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- EMDB-10498: CryoEM structure of the ternary DOCK2-ELMO1-RAC1 complex -

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基本情報

登録情報
データベース: EMDB / ID: EMD-10498
タイトルCryoEM structure of the ternary DOCK2-ELMO1-RAC1 complex
マップデータ
試料
  • 複合体: Ternary complex of DOCK2-ELMO1-RAC1
    • タンパク質・ペプチド: Dedicator of cytokinesis protein 2
    • タンパク質・ペプチド: Engulfment and cell motility protein 1ELMO1
    • タンパク質・ペプチド: Ras-related C3 botulinum toxin substrate 1
キーワードguanine nucleotide exchange factor (グアニンヌクレオチド交換因子) / cytoskeleton (細胞骨格) / actin (アクチン) / cryoEM (低温電子顕微鏡法) / SIGNALING PROTEIN
機能・相同性
機能・相同性情報


membrane raft polarization / alpha-beta T cell proliferation / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / 飲作用 / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 ...membrane raft polarization / alpha-beta T cell proliferation / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / 飲作用 / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / immunological synapse formation / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / negative thymic T cell selection / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / guanyl-nucleotide exchange factor complex / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / myoblast fusion / positive thymic T cell selection / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / phagocytosis, engulfment / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of phagocytosis / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / T cell receptor binding / GTPase activator activity / cell-matrix adhesion / cell chemotaxis / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / 低分子量GTPアーゼ / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1
類似検索 - 分子機能
Dedicator of cytokinesis protein 2 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / DOCKER, Lobe A ...Dedicator of cytokinesis protein 2 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe C / DHR-2, Lobe B / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / C2 DOCK-type domain profile. / DOCKER domain profile. / Pleckstrin homology domain / Variant SH3 domain / Small GTPase Rho / small GTPase Rho family profile. / C2 domain superfamily / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / 低分子量GTPアーゼ / 低分子量GTPアーゼ / Rab subfamily of small GTPases / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3ドメイン / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Ras-related C3 botulinum toxin substrate 1 / Engulfment and cell motility protein 1 / Dedicator of cytokinesis protein 2
類似検索 - 構成要素
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: 4.1 Å
データ登録者Chang L / Yang J
資金援助 英国, European Union, 3件
OrganizationGrant number国
Medical Research Council (United Kingdom)MC_UP_1201/6 英国
Cancer Research UKC576/A14109 英国
Marie Sklodowska-Curie Actions, FragNET ITN657725European Union
引用ジャーナル: Nat Commun / 年: 2020
タイトル: Structure of the DOCK2-ELMO1 complex provides insights into regulation of the auto-inhibited state.
著者: Leifu Chang / Jing Yang / Chang Hwa Jo / Andreas Boland / Ziguo Zhang / Stephen H McLaughlin / Afnan Abu-Thuraia / Ryan C Killoran / Matthew J Smith / Jean-Francois Côté / David Barford /
要旨: DOCK (dedicator of cytokinesis) proteins are multidomain guanine nucleotide exchange factors (GEFs) for RHO GTPases that regulate intracellular actin dynamics. DOCK proteins share catalytic (DOCK) ...DOCK (dedicator of cytokinesis) proteins are multidomain guanine nucleotide exchange factors (GEFs) for RHO GTPases that regulate intracellular actin dynamics. DOCK proteins share catalytic (DOCK) and membrane-associated (DOCK) domains. The structurally-related DOCK1 and DOCK2 GEFs are specific for RAC, and require ELMO (engulfment and cell motility) proteins for function. The N-terminal RAS-binding domain (RBD) of ELMO (ELMO) interacts with RHOG to modulate DOCK1/2 activity. Here, we determine the cryo-EM structures of DOCK2-ELMO1 alone, and as a ternary complex with RAC1, together with the crystal structure of a RHOG-ELMO2 complex. The binary DOCK2-ELMO1 complex adopts a closed, auto-inhibited conformation. Relief of auto-inhibition to an active, open state, due to a conformational change of the ELMO1 subunit, exposes binding sites for RAC1 on DOCK2, and RHOG and BAI GPCRs on ELMO1. Our structure explains how up-stream effectors, including DOCK2 and ELMO1 phosphorylation, destabilise the auto-inhibited state to promote an active GEF.
履歴
登録2019年11月15日-
ヘッダ(付随情報) 公開2020年7月29日-
マップ公開2020年7月29日-
更新2023年7月26日-
現状2023年7月26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: 0.04
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（半径に従い着色）
  • 表面レベル: 0.04
  • 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-6tgc
  • 表面レベル: 0.04
  • UCSF Chimeraによる作画
  • ダウンロード
  • 単純化した表面モデル + あてはめた原子モデル
  • 原子モデルPDB-6tgc
  • Jmol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_10498.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_10498.map.gz / 形式: CCP4 / 大きさ: 85.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
ボクセルのサイズX=Y=Z: 1.43 Å
密度
表面レベル登録者による: 0.04 / ムービー #1: 0.04
最小 - 最大-0.07212933 - 0.17415883
平均 (標準偏差)-0.000120875775 (±0.003674054)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ282282282
Spacing282282282
セルA=B=C: 403.25998 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z282282282
origin x/y/z0.0000.0000.000
length x/y/z403.260403.260403.260
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS282282282
D min/max/mean-0.0720.174-0.000

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添付データ

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追加マップ: #1

ファイルemd_10498_additional.map
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

ヒストグラム

ヒストグラム (対数)

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試料の構成要素

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全体 : Ternary complex of DOCK2-ELMO1-RAC1

全体名称: Ternary complex of DOCK2-ELMO1-RAC1
要素
  • 複合体: Ternary complex of DOCK2-ELMO1-RAC1
    • タンパク質・ペプチド: Dedicator of cytokinesis protein 2
    • タンパク質・ペプチド: Engulfment and cell motility protein 1ELMO1
    • タンパク質・ペプチド: Ras-related C3 botulinum toxin substrate 1

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超分子 #1: Ternary complex of DOCK2-ELMO1-RAC1

超分子名称: Ternary complex of DOCK2-ELMO1-RAC1 / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 600 KDa

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分子 #1: Dedicator of cytokinesis protein 2

分子名称: Dedicator of cytokinesis protein 2 / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 195.902516 KDa
組換発現生物種: Trichoplusia ni (イラクサキンウワバ)
配列文字列: MAPWRKADKE RHGVAIYNFQ GSGAPQLSLQ IGDVVRIQET CGDWYRGYLI KHKMLQGIFP KSFIHIKEVT VEKRRNTENI IPAEIPLAQ EVTTTLWEWG SIWKQLYVAS KKERFLQVQS MMYDLMEWRS QLLSGTLPKD ELKELKQKVT SKIDYGNKIL E LDLIVRDE ...文字列:
MAPWRKADKE RHGVAIYNFQ GSGAPQLSLQ IGDVVRIQET CGDWYRGYLI KHKMLQGIFP KSFIHIKEVT VEKRRNTENI IPAEIPLAQ EVTTTLWEWG SIWKQLYVAS KKERFLQVQS MMYDLMEWRS QLLSGTLPKD ELKELKQKVT SKIDYGNKIL E LDLIVRDE DGNILDPDNT SVISLFHAHE EATDKITERI KEEMSKDQP(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)GFPE IIMPGDVRND IYITLLQGDF DKYNKTTQRN VEVIMCVCAE DGKTLP NAI CVGAGDKPMN EYRSVVYYQV KQPRWMETVK VAVPIEDMQR IHLRFMFRHR SSLESKDKGE KNFAMSYVKL MKEDGTT LH DGFHDLVVLK GDSKKMEDAS AYLTLPSYRH HVENKGATLS RSSSSVGGLS VSSRDVFSIS TLVCST(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)IM MEH SQSDEY DILVFDALIY IIGLIADRKF Q(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)S SELVDFLMET FIMFKDLIGK NVYPGDWMAM SMVQNRVFLR AINKFAETMN QKFL EHTNF EFQLWNNYFH LAVAFITQDS LQLEQFSHAK YNKILNKYGD MRRLIGFSIR DMWYKLGQNK ICFIPGMVGP ILEMT LIPE AELRKATIPI FFDMMLCEYQ RSGDFKKFEN EIILKLDHEV EGGRGDEQYM QLLESILMEC AAEHPTIAKS VENFVN LVK GLLEKLLDYR GVMTDESKDN RMSCTVNLLN FYKDNNREEM YIRYLYKLRD LHLDCDNYTE AAYTLLLHTW LLKWSDE QC ASQVMQTGQQ HPQTHRQLKE TLYETIIGYF DKGKMWEEAI SLCKELAEQY EMEIFDYELL SQNLIQQAKF YESIMKIL R PKPDYFAVGY YGQGFPSFLR NKVFIYRGKE YERREDFQMQ LMTQFPNAEK MNTTSAPGDD VKNAPGQYIQ CFTVQPVLD EHPRFKNKPV PDQIINFYKS NYVQRFHYSR PVRRGTVDPE NEFASMWIER TSFVTAYKLP GILRWFEVVH MSQTTISPLE NAIETMSTA NEKILMMINQ YQSDETLPIN PLSMLLNGIV DPAVMGGFAK YEKAFFTEEY VRDHPEDQDK LTHLKDLIAW Q IPFLGAGI KIHEKRVSDN LRPFHDRMEE CFKNLKMKVE KEYGVREMPD FDDRRVGRPR SMLRSYRQMS IISLASMNSD CS TPSKPTS ESFDLELASP KTPRVEQEEP ISPGSTLPEV KLRRSKKRTK RSSVVFADEK AAAESDLKRL SRKHEFMSDT NLS EHAAIP LKASVLSQMS FASQSMPTIP ALALSVAGIP GLDEANTSPR LSQTFLQLSD GDKKTLTRKK VNQFFKTMLA SKSA EEGKQ IPDSLSTDL

UniProtKB: Dedicator of cytokinesis protein 2

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分子 #2: Engulfment and cell motility protein 1

分子名称: Engulfment and cell motility protein 1 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 83.891328 KDa
組換発現生物種: Trichoplusia ni (イラクサキンウワバ)
配列文字列: MPPPADIVKV AIEWPGAYPK LMEIDQKKPL SAIIKEVCDG WSLANHEYFA LQHADSSNFY ITEKNRNEIK NGTILRLTTS PAQNAQQLH ERIQSSSMDA KLEALKDLAS LSRDVTFAQE FINLDGISLL TQMVESGTEL YQKLQKIMKP CFGDMLSFTL T AFVELMDH ...文字列:
MPPPADIVKV AIEWPGAYPK LMEIDQKKPL SAIIKEVCDG WSLANHEYFA LQHADSSNFY ITEKNRNEIK NGTILRLTTS PAQNAQQLH ERIQSSSMDA KLEALKDLAS LSRDVTFAQE FINLDGISLL TQMVESGTEL YQKLQKIMKP CFGDMLSFTL T AFVELMDH GIVSWDTFSV AFIKKIASFV NKSAIDISIL QRSLAILESM VLNSHDLYQK VAQEITIGQL IPHLQGSDQE IQ TYTIAVI NALFLKAPDE RRQEMANILA QKQLRSIILT HVIRAQRAIN NEMAHQLYVL QVLTFNLLED RMMTKMDPQD QAQ RDIIFE LRRIAFDAES EPNNSSGSME KRKSMYTRDY KKLGFINHVN PAMDFTQTPP GMLALDNMLY FAKHHQDAYI RIVL ENSSR EDKHECPFGR SSIELTKMLC EILKVGELPS ETCNDFHPMF FTHDRSFEEF FCICIQLLNK TWKEMRATSE DFNKV MQVV KEQVMRALTT KPSSLDQFKS KLQNLSYTEI LKIRQSERMN QEDFQSRPIL ELKEKIQPEI LELIKQQRLN RLVEGT CFR KLNARRRQDK FWYCRLSPNH KVLHYGDLEE SPQGEVPHDS LQDKLPVADI KAVVTGKDCP HMKEKGALKQ NKEVLEL AF SILYDSNCQL NFIAPDKHEY CIWTDGLNAL LGKDMMSDLT RNDLDTLLSM EIKLRLLDLE NIQIPDAPPP IPKEPSNY D FVYDCN

UniProtKB: Engulfment and cell motility protein 1

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分子 #3: Ras-related C3 botulinum toxin substrate 1

分子名称: Ras-related C3 botulinum toxin substrate 1 / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO / EC番号: 低分子量GTPアーゼ
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 21.478113 KDa
組換発現生物種: Trichoplusia ni (イラクサキンウワバ)
配列文字列: MQAIKCVVVG DGAVGKTCLL ISYTTNAFPG EYIPTVFDNY SANVMVDGKP VNLGLWDTAG QEDYDRLRPL SYPQTDVFLI CFSLVSPAS FENVRAKWYP EVRHHCPNTP IILVGTKLDL RDDKDTIEKL KEKKLTPITY PQGLAMAKEI GAVKYLECSA L TQRGLKTV ...文字列:
MQAIKCVVVG DGAVGKTCLL ISYTTNAFPG EYIPTVFDNY SANVMVDGKP VNLGLWDTAG QEDYDRLRPL SYPQTDVFLI CFSLVSPAS FENVRAKWYP EVRHHCPNTP IILVGTKLDL RDDKDTIEKL KEKKLTPITY PQGLAMAKEI GAVKYLECSA L TQRGLKTV FDEAIRAVLC PPPVKKRKRK CLLL

UniProtKB: Ras-related C3 botulinum toxin substrate 1

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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0.2 mg/mL
緩衝液pH: 8
構成要素:
濃度式名称
20.0 mMC8H18N2O4SHepes
200.0 mMNaCl塩化ナトリウムsodium chloride塩化ナトリウム
グリッドモデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE
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 III

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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
特殊光学系エネルギーフィルター - 名称: GIF Quantum ER / 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: COUNTING / 平均電子線量: 50.0 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

初期モデルモデルのタイプ: INSILICO MODEL
詳細: e2initialmodel.py from the EMAN2 package was used for generation of the initial model
初期 角度割当タイプ: MAXIMUM LIKELIHOOD
最終 角度割当タイプ: MAXIMUM LIKELIHOOD
最終 再構成想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 1.4) / 使用した粒子像数: 245763

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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

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