+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17227 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. | |||||||||||||||
マップデータ | ||||||||||||||||
試料 |
| |||||||||||||||
キーワード | kinetochore / point centromere / CENP-A nucleosome / topological entrapment / centromeric DNA / CELL CYCLE | |||||||||||||||
機能・相同性 | 機能・相同性情報 Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / RAVE complex / Iron uptake and transport ...Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / RAVE complex / Iron uptake and transport / CBF3 complex / HDMs demethylate histones / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / PKMTs methylate histone lysines / Mis6-Sim4 complex / vacuolar proton-transporting V-type ATPase complex assembly / centromere complex assembly / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / septin ring assembly / ascospore formation / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / attachment of spindle microtubules to kinetochore / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / centromeric DNA binding / Assembly of the ORC complex at the origin of replication / CENP-A containing chromatin assembly / HDACs deacetylate histones / regulation of exit from mitosis / outer kinetochore / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / kinetochore assembly / condensed chromosome, centromeric region / regulation of metabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to kinetochore / replication fork protection complex / spindle pole body / positive regulation of glucose transmembrane transport / protein neddylation / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / postreplication repair / SUMOylation of chromatin organization proteins / mitotic intra-S DNA damage checkpoint signaling / vacuolar acidification / silent mating-type cassette heterochromatin formation / mitochondrial fusion / exit from mitosis / DNA binding, bending / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / positive regulation of transcription by RNA polymerase I / mitotic spindle assembly checkpoint signaling / Orc1 removal from chromatin / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / mitotic sister chromatid segregation / DNA replication origin binding / cullin family protein binding / Estrogen-dependent gene expression / Antigen processing: Ubiquitination & Proteasome degradation / rRNA transcription / chromosome, centromeric region / subtelomeric heterochromatin formation / DNA replication initiation / regulation of protein-containing complex assembly / heterochromatin organization / Ub-specific processing proteases / endomembrane system / protein localization to CENP-A containing chromatin / negative regulation of cytoplasmic translation / CENP-A containing nucleosome / nucleosomal DNA binding / regulation of mitotic cell cycle / meiotic cell cycle / chromosome segregation / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / G1/S transition of mitotic cell cycle / structural constituent of chromatin / G2/M transition of mitotic cell cycle / nucleosome / nucleosome assembly / chromatin organization / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / chromosome, telomeric region / protein dimerization activity 類似検索 - 分子機能 | |||||||||||||||
生物種 | Saccharomyces cerevisiae (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: 3.7 Å | |||||||||||||||
データ登録者 | Dendooven TD / Zhang Z / Yang J / McLaughlin S / Schwabb J / Scheres S / Yatskevich S / Barford D | |||||||||||||||
資金援助 | 英国, ドイツ, 4件
| |||||||||||||||
引用 | ジャーナル: Sci Adv / 年: 2023 タイトル: Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere. 著者: Tom Dendooven / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / Johannes Schwab / Sjors H W Scheres / Stanislau Yatskevich / David Barford / 要旨: The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) ...The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) complex and the microtubule-binding outer kinetochore KNL1-MIS12-NDC80 (KMN) network. The budding yeast inner kinetochore also contains the DNA binding centromere-binding factor 1 (CBF1) and CBF3 complexes. We determined the cryo-electron microscopy structure of the yeast inner kinetochore assembled onto the centromere-specific centromere protein A nucleosomes (CENP-A). This revealed a central CENP-A with extensively unwrapped DNA ends. These free DNA duplexes bind two CCAN protomers, one of which entraps DNA topologically, positioned on the centromere DNA element I (CDEI) motif by CBF1. The two CCAN protomers are linked through CBF3 forming an arch-like configuration. With a structural mechanism for how CENP-A can also be linked to KMN involving only CENP-QU, we present a model for inner kinetochore assembly onto a point centromere and how it organizes the outer kinetochore for chromosome attachment to the mitotic spindle. | |||||||||||||||
履歴 |
|
-構造の表示
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_17227.map.gz | 96.9 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-17227-v30.xml emd-17227.xml | 46.9 KB 46.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_17227.png | 83.3 KB | ||
その他 | emd_17227_additional_1.map.gz emd_17227_half_map_1.map.gz emd_17227_half_map_2.map.gz | 29.6 MB 131.5 MB 131.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17227 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17227 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_17227_validation.pdf.gz | 936.6 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_17227_full_validation.pdf.gz | 936.1 KB | 表示 | |
XML形式データ | emd_17227_validation.xml.gz | 14.5 KB | 表示 | |
CIF形式データ | emd_17227_validation.cif.gz | 17 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17227 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17227 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_17227.map.gz / 形式: CCP4 / 大きさ: 166.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.08 Å | ||||||||||||||||||||
密度 |
| ||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-追加マップ: #1
ファイル | emd_17227_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_17227_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_17227_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : A complex of CBF1-CCAN bound to centromeric C0N3 DNA
+超分子 #1: A complex of CBF1-CCAN bound to centromeric C0N3 DNA
+分子 #1: Centromere-binding protein 1
+分子 #2: Inner kinetochore subunit CTF3
+分子 #3: Inner kinetochore subunit MCM22
+分子 #4: Inner kinetochore subunit MCM16
+分子 #5: Inner kinetochore subunit IML3
+分子 #6: Inner kinetochore subunit CHL4
+分子 #7: Centromere DNA-binding protein complex CBF3 subunit C
+分子 #8: Centromere DNA-binding protein complex CBF3 subunit B
+分子 #9: Suppressor of kinetochore protein 1
+分子 #10: Inner kinetochore subunit CTF19
+分子 #11: Inner kinetochore subunit OKP1
+分子 #12: Inner kinetochore subunit MCM21
+分子 #13: Inner kinetochore subunit CNN1
+分子 #14: Inner kinetochore subunit AME1
+分子 #15: Inner kinetochore subunit WIP1
+分子 #16: Inner kinetochore subunit NKP1
+分子 #17: Inner kinetochore subunit NKP2
+分子 #20: Histone H4
+分子 #21: Histone H2B.1
+分子 #22: Histone H3-like centromeric protein CSE4
+分子 #23: Histone H2A.1
+分子 #18: C0N3
+分子 #19: C0N3
-実験情報
-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 |
-試料調製
緩衝液 | pH: 8 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 40.0 e/Å2 |
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: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.6 µm / 最小 デフォーカス(公称値): 1.0 µm |
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: NONE |
---|---|
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 108672 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |