+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10156 | |||||||||
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タイトル | Class 2B : CENP-A nucleosome in complex with CENP-C central region | |||||||||
マップデータ | Class 2B : CENP-A nucleosome in complex with CENP-C central region | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 spindle attachment to meiosis I kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / inner kinetochore / establishment of mitotic spindle orientation / mitotic cytokinesis ...spindle attachment to meiosis I kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / inner kinetochore / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Resolution of Sister Chromatid Cohesion / telomere organization / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / chromosome segregation / HDACs deacetylate histones / RHO GTPases Activate Formins / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / kinetochore / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / mitotic cell cycle / RUNX1 regulates transcription of genes involved in differentiation of HSCs / antibacterial humoral response / HATs acetylate histones / Processing of DNA double-strand break ends / midbody / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / cell division / chromatin binding / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
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 | Ali-Ahmad A / Bilokapic S / Halic M / Sekulic N | |||||||||
資金援助 | ノルウェー, ドイツ, 2件
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引用 | ジャーナル: EMBO Rep / 年: 2019 タイトル: CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail. 著者: Ahmad Ali-Ahmad / Silvija Bilokapić / Ingmar B Schäfer / Mario Halić / Nikolina Sekulić / 要旨: Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is ...Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is considered to be a central organizer of the CCAN. We provide new molecular insights into the structure of human CENP-A nucleosomes, in isolation and in complex with the CENP-C central region (CENP-C ), the main CENP-A binding module of human CENP-C. We establish that the short αN helix of CENP-A promotes DNA flexibility at the nucleosome ends, independently of the sequence it wraps. Furthermore, we show that, in vitro, two regions of human CENP-C (CENP-C and CENP-C ) both bind exclusively to the CENP-A nucleosome. We find CENP-C to bind with high affinity due to an extended hydrophobic area made up of CENP-A and CENP-A . Importantly, we identify two key conformational changes within the CENP-A nucleosome upon CENP-C binding. First, the loose DNA wrapping of CENP-A nucleosomes is further exacerbated, through destabilization of the H2A C-terminal tail. Second, CENP-C rigidifies the N-terminal tail of H4 in the conformation favoring H4 monomethylation, essential for a functional centromere. | |||||||||
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_10156.map.gz | 13.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10156-v30.xml emd-10156.xml | 10.3 KB 10.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_10156.png | 95.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10156 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10156 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10156_validation.pdf.gz | 264.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10156_full_validation.pdf.gz | 263.6 KB | 表示 | |
XML形式データ | emd_10156_validation.xml.gz | 5.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10156 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10156 | 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_10156.map.gz / 形式: CCP4 / 大きさ: 18.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Class 2B : CENP-A nucleosome in complex with CENP-C central region | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.3 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 : Class 2B : CENP-A nucleosome in complex with CENP-C central region
全体 | 名称: Class 2B : CENP-A nucleosome in complex with CENP-C central region |
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要素 |
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-超分子 #2: Class 2B : CENP-A nucleosome in complex with CENP-C central region
超分子 | 名称: Class 2B : CENP-A nucleosome in complex with CENP-C central region タイプ: complex / ID: 2 / 親要素: 0 / 含まれる分子: #1-#6 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli (大腸菌) |
-分子 #1: CENP-A nucleosome
分子 | 名称: CENP-A nucleosome / タイプ: other / ID: 1 / 分類: other |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSR LAREICVKFT RGVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV T LFPKDVQL ARRIRGLEEG LG MSGRGKG GKGLGKGGAK RHRKVLRDNI ...文字列: MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSR LAREICVKFT RGVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV T LFPKDVQL ARRIRGLEEG LG MSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMDV VYALKRQGRT LYGFGG GPL GMSGRGKQGG KARAKAKSRS SRAGLQFPVG RVHRLLRKGN YAERVGAGAP VYMAAVLEYL TAEILELAGN AARDNKKTRI IPRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K MPEPAKSA PAPKKGSKKA VTKAQKKDGK KRKRSRKESY SVYVYKVLKQ VHPDTGISSK AMGIMNSFVN DIFERIAGEA SRLAHYNKRS TITSREIQTA VRLLLPGELA KHAVSEGTKA VTKYTSSK A TCAGAATCCC GGTGCCGAGG CCGCTCAATT GGTCGTAGAC AGCTCTAGCA CCGCTTAAAC GCACGTACGC GCTGTCCCCC GCGTTTTAAC CGCCAAGGGG ATTACTCCCT AGTCTCCAGG CACGTGTCAG ATATATACAT CGAT ATCGA TGTATATATC TGACACGTGC CTGGAGACTA GGGAGTAATC CCCTTGGCGG TTAAAACGCG GGGGACAGCG CGTACGTGCG TTTAAGCGGT GCTAGAGCTG TCTACGACCA ATTGAGCGGC CTCGGCACCG GGATTCTGAT |
組換発現 | 生物種: Escherichia coli (大腸菌) |
-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 | 1.2 mg/mL |
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緩衝液 | pH: 7.5 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 100.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 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: 84000 |
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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 |