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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 | |||||||||
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![]() | Inflammasome / Activator / Biological process Immunity / Inflammatory response / Innate immunity / Transcription / Transcription regulation Ligand / ATP binding / Nucleotide binding / IMMUNE SYSTEM | |||||||||
機能・相同性 | ![]() NEK6-subfamily protein kinase / regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / small molecule sensor activity / detection of biotic stimulus / eukaryotic translation initiation factor 2alpha kinase activity / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / response to interferon-alpha / positive regulation of T-helper 2 cell differentiation ...NEK6-subfamily protein kinase / regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / small molecule sensor activity / detection of biotic stimulus / eukaryotic translation initiation factor 2alpha kinase activity / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / response to interferon-alpha / positive regulation of T-helper 2 cell differentiation / 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 / regulation of hematopoietic progenitor cell differentiation / positive regulation of type 2 immune response / positive regulation of stress-activated MAPK cascade / cellular response to potassium ion / NLRP3 inflammasome complex / protein phosphatase regulator activity / Nuclear Pore Complex (NPC) Disassembly / peptidoglycan binding / SUMOylation of immune response proteins / osmosensory signaling pathway / regulation of hematopoietic stem cell proliferation / phosphatidylinositol-4-phosphate binding / negative regulation of non-canonical NF-kappaB signal transduction / pattern recognition receptor signaling pathway / regulation of hematopoietic stem cell differentiation / negative regulation of interleukin-1 beta production / microtubule organizing center / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of viral genome replication / negative regulation of NF-kappaB transcription factor activity / positive regulation of interleukin-4 production / pyroptotic inflammatory response / positive regulation of telomere capping / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of acute inflammatory response / antiviral innate immune response / The NLRP3 inflammasome / protein maturation / spindle assembly / Purinergic signaling in leishmaniasis infection / signaling adaptor activity / positive regulation of chemokine production / EML4 and NUDC in mitotic spindle formation / endoplasmic reticulum unfolded protein response / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / regulation of mitotic cell cycle / cellular response to amino acid starvation / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / molecular function activator activity / non-specific protein-tyrosine kinase / 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 / non-membrane spanning protein tyrosine kinase activity / response to virus / PKR-mediated signaling / protein homooligomerization / Cytoprotection by HMOX1 / Evasion by RSV of host interferon responses / Metalloprotease DUBs / cellular response to virus / ISG15 antiviral mechanism / ADP binding / 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 / protein-macromolecule adaptor activity / kinase activity / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / DNA-binding transcription factor binding / defense response to virus / microtubule / sequence-specific DNA binding / positive regulation of MAPK cascade / protein autophosphorylation / molecular adaptor activity / negative regulation of translation / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / inflammatory response / translation / negative regulation of cell population proliferation / Golgi membrane / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
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 | |||||||||
![]() | Sharif H / Wang L / Wu H | |||||||||
資金援助 | ![]()
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![]() | ![]() 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. | |||||||||
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 48.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 15.7 KB 15.7 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 8.6 KB | 表示 | ![]() |
画像 | ![]() | 150.3 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 523 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 522.6 KB | 表示 | |
XML形式データ | ![]() | 10.4 KB | 表示 | |
CIF形式データ | ![]() | 13.3 KB | 表示 | |
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-関連構造データ
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EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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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: ![]() |
-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: ![]() |
-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: ![]() |
分子量 | 理論値: 117.890984 KDa |
組換発現 | 生物種: ![]() ![]() |
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: ![]() |
分子量 | 理論値: 32.01515 KDa |
組換発現 | 生物種: ![]() ![]() |
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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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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 |
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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: ![]() |
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 |
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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: |