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基本情報
登録情報 | データベース: EMDB / ID: EMD-23337 | ||||||||||||||||||||||||
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タイトル | Structure of full-length IP3R1 channel reconstituted into lipid nanodisc in the apo-state | ||||||||||||||||||||||||
![]() | Cryo-EM structure of full-length IP3R1 in nanodisc (apo-state) | ||||||||||||||||||||||||
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![]() | Calcium channel / lipid nanodisc / MEMBRANE PROTEIN | ||||||||||||||||||||||||
機能・相同性 | ![]() Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / negative regulation of calcium-mediated signaling / calcineurin complex / platelet dense granule membrane ...Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / negative regulation of calcium-mediated signaling / calcineurin complex / platelet dense granule membrane / epithelial fluid transport / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / regulation of postsynaptic cytosolic calcium ion concentration / inositol 1,4,5-trisphosphate-gated calcium channel activity / voluntary musculoskeletal movement / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / endoplasmic reticulum calcium ion homeostasis / positive regulation of hepatocyte proliferation / nuclear inner membrane / transport vesicle membrane / Ion homeostasis / dendrite development / intracellularly gated calcium channel activity / ligand-gated ion channel signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / GABA-ergic synapse / calcium channel inhibitor activity / release of sequestered calcium ion into cytosol / cellular response to cAMP / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / synaptic membrane / sarcoplasmic reticulum / liver regeneration / calcium-mediated signaling / calcium ion transmembrane transport / Schaffer collateral - CA1 synapse / cell morphogenesis / positive regulation of insulin secretion / positive regulation of neuron projection development / calcium ion transport / presynapse / nuclear envelope / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / cellular response to hypoxia / postsynapse / protein phosphatase binding / transmembrane transporter binding / postsynaptic density / response to hypoxia / positive regulation of apoptotic process / protein domain specific binding / neuronal cell body / synapse / calcium ion binding / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm 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: 3.3 Å | ||||||||||||||||||||||||
![]() | Baker MR / Fan G | ||||||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM structure of type 1 IPR channel in a lipid bilayer. 著者: Mariah R Baker / Guizhen Fan / Alexander B Seryshev / Melina A Agosto / Matthew L Baker / Irina I Serysheva / ![]() 要旨: Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved ...Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved in many physiological processes. Here, we present the cryo-EM structures of full-length rat IPR1 reconstituted in lipid nanodisc and detergent solubilized in the presence of phosphatidylcholine determined in ligand-free, closed states by single-particle electron cryo-microscopy. Notably, both structures exhibit the well-established IPR1 protein fold and reveal a nearly complete representation of lipids with similar locations of ordered lipids bound to the transmembrane domains. The lipid-bound structures show improved features that enabled us to unambiguously build atomic models of IPR1 including two membrane associated helices that were not previously resolved in the TM region. Our findings suggest conserved locations of protein-bound lipids among homotetrameric ion channels that are critical for their structural and functional integrity despite the diversity of structural mechanisms for their gating. | ||||||||||||||||||||||||
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「今月の分子」の関連する項目 |
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注釈 | Cryo-EM structure of full-length IP3R1 in nanodisc (apo-state) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 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 : Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein c...
全体 | 名称: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein complex |
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要素 |
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-超分子 #1: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein c...
超分子 | 名称: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein complex タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 1.3 MDa |
-分子 #1: Inositol 1,4,5-trisphosphate receptor type 1
分子 | 名称: Inositol 1,4,5-trisphosphate receptor type 1 / タイプ: protein_or_peptide / ID: 1 / コピー数: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 311.84825 KDa |
配列 | 文字列: SSFLHIGDIC SLYAEGSTNG FISTLGLVDD RCVVQPEAGD LNNPPKKFRD CLFKLCPMNR YSAQKQFWKA AKPGANSTTD AVLLNKLHH AADLEKKQNE TENRKLLGTV IQYGNVIQLL HLKSNKYLTV NKRLPALLEK NAMRVTLDEA GNEGSWFYIQ P FYKLRSIG ...文字列: SSFLHIGDIC SLYAEGSTNG FISTLGLVDD RCVVQPEAGD LNNPPKKFRD CLFKLCPMNR YSAQKQFWKA AKPGANSTTD AVLLNKLHH AADLEKKQNE TENRKLLGTV IQYGNVIQLL HLKSNKYLTV NKRLPALLEK NAMRVTLDEA GNEGSWFYIQ P FYKLRSIG DSVVIGDKVV LNPVNAGQPL HASSHQLVDN PGCNEVNSVN CNTSWKIVLF MKWSDNKDDI LKGGDVVRLF HA EQEKFLT CDEHRKKQHV FLRTTGRQSA TSATSSKALW EVEVVQHDPC RGGAGYWNSL FRFKHLATGH YLAAEVDPDF EEE CLEFQP SVDPDQDASR SRLRNAQEKM VYSLVSVPEG NDISSIFELD PTTLRGGDSL VPRNSYVRLR HLCTNTWVHS TNIP IDKEE EKPVMLKIGT SPLKEDKEAF AIVPVSPAEV RDLDFANDAS KVLGSIAGKL EKGTITQNER RSVTKLLEDL VYFVT GGTN SGQDVLEVVF SKPNRERQKL MREQNILKQI FKLLQAPFTD CGDGPMLRLE ELGDQRHAPF RHICRLCYRV LRHSQQ DYR KNQEYIAKQF GFMQKQIGYD VLAEDTITAL LHNNRKLLEK HITAAEIDTF VSLVRKNREP RFLDYLSDLC VSMNKSI PV TQELICKAVL NPTNADILIE TKLVLSRFEF EGVSTGENAL EAGEDEEEVW LFWRDSNKEI RSKSVRELAQ DAKEGQKE D RDVLSYYRYQ LNLFARMCLD RQYLAINEIS GQLDVDLILR CMSDENLPYD LRASFCRLML HMHVDRDPQE QVTPVKYAR LWSEIPSEIA IDDYDSSGAS KDEIKERFAQ TMEFVEEYLR DVVCQRFPFS DKEKNKLTFE VVNLARNLIY FGFYNFSDLL RLTKILLAI LDCVHVTTIF PISKMTKGEE NKGSNVMRSI HGVGELMTQV VLRGGGFLPM TPMAAAPEGN VKQAEPEKED I MVMDTKLK IIEILQFILN VRLDYRISCL LCIFKREFDE SNSQSSETSS GNSSQEGPSN VPGALDFEHI EEQAEGIFGG SE ENTPLDL DDHGGRTFLR VLLHLTMHDY PPLVSGALQL LFRHFSQRQE VLQAFKQVQL LVTSQDVDNY KQIKQDLDQL RSI VEKSEL WVYKGQGPDE PMDGASGENE HKKTEEGTSK PLKHESTSSY NYRVVKEILI RLSKLCVQES ASVRKSRKQQ QRLL RNMGA HAVVLELLQI PYEKAEDTKM QEIMRLAHEF LQNFCAGNQQ NQALLHKHIN LFLNPGILEA VTMQHIFMNN FQLCS EINE RVVQHFVHCI ETHGRNVQYI KFLQTIVKAE GKFIKKCQDM VMAELVNSGE DVLVFYNDRA SFQTLIQMMR SERDRM DEN SPLFMYHIHL VELLAVCTEG KNVYTEIKCN SLLPLDDIVR VVTHEDCIPE VKIAYINFLN HCYVDTEVEM KEIYTSN HM WKLFENFLVD ICRACNNTSD RKHADSVLEK YVTEIVMSIV TTFFSSPFSD QSTTLQTRQP VFVQLLQGVF RVYHCNWL M PSQKASVESC IRVLSDVAKS RAIAIPVDLD SQVNNLFLKS HNIVQKTAMN WRLSARNAAR RDSVLAASRD YRNIIERLQ DIVSALEDRL RPLVQAELSV LVDVLHRPEL LFPENTDARR KCESGGFICK LIKHTKQLLE ENEEKLCIKV LQTLREMMTK DRGYGEKQI SIDELENAEL PQPPEAENST EQELEPSPPL RQLEDHKRGE ALRQILVNRY YGNIRPSGRR ESLTSFGNGP L SPGGPSKP GGGGGGPGSG STSRGEMSLA EVQCHLDKEG ASNLVIDLIM NASSDRVFHE SILLAIALLE GGNTTIQHSF FC RLTEDKK SEKFFKVFYD RMKVAQQEIK ATVTVNTSDL GNKKKDDEVD RDAPSRKKAK EPTTQITEEV RDQLLEASAA TRK AFTTFR READPDDHYQ SGEGTQATTD KAKDDLEMSA VITIMQPILR FLQLLCENHN RDLQNFLRCQ NNKTNYNLVC ETLQ FLDCI CGSTTGGLGL LGLYINEKNV ALINQTLESL TEYCQGPCHE NQNCIATHES NGIDIITALI LNDINPLGKK RMDLV LELK NNASKLLLAI MESRHDSENA ERILYNMRPK ELVEVIKKAY MQGEVEFEDG ENGEDGAASP RNVGHNIYIL AHQLAR HNK ELQTMLKPGG QVDGDEALEF YAKHTAQIEI VRLDRTMEQI VFPVPSICEF LTKESKLRIY YTTERDEQGS KINDFFL RS EDLFNEMNWQ KKLRAQPVLY WCARNMSFWS SISFNLAVLM NLLVAFFYPF KGVRGGTLEP HWSGLLWTAM LISLAIVI A LPKPHGIRAL IASTILRLIF SVGLQPTLFL LGAFNVCNKI IFLMSFVGNC GTFTRGYRAM VLDVEFLYHL LYLLICAMG LFVHEFFYSL LLFDLVYREE TLLNVIKSVT RNGRPIILTA ALALILVYLF SIVGYLFFKD DFILEVDRLP NETAGPETGE SLANDFLYS DVCRVETGEN CTSPAPKEEL LPVEETEQDK EHTCETLLMC IVTVLSHGLR SGGGVGDVLR KPSKEEPLFA A RVIYDLLF FFMVIIIVLN LIFGVIIDTF ADLRSEKQKK EEILKTTCFI CGLERDKFDN KTVTFEEHIK EEHNMWHYLC FI VLVKVKD STEYTGPESY VAEMIRERNL DWFPRMRAMS LVSSDSEGEQ NELRNLQEKL ESTMKLVTNL SGQLSELKDQ MTE QRKQKQ RIGLLGHP UniProtKB: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR1 |
-分子 #2: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,...
分子 | 名称: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL タイプ: ligand / ID: 2 / コピー数: 28 / 式: PLX |
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分子量 | 理論値: 767.132 Da |
Chemical component information | ![]() ChemComp-PLX: |
-分子 #3: ZINC ION
分子 | 名称: ZINC ION / タイプ: ligand / ID: 3 / コピー数: 4 / 式: ZN |
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分子量 | 理論値: 65.409 Da |
-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: 7.4 |
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グリッド | モデル: Quantifoil / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 10 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 K / 装置: FEI VITROBOT MARK IV |
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電子顕微鏡法
顕微鏡 | TFS KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 検出モード: SUPER-RESOLUTION / デジタル化 - サイズ - 横: 3840 pixel / デジタル化 - サイズ - 縦: 3712 pixel / デジタル化 - 画像ごとのフレーム数: 2-35 / 実像数: 22000 / 平均露光時間: 0.2 sec. / 平均電子線量: 56.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 46943 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 0.8 µm / 倍率(公称値): 130000 |
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 |