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- EMDB-7129: Human PI4KIIIa lipid kinase complex -

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基本情報

登録情報
データベース: EMDB / ID: EMD-7129
タイトルHuman PI4KIIIa lipid kinase complex
マップデータHuman PI4KIIIa lipid kinase complex
試料
  • 複合体: Human phosphatidylinositol 4-kinase III alpha complex
    • タンパク質・ペプチド: Phosphatidylinositol 4-kinase III alpha (PI4KA)
    • タンパク質・ペプチド: Tetratricopeptide repeat protein 7B
    • タンパク質・ペプチド: Protein FAM126A
    • タンパク質・ペプチド: Phosphatidylinositol 4-kinase III alpha (PI4KA)
  • リガンド: 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide
キーワードkinase (キナーゼ) / phosphoinositide synthesis / Transferase-Signaling Protein complex
機能・相同性
機能・相同性情報


: / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / viral replication complex formation and maintenance / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / Golgi-associated vesicle membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol phosphate biosynthetic process ...: / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / viral replication complex formation and maintenance / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / Golgi-associated vesicle membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / 髄鞘 / protein localization to plasma membrane / kinase activity / neuron projection / cadherin binding / リン酸化 / viral RNA genome replication / focal adhesion / シグナル伝達 / extracellular exosome / ATP binding / 生体膜 / 細胞膜 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain ...Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Tetratricopeptide repeat / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Phosphatidylinositol 4-kinase alpha / Tetratricopeptide repeat protein 7B / Hyccin
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: 3.6 Å
データ登録者Lees JA / Zhang Y
資金援助 米国, 1件
OrganizationGrant number国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114068 米国
引用ジャーナル: Proc Natl Acad Sci U S A / 年: 2017
タイトル: Architecture of the human PI4KIIIα lipid kinase complex.
著者: Joshua A Lees / Yixiao Zhang / Michael S Oh / Curtis M Schauder / Xiaoling Yu / Jeremy M Baskin / Kerry Dobbs / Luigi D Notarangelo / Pietro De Camilli / Thomas Walz / Karin M Reinisch /
要旨: Plasma membrane (PM) phosphoinositides play essential roles in cell physiology, serving as both markers of membrane identity and signaling molecules central to the cell's interaction with its ...Plasma membrane (PM) phosphoinositides play essential roles in cell physiology, serving as both markers of membrane identity and signaling molecules central to the cell's interaction with its environment. The first step in PM phosphoinositide synthesis is the conversion of phosphatidylinositol (PI) to PI4P, the precursor of PI(4,5)P and PI(3,4,5)P This conversion is catalyzed by the PI4KIIIα complex, comprising a lipid kinase, PI4KIIIα, and two regulatory subunits, TTC7 and FAM126. We here report the structure of this complex at 3.6-Å resolution, determined by cryo-electron microscopy. The proteins form an obligate ∼700-kDa superassembly with a broad surface suitable for membrane interaction, toward which the kinase active sites are oriented. The structural complexity of the assembly highlights PI4P synthesis as a major regulatory junction in PM phosphoinositide homeostasis. Our studies provide a framework for further exploring the mechanisms underlying PM phosphoinositide regulation.
履歴
登録2017年11月27日-
ヘッダ(付随情報) 公開2017年12月13日-
マップ公開2017年12月13日-
更新2024年3月13日-
現状2024年3月13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: 0.05
  • 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: 0.05
  • 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-6bq1
  • 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_7129.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_7129.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Human PI4KIIIa lipid kinase complex
ボクセルのサイズX=Y=Z: 1.3 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-0.16651683 - 0.2872219
平均 (標準偏差)0.00042148505 (±0.0058580837)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ320320320
Spacing320320320
セルA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1670.2870.000

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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 : Human phosphatidylinositol 4-kinase III alpha complex

全体名称: Human phosphatidylinositol 4-kinase III alpha complex
要素
  • 複合体: Human phosphatidylinositol 4-kinase III alpha complex
    • タンパク質・ペプチド: Phosphatidylinositol 4-kinase III alpha (PI4KA)
    • タンパク質・ペプチド: Tetratricopeptide repeat protein 7B
    • タンパク質・ペプチド: Protein FAM126A
    • タンパク質・ペプチド: Phosphatidylinositol 4-kinase III alpha (PI4KA)
  • リガンド: 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide

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超分子 #1: Human phosphatidylinositol 4-kinase III alpha complex

超分子名称: Human phosphatidylinositol 4-kinase III alpha complex
タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#4
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 700 KDa

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分子 #1: Phosphatidylinositol 4-kinase III alpha (PI4KA)

分子名称: Phosphatidylinositol 4-kinase III alpha (PI4KA) / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO / EC番号: 1-phosphatidylinositol 4-kinase
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 173.821438 KDa
組換発現生物種: Homo sapiens (ヒト)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)MMQCV IAVADKVFDA FLNMM ADKA KTKENEEELE RHAQFLLVNF NHIHKRIRRV ADKYLSGLVD KFPHLLWSGT VLKTMLDILQ TLSLSLSADI HKDQPY YDI PDAPYRITVP DTYEARESIV KDFAARCGMI LQEAMKWAPT VTKSHLQEYL NKHQNWVSGL SQHTGLAMAT ESILHFA GY NKQNTTLGAT QLSERPACVK KDYSNFMASL NLRNRYAGEV YGMIRFSGTT GQMSDLNKMM VQDLHSALDR SHPQHYTQ A MFKLTAMLIS SKDCDPQLLH HLCWGPLRMF NEHGMETALA CWEWLLAGKD GVEVPFMREM AGAWHMTVEQ KFGLFSAEI KEADPLAASE ASQPKPCPPE VTPHYIWIDF LVQRFEIAKY CSSDQVEIFS SLLQRSMSLN IGGAKGSMNR HVAAIGPRFK LLTLGLSLL HADVVPNATI RNVLREKIYS TAFDYFSCPP KFPTQGEKRL REDISIMIKF WTAMFSDKKY LTASQLVPPD N QDTRSNLD ITVGSRQQAT QGWINTYPLS SGMSTISKKS GMSKKTNRGS QLHKYYMKRR TLLLSLLATE IERLITWYNP LS APELELD QAGENSVANW RSKYISLSEK QWKDNVNLAW SISPYLAVQL PARFKNTEAI GNEVTRLVRL DPGAVSDVPE AIK FLVTWH TIDADAPELS HVLCWAPTDP PTGLSYFSSM YPPHPLTAQY GVKVLRSFPP DAILFYIPQI VQALRYDKMG YVRE YILWA ASKSQLLAHQ FIWNMKTNIY LDEEGHQKDP DIGDLLDQLV EEITGSLSGP AKDFYQREFD FFNKITNVSA IIKPY PKGD ERKKACLSAL SEVKVQPGCY LPSNPEAIVL DIDYKSGTPM QSAAKAPYLA KFKVKRCGVS ELEKEGLRCR SDSEDE CST QEADGQKISW QAAIFKVGDD CRQDMLALQI IDLFKNIFQL VGLDLFVFPY RVVATAPGCG VIECIPDCTS RDQLGRQ TD FGMYDYFTRQ YGDESTLAFQ QARYNFIRSM AAYSLLLFLL QIKDRHNGNI MLDKKGHIIH IDFGFMFESS PGGNLGWE P DIKLTDEMVM IMGGKMEATP FKWFMEMCVR GYLAVRPYMD AVVSLVTLML DTGLPCFRGQ TIKLLKHRFS PNMTEREAA NFIMKVIQSC FLSNRSRTYD MIQYYQNDIP Y

UniProtKB: Phosphatidylinositol 4-kinase alpha

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分子 #2: Tetratricopeptide repeat protein 7B

分子名称: Tetratricopeptide repeat protein 7B / 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: 96.46057 KDa
組換発現生物種: Homo sapiens (ヒト)
配列文字列: MYPYDVPDYA AIAGAPDLKL MATKKAGSRL ETEIERCRSE CQWERIPELV KQLSAKLIAN DDMAELLLGE SKLEQYLKEH PLRQGASPR GPKPQLTEVR KHLTAALDRG NLKSEFLQES NLIMAKLNYV EGDYKEALNI YARVGLDDLP LTAVPPYRLR V IAEAYATK ...文字列:
MYPYDVPDYA AIAGAPDLKL MATKKAGSRL ETEIERCRSE CQWERIPELV KQLSAKLIAN DDMAELLLGE SKLEQYLKEH PLRQGASPR GPKPQLTEVR KHLTAALDRG NLKSEFLQES NLIMAKLNYV EGDYKEALNI YARVGLDDLP LTAVPPYRLR V IAEAYATK GLCLEKLPIS SSTSNLHVDR EQDVITCYEK AGDIALLYLQ EIERVILSNI QNRSPKPGPA PHDQELGFFL ET GLQRAHV LYFKNGNLTR GVGRFRELLR AVETRTTQNL RMTIARQLAE ILLRGMCEQS YWNPLEDPPC QSPLDDPLRK GAN TKTYTL TRRARVYSGE NIFCPQENTE EALLLLLISE SMANRDAVLS RIPEHKSDRL ISLQSASVVY DLLTIALGRR GQYE MLSEC LERAMKFAFE EFHLWYQFAL SLMAAGKSAR AVKVLKECIR LKPDDATIPL LAAKLCMGSL HWLEEAEKFA KTVVD VGEK TSEFKAKGYL ALGLTYSLQA TDASLRGMQE VLQRKALLAF QRAHSLSPTD HQAAFYLALQ LAISRQIPEA LGYVRQ ALQ LQGDDANSLH LLALLLSAQK HYHDALNIID MALSEYPENF ILLFSKVKLQ SLCRGPDEAL LTCKHMLQIW KSCYNLT NP SDSGRGSSLL DRTIADRRQL NTITLPDFSD PETGSVHATS VAASRVEQAL SEVASSLQSS APKQGPLHPW MTLAQIWL H AAEVYIGIGK PAEATACTQE AANLFPMSHN VLYMRGQIAE LRGSMDEARR WYEEALAISP THVKSMQRLA LILHQLGRY SLAEKILRDA VQVNSTAHEV WNGLGEVLQA QGNDAAATEC FLTALELEAS SPAVPFTIIP RVL

UniProtKB: Tetratricopeptide repeat protein 7B

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分子 #3: Protein FAM126A

分子名称: Protein FAM126A / タイプ: protein_or_peptide / ID: 3 / 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: 32.688514 KDa
組換発現生物種: Homo sapiens (ヒト)
配列文字列: GPGSFTSEKG VVEEWLSEFK TLPETSLPNY ATNLKDKSSL VSSLYKVIQE PQSELLEPVC HQLFEFYRSG EEQLLQFTLQ FLPELIWCY LAVSASRNVH SSGCIEALLL GVYNLEIVDK QGHTKVLSFT IPSLSKPSVY HEPSSIGSMA LTESALSQHG L SKVVYSGP ...文字列:
GPGSFTSEKG VVEEWLSEFK TLPETSLPNY ATNLKDKSSL VSSLYKVIQE PQSELLEPVC HQLFEFYRSG EEQLLQFTLQ FLPELIWCY LAVSASRNVH SSGCIEALLL GVYNLEIVDK QGHTKVLSFT IPSLSKPSVY HEPSSIGSMA LTESALSQHG L SKVVYSGP HPQREMLTAQ NRFEVLTFLL LCYNAALTYM PSVSLQSLCQ ICSRICVCGY PRQHVRKYKG ISSRIPVSSG FM VQMLTGI YFAFYNGEWD LAQKALDDII YRAQLELYPE PLLVANAIKA SLPHG

UniProtKB: Hyccin

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分子 #4: Phosphatidylinositol 4-kinase III alpha (PI4KA)

分子名称: Phosphatidylinositol 4-kinase III alpha (PI4KA) / タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO / EC番号: 1-phosphatidylinositol 4-kinase
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 173.906547 KDa
組換発現生物種: Homo sapiens (ヒト)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
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UniProtKB: Phosphatidylinositol 4-kinase alpha

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分子 #5: 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(...

分子名称: 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide
タイプ: ligand / ID: 5 / コピー数: 2 / 式: E4S
分子量理論値: 574.626 Da
Chemical component information

ChemComp-E4S:
5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide

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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0.25 mg/mL
緩衝液pH: 8
構成要素:
濃度名称式
50.0 mMTris-HClトリスヒドロキシメチルアミノメタン
200.0 mMSodium chloride塩化ナトリウムNaCl塩化ナトリウム
5.0 %Glycerolグリセリン
1.0 mMTCEP-HCl
グリッドモデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 400 / 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.
凍結凍結剤: ETHANE / チャンバー内湿度: 90 % / 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 TITAN KRIOS
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系C2レンズ絞り径: 100.0 µm / 最大 デフォーカス（補正後）: 3.7 µm / 最小 デフォーカス（補正後）: 1.8 µm / 倍率（補正後）: 38461 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス（公称値）: 3.5 µm / 最小 デフォーカス（公称値）: 2.0 µm / 倍率（公称値）: 22500
試料ステージ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
ホルダー冷却材: NITROGEN
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 / デジタル化 - 画像ごとのフレーム数: 1-40 / 実像数: 3280 / 平均露光時間: 10.0 sec. / 平均電子線量: 47.0 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: 508504
初期モデルモデルのタイプ: INSILICO MODEL
初期 角度割当タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION
最終 角度割当タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION
最終 再構成想定した対称性 - 点群: C2 (2回回転対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION / 使用した粒子像数: 64104
FSC曲線 (解像度の算出)

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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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