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- EMDB-4258: Structure of Ryanodine receptor 1 in nanodiscs in the presence of... -

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基本情報

登録情報
データベース: EMDB / ID: EMD-4258
タイトルStructure of Ryanodine receptor 1 in nanodiscs in the presence of calcium, ATP and ryanodine
マップデータ
試料
  • 複合体: Ryanodine receptor 1 reconstituted in lipid nanodiscs in the presence of calcium, ATP and ryanodine
    • タンパク質・ペプチド: Ryanodine receptor 1
  • リガンド: ZINC ION
  • リガンド: CALCIUM IONカルシウム
機能・相同性
機能・相同性情報


ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / 筋小胞体 / muscle contraction / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / 生体膜 / identical protein binding
類似検索 - 分子機能
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / リアノジン受容体 / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / リアノジン受容体 / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
類似検索 - ドメイン・相同性
Ryanodine receptor 1
類似検索 - 構成要素
生物種Oryctolagus cuniculus (ウサギ) / Rabbit (ウサギ)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.3 Å
データ登録者Willegems K / Efremov RG
資金援助 ベルギー, 2件
OrganizationGrant number国
IWT131261 ベルギー
FWOG.0266.15N ベルギー
引用ジャーナル: Structure / 年: 2018
タイトル: Influence of Lipid Mimetics on Gating of Ryanodine Receptor.
著者: Katrien Willegems / Rouslan G Efremov /
要旨: Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) ...Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) reconstituted into lipid nanodiscs. RyR1 is a homotetrameric giant ion channel that couples excitation of muscle cells to fast calcium release from the sarcoplasmic reticulum. Using single-particle cryo-EM we show that RyR1 reconstituted into lipid nanodiscs is stabilized in the open conformation when bound to the plant toxin ryanodine, but not in the presence of its physiological activators, calcium and ATP. Further, using ryanodine binding assays we show that membrane mimetics influence RyR1 transition between closed and open-channel conformations. We find that all detergents, including fluorinated detergents added to nanodiscs, stabilize closed state of RyR1. Our biochemical results correlate with available structural data and suggest optimal conditions for structural studies of RyR1 gating.
履歴
登録2018年1月9日-
ヘッダ(付随情報) 公開2018年3月14日-
マップ公開2018年8月8日-
更新2019年11月6日-
現状2019年11月6日処理サイト: PDBe / 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: 0.05
  • 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: 0.05
  • 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-6fg3
  • 表面レベル: 0.05
  • 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_4258.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_4258.map.gz / 形式: CCP4 / 大きさ: 209.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
ボクセルのサイズX=Y=Z: 1.355 Å
密度
表面レベル登録者による: 0.05 / ムービー #1: 0.05
最小 - 最大-0.08701025 - 0.21704483
平均 (標準偏差)0.0007965246 (±0.00919777)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ380380380
Spacing380380380
セルA=B=C: 514.9 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.3551.3551.355
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z514.900514.900514.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0870.2170.001

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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 1 reconstituted in lipid nanodiscs in the pres...

全体名称: Ryanodine receptor 1 reconstituted in lipid nanodiscs in the presence of calcium, ATP and ryanodine
要素
  • 複合体: Ryanodine receptor 1 reconstituted in lipid nanodiscs in the presence of calcium, ATP and ryanodine
    • タンパク質・ペプチド: Ryanodine receptor 1
  • リガンド: ZINC ION
  • リガンド: CALCIUM IONカルシウム

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超分子 #1: Ryanodine receptor 1 reconstituted in lipid nanodiscs in the pres...

超分子名称: Ryanodine receptor 1 reconstituted in lipid nanodiscs in the presence of calcium, ATP and ryanodine
タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1
由来(天然)生物種: Oryctolagus cuniculus (ウサギ) / 株: New Zealand white rabbit / 組織: skeletal muscle / 細胞中の位置: sarcoplasmic reticulum
分子量理論値: 2.2 MDa

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分子 #1: Ryanodine receptor 1

分子名称: Ryanodine receptor 1 / タイプ: protein_or_peptide / ID: 1
詳細: Poly Unk stretches correspond to polypeptide regions where the register is not assigned.
コピー数: 4 / 光学異性体: LEVO
由来(天然)生物種: Rabbit (ウサギ) / 株: New Zealand white rabbit / 組織: skeletal muscle
分子量理論値: 532.033062 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) 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ETRRAGERLG WAVQCQDPLT MMALHIPEEN RCMDILELSE RLDLQRFHSH TLRLYRAVCA LGNNRVAHAL CSHVDQA QL LHALEDAHLP GPLRAGYYDL LISIHLESAC RSRRSMLSEY IVPLTPETRA ITLFPPGRKG GNARRHGLPG VGVTTSLR P PHHFSPPCFV AALPAAGVAE APARLSPAIP LEALRDKALR MLGEAVRDGG QHARDPVGGS VEFQFVPVLK LVSTLLVMG IFGDEDVKQI LKMIEPEVFT EEEEEEEEEE EEEEEEEEDE EEKEEDEEEE EKEDAEKEEE EAPEGEKEDL EEGLLQMKLP ESVKLQMCN LLEYFCDQEL QHRVESLAAF AERYVDKLQA NQRSRYALLM RAFTMSAAET ARRTREFRSP PQEQINMLLH F KDEADEED CPLPEDIRQD LQDFHQDLLA HCGIQLEGEE EEPEEETSLS SRLRSLLETV RLVKKKEEKP EEELPAEEKK PQ SLQELVS HMVVRWAQED YVQSPELVRA MFSLLHRQYD GLGELLRALP RAYTISPSSV EDTMSLLECL GQIRSLLIVQ MGP QEENLM IQSIGNIMNN KVFYQHPNLM RALGMHETVM EVMVNVLGGG ETKEIRFPKM VTSCCRFLCY FCRISRQNQR SMFD HLSYL LENSGIGLGM QGSTPLDVAA ASVIDNNELA LALQEQDLEK VVSYLAGCGL QSCPMLLAKG YPDIGWNPCG GERYL DFLR FAVFVNGESV EENANVVVRL LIRKPECFGP ALRGEGGSGL LAAIEEAIRI SEDPARDGPG VRRDRRREHF GEEPPE ENR VHLGHAIMSF YAALIDLLGR CAPEMHLIQA GKGEALRIRA ILRSLVPLDD LVGIISLPLQ IPTL(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)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(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) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)TPLY NLPTHRACNM FLESYKAAWI LTEDHSFEDR MIDDLSKAGE QEEEEEEVEE KKPDPLHQLV LHFSRTALTE K SKLDEDYL YMAYADIMAK SCHLEEGGEN GEAEEEEVEV SFEEKEMEKQ RLLYQQSRLH TRGAAEMVLQ MISACKGETG AM VSSTLKL GISILNGGNA EVQQKMLDYL KDKKEVGFFQ SIQALMQTCS VLDLNAFERQ NKAEGLGMVN EDGTVINRQN GEK VMADDE FTQDLFRFLQ LLCEGHNNDF QNYLRTQTGN TTTINIIICT VDYLLRLQES ISDFYWYYSG KDVIEEQGKR NFSK AMSVA KQVFNSLTEY IQGPCTGNQQ SLAHSRLWDA VVGFLHVFAH MMMKLAQDSS QIELLKELLD LQKDMVVMLL SLLEG NVVN GMIARQMVDM LVESSSNVEM ILKFFDMFLK LKDIVGSEAF QDYVTDPRGL ISKKDFQKAM DSQKQFTGPE IQFLLS CSE ADENEMINFE EFANRFQEPA RDIGFNVAVL LTNLSEHVPH DPRLRNFLEL AESILEYFRP YLGRIEIMGA SRRIERI YF EISETNRAQW EMPQVKESKR QFIFDVVNEG GEAEKMELFV SFCEDTIFEM QIAAQISEPE GEPEADEDEG MGEAAAEG A EEGAAGAEGA AGTVAAGATA RLAAAAARAL RGLSYRSLRR RVRRLRRLTA REAATALAAL LWAVVARAGA AGAGAAAGA LRLLWGSLFG GGLVEGAKKV TVTELLAGMP DPTSDEVHGE QPAGPGGDAD GAGEGEGEGD AAEGDGDEEV AGHEAGPGGA EGVVAVADG GPFRPEGAGG LGDMGDTTPA EPPTPEGSPI LKRKLGVDGE EEELVPEPEP EPEPEPEKAD EENGEKEEVP E APPEPPKK APPSPPAKKE EAGGAGMEFW GELEVQRVKF LNYLSRNFYT LRFLALFLAF AINFILLFYK VSDSPPGEDD ME GSAAGDL AGAGSGGGSG WGSGAGEEAE GDEDENMVYY FLEESTGYME PALWCLSLLH TLVAFLCIIG YNCLKVPLVI FKR EKELAR KLEFDGLYIT EQPGDDDVKG QWDRLVLNTP SFPSNYWDKF VKRKVLDKHG DIFGRERIAE LLGMDLASLE ITAH NERKP DPPPGLLTWL MSIDVKYQIW KFGVIFTDNS FLYLGWYMVM SLLGHYNNFF FAAHLLDIAM GVKTLRTILS SVTHN GKQL VMTVGLLAVV VYLYTVVAFN FFRKFYNKSE DEDEPDMKCD DMMTCYLFHM YVGVRAGGGI GDEIEDPAGD EYELYR VVF DITFFFFVIV ILLAIIQGLI IDAFGELRDQ QEQVKEDMET KCFICGIGSD YFDTTPHGFE THTLEEHNLA NYMFFLM YL INKDETEHTG QESYVWKMYQ ERCWDFFPAG DCFRKQYEDQ LS

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分子 #2: ZINC ION

分子名称: ZINC ION / タイプ: ligand / ID: 2 / コピー数: 4 / 式: ZN
分子量理論値: 65.409 Da

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分子 #3: CALCIUM ION

分子名称: CALCIUM ION / タイプ: ligand / ID: 3 / コピー数: 4 / 式: CA
分子量理論値: 40.078 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

濃度3 mg/mL
緩衝液pH: 7.4
構成要素:
濃度式名称
20.0 mMC7H15NO4S3-morpholinopropane-1-sulfonic acid
200.0 mMNaCl塩化ナトリウムsodium chloride塩化ナトリウム
7.0 mMC10H16N5O13P3adenosine triphosphateアデノシン三リン酸
1.0 mMC4H10O2S2Dithiothreitolジチオトレイトール
0.2 mMC14H24N2O10EGTA
0.25 mMCaCl2calcium chloride
2.0 mg/mLC20H25F13O11fluorinated octyl maltoside
0.02 mMC25H35NO9ryanodineリアノジン
グリッドモデル: Quantifoil R2/1 / 材質: COPPER / 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 - 雰囲気: AIR / 前処理 - 気圧: 0.04 kPa
詳細: Glow discharged in ELMO plasma cleaner at current of 3 mA for 1 min.
凍結凍結剤: ETHANE / チャンバー内温度: 293.15 K / 装置: HOMEMADE PLUNGER

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
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: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / 最大 デフォーカス（公称値）: 3.0 µm / 最小 デフォーカス（公称値）: 2.0 µm / 倍率（公称値）: 59000
試料ステージホルダー冷却材: NITROGEN
撮影フィルム・検出器のモデル: FEI FALCON II (4k x 4k)
検出モード: COUNTING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / デジタル化 - サンプリング間隔: 14.0 µm / デジタル化 - 画像ごとのフレーム数: 1-7 / 撮影したグリッド数: 1 / 実像数: 3078 / 平均露光時間: 1.0 sec. / 平均電子線量: 28.0 e/Å2
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

粒子像選択選択した数: 75794
CTF補正ソフトウェア - 名称: CTFFIND (ver. 4)
初期モデルモデルのタイプ: OTHER
詳細: generated from class averages by EMAN2 initial_model routine
初期 角度割当タイプ: PROJECTION MATCHING
最終 3次元分類ソフトウェア - 名称: RELION (ver. 2)
最終 角度割当タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION (ver. 2)
最終 再構成想定した対称性 - 点群: C4 (4回回転対称) / 解像度のタイプ: BY AUTHOR / 解像度: 7.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2) / 使用した粒子像数: 61773
FSC曲線 (解像度の算出)

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原子モデル構築 1

精密化空間: REAL / プロトコル: FLEXIBLE FIT
得られたモデル

PDB-6fg3:
Structure of Ryanodine receptor 1 in nanodiscs in the presence of calcium, ATP and ryanodine

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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://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

他の情報も見る