+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13437 | ||||||||||||
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タイトル | Structure of the human CCAN CENP-A alpha-satellite complex | ||||||||||||
マップデータ | |||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 spindle attachment to meiosis I kinetochore / inner 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 / establishment of mitotic spindle orientation / chromosome, centromeric region ...spindle attachment to meiosis I kinetochore / inner 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 / establishment of mitotic spindle orientation / chromosome, centromeric region / mitotic cytokinesis / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / 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 / Resolution of Sister Chromatid Cohesion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNAメチル化 / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / chromosome segregation / RHO GTPases Activate Formins / HDACs deacetylate histones / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / 動原体 / PKMTs methylate histone lysines / RMTs methylate histone arginines / 遺伝的組換え / Pre-NOTCH Transcription and Translation / 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 / ヌクレオソーム / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic cell cycle / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / HATs acetylate histones / Processing of DNA double-strand break ends / midbody / antibacterial humoral response / 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 / 細胞分裂 / negative regulation of cell population proliferation / chromatin binding / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / 核質 / 生体膜 / identical protein binding 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: 2.68 Å | ||||||||||||
データ登録者 | Yatskevich S / Muir KW / Bellini D / Barford D | ||||||||||||
資金援助 | ドイツ, 3件
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引用 | ジャーナル: Science / 年: 2022 タイトル: Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome. 著者: Stanislau Yatskevich / Kyle W Muir / Dom Bellini / Ziguo Zhang / Jing Yang / Thomas Tischer / Masa Predin / Tom Dendooven / Stephen H McLaughlin / David Barford / 要旨: Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron ...Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron microscopy structures of the human inner kinetochore constitutive centromere associated network (CCAN) complex bound to CENP-A reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A, and a linker DNA segment of the α-satellite repeat emerges from the fully wrapped end of the nucleosome to thread through the central CENP-LN channel that tightly grips the DNA. The CENP-TWSX histone-fold module further augments DNA binding and partially wraps the linker DNA in a manner reminiscent of canonical nucleosomes. Our study suggests that the topological entrapment of the linker DNA by CCAN provides a robust mechanism by which kinetochores withstand both pushing and pulling forces exerted by the mitotic spindle. | ||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_13437.map.gz | 14.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13437-v30.xml emd-13437.xml | 18.8 KB 18.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_13437_fsc.xml | 13.6 KB | 表示 | FSCデータファイル |
画像 | emd_13437.png | 81.2 KB | ||
その他 | emd_13437_additional_1.map.gz | 170.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13437 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13437 | HTTPS FTP |
-関連構造データ
関連構造データ | 7piiMC 7pb4C 7pb8C 7pknC 7r5rC 7r5sC 7r5vC 7ywxC 7yyhC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_13437.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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: 0.831 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: #1
ファイル | emd_13437_additional_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : CENP-A nucleosome in complex with CENP-C
全体 | 名称: CENP-A nucleosome in complex with CENP-C |
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要素 |
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-超分子 #1: CENP-A nucleosome in complex with CENP-C
超分子 | 名称: CENP-A nucleosome in complex with CENP-C / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#7 |
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-分子 #1: Histone H3-like centromeric protein A
分子 | 名称: Histone H3-like centromeric protein A / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 16.02363 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV TLFPKDVQLA RRIRGLEEGL G |
-分子 #2: Histone H4
分子 | 名称: Histone H4 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 11.394426 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG |
-分子 #3: Histone H2A type 1-C
分子 | 名称: Histone H2A type 1-C / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 16.666334 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MGSSHHHHHH SPGLEVLFQG PRGMSGRGKQ GGKARAKAKS RSSRAGLQFP VGRVHRLLRK GNYAERVGAG APVYLAAVLE YLTAEILEL AGNAARDNKK TRIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK |
-分子 #4: Histone H2B type 1-C/E/F/G/I
分子 | 名称: Histone H2B type 1-C/E/F/G/I / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 13.937213 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK |
-分子 #7: Centromere protein C
分子 | 名称: Centromere protein C / タイプ: protein_or_peptide / ID: 7 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 61.943082 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MAASGLDHLK NGYRRRFCRP SRARDINTEQ GQNVLEILQD CFEEKSLAND FSTNSTKSVP NSTRKIKDTC IQSPSKECQK SHPKSVPVS SKKKEASLQF VVEPSEATNR SVQAHEVHQK ILATDVSSKN TPDSKKISSR NINDHHSEAD EEFYLSVGSP S VLLDAKTS ...文字列: MAASGLDHLK NGYRRRFCRP SRARDINTEQ GQNVLEILQD CFEEKSLAND FSTNSTKSVP NSTRKIKDTC IQSPSKECQK SHPKSVPVS SKKKEASLQF VVEPSEATNR SVQAHEVHQK ILATDVSSKN TPDSKKISSR NINDHHSEAD EEFYLSVGSP S VLLDAKTS VSQNVIPSSA QKRETYTFEN SVNMLPSSTE VSVKTKKRLN FDDKVMLKKI EIDNKVSDEE DKTSEGQERK PS GSSQNRI RDSEYEIQRQ AKKSFSTLFL ETVKRKSESS PIVRHAATAP PHSCPPDDTK LIEDEFIIDE SDQSFASRSW ITI PRKAGS LKQRTISPAE STALLQGRKS REKHHNILPK TLANDKHSHK PHPVETSQPS DKTVLDTSYA LIGETVNNYR STKY EMYSK NAEKPSRSKR TIKQKQRRKF MAKPAEEQLD VGQSKDENIH TSHITQDEFQ RNSDRNMEEH EEMGNDCVSK KQMPP VGSK KSSTRKDKEE SKKKRFSSES KNKLVPEEVT STVTKSRRIS RRPSDWWVVK SEESPVYSNS S |
-分子 #5: DNA (122-MER)
分子 | 名称: DNA (122-MER) / タイプ: dna / ID: 5 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 52.747801 KDa |
配列 | 文字列: (DC)(DT)(DA)(DC)(DA)(DA)(DA)(DA)(DA)(DG) (DA)(DG)(DT)(DG)(DT)(DT)(DT)(DC)(DA)(DA) (DA)(DA)(DC)(DT)(DG)(DC)(DT)(DC)(DT) (DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG)(DG)(DA) (DA) (DT)(DG)(DT)(DT)(DC) ...文字列: (DC)(DT)(DA)(DC)(DA)(DA)(DA)(DA)(DA)(DG) (DA)(DG)(DT)(DG)(DT)(DT)(DT)(DC)(DA)(DA) (DA)(DA)(DC)(DT)(DG)(DC)(DT)(DC)(DT) (DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG)(DG)(DA) (DA) (DT)(DG)(DT)(DT)(DC)(DA)(DA)(DC) (DT)(DC)(DT)(DG)(DT)(DG)(DA)(DG)(DT)(DT) (DG)(DA) (DA)(DT)(DG)(DC)(DA)(DA)(DT) (DC)(DA)(DT)(DC)(DA)(DC)(DA)(DA)(DA)(DG) (DA)(DA)(DG) (DT)(DT)(DT)(DC)(DT)(DG) (DA)(DG)(DA)(DA)(DT)(DG)(DC)(DT)(DT)(DC) (DT)(DG)(DT)(DT) (DT)(DA)(DG)(DT)(DT) (DT)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DA) (DG)(DA)(DT)(DA)(DT) (DT)(DC)(DC)(DC) (DG)(DT)(DT)(DT)(DC)(DC)(DA)(DA)(DC)(DG) (DA)(DA)(DG)(DG)(DC)(DC) (DT)(DC)(DA) (DA)(DA)(DG)(DC)(DG)(DG)(DT)(DC)(DC)(DA) (DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC) (DT)(DT)(DG)(DC)(DA)(DG)(DA)(DT)(DT) |
-分子 #6: DNA (123-MER)
分子 | 名称: DNA (123-MER) / タイプ: dna / ID: 6 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 52.800816 KDa |
配列 | 文字列: (DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DA)(DG) (DT)(DG)(DG)(DA)(DT)(DA)(DT)(DT)(DT)(DG) (DG)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DT) (DG)(DA)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DG) (DT) (DT)(DG)(DG)(DA)(DA) ...文字列: (DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DA)(DG) (DT)(DG)(DG)(DA)(DT)(DA)(DT)(DT)(DT)(DG) (DG)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DT) (DG)(DA)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DG) (DT) (DT)(DG)(DG)(DA)(DA)(DA)(DC)(DG) (DG)(DG)(DA)(DA)(DT)(DA)(DT)(DC)(DT)(DT) (DC)(DA) (DC)(DA)(DT)(DA)(DA)(DA)(DA) (DA)(DC)(DT)(DA)(DA)(DA)(DC)(DA)(DG)(DA) (DA)(DG)(DC) (DA)(DT)(DT)(DC)(DT)(DC) (DA)(DG)(DA)(DA)(DA)(DC)(DT)(DT)(DC)(DT) (DT)(DT)(DG)(DT) (DG)(DA)(DT)(DG)(DA) (DT)(DT)(DG)(DC)(DA)(DT)(DT)(DC)(DA)(DA) (DC)(DT)(DC)(DA)(DC) (DA)(DG)(DA)(DG) (DT)(DT)(DG)(DA)(DA)(DC)(DA)(DT)(DT)(DC) (DC)(DT)(DT)(DT)(DT)(DG) (DA)(DT)(DA) (DG)(DA)(DG)(DC)(DA)(DG)(DT)(DT)(DT)(DT) (DG)(DA)(DA)(DA)(DC)(DA)(DC) (DT)(DC) (DT)(DT)(DT)(DT)(DT)(DG)(DT)(DA)(DG) |
-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
緩衝液 | pH: 7.8 |
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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: GATAN K3 (6k x 4k) / 平均電子線量: 50.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |