+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0476 | |||||||||
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タイトル | Cryo-EM structure of NLRP3 bound to NEK7 | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Inflammasome / Activator / Biological process Immunity / Inflammatory response / Innate immunity / Transcription / Transcription regulation Ligand / ATP binding / Nucleotide binding / IMMUNE SYSTEM | |||||||||
機能・相同性 | 機能・相同性情報 NEK6-subfamily protein kinase / regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / molecular sensor activity / detection of biotic stimulus / eukaryotic translation initiation factor 2alpha kinase activity / cysteine-type endopeptidase activator activity / response to interferon-alpha / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation ...NEK6-subfamily protein kinase / regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / molecular sensor activity / detection of biotic stimulus / eukaryotic translation initiation factor 2alpha kinase activity / cysteine-type endopeptidase activator activity / response to interferon-alpha / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / NLRP3 inflammasome complex / Activation of NIMA Kinases NEK9, NEK6, NEK7 / negative regulation of osteoblast proliferation / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / osmosensory signaling pathway / regulation of hematopoietic progenitor cell differentiation / positive regulation of type 2 immune response / cellular response to potassium ion / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / Nuclear Pore Complex (NPC) Disassembly / peptidoglycan binding / pattern recognition receptor signaling pathway / SUMOylation of immune response proteins / regulation of hematopoietic stem cell differentiation / regulation of hematopoietic stem cell proliferation / negative regulation of non-canonical NF-kappaB signal transduction / phosphatidylinositol-4-phosphate binding / microtubule organizing center / negative regulation of interleukin-1 beta production / negative regulation of viral genome replication / positive regulation of NLRP3 inflammasome complex assembly / pyroptotic inflammatory response / positive regulation of interleukin-4 production / : / negative regulation of acute inflammatory response / positive regulation of telomere capping / The NLRP3 inflammasome / protein maturation / spindle assembly / Purinergic signaling in leishmaniasis infection / signaling adaptor activity / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / antiviral innate immune response / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / positive regulation of telomere maintenance via telomerase / cellular response to amino acid starvation / positive regulation of interleukin-1 beta production / molecular function activator activity / positive regulation of cytokine production / molecular condensate scaffold activity / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / ADP binding / response to virus / protein homooligomerization / PKR-mediated signaling / Cytoprotection by HMOX1 / cellular response to virus / Evasion by RSV of host interferon responses / Metalloprotease DUBs / ISG15 antiviral mechanism / defense response / negative regulation of inflammatory response / spindle pole / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / Interferon alpha/beta signaling / positive regulation of NF-kappaB transcription factor activity / kinase activity / protein-macromolecule adaptor activity / cellular response to lipopolysaccharide / defense response to virus / DNA-binding transcription factor binding / microtubule / protein autophosphorylation / sequence-specific DNA binding / positive regulation of MAPK cascade / molecular adaptor activity / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / ribosome / inflammatory response / protein phosphorylation / translation / negative regulation of cell population proliferation / Golgi membrane / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / negative regulation of apoptotic process 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: 3.8 Å | |||||||||
データ登録者 | Sharif H / Wang L / Wu H | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome. 著者: Humayun Sharif / Li Wang / Wei Li Wang / Venkat Giri Magupalli / Liudmila Andreeva / Qi Qiao / Arthur V Hauenstein / Zhaolong Wu / Gabriel Núñez / Youdong Mao / Hao Wu / 要旨: The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation ...The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation of the NLRP3 inflammasome in interphase. Here we report a cryo-electron microscopy structure of inactive human NLRP3 in complex with NEK7, at a resolution of 3.8 Å. The earring-shaped NLRP3 consists of curved leucine-rich-repeat and globular NACHT domains, and the C-terminal lobe of NEK7 nestles against both NLRP3 domains. Structural recognition between NLRP3 and NEK7 is confirmed by mutagenesis both in vitro and in cells. Modelling of an active NLRP3-NEK7 conformation based on the NLRC4 inflammasome predicts an additional contact between an NLRP3-bound NEK7 and a neighbouring NLRP3. Mutations to this interface abolish the ability of NEK7 or NLRP3 to rescue NLRP3 activation in NEK7-knockout or NLRP3-knockout cells. These data suggest that NEK7 bridges adjacent NLRP3 subunits with bipartite interactions to mediate the activation of the NLRP3 inflammasome. | |||||||||
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_0476.map.gz | 48.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0476-v30.xml emd-0476.xml | 15.7 KB 15.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0476_fsc.xml | 8.6 KB | 表示 | FSCデータファイル |
画像 | emd_0476.png | 150.3 KB | ||
Filedesc metadata | emd-0476.cif.gz | 6.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0476 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0476 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0476_validation.pdf.gz | 523 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0476_full_validation.pdf.gz | 522.6 KB | 表示 | |
XML形式データ | emd_0476_validation.xml.gz | 10.4 KB | 表示 | |
CIF形式データ | emd_0476_validation.cif.gz | 13.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0476 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0476 | 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_0476.map.gz / 形式: CCP4 / 大きさ: 52.7 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: 0.84 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 : NL3-NEK7
全体 | 名称: NL3-NEK7 |
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要素 |
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-超分子 #1: NL3-NEK7
超分子 | 名称: NL3-NEK7 / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #2 |
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-超分子 #2: NLRP3
超分子 | 名称: NLRP3 / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 詳細: The sequence is according to NP_001230062.1 isoform which lacks 2 residues from N-terminus. Total residues are 1034aa as compared to 1036 in UNP Q96P20. There are mutations in YRKKYRKY ...詳細: The sequence is according to NP_001230062.1 isoform which lacks 2 residues from N-terminus. Total residues are 1034aa as compared to 1036 in UNP Q96P20. There are mutations in YRKKYRKY instead its IYCAKYRAY mutations were intended to introduce so that the class of MBP and NLRP3 is avoided |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-超分子 #3: NEK7
超分子 | 名称: NEK7 / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: NACHT, LRR and PYD domains-containing protein 3
分子 | 名称: NACHT, LRR and PYD domains-containing protein 3 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 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: 117.890984 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MASTRCKLAR YLEDLEDVDL KKFKMHLEDY PPQKGCIPLP RGQTEKADHV DLATLMIDFN GEEKAWAMAV WIFAAINRRD LYEKAKRDE PKWGSDNARV SNPTVICQED SIEEEWMGLL EYLSRISICK MKKIYCAKYR AYVRSRFQCI EDRNARLGES V SLNKRYTR ...文字列: MASTRCKLAR YLEDLEDVDL KKFKMHLEDY PPQKGCIPLP RGQTEKADHV DLATLMIDFN GEEKAWAMAV WIFAAINRRD LYEKAKRDE PKWGSDNARV SNPTVICQED SIEEEWMGLL EYLSRISICK MKKIYCAKYR AYVRSRFQCI EDRNARLGES V SLNKRYTR LRLIKEHRSQ QEREQELLAI GKTKTCESPV SPIKMELLFD PDDEHSEPVH TVVFQGAAGI GKTILARKMM LD WASGTLY QDRFDYLFYI HCREVSLVTQ RSLGDLIMSC CPDPNPPIHK IVRKPSRILF LMDGFDELQG AFDEHIGPLC TDW QKAERG DILLSSLIRK KLLPEASLLI TTRPVALEKL QHLLDHPRHV EILGFSEAKR KEYFFKYFSD EAQARAAFSL IQEN EVLFT MCFIPLVCWI VCTGLKQQME SGKSLAQTSK TTTAVYVFFL SSLLQPRGGS QEHGLCAHLW GLCSLAADGI WNQKI LFEE SDLRNHGLQK ADVSAFLRMN LFQKEVDCEK FYSFIHMTFQ EFFAAMYYLL EEEKEGRTNV PGSRLKLPSR DVTVLL ENY GKFEKGYLIF VVRFLFGLVN QERTSYLEKK LSCKISQQIR LELLKWIEVK AKAKKLQIQP SQLELFYCLY EMQEEDF VQ RAMDYFPKIE INLSTRMDHM VSSFCIENCH RVESLSLGFL HNMPKEEEEE EKEGRHLDMV QCVLPSSSHA ACSHGLVN S HLTSSFCRGL FSVLSTSQSL TELDLSDNSL GDPGMRVLCE TLQHPGCNIR RLWLGRCGLS HECCFDISLV LSSNQKLVE LDLSDNALGD FGIRLLCVGL KHLLCNLKKL WLVSCCLTSA CCQDLASVLS TSHSLTRLYV GENALGDSGV AILCEKAKNP QCNLQKLGL VNSGLTSVCC SALSSVLSTN QNLTHLYLRG NTLGDKGIKL LCEGLLHPDC KLQVLELDNC NLTSHCCWDL S TLLTSSQS LRKLSLGNND LGDLGVMMFC EVLKQQSCLL QNLGLSEMYF NYETKSALET LQEEKPELTV VFEPSW UniProtKB: NACHT, LRR and PYD domains-containing protein 3 |
-分子 #2: Protein kinase R,Serine/threonine-protein kinase Nek7
分子 | 名称: Protein kinase R,Serine/threonine-protein kinase Nek7 タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO / EC番号: non-specific serine/threonine protein kinase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 32.01515 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: GSTDKRFGMD FRIEKKIGRG QFSEVYRAAC RLDGKTVALK KVQIFDLMDA KARADCIKEI DLLAQLNHPN VIKYYVCFIT GNELNIVLE LADAGDLSRM IKHFKKQKRL IPERTVWKYF VQLCSALEHM HSRRVMHRDI KPANVFITAT GVVKLGDLGL G RFFSSKTT ...文字列: GSTDKRFGMD FRIEKKIGRG QFSEVYRAAC RLDGKTVALK KVQIFDLMDA KARADCIKEI DLLAQLNHPN VIKYYVCFIT GNELNIVLE LADAGDLSRM IKHFKKQKRL IPERTVWKYF VQLCSALEHM HSRRVMHRDI KPANVFITAT GVVKLGDLGL G RFFSSKTT AAHSLVGTPY YMSPERIHEN GYNFKSDIWS LGCLLYEMAA LQSPFYGDKM NLYSLCKKIE QCDYPPLPSD HY SEELRQL VNMCINPDPE KRPDVTYVYD VAKRMHACTA SS UniProtKB: Interferon-induced, double-stranded RNA-activated protein kinase, Serine/threonine-protein kinase Nek7 |
-分子 #3: ADENOSINE-5'-DIPHOSPHATE
分子 | 名称: ADENOSINE-5'-DIPHOSPHATE / タイプ: ligand / ID: 3 / コピー数: 1 / 式: ADP |
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分子量 | 理論値: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-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: 7.5 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.1 K / 装置: FEI VITROBOT MARK II |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 55.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: OTHER / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): -3.0 µm / 最小 デフォーカス(公称値): -1.0 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-6npy: |