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- EMDB-22395: Functional Pathways of Biomolecules Retrieved from Single-particl... -

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基本情報

登録情報
データベース: EMDB / ID: EMD-22395
タイトルFunctional Pathways of Biomolecules Retrieved from Single-particle Snapshots - Frame 29 - State 3 (S3)
マップデータRyR1-CS2 frame 29 - state 3 (S3)
試料
  • 複合体: Ryanodine receptor 1 bound to FKBP1B
    • タンパク質・ペプチド: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • タンパク質・ペプチド: ryanodine receptor type 1
  • リガンド: ZINC ION
  • リガンド: CALCIUM ION
キーワードion channel / Ca2+ channel / excitation/contraction coupling / MEMBRANE PROTEIN
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 calcium-mediated signaling / 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 / response to redox state / protein maturation by protein folding / 'de novo' protein folding ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / 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 / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / FK506 binding / positive regulation of axon regeneration / channel regulator activity / smooth muscle contraction / response to vitamin E / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T cell proliferation / Ion homeostasis / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / calcium channel complex / sarcoplasmic reticulum membrane / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / response to hydrogen peroxide / Stimuli-sensing channels / Z disc / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / signaling receptor binding / membrane / cytosol / cytoplasm
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
類似検索 - ドメイン・相同性
Peptidyl-prolyl cis-trans isomerase FKBP1B
類似検索 - 構成要素
生物種Oryctolagus cuniculus (ウサギ) / 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: 4.5 Å
データ登録者Dashti A / des Georges A
資金援助 米国, 8件
OrganizationGrant number国
Department of Energy (DOE, United States)DE-SC0002164 米国
National Science Foundation (NSF, United States)STC 1231306 米国
National Science Foundation (NSF, United States)1551489 米国
Howard Hughes Medical Institute (HHMI)Joachim Frank 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM55440 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM29169 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133598 米国
Department of Energy (DOE, United States)DE-AC05-00OR22725 米国
引用
ジャーナル: Nat Commun / 年: 2020
タイトル: Retrieving functional pathways of biomolecules from single-particle snapshots.
著者: Ali Dashti / Ghoncheh Mashayekhi / Mrinal Shekhar / Danya Ben Hail / Salah Salah / Peter Schwander / Amedee des Georges / Abhishek Singharoy / Joachim Frank / Abbas Ourmazd /
要旨: A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an ...A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.
#1: ジャーナル: Nat Commun / 年: 2020
タイトル: Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots
著者: Dashti A / des Georges A / Singharoy A / Frank J / Ourmazd A
履歴
登録2020年7月31日-
ヘッダ(付随情報) 公開2020年8月12日-
マップ公開2020年8月12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: 0.16
  • 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: 0.16
  • 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-7jmi
  • 表面レベル: 0.16
  • 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_22395.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_22395.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈RyR1-CS2 frame 29 - state 3 (S3)
投影像・断面図

画像のコントロール

大きさ
明度
コントラスト
その他
軸Z (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 400 pix.
= 502. Å		1.26 Å/pix.
x 400 pix.
= 502. Å		1.26 Å/pix.
x 400 pix.
= 502. Å

表面

投影像

断面 (1/3)

断面 (1/2)

断面 (2/3)

画像は Spider により作成

ボクセルのサイズX=Y=Z: 1.255 Å
密度

ヒストグラム

ヒストグラム (対数)
表面レベル登録者による: 0.16 / ムービー #1: 0.16
最小 - 最大-0.23651816 - 0.54868877
平均 (標準偏差)0.0009594383 (±0.029728858)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ400400400
Spacing400400400
セルA=B=C: 502.0 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.2551.2551.255
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z502.000502.000502.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2370.5490.001

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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 bound to FKBP1B

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

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超分子 #1: Ryanodine receptor 1 bound to FKBP1B

超分子名称: Ryanodine receptor 1 bound to FKBP1B / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2
由来(天然)生物種: Oryctolagus cuniculus (ウサギ)
分子量理論値: 2.3 MDa

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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 type 1

分子名称: ryanodine receptor type 1 / 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: Oryctolagus cuniculus (ウサギ) / 組織: thigh
分子量理論値: 502.246719 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)MPL SAAMFLSERK NPAPQCP PR LEVQMLMPVS WSRMPNHFLQ VETRRAGERL GWAVQCQDPL TMMALHIPEE NRCMDILELS ERLDLQRFHS HTLRLYRA V CALGNNRVAH ALCSHVDQAQ LLHALEDAHL PGPLRAGYYD LLISIHLESA CRSRRSMLSE YIVPLTPETR AITLFPPGR KGGNARRHGL PGVGVTTSLR PPHHFSPPCF VAALPAAGVA EAPARLSPAI PLEALRDKAL RMLGEAVRDG GQHARDPVGG SVEFQFVPV LKLVSTLLVM GIFGDEDVKQ ILKMIEPEVF TEEEEEEEEE EEEEEEEEED EEEKEEDEEE EEKEDAEKEE E EAPEGEKE DLEEGLLQMK LPESVKLQMC NLLEYFCDQE LQHRVESLAA FAERYVDKLQ ANQRSRYALL MRAFTMSAAE TA RRTREFR SPPQEQINML LHFKDEADEE DCPLPEDIRQ DLQDFHQDLL AHCGIQLEGE EEEPEEETSL SSRLRSLLET VRL VKKKEE KPEEELPAEE KKPQSLQELV SHMVVRWAQE DYVQSPELVR AMFSLLHRQY DGLGELLRAL PRAYTISPSS VEDT MSLLE CLGQIRSLLI VQMGPQEENL MIQSIGNIMN NKVFYQHPNL MRALGMHETV MEVMVNVLGG GETKEIRFPK MVTSC CRFL CYFCRISRQN QRSMFDHLSY LLENSGIGLG MQGSTPLDVA AASVIDNNEL ALALQEQDLE KVVSYLAGCG LQSCPM LLA KGYPDIGWNP CGGERYLDFL RFAVFVNGES VEENANVVVR LLIRKPECFG PALRGEGGSG LLAAIEEAIR ISEDPAR DG PGVRRDRRRE HFGEEPPEEN RVHLGHAIMS FYAALIDLLG RCAPEMHLIQ AGKGEALRIR AILRSLVPLD DLVGIISL P LQIPTL(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)NFDP RPVETLNVII PEKLDSFINK F AEYTHEKW AFDKIQNNWS YGENVDEELK THPMLRPYKT FSEKDKEIYR WPIKESLKAM IAWEWTIEKA REGEEERTEK KK TRKISQT AQTYDPREGY NPQPPDLSGV TLSRELQAMA EQLAENYHNT WGRKKKQELE AKGGGTHPLL VPYDTLTAKE KAR DREKAQ ELLKFLQMNG YAVTR(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)TPLYNL PTHRACNMFL ESYKAAWILT EDHSFEDRMI DDLSKAGEQE EEEEEVEEKK PDPLHQLVL HFSRTALTEK SKLDEDYLYM AYADIMAKSC HLEEGGENGE AEEEEVEVSF EEKEMEKQRL LYQQSRLHTR GAAEMVLQMI SACKGETGA MVSSTLKLGI SILNGGNAEV QQKMLDYLKD KKEVGFFQSI QALMQTCSVL DLNAFERQNK AEGLGMVNED G TVINRQNG EKVMADDEFT QDLFRFLQLL CEGHNNDFQN YLRTQTGNTT TINIIICTVD YLLRLQESIS DFYWYYSGKD VI EEQGKRN FSKAMSVAKQ VFNSLTEYIQ GPCTGNQQSL AHSRLWDAVV GFLHVFAHMM MKLAQDSSQI ELLKELLDLQ KDM VVMLLS LLEGNVVNGM IARQMVDMLV ESSSNVEMIL KFFDMFLKLK DIVGSEAFQD YVTDPRGLIS KKDFQKAMDS QKQF TGPEI QFLLSCSEAD ENEMINFEEF ANRFQEPARD IGFNVAVLLT NLSEHVPHDP RLRNFLELAE SILEYFRPYL GRIEI MGAS RRIERIYFEI SETNRAQWEM PQVKESKRQF IFDVVNEGGE AEKMELFVSF CEDTIFEMQI AAQISEPEGE PEADED EGM GEAAAEGAEE GAAGAEGAAG TVAAGATARL AAAAARALRG LSYRSLRRRV RRLRRLTARE AATALAALLW AVVARAG AA GAGAAAGALR LLWGSLFGGG LVEGAKKVTV TELLAGMPDP TSDEVHGEQP AGPGGDADGA GEGEGEGDAA EGDGDEEV A GHEAGPGGAE GVVAVADGGP FRPEGAGGLG DMGDTTPAEP PTPEGSPILK RKLGVDGEEE ELVPEPEPEP EPEPEKADE ENGEKEEVPE APPEPPKKAP PSPPAKKEEA GGAGMEFWGE LEVQRVKFLN YLSRNFYTLR FLALFLAFAI NFILLFYKVS DSPPGEDDM EGSAAGDLAG AGSGGGSGWG SGAGEEAEGD EDENMVYYFL EESTGYMEPA LWCLSLLHTL VAFLCIIGYN C LKVPLVIF KREKELARKL EFDGLYITEQ PGDDDVKGQW DRLVLNTPSF PSNYWDKFVK RKVLDKHGDI FGRERIAELL GM DLASLEI TAHNERKPDP PPGLLTWLMS IDVKYQIWKF GVIFTDNSFL YLGWYMVMSL LGHYNNFFFA AHLLDIAMGV KTL RTILSS VTHNGKQLVM TVGLLAVVVY LYTVVAFNFF RKFYNKSEDE DEPDMKCDDM MTCYLFHMYV GVRAGGGIGD EIED PAGDE YELYRVVFDI TFFFFVIVIL LAIIQGLIID AFGELRDQQE QVKEDMETKC FICGIGSDYF DTTPHGFETH TLEEH NLAN YMFFLMYLIN KDETEHTGQE SYVWKMYQER CWDFFPAGDC FRKQYEDQLS

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分子 #3: ZINC ION

分子名称: ZINC ION / タイプ: ligand / ID: 3 / コピー数: 4 / 式: ZN
分子量理論値: 65.409 Da

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分子 #4: CALCIUM ION

分子名称: CALCIUM ION / タイプ: ligand / ID: 4 / 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3D array

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試料調製

濃度8 mg/mL
緩衝液pH: 7.4
グリッドモデル: UltrAuFoil / 材質: GOLD / 支持フィルム - 材質: GOLD / 支持フィルム - トポロジー: HOLEY ARRAY
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

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電子顕微鏡法

顕微鏡FEI POLARA 300
撮影フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
検出モード: COUNTING / 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD
試料ステージ試料ホルダーモデル: GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER
ホルダー冷却材: NITROGEN
実験機器
モデル: Tecnai Polara / 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: EMDB MAP
EMDB ID:

8391


詳細: RyR1-Cs2 (EGTA-only)
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: 4.5 Å / 解像度の算出法: OTHER
詳細: RESMAP and visual inspection. FSC not possible as no half-sets are available with the manifold embedding method
使用した粒子像数: 791956
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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原子モデル構築 1

初期モデルPDB ID:

5tb4


Chain - Source name: PDB / Chain - Initial model type: experimental model
詳細fitted to a model domain by domain with the rigid-body fit function in COOT 71, using multiple starting models to avoid model bias (PDB ID: 5TB4, 5T9R, 5TAP, 5T9V, 5TAL, 5TAQ) 22. The models were then refined in real-space using phenix.real_space_refine
精密化空間: REAL / プロトコル: OTHER
得られたモデル

PDB-7jmi:
Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots - Frame 29 - State 3 (S3)

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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