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基本情報

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データベース: PDB / ID: 7t9w
タイトルCrystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2
要素Papain-like protease nsp3
キーワードVIRAL PROTEIN (ウイルスタンパク質) / SARS-COV-2 (SARSコロナウイルス2) / COVID-19 (新型コロナウイルス感染症 (2019年)) / NON-STRUCTURAL PROTEIN 3 / NSP3 / BSM domain / Betacoronavirus-Specific Marker / G2M / group 2 marker / UNKNOWN FUNCTION / STRUCTURAL GENOMICS (構造ゲノミクス) / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES (アメリカ国立アレルギー・感染症研究所)
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / 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 / 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 / : / double membrane vesicle viral factory outer membrane / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ヘリカーゼ / 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
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)
手法X線回折 / 分子置換 / 解像度: 2.2 Å
データ登録者Stogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C 米国
引用ジャーナル: To Be Published
タイトル: Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2
著者: Stogios, P.J.
履歴
登録2021年12月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年12月29日Provider: repository / タイプ: Initial release
改定 1.12024年2月28日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond
改定 1.22024年4月3日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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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: Papain-like protease nsp3
B: Papain-like protease nsp3
C: Papain-like protease nsp3
D: Papain-like protease nsp3
E: Papain-like protease nsp3
F: Papain-like protease nsp3
G: Papain-like protease nsp3
H: Papain-like protease nsp3
I: Papain-like protease nsp3
J: Papain-like protease nsp3
K: Papain-like protease nsp3
L: Papain-like protease nsp3
M: Papain-like protease nsp3
N: Papain-like protease nsp3
O: Papain-like protease nsp3
P: Papain-like protease nsp3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)182,41119
ポリマ－182,19116
非ポリマー2203
水17,511972
1
A: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: Papain-like protease nsp3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)11,4222
ポリマ－11,3871
非ポリマー351
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
C: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: Papain-like protease nsp3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)11,4792
ポリマ－11,3871
非ポリマー921
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
5
E: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
6
F: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
7
G: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
8
H: Papain-like protease nsp3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)11,4792
ポリマ－11,3871
非ポリマー921
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
9
I: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
10
J: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
11
K: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
12
L: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
13
M: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
14
N: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
15
O: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
16
P: Papain-like protease nsp3


分子量 (理論値)分子数
合計 (水以外)11,3871
ポリマ－11,3871
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)157.462, 157.462, 79.619
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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要素

#1: タンパク質
Papain-like protease nsp3 / Non-structural protein 3 / nsp3 / PL2-PRO / Papain-like proteinase / PL-PRO


分子量: 11386.963 Da / 分子数: 16 / 断片: BSM (Betacoronavirus-Specific Marker) domain / 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 / プラスミド: pMCSG53 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): -Gold
参照: UniProt: P0DTD1, ubiquitinyl hydrolase 1, 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
#2: 化合物 ChemComp-CL / CHLORIDE ION / クロリド / 塩化物


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#3: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル / グリセリン


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#4: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 972 / 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: 2.71 Å3/Da / 溶媒含有率: 54.59 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6 / 詳細: 40% tacsimate, 0.5 M MES pH 6

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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: 回転陽極 / タイプ: RIGAKU MICROMAX-007 / 波長: 1.5418 Å
検出器タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2021年12月9日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.5418 Å / 相対比: 1
反射解像度: 2.2→30 Å / Num. obs: 98708 / % possible obs: 100 % / 冗長度: 7.5 % / Biso Wilson estimate: 34.28 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.04 / Net I/σ(I): 17.4
反射 シェル解像度: 2.2→2.24 Å / 冗長度: 6.1 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 4940 / CC1/2: 0.658 / Rpim(I) all: 0.389 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
HKL-3000データ削減
HKL-3000データスケーリング
PHASER位相決定
PHENIXモデル構築
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: Alphafold2 model

解像度: 2.2→29.42 Å / SU ML: 0.4037 / 交差検証法: FREE R-VALUE / σ(F): 0 / 位相誤差: 35.8544
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.3162 1875 1.99 %RANDOM
Rwork0.2616 92581 --
obs0.2627 94456 95.45 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 56.07 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→29.42 Å
タンパク質核酸リガンド溶媒全体
原子数10874 0 13 972 11859
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002611050
X-RAY DIFFRACTIONf_angle_d0.535415056
X-RAY DIFFRACTIONf_chiral_restr0.04231900
X-RAY DIFFRACTIONf_plane_restr0.00551881
X-RAY DIFFRACTIONf_dihedral_angle_d16.44054036
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.40231240.37636442X-RAY DIFFRACTION86.37
2.26-2.330.40551260.36546721X-RAY DIFFRACTION90.53
2.33-2.40.37271380.3516867X-RAY DIFFRACTION93.03
2.4-2.490.3351450.3327068X-RAY DIFFRACTION94.61
2.49-2.590.37431480.33837064X-RAY DIFFRACTION95.96
2.59-2.70.40141480.31987217X-RAY DIFFRACTION96.93
2.7-2.850.34131500.30657270X-RAY DIFFRACTION97.72
2.85-3.030.40771560.29017287X-RAY DIFFRACTION98.19
3.03-3.260.32271480.27057370X-RAY DIFFRACTION98.8
3.26-3.590.29951500.23377399X-RAY DIFFRACTION99.03
3.59-4.10.26991410.20687412X-RAY DIFFRACTION99.06
4.1-5.170.24451550.1927388X-RAY DIFFRACTION98.33
5.17-29.420.28241460.25117076X-RAY DIFFRACTION92.36
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)
14.728624173782.06970058199-0.310245742033.997433003971.638269057365.940790785640.1000475613050.293186501307-0.0724104466025-1.45880422166-1.04918515045-1.2939579664-0.7414553425440.6833439995260.9346792711620.7310485012860.03736449032280.1469363105650.6564563048030.3409396297911.02032395165-1.76732362104-59.9069429343-6.54201553619
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507.631282007431.238555927132.934102999165.962304727252.099326658332.08495121882-0.0866024950463-0.8328618163540.416800666494-0.0682518519987-0.0928940242240.247543360190.484027376659-0.9256147718060.07754733096340.3715088652710.0516531143810.06481559522890.4555307835080.05144295138860.46519608617415.9489674933-63.8541838584-20.0810169754
512.248151678880.412358002345-1.454400637622.6837339961-3.668032106086.107496001920.341662088407-1.21820880364-0.348491074751.257814682060.1582630347380.110065355467-0.08257077187780.215189944546-0.6190651913320.37434336681-0.0487255762014-0.1377627408040.5440525598240.01314367868580.45767639069819.8857037203-1.6084641366361.1053447158
523.968269421910.428357737049-0.2168934653961.976400684161.049799499540.6867284126470.009881738707270.2439478498750.0768535512513-0.0949891899742-0.0698004528665-0.150877867147-0.216430258175-0.06640530252740.09292552368290.3736769861420.0136655507539-0.1174150916130.2941818542050.04486848315570.32602047272621.20317935920.89423161968253.4667994549
530.4141968083980.141095899719-1.462595142278.578170117353.508336683189.761225868190.08458892309030.00359349800274-0.0835759222478-0.1674210159870.0980519590538-1.01560655964-0.5216402968260.951290611964-0.1130087893750.316396644226-0.0607822857065-0.04175942523230.3242299267370.1264246346160.4748398889226.8933971688-5.3375438774548.1447845782
549.34667783641-4.193298448324.23759474392.663170783580.07875283935096.88028135961-0.6852987347151.09209128745-0.0705419312279-0.0552313831909-0.763440328184-0.1023820887880.115817714721.014170355741.154874116130.4151156395490.1386599165830.06870175578360.4769570926180.2301448461160.64857460686429.2529084726-16.815412496639.6511061539
552.815930044790.865891968405-1.647290005152.562376743641.849464159535.2708697717-0.4141993747150.645829631821-0.2671639024170.194184166664-0.224881729511-0.1752199711470.6883437288970.04252112194340.4646308271060.3077020498820.0184506832265-0.05387478715690.179336046490.1211522290940.44000926089918.6736383777-13.306311214648.2745461286
564.48926798605-1.841590041321.299902382154.759422145542.224645163837.27772264485-0.07778385808070.280307959928-0.200923466782-0.7016079017230.0968875589364-0.189360522810.9040162140120.5313555647010.02825893701980.622800105660.04877226822630.2716805307490.3955583452610.1672779448610.77530607334325.4359488787-24.105602550339.4317203169
576.78127761535-2.503454551153.768793824792.116304713471.347490275588.1824048349-0.510695828228-0.644373393344-0.1423505470270.882377029756-0.0851227518470.378659535561-0.367035248738-0.416254423004-0.2507143728550.9083122411110.195984324031-0.5839439713320.006793056021010.6810121114170.6249317901180.925102270133-59.714494202338.9929763737
586.78390364003-1.06946536045-3.717371019430.2321751422280.5735848150434.97006014860.2845145071790.7921289449650.1514375101370.389674819962-0.2903223363980.0631254389999-0.385573878838-0.7938809953690.01141095331870.544367348455-0.0171160280673-0.05191212829590.3600977614410.1657778810670.5057624985421.19972573508-56.328601475729.9699477228
590.665385571835-0.577427439529-0.2526673115774.6179462281-0.4158232614474.449277255620.2905616927940.345833705257-0.1643361710940.376003349796-0.56540398895-1.15609342433-0.5026887874810.02493805804080.1950058411460.437187301964-0.076393362696-0.1095374018330.4645273022910.209584025480.48558796217913.8146786432-54.661673469622.4037779211
606.386554113390.92767880837-2.741721326462.04524700190.07544640136618.60891146651-0.24571486888-0.563608645391-0.4369107522910.458655239228-0.76406641518-0.5669031095050.4639271424520.8971819486010.822461868790.398151161232-0.0708369280995-0.07281249862570.3818561831730.2043495611440.47742052760113.1733474315-63.539963705227.8078925788
618.31616706535-0.3715426889155.067093961295.17658373922-0.4225650634533.268866245410.6070315720021.66118024655-0.0973108035170.244443427317-1.01155813214-2.30961182811-0.4901657764841.131287693460.6924541763430.576921659755-0.131042742124-0.1130978365940.6551046959290.6396241965970.98415087909423.9120725457-54.920754645118.2864953227
625.374129905491.39235317939-1.134741519486.67339345098-0.3497113663873.96010377638-0.137993734929-0.323913234848-0.1154228494730.240347824599-0.10204688355-0.5434794183320.1777638672191.484368100650.1760558839190.4965954342040.3111392175270.1927416466131.156917579850.4329481432460.80583497746740.7327008212-19.819490558939.2802385292
635.834957799360.413042483584-2.873972894410.824988565035-0.3364518233525.30024562309-0.959554740407-0.2557161424620.1926762923540.2803243117940.9604447706970.9689170856640.322254365557-0.0943357909374-0.127124030270.5108509572610.1648155438850.1231360142580.8181104557070.3202954201880.73203272695541.0032294768-16.395238438330.2655525377
641.50498914556-1.26615681796-2.031414737223.51710518533-0.6089036111883.96925745585-0.564634615271-1.10238838991-0.3509032263030.3265985916840.378643874618-0.0471244057520.1285520302170.2253993649920.1681168884330.3433102449570.133272277238-0.02357874289640.9027461033990.1752003435350.52815965542455.9026042949-17.422575741423.6129276106
651.63108145845-0.5611442270750.8934092414434.51326303105-1.506149800154.499005169220.002788918119550.138150051836-0.1362704439230.814709385893-0.36217125828-0.357057638141-0.4532126482960.5165955072180.287962822380.617150373285-0.166958637038-0.1449396716610.5391733761570.3027911995580.69254348418416.6074957891-39.251456569712.0520393674
661.97972264521.378321502480.2471501191121.01897054173-1.054748714763.794528765630.191602791381-0.626459520949-0.3827875938230.761354709392-0.414313596021-0.283130749432-0.191570688490.1726077086080.09954995914880.516928678418-0.0814102704085-0.0007857809635950.4996342491170.2085134497340.3402431238816.674694506-23.67393502874.88849856889
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 1241 through 1261 )AA1241 - 12611 - 21
22chain 'A' and (resid 1262 through 1273 )AA1262 - 127322 - 33
33chain 'A' and (resid 1274 through 1303 )AA1274 - 130334 - 63
44chain 'A' and (resid 1304 through 1328 )AA1304 - 132864 - 88
55chain 'B' and (resid 1238 through 1261 )BB1238 - 12611 - 24
66chain 'B' and (resid 1262 through 1329 )BB1262 - 132925 - 92
77chain 'C' and (resid 1240 through 1246 )CC1240 - 12461 - 7
88chain 'C' and (resid 1247 through 1251 )CC1247 - 12518 - 12
99chain 'C' and (resid 1252 through 1261 )CC1252 - 126113 - 22
1010chain 'C' and (resid 1262 through 1273 )CC1262 - 127323 - 34
1111chain 'C' and (resid 1274 through 1293 )CC1274 - 129335 - 54
1212chain 'C' and (resid 1294 through 1316 )CC1294 - 131655 - 77
1313chain 'C' and (resid 1317 through 1329 )CC1317 - 132978 - 90
1414chain 'D' and (resid 1240 through 1251 )DD1240 - 12511 - 12
1515chain 'D' and (resid 1252 through 1273 )DD1252 - 127313 - 34
1616chain 'D' and (resid 1274 through 1293 )DD1274 - 129335 - 54
1717chain 'D' and (resid 1294 through 1328 )DD1294 - 132855 - 89
1818chain 'E' and (resid 1240 through 1246 )EF1240 - 12461 - 7
1919chain 'E' and (resid 1247 through 1261 )EF1247 - 12618 - 22
2020chain 'E' and (resid 1262 through 1273 )EF1262 - 127323 - 34
2121chain 'E' and (resid 1274 through 1328 )EF1274 - 132835 - 89
2222chain 'F' and (resid 1241 through 1259 )FG1241 - 12591 - 19
2323chain 'F' and (resid 1260 through 1303 )FG1260 - 130320 - 63
2424chain 'F' and (resid 1304 through 1316 )FG1304 - 131664 - 76
2525chain 'F' and (resid 1317 through 1328 )FG1317 - 132877 - 88
2626chain 'G' and (resid 1240 through 1246 )GH1240 - 12461 - 7
2727chain 'G' and (resid 1247 through 1273 )GH1247 - 12738 - 34
2828chain 'G' and (resid 1274 through 1316 )GH1274 - 131635 - 77
2929chain 'G' and (resid 1317 through 1329 )GH1317 - 132978 - 90
3030chain 'H' and (resid 1239 through 1246 )HI1239 - 12461 - 8
3131chain 'H' and (resid 1247 through 1273 )HI1247 - 12739 - 35
3232chain 'H' and (resid 1274 through 1316 )HI1274 - 131636 - 78
3333chain 'H' and (resid 1317 through 1329 )HI1317 - 132979 - 91
3434chain 'I' and (resid 1241 through 1261 )IK1241 - 12611 - 21
3535chain 'I' and (resid 1262 through 1273 )IK1262 - 127322 - 33
3636chain 'I' and (resid 1274 through 1316 )IK1274 - 131634 - 76
3737chain 'I' and (resid 1317 through 1328 )IK1317 - 132877 - 88
3838chain 'J' and (resid 1240 through 1251 )JL1240 - 12511 - 12
3939chain 'J' and (resid 1252 through 1273 )JL1252 - 127313 - 34
4040chain 'J' and (resid 1274 through 1282 )JL1274 - 128235 - 43
4141chain 'J' and (resid 1283 through 1293 )JL1283 - 129344 - 54
4242chain 'J' and (resid 1294 through 1328 )JL1294 - 132855 - 89
4343chain 'K' and (resid 1240 through 1273 )KM1240 - 12731 - 34
4444chain 'K' and (resid 1274 through 1328 )KM1274 - 132835 - 89
4545chain 'L' and (resid 1241 through 1251 )LN1241 - 12511 - 11
4646chain 'L' and (resid 1252 through 1261 )LN1252 - 126112 - 21
4747chain 'L' and (resid 1262 through 1273 )LN1262 - 127322 - 33
4848chain 'L' and (resid 1274 through 1303 )LN1274 - 130334 - 63
4949chain 'L' and (resid 1304 through 1316 )LN1304 - 131664 - 76
5050chain 'L' and (resid 1317 through 1328 )LN1317 - 132877 - 88
5151chain 'M' and (resid 1239 through 1246 )MO1239 - 12461 - 8
5252chain 'M' and (resid 1247 through 1261 )MO1247 - 12619 - 23
5353chain 'M' and (resid 1262 through 1273 )MO1262 - 127324 - 35
5454chain 'M' and (resid 1274 through 1283 )MO1274 - 128336 - 45
5555chain 'M' and (resid 1284 through 1316 )MO1284 - 131646 - 78
5656chain 'M' and (resid 1317 through 1328 )MO1317 - 132879 - 90
5757chain 'N' and (resid 1240 through 1246 )NP1240 - 12461 - 7
5858chain 'N' and (resid 1247 through 1273 )NP1247 - 12738 - 34
5959chain 'N' and (resid 1274 through 1293 )NP1274 - 129335 - 54
6060chain 'N' and (resid 1294 through 1316 )NP1294 - 131655 - 77
6161chain 'N' and (resid 1317 through 1329 )NP1317 - 132978 - 90
6262chain 'O' and (resid 1240 through 1246 )OQ1240 - 12461 - 7
6363chain 'O' and (resid 1247 through 1273 )OQ1247 - 12738 - 34
6464chain 'O' and (resid 1274 through 1329 )OQ1274 - 132935 - 90
6565chain 'P' and (resid 1241 through 1273 )PR1241 - 12731 - 33
6666chain 'P' and (resid 1274 through 1329 )PR1274 - 132934 - 89

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万見について

-
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