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- PDB-8dru: Product structure of SARS-CoV-2 Mpro C145A mutant in complex with... -

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基本情報

登録情報
データベース: PDB / ID: 8dru
タイトルProduct structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp7-nsp8 (C7) cut site sequence
要素Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
キーワードVIRAL PROTEIN / Viral protease / SARS-CoV-2
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 / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / 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 / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / DNA helicase / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 / Lipocalin signature. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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. / : / 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 3Ecto domain profile. / : / 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
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Replicase polyprotein 1ab
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.31 Å
データ登録者Lee, J. / Kenward, C. / Worrall, L.J. / Vuckovic, M. / Paetzel, M. / Strynadka, N.C.J.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR) カナダ
引用ジャーナル: Nat Commun / 年: 2022
タイトル: X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.
著者: Lee, J. / Kenward, C. / Worrall, L.J. / Vuckovic, M. / Gentile, F. / Ton, A.T. / Ng, M. / Cherkasov, A. / Strynadka, N.C.J. / Paetzel, M.
履歴
登録2022年7月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年9月21日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
B: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
C: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
D: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
E: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
F: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
G: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)239,73231
ポリマ－237,0107
非ポリマー2,72224
水3,693205
1
A: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
ヘテロ分子

A: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,75612
ポリマ－67,7172
非ポリマー1,03910
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3560 Å2
ΔGint-15 kcal/mol
Surface area27520 Å2
手法PISA
2
B: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
E: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,5599
ポリマ－67,7172
非ポリマー8427
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-29 kcal/mol
Surface area26840 Å2
手法PISA
3
C: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
F: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,4389
ポリマ－67,7172
非ポリマー7217
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-19 kcal/mol
Surface area27610 Å2
手法PISA
4
D: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
G: Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,3587
ポリマ－67,7172
非ポリマー6405
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-25 kcal/mol
Surface area27640 Å2
手法PISA
単位格子
Length a, b, c (Å)166.110, 174.890, 96.330
Angle α, β, γ (deg.)90.000, 106.340, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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要素

#1: タンパク質
Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main ...3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase / nsp7


分子量: 33858.582 Da / 分子数: 7 / 変異: C145A / 由来タイプ: 組換発現
詳細: Mpro C145A catalytic mutant 1-300 with C-term extension of nsp7/nsp8 cut site sequence
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: rep, 1a-1b / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 8 / 由来タイプ: 合成 / 式: PO4
#3: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C4H10O3
#4: 化合物 ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / ペンタエチレングリコ-ル


分子量: 238.278 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H22O6 / コメント: 沈殿剤*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 205 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.79 Å3/Da / 溶媒含有率: 55.9 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 7 / 詳細: 0.1M HEPES 10% PEG 6K

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: CLSI / ビームライン: 08B1-1 / 波長: 1.5212 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2021年3月14日
放射モノクロメーター: Si(111) double crystal / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.5212 Å / 相対比: 1
反射解像度: 2.31→46.22 Å / Num. obs: 80942 / % possible obs: 93.1 % / 冗長度: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Net I/σ(I): 11.2
反射 シェル解像度: 2.31→2.535 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4047 / CC1/2: 0.566 / Rpim(I) all: 0.471 / % possible all: 62.4

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER2.8.3位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7JOY

7joy


解像度: 2.31→46.22 Å / SU ML: 0.3331 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 31.9862
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
詳細: Anisotropic correction performed using STARANISO Server.
Rfactor反射数%反射
Rfree0.2371 2000 2.47 %
Rwork0.19 78927 -
obs0.1911 80927 70.29 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 63.87 Å2
精密化ステップサイクル: LAST / 解像度: 2.31→46.22 Å
タンパク質核酸リガンド溶媒全体
原子数16471 0 168 205 16844
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.009417003
X-RAY DIFFRACTIONf_angle_d1.235523089
X-RAY DIFFRACTIONf_chiral_restr0.0692606
X-RAY DIFFRACTIONf_plane_restr0.00763002
X-RAY DIFFRACTIONf_dihedral_angle_d18.1896077
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.3736110.3403461X-RAY DIFFRACTION5.74
2.37-2.430.4279220.3234873X-RAY DIFFRACTION10.96
2.43-2.50.398410.28391593X-RAY DIFFRACTION20.02
2.5-2.580.3485740.29832937X-RAY DIFFRACTION36.76
2.58-2.680.28791130.30314440X-RAY DIFFRACTION55.25
2.68-2.780.32481430.28935646X-RAY DIFFRACTION70.96
2.78-2.910.3261790.28197053X-RAY DIFFRACTION87.86
2.91-3.060.32652000.26167916X-RAY DIFFRACTION99.1
3.06-3.260.26172030.23437987X-RAY DIFFRACTION99.57
3.26-3.510.29232020.20677964X-RAY DIFFRACTION99.39
3.51-3.860.23262020.17837960X-RAY DIFFRACTION99.17
3.86-4.420.20342020.14657987X-RAY DIFFRACTION99.44
4.42-5.570.18242030.14518019X-RAY DIFFRACTION99.6
5.57-46.220.19612050.16088091X-RAY DIFFRACTION99.47
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.51086742981-1.69870349113-0.1223633951262.23980560652-0.3457647071140.7356423208270.0952767196201-0.171441376706-0.1139352458260.104740717538-0.04673443507840.0166202169629-0.0960973337237-0.047511802526-0.03665151755370.288687517081-0.02255046038160.00951377424420.171647380631-0.002758623203940.19312301362212.283803682219.5996776651.61820356307
24.76650913485-1.68775459234-1.00648907873.104131548070.3473454400941.985171250340.172845197421-0.2039849267140.025087642410.0371387850818-0.0827066564428-0.05689773001810.09775461170220.120153963926-0.09218564957810.170727607292-0.066049720392-0.01581896181770.1612592991880.001501006804320.15266640727617.909212637820.35911723380.968779290324
34.67097890795-0.996814594790.03522427443941.78085958549-0.1920753808521.448706232840.4226728114150.3134702722231.26509429558-0.228467249957-0.287307358634-0.193243393067-0.3234473403250.02722784476690.03635825188590.3267697140240.02302785878050.162907127270.2341683996860.07706847078730.52700720927815.403209814634.5530826548-5.02758670403
43.221628650430.275485584448-1.472459022853.76117388181-1.746743925664.114775154860.3582620305841.193575603091.339304602840.0196570438633-0.1588866055410.451491879082-0.3147166450750.00427404198711-0.275670875910.7881930110190.2919059201260.3296143852730.9881802712150.3717850208911.31472878847.4483469797151.0542065934-17.6611085247
55.27746467671.0841727384.009248239334.01689460971-0.6393896245473.755114712030.3276120723041.027635707361.805989631220.19156448252-0.694256232730.770980602427-0.751253082742-0.6294316593230.4175392086310.9020413791720.2377849663360.2598021624780.6522816071860.1899423718421.081473233340.66039856623348.5456943671-13.8221921734
64.717590539550.8320665924532.986241440221.42032713493-0.2070519796692.143745381231.06435565860.546977176377-0.02506784228430.144222173064-0.495785666505-0.01212340529280.9642099366280.45637498508-0.7996184183210.7519982730090.3176613726680.049576633980.6605576164790.09905729049260.51724998809-9.1854041493933.8069644541-16.4565083323
72.067653472570.813742004036-0.4854458832163.28687925114-0.08534409527352.290770960310.173299967615-0.2500744245030.2404079748430.04209955253120.0532604694747-0.187581586838-0.2855318407630.240687095338-0.1697269481240.215772302622-0.03377356661310.0680114437430.25940800028-0.08319580721310.24513530454753.7442949027115.59539285526.7830277713
84.11077162265-0.21683538638-0.8818161279594.35255317257-2.389781171134.380554840420.1060414676430.155388788609-0.610942842943-0.396101437487-0.01819849580410.7249522896390.338830510661-0.5577991599590.04751438121760.318720717322-0.076930983793-0.0968705112090.390739770129-0.05665063276740.44146561623641.176288362989.42955441036.95408187188
91.35191795702-1.045956486860.7182690801863.50619377564-1.050648256071.36752313636-0.149750662661-0.0787573266978-0.185269963521-0.2776822348310.1977696744710.5524402391820.289689258933-0.484574627898-0.1313122814750.311417472868-0.0808901360902-0.04136655712680.380765572059-0.0233227304580.34492718257243.815579129387.173455677514.0681714995
101.49010501154-0.2291504250440.09708945889212.63270515266-0.02259526805472.697535779920.05504441430850.05217463565860.09660772824420.01721576661240.03358792342770.10683267239-0.05516340287550.0690648899397-0.09654566609480.1835680464160.01051784372030.009693353511280.1903688112730.03638170585720.22742445479917.2042889625151.9653923710.435124796078
115.58000514631-0.1213828768740.2723116084043.353086149190.1521858436450.09262991345731.110374387760.512311414264-1.4184185548-1.20875973416-0.5308095047930.2976406524531.642459698550.385869979332-0.2246626099231.065082761560.28396940691-0.2675101384210.529218420346-0.01356450935980.75143151199427.670228065118.422649551-1.67280874162
126.82492059583-2.987297142846.125480159991.12755164479-2.23150626325.185409425750.9270661365610.102018887177-0.739972000806-0.548054009373-0.3113932505130.3119201838991.16310145026-0.286676425527-0.4509874845190.7304380739740.0563246957516-0.04348096038170.4368792379250.03370331748120.52996822601630.2880396481121.9560701244.88245319466
134.181430795750.580362588337-0.7226575251613.26802285637-0.5251850660952.869566997470.10143038744-0.5706712668850.041224391220.4315066050470.0265965653097-0.2929836704020.02956007301670.523224952032-0.1282261368660.273632635796-0.0120333453558-0.071902364490.375487383103-0.02327612476410.23717029442455.855291339157.32112345927.8128645571
144.135885087880.0244170929484-0.4028998404283.933342291170.9792084462353.0427935697-0.0380458984680.7972537037340.155744177634-0.159325890814-0.0707529325390.513763218971-0.0425668795767-0.2032790295690.09304246020130.210867589031-0.0724084923875-0.01005541189730.3635020888280.02096548675410.3388891154841.520897878760.524438179811.7195148437
155.666926610120.237515906748-0.3280651389089.622671003611.767769326834.29387553139-0.2286861564882.63249958061-0.840867795799-1.34746519302-0.1739017766571.2763860107-0.568154735589-0.5650053979930.3072419027160.6101936698530.000938302755732-0.1021088351731.28717822038-0.1369441254260.73546272389832.495050458453.861924344-2.10219730641
162.271296087354.482863877490.6632455940429.12115351177-0.0969905329340.8334101373540.004268340164250.07106232051660.7368480509080.7612953067760.02168093404470.834044825432-0.456585878196-0.411389547686-0.05846626076310.5680013319290.03464306048170.1700739745220.568374365066-0.121700966910.71724256663928.038775933450.508386440510.3460639326
172.87291856882-0.2516795986030.3689555597834.07025587292-0.6909241595051.823114113660.104764569618-0.65704637299-0.8306122541230.913077871633-0.011993896583-0.1096284275750.3049396946120.353540152883-0.1832326495960.4888212398520.091969382527-0.07464218394360.6498473531020.1819502563330.48352715183552.109646494684.018045802746.4399104332
183.268823759090.25769320188-0.5488183422183.12926322132-0.1143777299382.61977888021-0.0687256421691-0.759925891046-0.269379659940.651473414461-0.1733129039930.1670621055510.295751000370.4718180094260.06455850720720.3775986465460.0265488508920.01980524166440.4259497417850.1108696492460.25405257630144.235908976688.852180596144.4317897615
190.962065341078-0.5652309439912.297768529766.314657456531.318153217556.47321920358-0.1096992934760.3002780687320.578810642034-0.478158450898-0.2239796622311.0578450681-0.228522881105-0.468062192690.349840990480.3637198662060.0140193582056-0.01920238611730.4580560893280.06546282210910.9710027913518.456566363101.49639800931.6396125135
201.295899816872.6243149547-1.411550106769.04930691623-1.218513847041.12432218571-0.02054961113460.4939982031810.10343399413-0.3610987730910.1784783056340.71849361046-0.0534571856075-0.287335661691-0.1041537123560.4208726514710.130414275534-0.09544292242580.44964273747-0.019244750490.67345193278124.4249702924106.72042114232.1041903237
213.08731210894-0.8396348554131.171604120391.09402611876-0.7214120903353.29206074689-0.266432360174-0.3900030381320.0560456990590.6289377742780.168806945354-0.183741142334-0.3898047516230.4005758810370.1107104780250.5898239085320.0891035236268-0.04327553752130.3736271049590.06332172519310.24141193724828.6193857031144.06816229427.1097395665
222.25939888014-0.216649643181.226386288213.18344984538-1.106370123993.5719341625-0.282118630489-0.3802029783060.005817281183491.08645769273-0.0715794284414-0.53442080464-0.7192187811960.5497472472720.3112870614081.036650696980.080753468109-0.166602262190.725415516148-0.006104529133260.37214534236936.5559302524144.15867881638.2134036747
233.611975907510.299597172471.179359335333.19292349214-1.141538696664.67605922570.0219346878487-0.267299838352-0.03160700696650.07461164222550.210890377620.380937824066-0.189099571299-0.0903966046757-0.2110154432430.4293859962260.1707875418720.04319850164650.3245974080680.09131750762340.26546853763121.853318908138.03645864825.3976426544
243.49931230505-1.053030983822.913886718551.910614605630.1399684216444.368963230120.301683813047-0.7565539584-0.967597198370.1161769371170.1780148928550.6159602231150.418745539604-0.728123200047-0.4064459567690.4981466571020.05017123547020.05592451670960.4762253424160.215718571960.5217185500714.0509771391129.71830407625.749762958
256.02143304705-0.362289870053-1.766877503320.872011970602-0.9169799963171.73848240532-0.0193698646786-2.24930747714-1.70010360521-0.3306808071290.7948251089931.307919168731.03559832244-1.89720452228-0.8677269504480.969315272382-0.35239473349-0.07352402541111.555099168620.6487129354671.228278654081.46190734337119.46373972327.2363893515
263.73799730462-3.557085028743.004256291934.17007532773-0.4913682254459.495173292120.626802239307-2.59130371243-1.864268323340.4166577004110.3224989920131.561041510991.58501511685-2.64972705414-0.3563457840160.632019227931-0.140291083572-0.05128280383191.396601564130.09731073174591.37039689335-3.96260747381128.65196469721.3552488878
274.73744492734-3.217210970372.2269531293.33474112159-2.998808328883.385717302330.1666414249370.419404487097-0.559508047062-0.185641138986-0.251056872118-0.09197935234490.522641170390.3186062769920.107161109570.4796281885320.05777725194840.001684907702350.404403478996-0.04947409425450.6020965376644.31998372893133.32945258211.2853087922
283.613959525940.0277687690819-0.01038413337383.150762081781.386897933122.95242865289-0.121591496484-0.27956087464-0.4695365447780.568114433411-0.2229963930840.4861575842430.80099793861-0.2995087637270.1348979482680.560247608978-0.1280190232670.1400896019410.2841310345330.04450575610750.40283414273430.147781147735.786574538631.8328609932
291.124445372361.405550343391.507059760444.089712941573.643841200413.21095255584-0.0368510058916-0.011627318001-0.132326291145-0.130833952992-0.6542971635931.01982922781-0.00539526284397-0.5004562804710.8008041952970.340414357254-0.04699348016560.06847328771240.505754046611-0.2047283170820.67251444090818.892756561652.463239407328.6643804562
302.400562849272.385346210750.5248523601478.72086284469-0.6732264375557.071798560820.5531380992350.05738751710820.9092357316760.377884370853-1.00280989941.52523720465-0.289486343477-0.0809329580196-0.08814589393420.6552156919520.0706637632618-0.001255289873980.6777609449960.04397938033491.0354156599214.114927253768.665629967531.5841832488
313.568429872733.78605519595-0.003755249364128.670230797150.6280651404160.2152351565090.7317941866530.8921236833160.1878925827-0.553230822676-0.4934176161150.5813290235890.117905675418-0.196917392814-0.3000943683350.6637346574410.1588514343220.01823314080520.648250169629-0.06740396038560.42721022235525.500203468668.946283478230.0210119162
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )AA1 - 431 - 43
22chain 'A' and (resid 44 through 155 )AA44 - 15544 - 155
33chain 'A' and (resid 156 through 214 )AA156 - 214156 - 214
44chain 'A' and (resid 215 through 249 )AA215 - 249215 - 249
55chain 'A' and (resid 250 through 292 )AA250 - 292250 - 292
66chain 'A' and (resid 293 through 306 )AA293 - 306293 - 306
77chain 'B' and (resid 1 through 200 )BB1 - 2001 - 200
88chain 'B' and (resid 201 through 243 )BB201 - 243201 - 243
99chain 'B' and (resid 244 through 306 )BB244 - 306244 - 306
1010chain 'C' and (resid 1 through 200 )CC1 - 2001 - 200
1111chain 'C' and (resid 201 through 243 )CC201 - 243201 - 243
1212chain 'C' and (resid 244 through 306 )CC244 - 306244 - 306
1313chain 'D' and (resid 1 through 139 )DD1 - 1391 - 139
1414chain 'D' and (resid 140 through 243 )DD140 - 243140 - 243
1515chain 'D' and (resid 244 through 273 )DD244 - 273244 - 273
1616chain 'D' and (resid 274 through 306 )DD274 - 306274 - 306
1717chain 'E' and (resid 1 through 70 )EE1 - 701 - 70
1818chain 'E' and (resid 71 through 200 )EE71 - 20071 - 200
1919chain 'E' and (resid 201 through 243 )EE201 - 243201 - 243
2020chain 'E' and (resid 244 through 306 )EE244 - 306244 - 306
2121chain 'F' and (resid 1 through 43 )FF1 - 431 - 43
2222chain 'F' and (resid 44 through 100 )FF44 - 10044 - 100
2323chain 'F' and (resid 101 through 155 )FF101 - 155101 - 155
2424chain 'F' and (resid 156 through 226 )FF156 - 226156 - 226
2525chain 'F' and (resid 227 through 243 )FF227 - 243227 - 243
2626chain 'F' and (resid 244 through 274 )FF244 - 274244 - 274
2727chain 'F' and (resid 275 through 306 )FF275 - 306275 - 306
2828chain 'G' and (resid 1 through 180 )GG1 - 1801 - 180
2929chain 'G' and (resid 181 through 214 )GG181 - 214181 - 214
3030chain 'G' and (resid 215 through 250 )GG215 - 250215 - 250
3131chain 'G' and (resid 251 through 306 )GG251 - 306251 - 306

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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://pdbjlvh1.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