+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31365 | ||||||||||||
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タイトル | Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5 in a 2:1:1 ratio | ||||||||||||
マップデータ | |||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 G protein-coupled glycine receptor activity / GTPase activator complex / light adaption / dark adaptation / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / positive regulation of potassium ion transmembrane transport / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / negative regulation of G protein-coupled receptor signaling pathway ...G protein-coupled glycine receptor activity / GTPase activator complex / light adaption / dark adaptation / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / positive regulation of potassium ion transmembrane transport / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / negative regulation of G protein-coupled receptor signaling pathway / G protein-coupled dopamine receptor signaling pathway / regulation of synapse organization / G-protein alpha-subunit binding / enzyme activator activity / response to amphetamine / GTPase activator activity / positive regulation of GTPase activity / cell projection / protein localization to plasma membrane / brain development / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / cognition / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / transmembrane signaling receptor activity / heterotrimeric G-protein complex / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / nuclear envelope / presynapse / protein-folding chaperone binding / presynaptic membrane / Ca2+ pathway / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / postsynaptic membrane / response to ethanol / Extra-nuclear estrogen signaling / intracellular signal transduction / neuron projection / G protein-coupled receptor signaling pathway / GTPase activity / signal transduction / protein-containing complex / nucleus / plasma membrane / cytosol / cytoplasm 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: 3.95 Å | ||||||||||||
データ登録者 | Kim Y / Jeong E / Jeong J / Cho Y | ||||||||||||
資金援助 | 韓国, 3件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Structure of the class C orphan GPCR GPR158 in complex with RGS7-Gβ5. 著者: Eunyoung Jeong / Yoojoong Kim / Jihong Jeong / Yunje Cho / 要旨: GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding ...GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding domain and terminates Gαi/o protein signaling through the RGS7-Gβ5 heterodimer. Here, we report the cryo-EM structures of GPR158 alone and in complex with one or two RGS7-Gβ5 heterodimers. GPR158 dimerizes through Per-Arnt-Sim-fold extracellular and transmembrane (TM) domains connected by an epidermal growth factor-like linker. The TM domain (TMD) reflects both inactive and active states of other class C GPCRs: a compact intracellular TMD, conformations of the two intracellular loops (ICLs) and the TMD interface formed by TM4/5. The ICL2, ICL3, TM3, and first helix of the cytoplasmic coiled-coil provide a platform for the DHEX domain of one RGS7 and the second helix recruits another RGS7. The unique features of the RGS7-binding site underlie the selectivity of GPR158 for RGS7. | ||||||||||||
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_31365.map.gz | 154.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31365-v30.xml emd-31365.xml | 15.3 KB 15.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31365.png | 55.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31365 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31365 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_31365_validation.pdf.gz | 330.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_31365_full_validation.pdf.gz | 329.8 KB | 表示 | |
XML形式データ | emd_31365_validation.xml.gz | 6.9 KB | 表示 | |
CIF形式データ | emd_31365_validation.cif.gz | 7.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31365 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31365 | 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_31365.map.gz / 形式: CCP4 / 大きさ: 163.6 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: 1.06995 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 : Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5...
全体 | 名称: Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5 in a 2:1:1 ratio |
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要素 |
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-超分子 #1: Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5...
超分子 | 名称: Locally refined cryo-EM map of GPR158 in complex with RGS7-Gbeta5 in a 2:1:1 ratio タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
-分子 #1: GPR158
分子 | 名称: GPR158 / タイプ: protein_or_peptide / ID: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTG DSHQLKRANC SGRYELAGLP GKWPALASAH PSLHRALDTL THATNFLNVM LQSNKSREQN LQDDLDWYQA L VWSLLEGE ...文字列: MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTG DSHQLKRANC SGRYELAGLP GKWPALASAH PSLHRALDTL THATNFLNVM LQSNKSREQN LQDDLDWYQA L VWSLLEGE PSISRAAITF STDSLSAPAP QVFLQATREE SRILLQDLSS SAPHLANATL ETEWFHGLRR KWRPHLHRRG PN QGPRGLG HSWRRKDGLG GDKSHFKWSP PYLECENGSY KPGWLVTLSS AIYGLQPNLV PEFRGVMKVD INLQKVDIDQ CSS DGWFSG THKCHLNNSE CMPIKGLGFV LGAYECICKA GFYHPGVLPV NNFRRRGPDQ HISGSTKDVS EEAYVCLPCR EGCP FCADD SPCFVQEDKY LRLAIISFQA LCMLLDFVSM LVVYHFRKAK SIRASGLILL ETILFGSLLL YFPVVILYFE PSTFR CILL RWARLLGFAT VYGTVTLKLH RVLKVFLSRT AQRIPYMTGG RVMRMLAVIL LVVFWFLIGW TSSVCQNLEK QISLIG QGK TSDHLIFNMC LIDRWDYMTA VAEFLFLLWG VYLCYAVRTV PSAFHEPRYM AVAVHNELII SAIFHTIRFV LASRLQS DW MLMLYFAHTH LTVTVTIGLL LIPKFSHSSN NPRDDIATEA YEDELDMGRS GSYLNSSINS AWSEHSLDPE DIRDELKK L YAQLEIYKRK KMITNNPHLQ KKRCSKKGLG RSIMRRITEI PETVSRQCSK EDKEGADHGT AKGTALIRKN PPESSGNTG KSKEETLKNR VFSLKKSHST YDHVRDQTEE SSSLPTESQE EETTENSTLE SLSGKKLTQK LKE RGRLEV LFQGPGGSMS KGEE LFTGV VPILVELDGD VNGHK FSVR GEGEGDATNG KLTLKF ICT TGKLPVPWPT LVTTLTY GV QCFSRYPDHM KRHDFFKS A MPEGYVQERT ISFKDDGTY KTRAEVKFEG DTLVNRIELK GIDFKEDGN ILGHKLEYNF N SHNVYITA DKQKNGIKAN FK IRHNVED GSVQLADHYQ QNT PIGDGP VLLPDNHYLS TQSV LSKDP NEKRDHMVLL EFVTA AGIT HGGSWSHPQF EKGGGS GGG SGGSAWSHPQ FE |
-分子 #2: GPR158
分子 | 名称: GPR158 / タイプ: protein_or_peptide / ID: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTGD SHQLKRANCS GRYELAGLPG KWPALASAHP SLHRALDTLT HATNFLNVML QSNKSREQNL QDDLDWYQAL VWSLLEGEPS ...文字列: MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTGD SHQLKRANCS GRYELAGLPG KWPALASAHP SLHRALDTLT HATNFLNVML QSNKSREQNL QDDLDWYQAL VWSLLEGEPS ISRAAITFST DSLSAPAPQV FLQATREESR ILLQDLSSSA PHLANATLET EWFHGLRRKW RPHLHRRGPN QGPRGLGHSW RRKDGLGGDK SHFKWSPPYL ECENGSYKPG WLVTLSSAIY GLQPNLVPEF RGVMKVDINL QKVDIDQCSS DGWFSGTHKC HLNNSECMPI KGLGFVLGAY ECICKAGFYH PGVLPVNNFR RRGPDQHISG STKDVSEEAY VCLPCREGCP FCADDSPCFV QEDKYLRLAI ISFQALCMLL DFVSMLVVYH FRKAKSIRAS GLILLETILF GSLLLYFPVV ILYFEPSTFR CILLRWARLL GFATVYGTVT LKLHRVLKVF LSRTAQRIPY MTGGRVMRML AVILLVVFWF LIGWTSSVCQ NLEKQISLIG QGKTSDHLIF NMCLIDRWDY MTAVAEFLFL LWGVYLCYAV RTVPSAFHEP RYMAVAVHNE LIISAIFHTI RFVLASRLQS DWMLMLYFAH THLTVTVTIG LLLIPKFSHS SNNPRDDIAT EAYEDELDMG RSGSYLNSSI NSAWSEHSLD PEDIRDELKK LYAQLEIYKR KKMITNNPHL QKKRCSKKGL GRSIMRRITE IPETVSRQCS KEDKEGADHG TAKGTALIRK NPPESSGNTG KSKEETLKNR VFSLKKSHST YDHVRDQTEE SSSLPTESQE EETTENSTLE SLSGKKLTQK LKEDSEAEST ESVPLVCKSA SAHNLSSEKK TGHPRTSMLQ KSLSVIASAK EKTLGLAGKT QTAGVEERTK SQKPLPKDKE TNRNHSNSDN TETKDPAPQN SNPAEEPRKP QKSGIMKQQR VNPTTANSDL NPGTTQMKDN FDIGEVCPWE VYDLTPGPVP SESKVQKHVS IVASEMEKNP TFSLKEKSHH KPKAAEVCQQ SNQKRIDKAE VCLWESQGQS ILEDEKLLIS KTPVLPERAK EENGGQPRAA NVCAGQSEEL PPKAVASKTE NENLNQIGHQ EKKTSSSEEN VRGSYNSSNN FQQPLTSRAE VCPWEFETPA QPNAGRSVAL PASSALSANK IAGPRKEEIW DSFKV |
-分子 #3: Regulator of G-protein signaling 7
分子 | 名称: Regulator of G-protein signaling 7 / タイプ: protein_or_peptide / ID: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MAQGNNYGQT SNGVADESPN MLVYRKMEDV IARMQDEKNG IPIRTVKSFL SKIPSVFSGS DIVQWLIKNL TIEDPVEALH LGTLMAAHG YFFPISDHVL TLKDDGTFYR FQTPYFWPSN CWEPENTDYA VYLCKRTMQN KARLELADYE AESLARLQRA F ARKWEFIF ...文字列: MAQGNNYGQT SNGVADESPN MLVYRKMEDV IARMQDEKNG IPIRTVKSFL SKIPSVFSGS DIVQWLIKNL TIEDPVEALH LGTLMAAHG YFFPISDHVL TLKDDGTFYR FQTPYFWPSN CWEPENTDYA VYLCKRTMQN KARLELADYE AESLARLQRA F ARKWEFIF MQAEAQAKVD KKRDKIERKI LDSQERAFWD VHRPVPGCVN TTEVDIKKSS RMRNPHKTRK SVYGLQNDIR SH SPTHTPT PETKPPTEDE LQQQIKYWQI QLDRHRLKMS KVADSLLSYT EQYLEYDPFL LPPDPSNPWL SDDTTFWELE ASK EPSQQR VKRWGFGMDE ALKDPVGREQ FLKFLESEFS SENLRFWLAV EDLKKRPIKE VPSRVQEIWQ EFLAPGAPSA INLD SKSYD KTTQNVKEPG RYTFEDAQEH IYKLMKSDSY PRFIRSSAYQ ELLQAKKKSG NSMDRRTSFE KFAQNVGRNI PIFPC HKNC TPTLRASTNL LRGRGGSENL YFQGGSGSGG DYKDDDDKDY KDDDDK |
-分子 #4: Guanine nucleotide-binding protein subunit beta-5
分子 | 名称: Guanine nucleotide-binding protein subunit beta-5 / タイプ: protein_or_peptide / ID: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MCDQTFLVNV FGSCDKCFKQ RALRPVFKKS QQLSYCSTCA EIMATEGLHE NETLASLKSE AESLKGKLEE ERAKLHDVEL HQVAERVEAL GQFVMKTRRT LKGHGNKVLC MDWCKDKRRI VSSSQDGKVI VWDSFTTNKE HAVTMPCTWV MACAYAPSGC AIACGGLDNK ...文字列: MCDQTFLVNV FGSCDKCFKQ RALRPVFKKS QQLSYCSTCA EIMATEGLHE NETLASLKSE AESLKGKLEE ERAKLHDVEL HQVAERVEAL GQFVMKTRRT LKGHGNKVLC MDWCKDKRRI VSSSQDGKVI VWDSFTTNKE HAVTMPCTWV MACAYAPSGC AIACGGLDNK CSVYPLTFDK NENMAAKKKS VAMHTNYLSA CSFTNSDMQI LTASGDGTCA LWDVESGQLL QSFHGHGADV LCLDLAPSET GNTFVSGGCD KKAMVWDMRS GQCVQAFETH ESDINSVRYY PSGDAFASGS DDATCRLYDL RADREVAIYS KESIIFGASS VDFSLSGRLL FAGYNDYTIN VWDVLKGSRV SILFGHENRV STLRVSPDGT AFCSGSWDHT LRVWA |
-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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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % |
-電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
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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 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: DIFFRACTION |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.95 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 362999 |
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初期 角度割当 | タイプ: OTHER |
最終 角度割当 | タイプ: OTHER |