[日本語] English
万見
- PDB-7rqg: Crystal structure of the Nsp3 Y3 domain from SARS-CoV-2 -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7rqg
タイトルCrystal structure of the Nsp3 Y3 domain from SARS-CoV-2
要素Non-structural protein 3
キーワードVIRAL PROTEIN / SARS-CoV-2 / COVID-19 / non-structural protein 3 / nsp3 / Y3 domain / unknown function / structural genomics / CSGID / center for structural genomics of infectious diseases / NIAID / national institute of allergy and infectious diseases
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 / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / 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.
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 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.17 Å
データ登録者Stogios, P.J. / Skarina, T. / Chang, C. / 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 Y3 domain from SARS-CoV-2
著者: Stogios, P.J.
履歴
登録2021年8月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年8月18日Provider: repository / タイプ: Initial release
改定 1.12024年4月3日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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

-
集合体

登録構造単位
A: Non-structural protein 3
B: Non-structural protein 3
C: Non-structural protein 3
D: Non-structural protein 3


分子量 (理論値)分子数
合計 (水以外)45,9374
ポリマ－45,9374
非ポリマー00
水4,540252
1
A: Non-structural protein 3


分子量 (理論値)分子数
合計 (水以外)11,4841
ポリマ－11,4841
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Non-structural protein 3


分子量 (理論値)分子数
合計 (水以外)11,4841
ポリマ－11,4841
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Non-structural protein 3


分子量 (理論値)分子数
合計 (水以外)11,4841
ポリマ－11,4841
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Non-structural protein 3


分子量 (理論値)分子数
合計 (水以外)11,4841
ポリマ－11,4841
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)41.590, 49.141, 54.630
Angle α, β, γ (deg.)80.217, 89.649, 77.938
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
要素

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


分子量: 11484.261 Da / 分子数: 4 / 断片: Y3 domain / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
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: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 252 / 由来タイプ: 天然 / 式: H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.36 Å3/Da / 溶媒含有率: 47.9 %
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: 7.5
詳細: 1.1 sodium citrate, M, 0.1 M Hepes pH 7.5; Cryoprotectant paratone

-
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: APS / ビームライン: 19-ID / 波長: 0.97918 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2021年7月29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: 0.97918 Å / 相対比: 1
反射解像度: 2.17→30 Å / Num. obs: 19504 / % possible obs: 90.5 % / 冗長度: 2.9 % / Biso Wilson estimate: 37.12 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.073 / Net I/σ(I): 15.26
反射 シェル解像度: 2.18→2.22 Å / 冗長度: 2.7 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 960 / CC1/2: 0.536 / Rpim(I) all: 0.487 / % possible all: 89.2

-
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
PHENIX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: 2.17→28.05 Å / SU ML: 0.2648 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 28.8747
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2417 975 5 %
Rwork0.1968 18516 -
obs0.1991 19491 89.04 %
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: 51.37 Å2
精密化ステップサイクル: LAST / 解像度: 2.17→28.05 Å
タンパク質核酸リガンド溶媒全体
原子数2990 0 0 252 3242
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00223031
X-RAY DIFFRACTIONf_angle_d0.45274091
X-RAY DIFFRACTIONf_chiral_restr0.0407490
X-RAY DIFFRACTIONf_plane_restr0.0036518
X-RAY DIFFRACTIONf_dihedral_angle_d18.12211143
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.290.30551270.25452431X-RAY DIFFRACTION81.26
2.29-2.430.29771440.23862735X-RAY DIFFRACTION92.22
2.43-2.620.27491430.22812707X-RAY DIFFRACTION91.61
2.62-2.880.29051340.2192551X-RAY DIFFRACTION85.89
2.88-3.30.27411470.20422791X-RAY DIFFRACTION94.11
3.3-4.160.19451380.17572627X-RAY DIFFRACTION87.56
4.16-28.050.221420.17752674X-RAY DIFFRACTION90.81
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)
16.2062896533-1.49250984092-3.392144536829.69813120991-4.60140942435.010328629250.2020598238260.266188971053-0.500159783884-0.8034820245760.3629258940592.00178657761.19860296727-1.48968661342-0.08117576641470.497039072714-0.017783948909-0.1168015261860.493831140021-0.0213736706650.635785713556-14.72813255855.905438622112.72855154301
26.4218145347-1.8607606582-3.585190371495.278021750876.593560932498.595837543630.32581724573-1.04216371671-0.8333813803421.017013462050.825420640780.470256381207-0.106861653582-1.07045912675-0.6636667858080.4938832455070.1057203759550.003090832180980.503642136460.1928196668380.352639505256-2.879492867015.482211527719.67632213619
38.409633779893.9678758211-5.34609176849.45433881016-5.971799098094.99778384093-0.6231793181610.751749427176-0.353210535395-0.9332704581560.12042738456-0.2259986866451.103126819840.7907209848730.4976439395220.3849958690210.0736293466661-0.03334180809840.374186258994-0.06168543572590.3274825738683.356409036670.482683428655-7.08274326612
43.868101153193.722926443710.9273536936578.50405234211-3.139600408643.62017539223-0.427286410529-0.4152404804780.617781263441-0.3726575089070.4932018803410.104038371875-1.12985082644-0.512611339768-0.05990703585430.295184134998-0.00393436234172-0.02555379760490.317351491451-0.02808182165470.2340816701196.2468677860511.625292613-5.23928662325
54.741187653860.23673934194-2.146927984318.28263670489-0.9545904744568.57201366642-0.132899950599-0.206032158706-0.8349152718720.4570560196890.2050570176820.811798685790.9358597866640.506735765383-0.04625244708660.236499777980.0446431736620.004739731961940.2711642974760.03718284919790.5649420244860.616380897887-4.694709934913.77588449418
68.78196595942.57137427682-5.460471977886.926488047321.082695829249.271156051530.4801050171710.1601411159490.823486407264-0.8514381566680.45014845370.148022087554-1.208977507990.506622354052-0.6406458215150.138176294910.00798028416905-0.08980521853530.2940912737040.002327371932590.241254927673-3.4035061435610.10858583080.764292984536
72.154960890585.91106153178-1.607024637474.519822781-0.9378448889469.099311007950.4130580736920.786622886667-0.141586856907-2.21954374835-0.4846266916010.6826075461080.2210620983560.0212353916253-0.008821407988390.4878324374990.0861959929566-0.105991569940.424544828427-0.1111113583870.448232613208-6.460210569123.15486450031-7.49105044412
86.14691333116-0.3815113625541.266356908148.542760042526.43298007148.300402294330.0133209430741-0.2650769195430.03712264071120.231691408061-0.02683477650360.6090758648440.5081131154110.2920256208190.004218222636380.302898470193-0.0486625172254-0.02028024494670.2683862771270.08306304039630.271207166804-6.005377012753.67691122315.54833799598
91.998535681143.08342775168-4.400866316191.358588927110.424162694947.17679935363-3.80888164732-1.28120516067-2.844031142583.651744371982.451188921380.688420226212.497550813443.11776087370.6459071645791.18332931140.5175515061140.05744442428181.270499223160.2017669357920.7167128377772.91763141086-1.9108588863212.3791170847
104.2096928755.27029891419-2.573024819587.17488670013-2.178470344293.69460804696-0.6182473474670.194971944162-1.10524831972-0.0727929930783-0.446494186152-2.279822130890.5362435039661.573396749131.111878237520.4938426428690.1808777887770.05220040495480.5110626190360.07010906957230.45595891453410.98630494750.782273483563-0.428124770878
117.812728125433.26855370034-2.12018005766.56446362099-5.481413613088.67601979411-1.301663737131.73988335808-0.984694174907-3.30968715197-0.484946883567-1.494088897621.66492511238-0.05005122389650.7940850248910.7902348899470.1526558434070.2018458386860.4972552138720.1940417342550.377715555780.91521656457322.611333647512.5411135782
125.77576375143-3.051502362353.991626569985.91978762870.6316743566756.25764351757-0.2806807009820.9021201202350.0666361823959-0.01882704580610.324200984854-0.0773477938218-0.2917350270140.2830550683310.0294425162760.33424787583-0.02036064025330.0602839376580.2651964700490.08045185217140.2056215744527.6345208398115.555543193723.4278935007
134.899164303754.986859590111.10068488545.372942626391.969064003592.623995748140.1654630798820.667940600624-1.069550778290.107397053750.350290426333-2.05543816635-0.2313662219551.24132641237-0.5123898276150.477396891141-0.0103868695545-0.005215382429840.660473754065-0.06427171581480.61200915555415.685617096921.684565259933.7545403196
146.469828998334.053199008536.351727295452.54455123364.110329327129.15654976084-0.5115960014580.1434473892430.532779682953-0.04204906625940.604380571370.437671509327-1.60393325911-0.17053524048-0.1378233228730.5616554030260.009280169910090.09445390890840.543046194558-0.02520758016950.300136895036.3271431726321.944826036435.5105560474
153.07841993288-2.30449264098-2.162199847288.280536493291.408867750955.013210435680.000210504528919-0.125686790539-1.10439085339-0.314887254208-0.124257166722-0.2989471449550.5937437092340.1454491276590.1305684984220.370103349050.019020542018-0.05300838816350.309522612999-0.05030434187010.33887439363810.173042766210.041781496520.9006475014
162.401687149612.233835926311.852877231285.183540295492.984806105292.457920721750.0896217052362-0.741896531184-0.0006574227854120.2591279157550.008705835393440.177509212276-0.300339599406-0.07707224393960.03791082365770.3470470003830.05875586260920.04948842258670.2795143120770.00262914823410.2534809977131.537177773922.608024709625.2484968848
175.40393483912-2.3318398775-5.42819236013.444834891622.928800896745.569292831190.0101407893159-0.4572353165360.4539429147560.1207741774540.1684445246640.322483481862-1.092383399940.68605053879-0.2270867688830.415759768213-0.0795875269212-0.02630389862240.3886845469230.01587261980890.39279819326311.698991912725.441053656521.7580830801
182.265449610010.319909293199-0.7744255665472.750553011920.1862495153560.643642805039-0.3302095974690.26277438033-0.613634514579-0.2152211485850.21473678664-0.1045705635070.08547901674360.108150165850.1184144395640.3600814311050.0002771560923380.05550637980060.267002345014-0.0074309244010.2096793259846.8453364139818.225038663115.6098846627
196.53169800707-0.3479945897655.666005162477.03611286239-4.658092613048.490327472030.227010092301-1.822852606541.410566617541.33374130160.0931147570703-0.00517898572557-1.16575804984-0.255021077587-0.6205422975120.382735201541-0.02331913695640.2394483137540.4759402726760.04862100661840.735978510369-6.0991343461815.406506456824.2206575188
206.602711781261.76254532351-3.341918764012.5524073884-2.648101544494.41059960789-0.06259403844240.379145519519-3.60213061142-0.97674598662-0.1655850415011.908945258830.922474534091-0.5655431852870.005666902587270.611574270494-0.1084847452840.09878268820580.514120209006-0.1517217483740.9041202433932.995410474735.0776605120724.3873006373
216.441460582864.84042580413.055419732453.591303059412.308338214532.26940250872-0.0803849631917-0.442988374126-1.018684612371.324221246050.727875982722-0.3880043643562.064709629811.18832516203-0.7651423618090.5038500862440.104714093710.0044859310270.37571008618-0.02333317070980.42573570294510.512212741310.547093587632.9646362728
226.67071177522-0.762692425132.714059120977.13786269831.504219244268.66401654838-0.948592609177-0.02667807419951.138332662510.3972357709950.331689366235-1.65444096289-0.3302777929831.132693335510.3862246065060.3606520202-0.0274253202931-0.08178556726510.4013403597860.05898173714340.616992801486-12.137806461321.48832562035.8404370727
238.783203243582.956499026033.130720417335.001197772892.23385892344.37230999475-0.5506694497721.15145518675-0.291748319747-1.283969344480.36491452457-0.6099465877850.126722092860.4131665797080.1321684396420.440351299073-0.006894841720620.04145997404430.357856051022-0.02233908152320.355767508736-24.578349194218.925531975-7.67261158505
248.4298409817-5.04952675297-1.431414132763.88441801301-1.54990863296.79546655760.0137653155537-0.165810443280.977551167332-0.2358360276190.1645408034920.409836499185-0.883600036104-0.470240343136-0.1743179603250.3639635369180.0232657214395-0.05437629091580.282832100629-0.009304744313270.285761623834-22.318859531430.30091608970.990622270414
251.29913753175-1.592889592360.8246284300665.94155515604-0.6995045559436.0190409169-0.1364818902310.470589255456-0.333091602099-0.2128080203120.296939639089-0.1792564566310.472504670007-0.215915393369-0.2135436458720.178039783462-0.02475009051780.02379312496690.305218622566-0.0002932375564460.380336380663-16.897190432315.44603468210.186023938875
264.411739988572.830846588791.342472589583.89056881587-1.761553450736.11559700616-0.2489259937261.57248467078-0.941222514177-1.539305105690.0679709330709-1.845446825750.338546398320.9249580419810.1616834965780.535677013106-0.08313806389470.1664839469610.574647833522-0.04956001496530.440539786574-13.997646034321.5721639846-8.61039102277
277.55769122891.03205278568-0.280853902414.62981965293-3.181163720176.78820047539-0.165870640963-0.01768123938190.4451012180710.6706893124780.240685225093-0.511279630013-0.846349751591-0.511311682238-0.09516348110670.354057389570.01177697890850.002881054215350.256808037624-0.06656514023640.302426125776-17.329076860624.31605459695.80238407343
287.481651698826.085049844194.24458121289.302584289485.6457784283.548582697040.2831044925960.345065568457-0.185417904099-0.847457130476-0.4724058713330.609377797667-0.03513953465-0.9475436353890.3084961361530.6286371474650.130166323998-0.1455873098060.382305002206-0.04959587212630.41879406383-31.198707867124.2198603552-3.71162118681
296.85193777901-0.112855447316-1.116356994218.19542684492-1.898378920095.84251305513-0.0588271489717-0.38205707886-0.464368286280.4174399387620.07993919357360.02712024459310.3197660489510.2078199585050.03517786768210.2967429645090.00914338693598-0.0271841012480.439667004805-0.01174512814370.446476013871-8.466896511641.488070909417.9146744947
307.11421268412-0.459736012782.589600156020.9941045489522.392645152438.53042017071.765719487-0.239573263821-0.846840010323-2.983810447480.15135425776-0.14640968512.855669878250.720027996285-1.474932616211.88692301757-0.0688483714251-0.07971059184530.6213949361010.05675927073150.783524949769-7.4878222173144.26585188267.84662634701
318.361463268272.22183708788-2.431318628659.77906045997-4.819193770952.85271078067-0.2480531316430.2980035221320.3589768080741.29753466540.6224905757020.201872304543-0.60623527096-0.252471778584-0.3058995454980.5808797996990.134359113406-0.05470784941830.386266254555-0.01622220232340.480598140096-12.362037420346.953221568819.5685280517
328.01433410597-1.19217516059-0.9133699255994.10180661067-0.2551559931195.03872524611-0.551980538783-0.9089996604020.5712978505650.7764877123390.109592178611-1.8165541839-0.5597138293130.896035487080.2477333241930.7471403221560.0235737781451-0.2712456439640.4615976999650.03852794660850.724942175087-2.106783123937.083153522120.7415435812
335.54116382346-4.365207246252.780970434364.25362414876-2.499532589961.57603560666-1.31697905855-0.5541529347790.2003891625490.3270626128460.5090303002921.05969188478-1.4105600412-1.155057645280.9546067409750.7384115433760.0810770181445-0.2451078380180.378482860634-0.03936157747490.80351205325-12.263283405830.507768371412.4801278934
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 1842 through 1848 )AA1842 - 18481 - 7
22chain 'A' and (resid 1849 through 1854 )AA1849 - 18548 - 13
33chain 'A' and (resid 1855 through 1866 )AA1855 - 186614 - 25
44chain 'A' and (resid 1867 through 1875 )AA1867 - 187526 - 34
55chain 'A' and (resid 1876 through 1892 )AA1876 - 189235 - 51
66chain 'A' and (resid 1893 through 1904 )AA1893 - 190452 - 63
77chain 'A' and (resid 1905 through 1917 )AA1905 - 191764 - 76
88chain 'A' and (resid 1918 through 1930 )AA1918 - 193077 - 89
99chain 'A' and (resid 1931 through 1935 )AA1931 - 193590 - 94
1010chain 'A' and (resid 1936 through 1943 )AA1936 - 194395 - 102
1111chain 'B' and (resid 1844 through 1848 )BB1844 - 18481 - 5
1212chain 'B' and (resid 1849 through 1861 )BB1849 - 18616 - 18
1313chain 'B' and (resid 1862 through 1866 )BB1862 - 186619 - 23
1414chain 'B' and (resid 1867 through 1875 )BB1867 - 187524 - 32
1515chain 'B' and (resid 1876 through 1892 )BB1876 - 189233 - 49
1616chain 'B' and (resid 1893 through 1904 )BB1893 - 190450 - 61
1717chain 'B' and (resid 1905 through 1917 )BB1905 - 191762 - 74
1818chain 'B' and (resid 1918 through 1925 )BB1918 - 192575 - 82
1919chain 'B' and (resid 1926 through 1930 )BB1926 - 193083 - 87
2020chain 'B' and (resid 1931 through 1935 )BB1931 - 193588 - 92
2121chain 'B' and (resid 1936 through 1943 )BB1936 - 194393 - 100
2222chain 'C' and (resid 1844 through 1854 )CC1844 - 18541 - 11
2323chain 'C' and (resid 1855 through 1875 )CC1855 - 187512 - 32
2424chain 'C' and (resid 1876 through 1892 )CC1876 - 189233 - 49
2525chain 'C' and (resid 1893 through 1904 )CC1893 - 190450 - 61
2626chain 'C' and (resid 1905 through 1917 )CC1905 - 191762 - 74
2727chain 'C' and (resid 1918 through 1935 )CC1918 - 193575 - 92
2828chain 'C' and (resid 1936 through 1943 )CC1936 - 194393 - 100
2929chain 'D' and (resid 1844 through 1864 )DD1844 - 18641 - 21
3030chain 'D' and (resid 1865 through 1878 )DD1865 - 187822 - 27
3131chain 'D' and (resid 1879 through 1892 )DD1879 - 189228 - 41
3232chain 'D' and (resid 1893 through 1925 )DD1893 - 192542 - 74
3333chain 'D' and (resid 1926 through 1931 )DD1926 - 193175 - 80

+
万見について

-
お知らせ

-
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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlc1.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

+
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

+
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

+
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。

-
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