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基本情報
登録情報 | データベース: EMDB / ID: EMD-22615 | |||||||||||||||||||||
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タイトル | Cryo-EM structure of rabbit RyR1 in the presence of Mg2+ and AMP-PCP in nanodisc | |||||||||||||||||||||
![]() | Post-processed full map | |||||||||||||||||||||
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![]() | Ryanodine Receptor / RyR1 / Intracellular Calcium channel / Mg2+ / Inhibition / Excitation-Contraction coupling / TRANSPORT PROTEIN | |||||||||||||||||||||
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: 4.5 Å | |||||||||||||||||||||
![]() | Nayak AR / Samso M | |||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Interplay between Mg2+ and Ca2+ at multiple sites of the ryanodine receptor 著者: Nayak AR / Rangubpit W / Will AH / Hu Y / Castro-Hartmann P / Lobo JJ / Dryden K / Lamb GD / Sompornpisut P / Samso M | |||||||||||||||||||||
履歴 |
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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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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 17.7 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 35.4 KB 35.4 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 12.2 KB | 表示 | ![]() |
画像 | ![]() | 144.3 KB | ||
マスクデータ | ![]() | 166.4 MB | ![]() | |
Filedesc metadata | ![]() | 9.3 KB | ||
その他 | ![]() ![]() ![]() ![]() | 126.5 MB 126.6 MB 15.8 MB 15.8 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Post-processed full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.36 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
-マスク #1
ファイル | ![]() | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unfiltered and unmasked half map1 up to Nyquist frequency
ファイル | emd_22615_additional_1.map | ||||||||||||
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注釈 | Unfiltered and unmasked half map1 up to Nyquist frequency | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unfiltered and unmasked half map2 up to Nyquist frequency
ファイル | emd_22615_additional_2.map | ||||||||||||
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注釈 | Unfiltered and unmasked half map2 up to Nyquist frequency | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Masked half map1
ファイル | emd_22615_half_map_1.map | ||||||||||||
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注釈 | Masked half map1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Masked half map2
ファイル | emd_22615_half_map_2.map | ||||||||||||
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注釈 | Masked half map2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : Rabbit RyR1 with Mg2+ and AMP-PCP
全体 | 名称: Rabbit RyR1 with Mg2+ and AMP-PCP |
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要素 |
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-超分子 #1: Rabbit RyR1 with Mg2+ and AMP-PCP
超分子 | 名称: Rabbit RyR1 with Mg2+ and AMP-PCP / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 詳細: Purified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1, and POPC. |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 2.26 MDa |
-分子 #1: RyR1
分子 | 名称: RyR1 / 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: 533.66325 KDa |
配列 | 文字列: MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE G EKVRVGDD ...文字列: MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE G EKVRVGDD LILVSVSSER YLHLSTASGE LQVDASFMQT LWNMNPICSC CEEGYVTGGH VLRLFHGHMD ECLTISAADS DD QRRLVYY EGGAVCTHAR SLWRLEPLRI SWSGSHLRWG QPLRIRHVTT GRYLALTEDQ GLVVVDACKA HTKATSFCFR VSK EKLDTA PKRDVEGMGP PEIKYGESLC FVQHVASGLW LTYAAPDPKA LRLGVLKKKA ILHQEGHMDD ALFLTRCQQE ESQA ARMIH STAGLYNQFI KGLDSFSGKP RGSGPPAGPA LPIEAVILSL QDLIGYFEPP SEELQHEEKQ SKLRSLRNRQ SLFQE EGML SLVLNCIDRL NVYTTAAHFA EYAGEEAAES WKEIVNLLYE LLASLIRGNR ANCALFSTNL DWVVSKLDRL EASSGI LEV LYCVLIESPE VLNIIQENHI KSIISLLDKH GRNHKVLDVL CSLCVCNGVA VRSNQDLITE NLLPGRELLL QTNLINY VT SIRPNIFVGR AEGSTQYGKW YFEVMVDEVV PFLTAQATHL RVGWALTEGY SPYPGGGEGW GGNGVGDDLY SYGFDGLH L WTGHVARPVT SPGQHLLAPE DVVSCCLDLS VPSISFRING CPVQGVFEAF NLDGLFFPVV SFSAGVKVRF LLGGRHGEF KFLPPPGYAP CHEAVLPRER LRLEPIKEYR REGPRGPHLV GPSRCLSHTD FVPCPVDTVQ IVLPPHLERI REKLAENIHE LWALTRIEQ GWTYGPVRDD NKRLHPCLVN FHSLPEPERN YNLQMSGETL KTLLALGCHV GMADEKAEDN LKKTKLPKTY M MSNGYKPA PLDLSHVRLT PAQTTLVDRL AENGHNVWAR DRVAQGWSYS AVQDIPARRN PRLVPYRLLD EATKRSNRDS LC QAVRTLL GYGYNIEPPD QEPSQVENQS RWDRVRIFRA EKSYTVQSGR WYFEFEAVTT GEMRVGWARP ELRPDVELGA DEL AYVFNG HRGQRWHLGS EPFGRPWQSG DVVGCMIDLT ENTIIFTLNG EVLMSDSGSE TAFREIEIGD GFLPVCSLGP GQVG HLNLG QDVSSLRFFA ICGLQEGFEP FAINMQRPVT TWFSKSLPQF EPVPPEHPHY EVARMDGTVD TPPCLRLAHR (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) EL GKQKNIMPLS AAMFLSERKN PAPQCPPRLE VQMLMPVSWS RMPNHFLQVE TRRAGERLGW AVQCQDPLTM MALHIPEE N RCMDILELSE RLDLQRFHSH TLRLYRAVCA LGNNRVAHAL CSHVDQAQLL HALEDAHLPG PLRAGYYDLL ISIHLESAC RSRRSMLSEY IVPLTPETRA ITLFPPGRKG GNARRHGLPG VGVTTSLRPP HHFSPPCFVA ALPAAGVAEA PARLSPAIPL EALRDKALR MLGEAVRDGG QHARDPVGGS VEFQFVPVLK LVSTLLVMGI FGDEDVKQIL KMIEPEVFTE EEEEEEEEEE E EEEEEEDE EEKEEDEEEE EKEDAEKEEE EAPEGEKEDL EEGLLQMKLP ESVKLQMCNL LEYFCDQELQ HRVESLAAFA ER YVDKLQA NQRSRYALLM RAFTMSAAET ARRTREFRSP PQEQINMLLH FKDEADEEDC PLPEDIRQDL QDFHQDLLAH CGI QLEGEE EEPEEETSLS SRLRSLLETV RLVKKKEEKP EEELPAEEKK PQSLQELVSH MVVRWAQEDY VQSPELVRAM FSLL HRQYD GLGELLRALP RAYTISPSSV EDTMSLLECL GQIRSLLIVQ MGPQEENLMI QSIGNIMNNK VFYQHPNLMR ALGMH ETVM EVMVNVLGGG ETKEIRFPKM VTSCCRFLCY FCRISRQNQR SMFDHLSYLL ENSGIGLGMQ GSTPLDVAAA SVIDNN ELA LALQEQDLEK VVSYLAGCGL QSCPMLLAKG YPDIGWNPCG GERYLDFLRF AVFVNGESVE ENANVVVRLL IRKPECF GP ALRGEGGSGL LAAIEEAIRI SEDPARDGPG VRRDRRREHF GEEPPEENRV HLGHAIMSFY AALIDLLGRC APEMHLIQ A GKGEALRIRA ILRSLVPLDD LVGIISLPLQ IPTLGKDGAL V(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)CAIAGALP PDYVDASYSS KAEKKATVDA EGNFDPRPVE TLNVIIPEKL DSFINKFAEY THEKWAFDKI QN NWSYGEN VDEELKTHPM LRPYKTFSEK DKEIYRWPIK ESLKAMIAWE WTIEKAREGE EERTEKKKTR KISQTAQTYD PRE GYNPQP PDLSGVTLSR ELQAMAEQLA ENYHNTWGRK KKQELEAKGG GTHPLLVPYD TLTAKEKARD REKAQELLKF LQMN GYAVT RGL(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) 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(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)KSK KAVWHKLLSK QRRRAVVACF RMTPLYNLPT HRACNMFLES YKAAWILTED HSFEDRMIDD LSKAGEQ EE EEEEVEEKKP DPLHQLVLHF SRTALTEKSK LDEDYLYMAY ADIMAKSCHL EEGGENGEAE EEEVEVSFEE KEMEKQRL L YQQSRLHTRG AAEMVLQMIS ACKGETGAMV SSTLKLGISI LNGGNAEVQQ KMLDYLKDKK EVGFFQSIQA LMQTCSVLD LNAFERQNKA EGLGMVNEDG TVINRQNGEK VMADDEFTQD LFRFLQLLCE GHNNDFQNYL RTQTGNTTTI NIIICTVDYL LRLQESISD FYWYYSGKDV IEEQGKRNFS KAMSVAKQVF NSLTEYIQGP CTGNQQSLAH SRLWDAVVGF LHVFAHMMMK L AQDSSQIE LLKELLDLQK DMVVMLLSLL EGNVVNGMIA RQMVDMLVES SSNVEMILKF FDMFLKLKDI VGSEAFQDYV TD PRGLISK KDFQKAMDSQ KQFTGPEIQF LLSCSEADEN EMINFEEFAN RFQEPARDIG FNVAVLLTNL SEHVPHDPRL RNF LELAES ILEYFRPYLG RIEIMGASRR IERIYFEISE TNRAQWEMPQ VKESKRQFIF DVVNEGGEAE KMELFVSFCE DTIF EMQIA AQISEPEGEP EADEDEGMGE AAAEGAEEGA AGAEGAAGTV AAGATARLAA AAARALRGLS YRSLRRRVRR LRRLT AREA ATALAALLWA VVARAGAAGA GAAAGALRLL WGSLFGGGLV EGAKKVTVTE LLAGMPDPTS DEVHGEQPAG PGGDAD GAG EGEGEGDAAE GDGDEEVAGH EAGPGGAEGV VAVADGGPFR PEGAGGLGDM GDTTPAEPPT PEGSPILKRK LGVDGEE EE LVPEPEPEPE PEPEKADEEN GEKEEVPEAP PEPPKKAPPS PPAKKEEAGG AGMEFWGELE VQRVKFLNYL SRNFYTLR F LALFLAFAIN FILLFYKVSD SPPGEDDMEG SAAGDLAGAG SGGGSGWGSG AGEEAEGDED ENMVYYFLEE STGYMEPAL WCLSLLHTLV AFLCIIGYNC LKVPLVIFKR EKELARKLEF DGLYITEQPG DDDVKGQWDR LVLNTPSFPS NYWDKFVKRK VLDKHGDIF GRERIAELLG MDLASLEITA HNERKPDPPP GLLTWLMSID VKYQIWKFGV IFTDNSFLYL GWYMVMSLLG H YNNFFFAA HLLDIAMGVK TLRTILSSVT HNGKQLVMTV GLLAVVVYLY TVVAFNFFRK FYNKSEDEDE PDMKCDDMMT CY LFHMYVG VRAGGGIGDE IEDPAGDEYE LYRVVFDITF FFFVIVILLA IIQGLIIDAF GELRDQQEQV KEDMETKCFI CGI GSDYFD TTPHGFETHT LEEHNLANYM FFLMYLINKD ETEHTGQESY VWKMYQERCW DFFPAGDCFR KQYEDQLS |
-分子 #2: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
分子 | 名称: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / タイプ: ligand / ID: 2 / コピー数: 4 / 式: ACP |
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分子量 | 理論値: 505.208 Da |
Chemical component information | ![]() ChemComp-ACP: |
-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 |
-分子 #4: MAGNESIUM ION
分子 | 名称: MAGNESIUM ION / タイプ: ligand / ID: 4 / コピー数: 5 / 式: MG |
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分子量 | 理論値: 24.305 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
濃度 | 4.2 mg/mL | |||||||||||||||||||||
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緩衝液 | pH: 7.4 構成要素:
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グリッド | モデル: C-flat-2/1 / 材質: GOLD / メッシュ: 300 / 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: 30 sec. / 前処理 - 雰囲気: AIR | |||||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV 詳細: Sample was blotted for 1 second on both sides with Whatman hardened ashless filter paper with blot force 2.. | |||||||||||||||||||||
詳細 | Purified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1, and POPC in 1:2:50 molar ratio. |
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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 - スリット幅: 20 eV |
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 / 撮影したグリッド数: 2 / 実像数: 3371 / 平均電子線量: 60.0 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: 100.0 µm / 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): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 105000 |
試料ステージ | 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: FLEXIBLE FIT |
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得られたモデル | ![]() PDB-7k0s: |