+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13972 | ||||||||||||
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タイトル | Desensitized state of GluA1/2 AMPA receptor in complex with TARP-gamma 8 (TMD-LBD) | ||||||||||||
マップデータ | PostProcessed map of the GluA1/2/TARP-gamma8 in the desentitised state obtained in relion | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / cellular response to ammonium ion ...Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / cellular response to ammonium ion / proximal dendrite / neurotransmitter receptor transport, postsynaptic endosome to lysosome / L-type voltage-gated calcium channel complex / response to sucrose / LGI-ADAM interactions / myosin V binding / Trafficking of AMPA receptors / neuron spine / cellular response to dsRNA / cellular response to L-glutamate / regulation of AMPA receptor activity / protein phosphatase 2B binding / conditioned place preference / neurotransmitter receptor internalization / response to arsenic-containing substance / postsynaptic neurotransmitter receptor diffusion trapping / regulation of monoatomic ion transmembrane transport / dendritic spine membrane / Synaptic adhesion-like molecules / long-term synaptic depression / response to morphine / cellular response to peptide hormone stimulus / beta-2 adrenergic receptor binding / protein kinase A binding / peptide hormone receptor binding / response to psychosocial stress / spine synapse / dendritic spine neck / spinal cord development / neuronal cell body membrane / dendritic spine head / Activation of AMPA receptors / behavioral response to pain / perisynaptic space / AMPA glutamate receptor activity / transmission of nerve impulse / ligand-gated monoatomic cation channel activity / channel regulator activity / cellular response to organic cyclic compound / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / regulation of postsynaptic membrane neurotransmitter receptor levels / AMPA glutamate receptor complex / excitatory synapse / adenylate cyclase binding / kainate selective glutamate receptor activity / positive regulation of excitatory postsynaptic potential / ionotropic glutamate receptor complex / regulation of postsynaptic membrane potential / cellular response to glycine / postsynaptic density, intracellular component / asymmetric synapse / neuronal action potential / calcium channel regulator activity / regulation of receptor recycling / G-protein alpha-subunit binding / Unblocking of NMDA receptors, glutamate binding and activation / voltage-gated calcium channel activity / glutamate receptor binding / positive regulation of synaptic transmission / response to electrical stimulus / long-term memory / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / synapse assembly / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / SNARE binding / dendritic shaft / response to cocaine / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / cellular response to amino acid stimulus / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding 類似検索 - 分子機能 | ||||||||||||
生物種 | Rattus norvegicus (ドブネズミ) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | ||||||||||||
データ登録者 | Herguedas B / Kohegyi B / Dohrke JN / Watson JF / Zhang D / Ho H / Shaikh S / Lape R / Krieger JM / Greger IH | ||||||||||||
資金援助 | 英国, 3件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. 著者: Beatriz Herguedas / Bianka K Kohegyi / Jan-Niklas Dohrke / Jake F Watson / Danyang Zhang / Hinze Ho / Saher A Shaikh / Remigijus Lape / James M Krieger / Ingo H Greger / 要旨: AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor's ligand-binding domains (LBDs) leads to ion channel ...AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor's ligand-binding domains (LBDs) leads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission and are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs) through currently incompletely resolved mechanisms. Here, electron cryo-microscopy structures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states (at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop ('β1'), elucidating how this TARP stabilizes specific gating states. We further show how TARPs alter channel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we reveal that the Q/R-editing site couples the channel constriction at the filter entrance to the gate, and forms the major cation binding site in the conduction path. Our results provide a mechanistic framework of how TARPs modulate AMPAR gating and conductance. | ||||||||||||
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_13972.map.gz | 116.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13972-v30.xml emd-13972.xml | 27.7 KB 27.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_13972_fsc.xml | 11.4 KB | 表示 | FSCデータファイル |
画像 | emd_13972.png | 51.1 KB | ||
その他 | emd_13972_additional_1.map.gz emd_13972_half_map_1.map.gz emd_13972_half_map_2.map.gz | 6.8 MB 96.7 MB 97 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13972 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13972 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_13972_validation.pdf.gz | 485.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_13972_full_validation.pdf.gz | 485.4 KB | 表示 | |
XML形式データ | emd_13972_validation.xml.gz | 18.4 KB | 表示 | |
CIF形式データ | emd_13972_validation.cif.gz | 23.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13972 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13972 | 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_13972.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | PostProcessed map of the GluA1/2/TARP-gamma8 in the desentitised state obtained in relion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.06 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
-追加マップ: Composite map generated from focused refinement of TMD...
ファイル | emd_13972_additional_1.map | ||||||||||||
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注釈 | Composite map generated from focused refinement of TMD and LBD regions. This map was used for manual model building | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map obtained in 3D refinement
ファイル | emd_13972_half_map_1.map | ||||||||||||
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注釈 | Half map obtained in 3D refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map obtained in 3D refinement
ファイル | emd_13972_half_map_2.map | ||||||||||||
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注釈 | Half map obtained in 3D refinement | ||||||||||||
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 : Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP ...
全体 | 名称: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8 |
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要素 |
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-超分子 #1: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP ...
超分子 | 名称: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8 タイプ: complex / キメラ: Yes / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3 / 詳細: GluA2 and TARP8 are expressed as a tandem construct |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換細胞: HEK293 EXPI / 組換プラスミド: PRK5 |
分子量 | 理論値: 490 KDa |
-分子 #1: Isoform Flip of Glutamate receptor 1
分子 | 名称: Isoform Flip of Glutamate receptor 1 / 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: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 102.66193 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR ...文字列: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR VLDTAAEKNW QVTAVNILTT TEEGYRMLFQ DLEKKKERLV VVDCESERLN AILGQIVKLE KNGIGYHYIL AN LGFMDID LNKFKESGAN VTGFQLVNYT DTIPARIMQQ WRTSDSRDHT RVDWKRPKYT SALTYDGVKV MAEAFQSLRR QRI DISRRG NAGDCLANPA VPWGQGIDIQ RALQQVRFEG LTGNVQFNEK GRRTNYTLHV IEMKHDGIRK IGYWNEDDKF VPAA TDAQA GGDNSSVQNR TYIVTTILED PYVMLKKNAN QFEGNDRYEG YCVELAAEIA KHVGYSYRLE IVSDGKYGAR DPDTK AWNG MVGELVYGRA DVAVAPLTIT LVREEVIDFS KPFMSLGISI MIKKPQKSKP GVFSFLDPLA YEIWMCIVFA YIGVSV VLF LVSRFSPYEW HSEEFEEGRD QTTSDQSNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTA NL AAFLTVERMV SPIESAEDLA KQTEIAYGTL EAGSTKEFFR RSKIAVFEKM WTYMKSAEPS VFVRTTEEGM IRVRKSKG K YAYLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGIATPKG SALRGPVNLA VLKLSEQGVL DKLKSKWWYD KGECGSKDS GSKDKTSALS LSNVAGVFYI LIGGLGLAML VALIEFCYKS RSESKRMKGF CLIPQQSINE AIRTSTLPRN SGAGASGGGG SGENGRVVS QDFPKSMQSI PCMSHSSGMP LGATGL |
-分子 #2: Isoform Flip of Glutamate receptor 2
分子 | 名称: Isoform Flip of Glutamate receptor 2 / 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: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 96.247055 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA ...文字列: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA AEKKWQVTAI NVGNINNDKK DETYRSLFQD LELKKERRVI LDCERDKVND IVDQVITIGK HVKGYHYIIA NL GFTDGDL LKIQFGGANV SGFQIVDYDD SLVSKFIERW STLEEKEYPG AHTATIKYTS ALTYDAVQVM TEAFRNLRKQ RIE ISRRGN AGDCLANPAV PWGQGVEIER ALKQVQVEGL SGNIKFDQNG KRINYTINIM ELKTNGPRKI GYWSEVDKMV VTLT ELPSG NDTSGLENKT VVVTTILESP YVMMKKNHEM LEGNERYEGY CVDLAAEIAK HCGFKYKLTI VGDGKYGARD ADTKI WNGM VGELVYGKAD IAIAPLTITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVV LFL VSRFSPYEWH TEEFEDGRET QSSESTNEFG IFNSLWFSLG AFMRQGCDIS PRSLSGRIVG GVWWFFTLII ISSYTAN LA AFLTVERMVS PIESAEDLSK QTEIAYGTLD SGSTKEFFRR SKIAVFDKMW TYMRSAEPSV FVRTTAEGVA RVRKSKGK Y AYLLESTMNE YIEQRKPCDT MKVGGNLDSK GYGIATPKGS SLGTPVNLAV LKLSEQGVLD KLKNKWWYDK GECGAKDSG SKEKTSALSL SNVAGVFYIL VGGLGLAMLV ALIEFCYKSR AEAKRMKVAK NPQNINPSSS |
-分子 #3: Voltage-dependent calcium channel gamma-8 subunit
分子 | 名称: Voltage-dependent calcium channel gamma-8 subunit / 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: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 43.576004 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: GESLKRWNEE RGLWCEKGVQ VLLTTIGAFA AFGLMTIAIS TDYWLYTRAL ICNTTNLTAG DDGPPHRGGS GSSEKKDPGG LTHSGLWRI CCLEGLKRGV CVKINHFPED TDYDHDSAEY LLRVVRASSI FPILSAILLL LGGVCVAASR VYKSKRNIIL G AGILFVAA ...文字列: GESLKRWNEE RGLWCEKGVQ VLLTTIGAFA AFGLMTIAIS TDYWLYTRAL ICNTTNLTAG DDGPPHRGGS GSSEKKDPGG LTHSGLWRI CCLEGLKRGV CVKINHFPED TDYDHDSAEY LLRVVRASSI FPILSAILLL LGGVCVAASR VYKSKRNIIL G AGILFVAA GLSNIIGVIV YISANAGEPG PKRDEEKKNH YSYGWSFYFG GLSFILAEVI GVLAVNIYIE RSREAHCQSR SD LLKAGGG AGGSGGSGPS AILRLPSYRF RYRRRSRSSS RGSSEASPSR DASPGGPGGP GFASTDISMY TLSRDPSKGS VAA GLASAG GGGGGAGVGA YGGAAGAAGG GGTGSERDRG SSAGFLTLHN AFPKEAASGV TVTVTGPPAA PAPAPPAPAA PAPG TLSKE AAASNTNTLN RKLEVLFQ |
-分子 #4: GLUTAMIC ACID
分子 | 名称: GLUTAMIC ACID / タイプ: ligand / ID: 4 / コピー数: 4 / 式: GLU |
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分子量 | 理論値: 147.129 Da |
Chemical component information | ChemComp-GLU: |
-分子 #5: PALMITOLEIC ACID
分子 | 名称: PALMITOLEIC ACID / タイプ: ligand / ID: 5 / コピー数: 10 / 式: PAM |
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分子量 | 理論値: 254.408 Da |
Chemical component information | ChemComp-PAM: |
-分子 #6: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
分子 | 名称: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / タイプ: ligand / ID: 6 / コピー数: 2 / 式: OLC |
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分子量 | 理論値: 356.54 Da |
Chemical component information | ChemComp-OLC: |
-分子 #7: (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate
分子 | 名称: (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / タイプ: ligand / ID: 7 / コピー数: 2 / 式: 79N |
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分子量 | 理論値: 328.487 Da |
Chemical component information | ChemComp-79N: |
-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 | 2.5 mg/mL |
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緩衝液 | pH: 8 詳細: 25 mM TRIS 150 mM NaCl 0.02 % GDN 87 uM CTZ 100 mM L-Glu |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE |
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 / 詳細: 3-4 second blots. |
詳細 | Sample was incubated with 87 uM CTZ for 30 minutes and 100 mM L-Glutamate was added before grid preparation |
-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 K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 9664 / 平均露光時間: 4.0 sec. / 平均電子線量: 51.0 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: OTHER / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.2 µm / 最小 デフォーカス(公称値): 0.34 µm / 倍率(公称値): 81000 |
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
初期モデル | (PDB ID: , ) |
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詳細 | First, rigid body fit was performed in Chimera using the coordinates of the TMD of 6QKC and the coordinates of the LBD in PDB code 3TKD. Manual model building was performed with Coot and Refinement was performed with Refmac. The TMD and LBD maps obtained independently aided model building but were not used for refinement. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-7qhh: |