+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5g5p | ||||||
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タイトル | Structure of the Saccharomyces cerevisiae TREX-2 complex | ||||||
要素 |
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キーワード | TRANSPORT PROTEIN / MRNA / MRNA EXPORT | ||||||
機能・相同性 | 機能・相同性情報 actin filament-based process / cellular bud site selection / SAGA complex localization to transcription regulatory region / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / maintenance of DNA trinucleotide repeats / filamentous growth / proteasome regulatory particle, lid subcomplex ...actin filament-based process / cellular bud site selection / SAGA complex localization to transcription regulatory region / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / maintenance of DNA trinucleotide repeats / filamentous growth / proteasome regulatory particle, lid subcomplex / mRNA 3'-end processing / poly(A)+ mRNA export from nucleus / proteasome storage granule / proteasome assembly / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / protein folding chaperone / protein export from nucleus / proteasome complex / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / ribosomal small subunit biogenesis / nuclear envelope / mitotic cell cycle / double-stranded DNA binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / regulation of cell cycle / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | SACCHAROMYCES CEREVISIAE (パン酵母) | ||||||
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: 5.3 Å | ||||||
データ登録者 | Aibara, S. / Bai, X.C. / Stewart, M. | ||||||
引用 | ジャーナル: J Struct Biol / 年: 2016 タイトル: The Sac3 TPR-like region in the Saccharomyces cerevisiae TREX-2 complex is more extensive but independent of the CID region. 著者: Shintaro Aibara / Xiao-Chen Bai / Murray Stewart / 要旨: Transcription-export complex 2 (TREX-2 complex) facilitates the localization of actively transcribing genes to the nuclear periphery and also functions to contribute to the generation of export- ...Transcription-export complex 2 (TREX-2 complex) facilitates the localization of actively transcribing genes to the nuclear periphery and also functions to contribute to the generation of export-competent mRNPs through interactions with the general mRNA nuclear export factor Mex67:Mtr2. The TREX-2 complex is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31, and Sus1 bind. TREX-2 can be subdivided into two modules: one, in which Thp1 and Sem1 bind to the Sac3(M) region (residues ∼100-551), and the other in which Cdc31 and two Sus1 chains bind to the Sac3(CID) region (residues ∼710-805). Complementary structural analyses using X-ray crystallography, electron microscopy, and small-angle X-ray scattering of the Saccharomyces cerevisiae TREX-2 complex, expressed using Baculovirus-infected Sf9 cells, have indicated that the TPR-like repeats of the Sac3(M) region extend considerably further towards the N-terminus than previously thought, and also indicate that this region and Sac3(CID):Sus1:Cdc31 region of the S. cerevisiae complex are structurally independent. Although the density visible accounted for only ∼100kDa, a 5.3Å resolution cryo-EM reconstruction was obtained of the M-region of TREX-2 that showed an additional three putative α-helices extending towards the Sac3 N-terminus and these helices were also seen in a 4.9Å resolution structure obtained by X-ray crystallography. SUMMARY STATEMENT: We describe the expression, purification and structural characterization of the S. cerevisiae TREX-2 complex and demonstrate that the Sac3 TPR-like repeats are more extensive than ...SUMMARY STATEMENT: We describe the expression, purification and structural characterization of the S. cerevisiae TREX-2 complex and demonstrate that the Sac3 TPR-like repeats are more extensive than previously thought and that the M- and CID-regions do not appear to have a defined spatial orientation. | ||||||
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 | 5g5p.cif.gz | 220.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5g5p.ent.gz | 150.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5g5p.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 | 5g5p_validation.pdf.gz | 748.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5g5p_full_validation.pdf.gz | 755.8 KB | 表示 | |
XML形式データ | 5g5p_validation.xml.gz | 27.9 KB | 表示 | |
CIF形式データ | 5g5p_validation.cif.gz | 40.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/g5/5g5p ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g5p | 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: タンパク質 | 分子量: 93213.320 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) SACCHAROMYCES CEREVISIAE (パン酵母) プラスミド: PACEBACRZ / 細胞株 (発現宿主): SF9 発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ) 参照: UniProt: P46674 | ||
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#2: タンパク質 | 分子量: 52734.820 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) SACCHAROMYCES CEREVISIAE (パン酵母) プラスミド: PACEBACRZ / 細胞株 (発現宿主): SF9 発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ) 参照: UniProt: Q08231 | ||
#3: タンパク質 | 分子量: 10397.102 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) SACCHAROMYCES CEREVISIAE (パン酵母) プラスミド: PACEBACRZ / 細胞株 (発現宿主): SF9 発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ) 参照: UniProt: O94742 | ||
#4: タンパク質 | 分子量: 68527.133 Da / 分子数: 3 / 由来タイプ: 組換発現 / 詳細: CHAINS D, F AND E ARE MODELLED AS POLYALA 由来: (組換発現) SACCHAROMYCES CEREVISIAE (パン酵母) プラスミド: PACEBACRZ / 細胞株 (発現宿主): SF9 発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ) 配列の詳細 | CHAINS D, E AND F ARE BUILT AS POLYALA DUE TO RESOLUTION | |
-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: Sac3 in complex with Thp1 and Sem1 / タイプ: COMPLEX / Oligomeric details: One heterotrimer / 由来: MULTIPLE SOURCES |
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分子量 | 値: 0.19 MDa / 実験値: NO |
緩衝液 | 名称: 20 MM HEPES, 300 MM NACL, 5 MM DTT / pH: 8 / 詳細: 20 mM HEPES, 300 mM NaCl, 5 mM DTT |
試料 | 濃度: 0.015 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: OTHER |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / Temp: 85 K / 湿度: 100 % / 詳細: LIQUID ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2015年11月3日 |
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): 81000 X / 倍率(補正後): 35714 X / 最大 デフォーカス(公称値): 4500 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 / 最高温度: 90 K / 最低温度: 80 K |
撮影 | 電子線照射量: 40 e/Å2 フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) |
画像スキャン | デジタル画像の数: 496 |
-解析
EMソフトウェア | 名称: RELION / カテゴリ: 3次元再構成 | ||||||||||||
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粒子像の選択 | 詳細: The particles were processed using Relion | ||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 解像度: 5.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 81559 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / 対称性のタイプ: POINT | ||||||||||||
精密化 | 最高解像度: 5.3 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 5.3 Å
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