+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0095 | |||||||||
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タイトル | Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore | |||||||||
マップデータ | CBF3-core-Ndc10-DBD | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly / mitotic spindle elongation ...RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly / mitotic spindle elongation / centromeric DNA binding / regulation of exit from mitosis / Antigen processing: Ubiquitination & Proteasome degradation / vacuolar acidification / kinetochore assembly / condensed chromosome, centromeric region / regulation of metabolic process / exit from mitosis / spindle pole body / positive regulation of glucose transmembrane transport / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / mitochondrial fusion / DNA binding, bending / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF複合体 / mitotic spindle assembly checkpoint signaling / DNA replication origin binding / regulation of mitotic cell cycle / cullin family protein binding / subtelomeric heterochromatin formation / regulation of protein-containing complex assembly / spindle midzone / 細胞内膜系 / negative regulation of cytoplasmic translation / chromosome segregation / G1/S transition of mitotic cell cycle / spindle / 動原体 / G2/M transition of mitotic cell cycle / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / chromosome, telomeric region / protein ubiquitination / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA binding / zinc ion binding / identical protein binding / 細胞核 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288C (パン酵母) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | |||||||||
データ登録者 | Yan K / Zhang Z / Yang J / McLaughlin SH / Barford D | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2018 タイトル: Architecture of the CBF3-centromere complex of the budding yeast kinetochore. 著者: Kaige Yan / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / David Barford / 要旨: Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into ...Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are associated with the centromere-specific nucleosome Cse4. Deposition of Cse4 at CEN loci is dependent on the CBF3 complex that engages CDEIII to direct Cse4 nucleosomes to CDEII. To understand how CBF3 recognizes CDEIII and positions Cse4, we determined a cryo-EM structure of a CBF3-CEN complex. CBF3 interacts with CEN DNA as a head-to-head dimer that includes the whole of CDEIII and immediate 3' regions. Specific CEN-binding of CBF3 is mediated by a Cep3 subunit of one of the CBF3 protomers that forms major groove interactions with the conserved and essential CCG and TGT motifs of CDEIII. We propose a model for a CBF3-Cse4-CEN complex with implications for understanding CBF3-directed deposition of the Cse4 nucleosome at CEN loci. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_0095.map.gz | 2.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0095-v30.xml emd-0095.xml | 18.4 KB 18.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0095.png | 30.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0095 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0095 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_0095.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | CBF3-core-Ndc10-DBD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : CBF3-core-Ndc10-DBD complex
+超分子 #1: CBF3-core-Ndc10-DBD complex
+分子 #1: Centromere DNA-binding protein complex CBF3 subunit B
+分子 #2: Centromere DNA-binding protein complex CBF3 subunit C
+分子 #3: Centromere DNA-binding protein complex CBF3 subunit B
+分子 #4: Suppressor of kinetochore protein 1
+分子 #5: Centromere DNA-binding protein complex CBF3 subunit A
+分子 #6: METHIONINE
+分子 #7: PHENYLALANINE
+分子 #8: ASPARAGINE
+分子 #9: ARGININE
+分子 #10: THREONINE
+分子 #11: GLUTAMINE
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.4 mg/mL |
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緩衝液 | pH: 8 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: COUNTING / 平均電子線量: 27.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: OTHER / 詳細: Initial model was from SIMPLE_PRIME. |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 73894 |
-原子モデル構築 1
精密化 | プロトコル: OTHER |
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得られたモデル | PDB-6gyp: |