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- PDB-7tj2: SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA -

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基本情報

登録情報
データベース: PDB / ID: 7tj2
タイトルSARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA
要素
  • (RNA (31-MER)) x 2
  • Uridylate-specific endoribonuclease nsp15
キーワードVIRAL PROTEIN/RNA (ウイルス性) / endoribonuclease / VIRAL PROTEIN (ウイルスタンパク質) / VIRAL PROTEIN-RNA complex (ウイルス性)
機能・相同性
機能・相同性情報


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / 3C様プロテアーゼ / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / : / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / ヘリカーゼ / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / ヘリカーゼ / induction by virus of host autophagy / RNA依存性RNAポリメラーゼ / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / タンパク質分解 / RNA binding / zinc ion binding / ATP binding / 生体膜
類似検索 - 分子機能
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Lipocalin signature. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus
類似検索 - ドメイン・相同性
リボ核酸 / RNA (> 10) / Replicase polyprotein 1ab
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
synthetic construct (人工物)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.2 Å
データ登録者Frazier, M.N. / Krahn, J.M. / Butay, K.J. / Dillard, L.B. / Borgnia, M.J. / Stanley, R.E.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES103247 米国
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC ES103326 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAES103340 米国
引用
ジャーナル: Nucleic Acids Res / 年: 2022
タイトル: Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease.
著者: Meredith N Frazier / Isha M Wilson / Juno M Krahn / Kevin John Butay / Lucas B Dillard / Mario J Borgnia / Robin E Stanley
要旨: Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, ...Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is a uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
#1: ジャーナル: bioRxiv / 年: 2022
タイトル: Flipped Over U: Structural Basis for dsRNA Cleavage by the SARS-CoV-2 Endoribonuclease.
著者: Meredith N Frazier / Isha M Wilson / Juno M Krahn / Kevin John Butay / Lucas B Dillard / Mario J Borgnia / Robin E Stanley /
要旨: Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, ...Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
履歴
登録2022年1月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年3月23日Provider: repository / タイプ: Initial release
改定 1.12022年12月7日Group: Database references / カテゴリ: citation / citation_author

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Uridylate-specific endoribonuclease nsp15
B: Uridylate-specific endoribonuclease nsp15
C: Uridylate-specific endoribonuclease nsp15
D: Uridylate-specific endoribonuclease nsp15
E: Uridylate-specific endoribonuclease nsp15
F: Uridylate-specific endoribonuclease nsp15
G: RNA (31-MER)
H: RNA (31-MER)


分子量 (理論値)分子数
合計 (水以外)268,7908
ポリマ－268,7908
非ポリマー00
水0
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法
タイプ名称対称操作数
identity operation1_5551
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "C" and (resid 0 or (resid 1 and (name...
d_2ens_1(chain "B" and resid 0 through 47)
d_3ens_1(chain "A" and resid 0 through 47)
d_4ens_1(chain "D" and resid 0 through 47)
d_5ens_1(chain "E" and resid 0 through 47)
d_6ens_1(chain "F" and resid 0 through 47)
d_1ens_2(chain "C" and resid 50 through 188)
d_2ens_2(chain "B" and resid 50 through 188)
d_3ens_2(chain "A" and resid 50 through 188)
d_4ens_2(chain "D" and resid 50 through 188)
d_5ens_2(chain "E" and resid 50 through 188)
d_6ens_2(chain "F" and resid 50 through 188)
d_1ens_3(chain "A" and (resid 195 through 206 or resid 249 through 299))
d_2ens_3(chain "B" and (resid 195 through 206 or resid 249 through 299))
d_3ens_3(chain "C" and (resid 195 through 206 or resid 249 through 299))
d_4ens_3(chain "D" and resid 195 through 299)
d_5ens_3(chain "E" and (resid 195 through 206 or resid 249 through 299))
d_6ens_3(chain "F" and (resid 195 through 206 or resid 249 through 299))
d_1ens_4(chain "B" and (resid 314 through 334 or resid 341 through 345))
d_2ens_4(chain "C" and (resid 314 through 334 or resid 341 through 345))
d_3ens_4(chain "E" and (resid 314 through 334 or resid 341 through 345))
d_4ens_4(chain "F" and (resid 314 through 334 or resid 341 through 345))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLULYSC2 - 49
d_21ens_1GLULYSB2 - 49
d_31ens_1GLULYSA2 - 49
d_41ens_1GLULYSD2 - 49
d_51ens_1GLULYSE2 - 49
d_61ens_1GLULYSF2 - 49
d_11ens_2LEUGLNC52 - 190
d_21ens_2LEUGLNB52 - 190
d_31ens_2LEUGLNA52 - 190
d_41ens_2LEUGLND52 - 190
d_51ens_2LEUGLNE52 - 190
d_61ens_2LEUGLNF52 - 190
d_11ens_3PHEPROA197 - 208
d_12ens_3LEULEUA251 - 301
d_21ens_3PHEPROB197 - 208
d_22ens_3LEULEUB251 - 301
d_31ens_3PHEPROC197 - 208
d_32ens_3LEULEUC251 - 301
d_41ens_3PHELEUD197 - 259
d_51ens_3PHEPROE197 - 208
d_52ens_3LEULEUE251 - 301
d_61ens_3PHEPROF197 - 208
d_62ens_3LEULEUF251 - 301
d_11ens_4VALCYSB316 - 336
d_12ens_4THRLYSB343 - 347
d_21ens_4VALCYSC316 - 336
d_22ens_4THRLYSC343 - 347
d_31ens_4VALCYSE316 - 336
d_32ens_4THRLYSE343 - 347
d_41ens_4VALCYSF316 - 336
d_42ens_4THRLYSF343 - 347

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixベクター
1given(-0.45149147147, -0.87348987978, -0.182128748724), (0.830613911613, -0.486003937748, 0.271810048248), (-0.325938615424, -0.0285587537509, 0.944959478792)300.555212585, 54.2275886359, 48.3671155526
2given(-0.460959827356, 0.826621670707, -0.322819843073), (-0.870003191972, -0.492670044069, -0.0192528863949), (-0.174958519431, 0.271979486717, 0.946264590526)107.537062572, 289.684084037, -6.82935369216
3given(0.330694474661, 0.930774218974, 0.155886233268), (0.932770750628, -0.34747053506, 0.0959320282164), (0.14345693152, 0.113681927144, -0.983105552949)-52.5079653968, 44.54917187, 188.207488687
4given(-0.989117311799, -0.145258079507, 0.0233887544913), (-0.147038849427, 0.970376954654, -0.191698050684), (0.00514978233118, -0.19305091612, -0.9811752257)251.923241058, 42.3050556955, 242.264947649
5given(0.571599128168, -0.748364771507, 0.336488640885), (-0.74703601192, -0.644268330551, -0.163876524074), (0.339428392407, -0.157697454055, -0.927318650418)105.804835134, 309.603399816, 192.168969573
6given(-0.461444336885, -0.869749061967, -0.174944828914), (0.825474081215, -0.493175676623, 0.274536506187), (-0.325056403103, -0.0177291058625, 0.945528430882)300.418149322, 55.2787799224, 46.9341560261
7given(-0.448697602298, 0.832423146911, -0.325180205699), (-0.875987770688, -0.481715292259, -0.0244090722876), (-0.176962954592, 0.273901591252, 0.945336993358)105.922775969, 289.888557243, -6.75559331331
8given(0.323603361261, 0.933830482688, 0.1524516126), (0.93302580994, -0.341716837134, 0.112660734975), (0.157301311395, 0.105783896803, -0.981868659552)-51.5879685365, 41.6637950433, 187.177688094
9given(-0.989041598602, -0.147596836512, 0.00344820050502), (-0.145250733773, 0.968607133686, -0.201748469415), (0.0264374842492, -0.200038482359, -0.979431296724)254.598957054, 43.6901610321, 240.164783234
10given(0.571085186312, -0.747592431329, 0.33906823295), (-0.746364101659, -0.644840148714, -0.164687007264), (0.341763569928, -0.15901804686, -0.926234809885)105.47522708, 309.664543566, 191.941686781
11given(-0.458584967506, 0.828350613947, -0.321768687027), (-0.87077093027, -0.491134750166, -0.0233376129215), (-0.177363509706, 0.269484540471, 0.946530648142)106.990833615, 290.291345359, -6.31902528409
12given(-0.455505258748, -0.873843820956, -0.170035101757), (0.828353170939, -0.48600693319, 0.278618529691), (-0.326107318914, -0.0139369102527, 0.94523001385)299.712892342, 53.4343655231, 46.8843107609
13given(0.581385741976, -0.739139564564, 0.340093109491), (-0.740021005843, -0.654110865601, -0.156549948619), (0.338170859089, -0.160660136931, -0.92726953496)103.141183735, 309.219212966, 192.504951576
14given(0.327933157677, 0.936932934788, 0.120898799848), (0.934363137004, -0.340558316062, 0.104812029699), (0.139374934277, 0.0785920420243, -0.98711596007)-48.5478364934, 42.19520986, 192.758584061
15given(-0.988840961568, -0.148475493912, 0.0121893573336), (-0.147718528852, 0.966608919841, -0.209395397077), (0.0193077434781, -0.208859339727, -0.977755075288)253.759146612, 45.0152683665, 241.83136288
16given(-0.449536595511, 0.834323185344, -0.319095082529), (-0.882083766444, -0.470957624655, 0.0112758483486), (-0.140872560395, 0.286537498729, 0.947655624977)104.744149755, 283.398144323, -12.3786568875
17given(0.575168522279, -0.745538181632, 0.336680843987), (-0.750382000572, -0.644732064051, -0.145764943669), (0.325742266519, -0.168799838015, -0.930268020782)104.756292486, 307.499038363, 195.520404301
18given(0.337687474201, 0.929197972893, 0.150194197424), (0.928520947526, -0.355011523299, 0.108699900326), (0.154324397855, 0.102751863718, -0.982662726844)-52.0985463815, 44.4227185606, 188.411101275

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要素

#1: タンパク質
Uridylate-specific endoribonuclease nsp15 / NendoU / Non-structural protein 15 / nsp15


分子量: 39246.684 Da / 分子数: 6 / 変異: H235A / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
遺伝子: rep, 1a-1b / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P0DTD1, 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; -
#2: RNA鎖 RNA (31-MER)


分子量: 16781.023 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: RNA鎖 RNA (31-MER)


分子量: 16528.768 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Structural Basis for dsRNA cleavage by the SARS-CoV-2 Endoribonuclease
タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
分子量値: 0.250 MDa / 実験値: NO
由来(天然)生物種: Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
由来(組換発現)生物種: Escherichia coli (大腸菌)
緩衝液pH: 7.5
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELDBright-field microscopy / 最大 デフォーカス（公称値）: -1200 nm / 最小 デフォーカス（公称値）: 2200 nm
撮影電子線照射量: 60 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)

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解析

ソフトウェア
名称バージョン分類
phenix.real_space_refine1.20_4459精密化
PHENIX1.20_4459精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 396312 / 対称性のタイプ: POINT
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 65.86 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.001717556
ELECTRON MICROSCOPYf_angle_d0.3724111
ELECTRON MICROSCOPYf_chiral_restr0.04052824
ELECTRON MICROSCOPYf_plane_restr0.00292873
ELECTRON MICROSCOPYf_dihedral_angle_d8.29756555
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints7.92120752241E-13
ens_1d_3CELECTRON MICROSCOPYNCS constraints1.28611694809E-10
ens_1d_4CELECTRON MICROSCOPYNCS constraints6.36512965017E-13
ens_1d_5CELECTRON MICROSCOPYNCS constraints1.45951644508E-11
ens_1d_6CELECTRON MICROSCOPYNCS constraints1.17273933076E-13
ens_2d_2CELECTRON MICROSCOPYNCS constraints6.14190293656E-13
ens_2d_3CELECTRON MICROSCOPYNCS constraints7.14321987524E-12
ens_2d_4CELECTRON MICROSCOPYNCS constraints5.81989938182E-13
ens_2d_5CELECTRON MICROSCOPYNCS constraints1.57007586849E-13
ens_2d_6CELECTRON MICROSCOPYNCS constraints1.27904376578E-13
ens_3d_2AELECTRON MICROSCOPYNCS constraints1.43554687961E-11
ens_3d_3AELECTRON MICROSCOPYNCS constraints2.55132225767E-12
ens_3d_4AELECTRON MICROSCOPYNCS constraints1.36424263776E-13
ens_3d_5AELECTRON MICROSCOPYNCS constraints1.00484924407E-13
ens_3d_6AELECTRON MICROSCOPYNCS constraints1.26281393919E-12
ens_4d_2BELECTRON MICROSCOPYNCS constraints1.48113857705E-11
ens_4d_3BELECTRON MICROSCOPYNCS constraints8.42019887778E-11
ens_4d_4BELECTRON MICROSCOPYNCS constraints4.73066128445E-11

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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