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万見
- EMDB-22016: Wt pig RyR1 in complex with apoCaM, EGTA condition (class 3, open) -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: EMDB / ID: EMD-22016
タイトルWt pig RyR1 in complex with apoCaM, EGTA condition (class 3, open)
マップデータRyR1, FKBP12.6, CaM
試料
  • 複合体: ryanodine receptor-FKBP1B-Calmodulin complex
    • 複合体: ryanodine receptor
      • タンパク質・ペプチド: Ryanodine Receptor
    • 複合体: FKBP1B
      • タンパク質・ペプチド: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • 複合体: Calmodulin
      • タンパク質・ペプチド: Calmodulin-1
  • リガンド: ZINC ION
キーワードreceptor / calcium / channel / complex / TRANSPORT PROTEIN-ISOMERASE-CALCIUM BINDING PROTEIN complex
機能・相同性
機能・相同性情報


positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / cell communication by electrical coupling involved in cardiac conduction ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / cell communication by electrical coupling involved in cardiac conduction / Calmodulin induced events / response to redox state / protein maturation by protein folding / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / 'de novo' protein folding / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of heart rate / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of phosphoprotein phosphatase activity / Activation of RAC1 downstream of NMDARs / FK506 binding / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of axon regeneration / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / : / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / smooth muscle contraction / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / response to vitamin E / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / protein peptidyl-prolyl isomerization / eNOS activation / T cell proliferation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / Ion homeostasis / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation
類似検索 - 分子機能
FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
類似検索 - ドメイン・相同性
Calmodulin-1 / Peptidyl-prolyl cis-trans isomerase FKBP1B
類似検索 - 構成要素
生物種Sus scrofa (ブタ) / 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: 4.2 Å
データ登録者Woll KW / Haji-Ghassemi O
資金援助1件
OrganizationGrant number国
Canadian Institutes of Health Research (CIHR)
引用ジャーナル: Nat Commun / 年: 2021
タイトル: Pathological conformations of disease mutant Ryanodine Receptors revealed by cryo-EM.
著者: Kellie A Woll / Omid Haji-Ghassemi / Filip Van Petegem /
要旨: Ryanodine Receptors (RyRs) are massive channels that release Ca from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and ...Ryanodine Receptors (RyRs) are massive channels that release Ca from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and arrhythmias. Here, we explore the first MH mutation identified in humans by providing cryo-EM snapshots of the pig homolog, R615C, showing that it affects an interface between three solenoid regions. We also show the impact of apo-calmodulin (apoCaM) and how it can induce opening by bending of the bridging solenoid, mediated by its N-terminal lobe. For R615C RyR1, apoCaM binding abolishes a pathological 'intermediate' conformation, distributing the population to a mixture of open and closed channels, both different from the structure without apoCaM. Comparisons show that the mutation primarily affects the closed state, inducing partial movements linked to channel activation. This shows that disease mutations can cause distinct pathological conformations of the RyR and facilitate channel opening by disrupting interactions between different solenoid regions.
履歴
登録2020年5月21日-
ヘッダ(付随情報) 公開2021年1月13日-
マップ公開2021年1月13日-
更新2024年3月6日-
現状2024年3月6日処理サイト: RCSB / 状態: 公開

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構造の表示

ムービー
  • 表面図（断面を密度値に従い着色）
  • 表面レベル: 0.022
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（円筒半径に従い着色）
  • 表面レベル: 0.022
  • UCSF Chimeraによる作画
  • ダウンロード
  • あてはめたモデルとの重ね合わせ
  • 原子モデル: PDB-6x33
  • 表面レベル: 0.022
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューアEMマップ:
SurfViewMolmilJmol/JSmol
添付画像

emd_22016.png

ダウンロードとリンク

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マップ

ファイルダウンロード / ファイル: emd_22016.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈RyR1, FKBP12.6, CaM
ボクセルのサイズX=Y=Z: 1.09 Å
密度
表面レベル登録者による: 0.022 / ムービー #1: 0.022
最小 - 最大-0.13581067 - 0.17267257
平均 (標準偏差)-0.000000000013079 (±0.0043265284)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ480480480
Spacing480480480
セルA=B=C: 523.2 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z523.200523.200523.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ410410410
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.1360.173-0.000

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添付データ

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試料の構成要素

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全体 : ryanodine receptor-FKBP1B-Calmodulin complex

全体名称: ryanodine receptor-FKBP1B-Calmodulin complex
要素
  • 複合体: ryanodine receptor-FKBP1B-Calmodulin complex
    • 複合体: ryanodine receptor
      • タンパク質・ペプチド: Ryanodine Receptor
    • 複合体: FKBP1B
      • タンパク質・ペプチド: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • 複合体: Calmodulin
      • タンパク質・ペプチド: Calmodulin-1
  • リガンド: ZINC ION

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超分子 #1: ryanodine receptor-FKBP1B-Calmodulin complex

超分子名称: ryanodine receptor-FKBP1B-Calmodulin complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3

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超分子 #2: ryanodine receptor

超分子名称: ryanodine receptor / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #2
由来(天然)生物種: Sus scrofa (ブタ) / 組織: Skeletal Muscle

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超分子 #3: FKBP1B

超分子名称: FKBP1B / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #1
由来(天然)生物種: Homo sapiens (ヒト)

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超分子 #4: Calmodulin

超分子名称: Calmodulin / タイプ: complex / ID: 4 / 親要素: 1 / 含まれる分子: #3
由来(天然)生物種: Homo sapiens (ヒト)

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分子 #1: Peptidyl-prolyl cis-trans isomerase FKBP1B

分子名称: Peptidyl-prolyl cis-trans isomerase FKBP1B / タイプ: protein_or_peptide / ID: 1 / コピー数: 4 / 光学異性体: LEVO / EC番号: peptidylprolyl isomerase
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 11.667305 KDa
組換発現生物種: Escherichia coli (大腸菌)
配列文字列:
GVEIETISPG DGRTFPKKGQ TCVVHYTGML QNGKKFDSSR DRNKPFKFRI GKQEVIKGFE EGAAQMSLGQ RAKLTCTPDV AYGATGHPG VIPPNATLIF DVELLNLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

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分子 #2: Ryanodine Receptor

分子名称: Ryanodine Receptor / タイプ: protein_or_peptide / ID: 2 / コピー数: 4 / 光学異性体: LEVO
由来(天然)生物種: Sus scrofa (ブタ)
分子量理論値: 425.09225 KDa
配列文字列: QFLRTDDEVV LQCNATVLKE QLKLCLAAEG FGNRLCFLEP TSNAQNVPPD LAICCFVLEQ SLSVRALQEM LANGHRTLLY GHAILLRHA HSGMYLSCLT TSRSMTDKLA FDVGLQEDAT GEACWWTTHP ASKQRSEGEK VRVGDDLILV SVSSERYLHL S TASGELQV ...文字列:
QFLRTDDEVV LQCNATVLKE QLKLCLAAEG FGNRLCFLEP TSNAQNVPPD LAICCFVLEQ SLSVRALQEM LANGHRTLLY GHAILLRHA HSGMYLSCLT TSRSMTDKLA FDVGLQEDAT GEACWWTTHP ASKQRSEGEK VRVGDDLILV SVSSERYLHL S TASGELQV DASFMQTLWN MNPICSGCEE GYVTGGHVLR LFHGHMDECL TISPADSDDQ RRLVYYEGGS VCTHARSLWR LE PLRISWS GSHLRWGQPL RIRHVTTGRY LALIEDQGLV VVDASKAHTK ATSFCFRISK EKLKRDVEGM GPPEIKYGES LCF VQHVAS GLWLTYAALK KKAILHQEGH MDDALSLTRC QQEESQAARM IYSTAGLYNH FIKGLDSFSG KPRGSGAPAG TALP LEGVI LSLQDLIGYF EPPSEELQHE EKQSKLRSLR NRQSLFQEEG MLSLVLNCID RLNVYTTAAH FAEFAGEEAA ESWKE IVNL LYEILASLIR GNRANCALFS NNLDWLVSKL DRLEASSGIL EVLYCVLIES PEVLNIIQEN HIKSIISLLD KHGRNH KVL DVLCSLCVCN GVAVRSNQDL ITENLLPGRE LLLQTNLINY VTSIRPNIFV GRAEGTTQYS KWYFEVMVDE VVPFLTA QA THLRVGWALT EGYSPYPGGG EGWGGNGVGD DLYSYGFDGL HLWTGHVPRL VTSPGQHLLA PEDVVSCCLD LSVPSISF R INGCPVQGVF EAFNLNGLFF PVVSFSAGVK VRFLLGGRHG EFKFLPPPGY APCHEAVLPR ERLRLEPIKE YRREGPRGP HLVGPSRCLS HTDFVPCHLE RIREKLAENI HELWALTRIE QGWTYGPVRD DNKRLHPCLV DFHSLPEPER NYNLQMSGET LKTLLALGC HVGMADEKAE DNLRKTKLPK TYMMSNGYKP APLDLSHVRL TPAQTTLVDR LAENGHNVWA RDRVAQGWSY S AVQDIPAR RNPRLVPYRL LDEATKRSNR DSLCQAVRTL LGYGYNIERV RIFRAEKSYA VQSGRWYFEF EAVTTGEMRV GW ARPELRP DVELGADELA YVFNGHRGQR WHLGSELFGR PWQSGDVVGC MIDLTENTII FTLNGEVLMS DSGSETAFRD IEV GDGFLP VCSLGPGQVG HLNLGQDVSS LRFFAICGLQ EGFEPFAINM QRPVTTWFSK SLPQFEAVPL EHPHYEVSRV DGTV DTPPC LRLTHRSLVE MLFLRLSLPV QFHQLNTTTY YYSVRVFAGQ EPSCVWVGWV TPDYHQHDMN FDLTKVRAVT VTMGD NIHS SLKCSNCYMV WGGDFVSHTD LVIGCLVDLA TGLMTFTANG KESNTFFQVE PNTKLFPAVF VLPTHQNVIQ FELGKQ KNI MPLSAAMFLS ERKNPAPQCP PRLEMQMLMP VSWSRMPNHF LRVETRRAGE RLGWAVQCQE PLTMMALHIP EENRCMD IL ELSERLDLQQ FHSHTLRLYR AVCALGNNRV AHALCSHVDQ AQLLHALEDA HLPGPLRAGY YDLLISIHLE SACRSRRS M LSEYIVPLTP ETRAITLFPP RHGLPGVGVT TSLRPPHHFS APCFVAALPE APARLSPSIP LEALRDKALR MLGEAVRDG GQHARDPVGG SVEFQFVPVL KLVSTLLVMG IFGDEDVKQI LKMIEPEVEE GLLQMKLPES VKLQMCNLLE YFCDQELQHR VESLAAFAE RYVDKLQANQ RDRYGILMKA FTMTAAETAR RTREFRSPPQ EQINMLLHFK PLPDEIRQDL LEFHQDLLTH C GIQLQSLQ ELVSHTVVRW AQEDFVQSPE LVRAMFSLLH RQYDGLGELL RALPRAYTIS PSSVEDTMSL LECLGQIRSL LI VQMGPQE ENLMIQSIGN IMNNKVFYQH PNLMRALGMH ETVMEVMVNV LRFPKMVTSC CRFLCYFCRI SRQNQRSMFD HLS YLLENS GGMQGSTPLD VAAASVIDNN ELALALQEQD LEKVVSYLAG CGLQSCPMLL AKGYPDIGWN PCGGERYLDF LRFA VFVNG ESVEENANVV VRLLIRKPEC FGPALRGEGG SGLLATIEEA IHLGHAIMSF YAALIDLLGR CAPEMHLIQA GKGEA LRIR AILRSLVPLD DLVGIISLPL QIPMSASFVP DHKASMVLFL DRVYGIENQD FLLHVLDVGF LPDMRAAALA LNRYLC LAV LPLITKCAPL FAMVDSMLHT VYRLSRGRSL TKAQRDVIEE CLMALCRYIR PSMLQHLLRR LVF(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)DPRPVETL NVIIPEKLDS FI NKFAEYT HEKWAFDKIQ NNWSYGENID EELKTHPMLR PYKTFSEKDK EIYRWPIKES LKAMIAWEWT IEKAREGEYN PQP PDLSGV TLSRELQAMA EQLAENYHNT WGRKKKQELE AKGGGTHPLL VPYDTLTAKE KARDREKAQE LLKFLQMNGY AVTR (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)F SVLCRDLYAL YPLL IRYVD NNRAHWLTEP NPSAEELFRM VGEIFIYWSK SHNFKREEQN FVV(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)HKLLS KQRRR AVVA CFRMTPLYNL PTHRACNMFL ESYKAAWILT EDHSFEDRMI DDLSKAGEQE EEEEEVEEKK PDPLHQLVLH FSRTAL TEK SKLDEDYLYM AYADIMAKSC HLEESFEEKE MEKQRLLYQQ ARLHNRGAAE MVLQMISACK GETGAMVSST LKLGISI LN GGNADVQQKM LDYLKDKKEV GFFQSIQALM QTCSVLDLNA FERQNKAEGL GMVNEDGTVI GEKVMADDEF TQDLFRFL Q LLCEGHNNDF QNYLRTQTGN TTTINIIICT VDYLLRLQES ISDFYWYYSG KDVIEEQGKR NFSKAMSVAK QVFNSLTEY IQGPCTGNQQ SLAHSRLWDA VVGFLHVFAH MMMKLAQDSS QIELLKELLD LQKDMVVMLL SLLEGNVVNG MIARQMVDML VESSSNVEM ILKFFDMFLK LKDIVGSEAF QDYVTDPRGL ISKKDFQK(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)EFA NR FQEPARDIGF NVAVLLTNLS EHVPHDPRLR NFLELAESIL EYFRPYLGRI EIMGASRRIE RIYFEISETN RAQWEMPQ V KESKRQFIFD VVNEKMELFV SFCEDTIFEM QIAAQ(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)EVQRVKF LNYLSRNFYT LRFLALFLAF AINFILLF Y KVSDSPPVYY FLEESTGYME PALRCLSLLH TLVAFLCIIG YNCLKVPLVI FKREKELARK LEFDGLYITE QPEDDDVKG QWDRLVLNTP SFPSNYWDKF VKRKVLDKHG DIYGRERIAE IDVKYQIWKF GVIFTDNSFL YLGWYMVMSL LGHYNNFFFA AHLLDIAMG VKTLRTILSS VTHNGKQLVM TVGLLAVVVY LYTVVAFNFF RKFYNKMKCD DMMTCYLFHM YVGVRAGGGI G DEIEDPAG DEYELYRVVF DITFFFFVIV ILLAIIQGLI IDAFGELRDQ QEQVREDMET KCFICGIGSD YFDTTPHRFE TH TLEEHNL ANYMFFLMYL INKDETEHTG QESYVWKMYQ ERCWDFFPAG DCFRKQYEDQ L

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分子 #3: Calmodulin-1

分子名称: Calmodulin-1 / タイプ: protein_or_peptide / ID: 3 / コピー数: 4 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 16.723365 KDa
組換発現生物種: Escherichia coli (大腸菌)
配列文字列:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTA

UniProtKB: Calmodulin-1

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分子 #4: ZINC ION

分子名称: ZINC ION / タイプ: ligand / ID: 4 / コピー数: 4 / 式: ZN
分子量理論値: 65.409 Da

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実験情報

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構造解析

手法クライオ電子顕微鏡法
解析単粒子再構成法
試料の集合状態particle

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試料調製

緩衝液pH: 7.5
グリッド詳細: unspecified
凍結凍結剤: ETHANE

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
撮影フィルム・検出器のモデル: FEI FALCON III (4k x 4k)
平均電子線量: 50.0 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: DIFFRACTION
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

初期モデルモデルのタイプ: PDB ENTRY
最終 再構成解像度のタイプ: BY AUTHOR / 解像度: 4.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: PHENIX (ver. dev-3714) / 使用した粒子像数: 25122
初期 角度割当タイプ: MAXIMUM LIKELIHOOD
最終 角度割当タイプ: MAXIMUM LIKELIHOOD

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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