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- EMDB-5976: Structures of yeast 80S ribosome-tRNA complexes in the rotated an... -

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基本情報

登録情報
データベース: EMDB / ID: EMD-5976
タイトルStructures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - 1 tRNA in rotated conformation)
マップデータReconstruction of a yeast 80S ribosome in the rotated state with 1 tRNA bound. (Class II)
試料
  • 試料: 80S ribosome bound to mRNA containing Kozak sequence and to one tRNA
  • 複合体: 80S ribosome
  • RNA: mRNA
  • RNA: transfer RNA
キーワード80S ribosome / Kozak sequence / translation
機能・相同性
機能・相同性情報


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / hexon binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / preribosome, small subunit precursor / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / Ub-specific processing proteases / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / viral capsid / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / host cell nucleus / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
類似検索 - 分子機能
60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : ...60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L1, conserved site / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L1 signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / S27a-like superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L10e, conserved site / Plectin/S10 domain / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal_L40e
類似検索 - ドメイン・相同性
Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A ...Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Pre-hexon-linking protein VIII / Small ribosomal subunit protein uS9A / Large ribosomal subunit protein uL11A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS26A / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / Large ribosomal subunit protein eL13A / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母) / Escherichia coli (大腸菌)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.2 Å
データ登録者Svidritskiy E / Brilot AF / Koh CS / Grigorieff N / Korostelev AA
引用ジャーナル: Structure / 年: 2014
タイトル: Structures of yeast 80S ribosome-tRNA complexes in the rotated and nonrotated conformations.
著者: Egor Svidritskiy / Axel F Brilot / Cha San Koh / Nikolaus Grigorieff / Andrei A Korostelev /
要旨: The structural understanding of eukaryotic translation lags behind that of translation on bacterial ribosomes. Here, we present two subnanometer resolution structures of S. cerevisiae 80S ribosome ...The structural understanding of eukaryotic translation lags behind that of translation on bacterial ribosomes. Here, we present two subnanometer resolution structures of S. cerevisiae 80S ribosome complexes formed with either one or two tRNAs and bound in response to an mRNA fragment containing the Kozak consensus sequence. The ribosomes adopt two globally different conformations that are related to each other by the rotation of the small subunit. Comparison with bacterial ribosome complexes reveals that the global structures and modes of intersubunit rotation of the yeast ribosome differ significantly from those in the bacterial counterpart, most notably in the regions involving the tRNA, small ribosomal subunit, and conserved helix 69 of the large ribosomal subunit. The structures provide insight into ribosome dynamics implicated in tRNA translocation and help elucidate the role of the Kozak fragment in positioning an open reading frame during translation initiation in eukaryotes.
履歴
登録2014年5月21日-
ヘッダ(付随情報) 公開2014年7月30日-
マップ公開2014年8月6日-
更新2015年10月7日-
現状2015年10月7日処理サイト: RCSB / 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: 0.12
  • 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: 0.12
  • 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-3j77
  • 表面レベル: 0.12
  • 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

400_5976.gif

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_5976.map.gz / 形式: CCP4 / 大きさ: 173.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Reconstruction of a yeast 80S ribosome in the rotated state with 1 tRNA bound. (Class II)
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.)
1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. 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: 1.05 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: 0.12 / ムービー #1: 0.12
最小 - 最大-0.18186775 - 0.47021329
平均 (標準偏差)0.00601077 (±0.04798295)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ360360360
Spacing360360360
セルA=B=C: 377.99997 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1820.4700.006

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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 : 80S ribosome bound to mRNA containing Kozak sequence and to one tRNA

全体名称: 80S ribosome bound to mRNA containing Kozak sequence and to one tRNA
要素
  • 試料: 80S ribosome bound to mRNA containing Kozak sequence and to one tRNA
  • 複合体: 80S ribosome
  • RNA: mRNA
  • RNA: transfer RNA

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超分子 #1000: 80S ribosome bound to mRNA containing Kozak sequence and to one tRNA

超分子名称: 80S ribosome bound to mRNA containing Kozak sequence and to one tRNA
タイプ: sample / ID: 1000 / 詳細: Sample was monodisperse. / Number unique components: 3
分子量実験値: 3.5 MDa

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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 / データベース: NCBI / Ribosome-details: ribosome-eukaryote: ALL
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母) / 別称: Yeast
分子量実験値: 3.5 MDa

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分子 #1: mRNA

分子名称: mRNA / タイプ: rna / ID: 1 / 分類: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 5 KDa
配列文字列:
AAAAAUGUAA AAAA

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分子 #2: transfer RNA

分子名称: transfer RNA / タイプ: rna / ID: 2 / Name.synonym: tRNA / 詳細: tRNA fmet / 分類: TRANSFER / Structure: OTHER / Synthetic?: No
由来(天然)生物種: Escherichia coli (大腸菌)
分子量理論値: 25 KDa

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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1.2 mg/mL
緩衝液pH: 7.5
詳細: 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2, 0.3 U/uL RNasin
凍結凍結剤: ETHANE / チャンバー内湿度: 95 % / 装置: FEI VITROBOT MARK II

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
日付2013年1月2日
撮影カテゴリ: CCD
フィルム・検出器のモデル: FEI FALCON I (4k x 4k)
デジタル化 - サンプリング間隔: 14 µm / 実像数: 4754 / 平均電子線量: 30 e/Å2 / ビット/ピクセル: 16
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系倍率（補正後）: 133333 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 0.01 mm / 最大 デフォーカス（公称値）: 4.844 µm / 最小 デフォーカス（公称値）: 1.159 µm / 倍率（公称値）: 133333
試料ステージ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

CTF補正詳細: CTFFIND3, FREALIGN per micrograph
最終 再構成アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 6.2 Å / 解像度の算出法: OTHER
ソフトウェア - 名称: EMAN2, IMAGIC, FREALIGN, RSAMPLE, CTFFIND3
使用した粒子像数: 25136

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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, CNS
詳細3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B.
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-3j77:
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA)

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原子モデル構築 2

初期モデルPDB ID:

3u5c
PDB 未公開エントリ

ソフトウェア名称: Chimera, CNS
詳細3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B.
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-3j77:
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA)

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原子モデル構築 3

初期モデルPDB ID:

3u5d
PDB 未公開エントリ

ソフトウェア名称: Chimera, CNS
詳細3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B.
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-3j77:
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA)

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原子モデル構築 4

初期モデルPDB ID:

3u5e
PDB 未公開エントリ

ソフトウェア名称: Chimera, CNS
詳細3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B.
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-3j77:
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA)

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原子モデル構築 5

初期モデルPDB ID:

4gd1
PDB 未公開エントリ


Chain - #0 - Chain ID: V / Chain - #1 - Chain ID: X
ソフトウェア名称: Chimera, CNS
詳細3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B.
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-3j77:
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA)

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原子モデル構築 6

初期モデルPDB ID:

3j3b
PDB 未公開エントリ

ソフトウェア名称: Chimera, CNS
詳細3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B.
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-3j77:
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA)

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  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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