- EMDB-4241: Cryo-EM structure of the core Centromere Binding Factor 3 complex -
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基本情報
登録情報
データベース: EMDB / ID: EMD-4241
タイトル
Cryo-EM structure of the core Centromere Binding Factor 3 complex
マップデータ
試料
複合体: The core Centromere Binding Factor 3 complex
タンパク質・ペプチド: Centromere DNA-binding protein complex CBF3 subunit B
タンパク質・ペプチド: Suppressor of kinetochore protein 1
タンパク質・ペプチド: Centromere DNA-binding protein complex CBF3 subunit C
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 / septin ring assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin ...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 / septin ring assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / centromeric DNA binding / regulation of exit from mitosis / Antigen processing: Ubiquitination & Proteasome degradation / kinetochore assembly / regulation of metabolic process / exit from mitosis / vacuolar acidification / positive regulation of glucose transmembrane transport / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / mitochondrial fusion / silent mating-type cassette heterochromatin formation / DNA binding, bending / SCF複合体 / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / mitotic spindle assembly checkpoint signaling / DNA replication origin binding / cullin family protein binding / subtelomeric heterochromatin formation / regulation of protein-containing complex assembly / 細胞内膜系 / negative regulation of cytoplasmic translation / regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / zinc ion binding / identical protein binding / 細胞核 / 細胞質 類似検索 - 分子機能
Centromere DNA-binding protein complex CBF3 subunit C / Centromere DNA-binding protein complex CBF3 subunit B / Suppressor of kinetochore protein 1 類似検索 - 構成要素
Biotechnology and Biological Sciences Research Council
BB/J007595/1
英国
引用
ジャーナル: Cell Rep / 年: 2018 タイトル: Insights into Centromere DNA Bending Revealed by the Cryo-EM Structure of the Core Centromere Binding Factor 3 with Ndc10. 著者: Wenjuan Zhang / Natalya Lukoyanova / Shomon Miah / Jonathan Lucas / Cara K Vaughan / 要旨: The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the ...The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the kinetochore in these organisms, as it facilitates genetic centromere specification and allows association of all other kinetochore components. We determined high-resolution structures of the core complex of CBF3 alone and in association with a monomeric construct of Ndc10, using cryoelectron microscopy (cryo-EM). We identify the DNA-binding site of the complex and present a model in which CBF3 induces a tight bend in centromeric DNA, thus facilitating assembly of the centromeric nucleosome.
タンパク質・ペプチド: Centromere DNA-binding protein complex CBF3 subunit B
タンパク質・ペプチド: Suppressor of kinetochore protein 1
タンパク質・ペプチド: Centromere DNA-binding protein complex CBF3 subunit C
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超分子 #1: The core Centromere Binding Factor 3 complex
超分子
名称: The core Centromere Binding Factor 3 complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: The core CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, and full length Skp1 and Ctf13 components.
由来(天然)
生物種: Saccharomyces cerevisiae (パン酵母)
組換発現
生物種: Saccharomyces cerevisiae (パン酵母)
分子量
理論値: 220 KDa
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分子 #1: Centromere DNA-binding protein complex CBF3 subunit B
分子
名称: Centromere DNA-binding protein complex CBF3 subunit B タイプ: protein_or_peptide / ID: 1 / 詳細: Model is numbered according to / コピー数: 2 / 光学異性体: LEVO
クラス数: 4 / 平均メンバー数/クラス: 17348 / ソフトウェア - 名称: RELION (ver. 2.0) 詳細: The automatically picked particles were screened manually followed by reference-free 2D classification, which yielded 69,392 particles for subsequent 3D classification.
使用したクラス数: 4 / 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2.0) 詳細: 3D auto-refinement of all the good particles from 2D classification, provided a reconstruction at 4.7 angstrom overall resolution. After post-process by RELION and sharpened by a negative B- ...詳細: 3D auto-refinement of all the good particles from 2D classification, provided a reconstruction at 4.7 angstrom overall resolution. After post-process by RELION and sharpened by a negative B-factor using an automated procedure resulting in a 4.1 angstrom reconstruction. 使用した粒子像数: 69392
詳細
The selected images were high-pass filtered and normalized.
Image processing ID
1
Image recording ID
1
FSC曲線 (解像度の算出)
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画像解析 #2
粒子像選択
選択した数: 289281
CTF補正
ソフトウェア - 名称: CTFFIND (ver. 4.0) ソフトウェア - 詳細: CTF parameters were estimated using CTFFIND4
初期モデル
モデルのタイプ: OTHER 詳細: An ovoid generated from SPIDER was used as an initial model for 3D classification.
クラス数: 3 / 平均メンバー数/クラス: 94038 / ソフトウェア - 名称: RELION (ver. 2.0) 詳細: After joining the two dataset of selection from 2D classification , 282,116 particles were input to 3D classification using an initial 3D reference obtained by low pass-filtering the ...詳細: After joining the two dataset of selection from 2D classification , 282,116 particles were input to 3D classification using an initial 3D reference obtained by low pass-filtering the reconstruction of map from the first dataset, resulting two best 3D classes, which in total contain 67 percent of the whole particles.
使用したクラス数: 2 / 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: FOURIER SPACE / 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 / ソフトウェア - 名称: RELION (ver. 2.0) 詳細: 187, 606 particles were in the best two 3D classes. 3D auto-refinement of the 3D joined classes against the corresponding particles resulted in a final reconstruction. 使用した粒子像数: 187606
詳細
The selected images were high-pass filtered and normalized.