MARK IV / 手法: Wait 30 sec, Blot 6 seconds, plunge

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電子顕微鏡法

顕微鏡FEI POLARA 300
日付2011年1月1日
撮影カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM
デジタル化 - スキャナー: NIKON SUPER COOLSCAN 9000
実像数: 1000 / 平均電子線量: 25 e/Å2 / ビット/ピクセル: 32
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.26 mm / 最大 デフォーカス（公称値）: 4.0 µm / 最小 デフォーカス（公称値）: 1.5 µm / 倍率（公称値）: 59000
試料ステージ試料ホルダーモデル: SIDE ENTRY, EUCENTRIC
実験機器
モデル: Tecnai Polara / 画像提供: FEI Company

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画像解析

詳細Data were processed using SPIDER. The particles windows were automatically extracted from 1000 film-recorded micrographs and inspected manually. Standard SPIDER protocols for reference-based reconstruction, except that contrast transfer function (CTF) of the reconstructions was corrected by phase-flipping the particles using the defocus value estimated for each micrograph and a single reconstruction was obtained from the entire dataset using conjugate gradients with regularization (BP CG in SPIDER).
CTF補正詳細: Phase-flip on each particle
最終 再構成想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 5.57 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: Spider / 使用した粒子像数: 164000
FSC曲線 (解像度の算出)

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原子モデル構築 1

初期モデルPDB ID:

3u5b
PDB 未公開エントリ

ソフトウェア名称: Chimera
詳細Protocol: Rigid body. The structure of the 80S from Yeast (3U5B and others) as well as the structure of the 60S from Tetrahymena thermophila (4A17 and others) were used as starting model for the 60S subunit model. The 40S from Tetrahymena thermophila (2XZM and 2XZN) as well as the 80S from Yeast were used as starting model for the 40S subunit model. The 80S model of Triticum aestivum (3IZR and others) was used to fit missing proteins form the two X-ray structures.
精密化空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross correlation
得られたモデル

PDB-4v8m:
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome

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原子モデル構築 2

初期モデルPDB ID:

2xzm
PDB 未公開エントリ

ソフトウェア名称: Chimera
詳細Protocol: Rigid body. The structure of the 80S from Yeast (3U5B and others) as well as the structure of the 60S from Tetrahymena thermophila (4A17 and others) were used as starting model for the 60S subunit model. The 40S from Tetrahymena thermophila (2XZM and 2XZN) as well as the 80S from Yeast were used as starting model for the 40S subunit model. The 80S model of Triticum aestivum (3IZR and others) was used to fit missing proteins form the two X-ray structures.
精密化空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross correlation
得られたモデル

PDB-4v8m:
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome

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原子モデル構築 3

初期モデルPDB ID:

3izr
PDB 未公開エントリ

ソフトウェア名称: Chimera
詳細Protocol: Rigid body. The structure of the 80S from Yeast (3U5B and others) as well as the structure of the 60S from Tetrahymena thermophila (4A17 and others) were used as starting model for the 60S subunit model. The 40S from Tetrahymena thermophila (2XZM and 2XZN) as well as the 80S from Yeast were used as starting model for the 40S subunit model. The 80S model of Triticum aestivum (3IZR and others) was used to fit missing proteins form the two X-ray structures.
精密化空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross correlation
得られたモデル

PDB-4v8m:
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome

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