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- PDB-5tl7: Crystal structure of SARS-CoV papain-like protease in complex wit... -

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基本情報

登録情報
データベース: PDB / ID: 5tl7
タイトルCrystal structure of SARS-CoV papain-like protease in complex with C-terminal domain mouse ISG15
要素
  • Replicase polyprotein 1ab
  • Ubiquitin-like protein ISG15
キーワードSignaling protein/Hydrolase / Signaling protein / Hydrolase / Signaling protein-Hydrolase complex
機能・相同性
機能・相同性情報


Modulation of host responses by IFN-stimulated genes / ISG15 antiviral mechanism / Termination of translesion DNA synthesis / positive regulation of protein oligomerization / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs ...Modulation of host responses by IFN-stimulated genes / ISG15 antiviral mechanism / Termination of translesion DNA synthesis / positive regulation of protein oligomerization / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein localization to mitochondrion / response to type I interferon / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / K63-linked deubiquitinase activity / host cell endoplasmic reticulum / viral transcription / positive regulation of interleukin-10 production / SARS-CoV-1 modulates host translation machinery / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / integrin-mediated signaling pathway / response to bacterium / modification-dependent protein catabolic process / integrin binding / positive regulation of type II interferon production / response to virus / protein tag activity / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / endonuclease activity / 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 / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / mRNA guanylyltransferase activity / defense response to virus / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / DNA helicase / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell Golgi apparatus / methyltransferase cap1 activity / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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 / lyase activity / defense response to bacterium / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / innate immune response / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / ubiquitin protein ligase binding / DNA-templated transcription / ATP hydrolysis activity / proteolysis / extracellular region / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm
類似検索 - 分子機能
Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / : / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / : / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / RNA-dependent RNA polymerase, SARS-CoV-like / Ubiquitin-like domain / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / 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 / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) 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 / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / 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. / 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 / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / Betacoronavirus single-stranded poly(A) binding domain / 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 / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) 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, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / : / Coronavirus replicase NSP2, N-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus
類似検索 - ドメイン・相同性
Replicase polyprotein 1ab / Ubiquitin-like protein ISG15
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
SARS coronavirus (SARS コロナウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.44 Å
データ登録者Daczkowski, C.D. / Dzimianski, J.V. / Pegan, S.D.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI109008 米国
United States Department of Agriculture (USDA)58-5030-5-034 米国
引用ジャーナル: J. Mol. Biol. / 年: 2017
タイトル: Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species.
著者: Daczkowski, C.M. / Dzimianski, J.V. / Clasman, J.R. / Goodwin, O. / Mesecar, A.D. / Pegan, S.D.
履歴
登録2016年10月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年5月3日Provider: repository / タイプ: Initial release
改定 1.12017年6月14日Group: Database references / カテゴリ: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
改定 1.22017年9月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
改定 1.52024年10月16日Group: Derived calculations / Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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: Ubiquitin-like protein ISG15
B: Replicase polyprotein 1ab
C: Ubiquitin-like protein ISG15
D: Replicase polyprotein 1ab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)90,3116
ポリマ－90,1814
非ポリマー1312
水2,198122
1
A: Ubiquitin-like protein ISG15
B: Replicase polyprotein 1ab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1563
ポリマ－45,0902
非ポリマー651
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Ubiquitin-like protein ISG15
D: Replicase polyprotein 1ab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1563
ポリマ－45,0902
非ポリマー651
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)75.981, 98.191, 106.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質 Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein


分子量: 9280.692 Da / 分子数: 2 / 断片: C-terminal domain (UNP residues 78-155 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Isg15, G1p2, Ucrp / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q64339
#2: タンパク質 Replicase polyprotein 1ab / pp1ab / ORF1ab polyprotein


分子量: 35809.629 Da / 分子数: 2 / 断片: UNP residues 1541-1855 / 由来タイプ: 組換発現
由来: (組換発現) SARS coronavirus (SARS コロナウイルス)
遺伝子: rep, 1a-1b / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P0C6X7, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, 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, ...参照: UniProt: P0C6X7, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, 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, RNA-directed RNA polymerase, DNA helicase, RNA helicase, 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの, 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, 加水分解酵素; エステル加水分解酵素
#3: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 122 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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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: 2.21 Å3/Da / 溶媒含有率: 44.23 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: 65% (v/v) MPD, 0.1 M Tris [pH 8.0], supplemented with 30% (w/v) Trimethylamine N-oxide dihydrate additive in a 1:5 dilution

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 21-ID-G / 波長: 0.9786 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2015年6月26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: 0.9786 Å / 相対比: 1
反射解像度: 2.44→72.23 Å / Num. obs: 29922 / % possible obs: 99.1 % / 冗長度: 2.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 18
反射 シェル解像度: 2.44→2.53 Å / Rmerge(I) obs: 0.742

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0073精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3E9S,5JZE

3e9s

5jze


解像度: 2.44→72.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.905 / SU B: 24.002 / SU ML: 0.264 / 交差検証法: THROUGHOUT / ESU R: 0.697 / ESU R Free: 0.315 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.26744 1529 5.1 %RANDOM
Rwork0.19211 ---
obs0.19615 28405 98.88 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 64.266 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.08 Å2
精密化ステップサイクル: 1 / 解像度: 2.44→72.23 Å
タンパク質核酸リガンド溶媒全体
原子数6226 0 2 122 6350
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196362
X-RAY DIFFRACTIONr_bond_other_d0.0010.026006
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9518602
X-RAY DIFFRACTIONr_angle_other_deg0.754313822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39524.364291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.493151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.281528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021495
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0093.5093120
X-RAY DIFFRACTIONr_mcbond_other2.0083.5093119
X-RAY DIFFRACTIONr_mcangle_it2.9575.263893
X-RAY DIFFRACTIONr_mcangle_other2.9585.2613894
X-RAY DIFFRACTIONr_scbond_it2.4763.7843242
X-RAY DIFFRACTIONr_scbond_other2.4763.7843243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8115.5674710
X-RAY DIFFRACTIONr_long_range_B_refined6.4128.1866933
X-RAY DIFFRACTIONr_long_range_B_other6.4128.1236917
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 2.442→2.506 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.306 118 -
Rwork0.263 1983 -
obs--96.6 %
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)
112.5229-3.7431-7.69877.00575.289210.67310.2448-0.29070.92630.24670.0449-0.2775-0.22910.0127-0.28960.35830.0238-0.05480.16040.02360.226-34.6124.17436.5
28.1204-1.40476.89571.1784-1.658322.11280.46661.17230.0733-0.0605-0.34230.10220.43210.3199-0.12420.43740.0344-0.01360.3239-0.010.2834-24.761115.83726.756
38.065-3.3124-12.946211.06621.073430.44050.92920.20960.2298-0.5522-0.46590.1787-0.7624-0.2081-0.46320.2904-0.018-0.03560.2588-0.00230.1741-35.345119.60632.436
42.0357-0.2247-2.54045.12753.4386.4802-0.1487-0.287-0.1550.0774-0.00670.43170.10210.09570.15540.29060.03380.00050.23160.03850.2372-33.57117.64144.355
59.9527-0.7030.70167.4284-0.1978.34720.21880.035-0.2445-0.418-0.39690.61520.3177-0.67080.17810.3421-0.0108-0.09020.2628-0.08880.3082-34.7110.99134.753
66.0304-5.9165-0.28217.02022.67996.0870.12290.0111-0.21820.0720.0747-0.13370.377-0.1731-0.19760.29540.0034-0.01510.2031-0.06610.3537-25.024111.4638.487
710.63853.1741-4.98633.59481.40495.53570.1692-0.66770.34620.2266-0.01470.05210.1530.4782-0.15450.35610.0351-0.03830.2033-0.01940.2395-23.97119.86846.496
813.22060.97910.47388.1021-2.32522.4967-0.1433-0.25460.4773-0.02240.40260.1433-0.35510.069-0.25930.34630.02080.03260.2203-0.04460.2431-28.352124.49345.111
98.5577-4.30510.67826.69580.64085.41760.29490.16310.5586-0.6617-0.1381-0.0519-0.44360.1278-0.15680.3744-0.00940.0220.2050.03450.2732-28.987126.57435.776
105.5999-3.9993-1.66446.9147-3.55756.0947-0.23590.0645-0.4589-0.03550.36980.48290.3532-0.5211-0.13390.3534-0.0424-0.03530.1495-0.0690.3171-19.869108.46336.304
113.83360.9997-1.14970.8352-1.24972.0092-0.2392-0.3856-0.4351-0.06530.1896-0.05570.2901-0.37360.04960.50450.02110.04350.26860.02580.3434-23.32199.66767.146
126.01393.42011.37079.29530.20795.3872-0.0241-0.1186-0.25620.0916-0.16050.23560.2804-0.15670.18460.26730.02320.04740.2065-0.01370.2068-22.212101.04963.665
130.93542.9832-1.828714.96082.302517.80130.2958-0.2015-0.0360.7804-0.2183-0.2373-0.01090.1765-0.07750.6717-0.14240.02450.70020.01820.5503-17.218121.92766.489
144.407-1.1045-1.7694.0923-0.0973.4118-0.039-0.2782-0.20930.099-0.03250.07940.06450.29410.07140.2225-0.0255-0.08080.07180.0010.1428-8.04109.58455.284
151.34510.28820.13581.31010.71752.93770.0094-0.0118-0.0172-0.1408-0.0756-0.117-0.03890.28970.06620.30140.03040.00290.0532-0.00990.2476-6.29112.19248.642
161.6988-0.38292.62520.9458-1.8396.2841-0.09860.32580.2776-0.0537-0.15-0.0215-0.35940.41250.24860.4310.09030.02170.22270.0290.3086-12.647126.72832.695
170.90231.04860.52243.5497-1.03664.2327-0.04390.16610.1608-0.5106-0.1040.3718-0.2389-0.18570.1480.45380.0641-0.04230.21380.04790.2945-11.126123.58827.632
182.3230.16660.39522.3029-0.86362.4508-0.04960.33750.0124-0.3116-0.01150.0662-0.03790.2510.06110.46450.03730.0310.2288-0.0520.2108-7.463114.03329.008
1910.22514.7898-8.02934.84610.391113.4894-0.0459-0.2424-0.0446-0.41560.0096-0.1877-0.1960.57720.03630.45460.17030.0590.37920.03740.35726.657102.7835.197
201.51370.40480.02638.07650.92792.20680.19450.37310.1741-0.3186-0.1823-0.276-0.17520.3949-0.01230.3697-0.01120.02150.32670.01540.2208-2.384119.59427.251
2113.6713-1.51294.07552.7622-0.16372.9611-0.1167-0.30620.11430.36690.07920.2311-0.2328-0.28440.03760.4066-0.0329-0.00280.27330.02120.333418.191135.3482.494
221.7548-2.437-3.627920.973823.525427.06840.35410.3626-0.1384-0.40530.3709-1.0334-0.47510.3677-0.7250.72450.08150.05440.72960.27490.920632.269131.7463.495
238.0512-0.32192.65938.9023-3.743512.5586-0.23240.5530.84460.1104-0.0246-0.5514-0.6581-0.03290.25710.3347-0.03960.02130.16470.03030.397421.719136.965-1.224
241.6906-3.15041.8367.2328-1.66694.3160.0042-0.081-0.0716-0.11750.12530.1486-0.0286-0.1684-0.12950.30870.0146-0.00480.21410.03570.369311.115129.759-3.897
2511.84522.93632.27074.2603-7.420218.5-0.1810.2963-0.3231-0.25280.0847-0.14030.3782-0.04160.09630.33090.094-0.06530.28520.01430.354119.128126.55-6.397
266.50931.93845.011724.02683.60444.0692-0.25640.14970.2348-0.53440.2278-0.5687-0.23930.09350.02870.3270.03340.0420.32560.0970.502326.209131.091-6.453
272.03462.33483.36298.1624-1.89411.6742-0.23680.1241-0.2625-0.99290.3586-0.64320.4174-0.1447-0.12180.3520.00120.03190.28670.06730.471226.741122.728-3.057
285.62692.75496.97369.72726.839614.45190.214-0.2529-0.3127-0.0054-0.1710.0821-0.06260.0073-0.04290.24730.01440.04030.2390.05320.35115.816121.9524.691
298.4177-4.5084-2.79894.00822.79428.963-0.1588-0.2279-0.00850.16230.1420.50610.374-0.99260.01670.31470.01640.02350.19550.03290.451310.573125.8991.89
305.1971-5.3298-0.879210.49440.40460.59940.0330.28080.2380.2773-0.2549-0.0236-0.2649-0.01430.22190.35280.013-0.04860.23810.01990.273923.967125.8393.901
315.94350.9135-0.00283.53650.19466.8080.01540.5426-0.6788-0.5072-0.09870.22120.5757-0.08540.08320.41260.0028-0.07280.1191-0.07370.446910.79298.412-14.159
328.0826-0.7244-2.04284.5782-0.04848.8440.06840.1985-0.1779-0.2015-0.15730.02060.05710.17660.0890.37180.0022-0.11270.1279-0.01760.361212.627102.044-12.754
3315.9582-4.15392.94533.5132-0.64428.08110.0394-0.3178-0.394-0.2044-0.0350.24440.1246-0.5255-0.00430.3391-0.03830.01150.27990.00390.46560.536107.1046.436
343.1288-0.07280.07491.9955-0.07741.97730.04210.0748-0.17220.0225-0.00080.24980.26460.043-0.04140.2460.0026-0.0150.0050.01780.258721.728101.4387.344
353.5106-3.9346-0.570410.7915-1.28680.7343-0.0868-0.1918-0.28120.614-0.05930.1842-0.00170.05330.14620.4422-0.07920.07670.27340.03950.351415.412101.65116.626
362.22470.37440.30032.01811.27192.8376-0.0101-0.20270.143-0.0348-0.00690.2008-0.0046-0.03060.0170.2369-0.0145-0.0060.03270.05180.324320.978109.056.884
374.2083.9225-0.61996.6375-0.96922.8010.3851-0.19320.52850.2149-0.38330.4046-0.1154-0.146-0.00180.27170.10.03750.1449-0.03130.414925.792129.38321.369
381.23220.1538-0.44891.9835-0.05151.83870.1283-0.11950.36710.22870.06640.0199-0.10360.0735-0.19460.28470.02240.03120.0702-0.02270.30535.449121.64919.115
391.9553-0.99372.81864.0287-2.19557.72430.0877-0.0438-0.03650.0649-0.0702-0.03720.050.1623-0.01750.20560.01030.03150.1855-0.02370.241838.8103.21513.061
402.1449-1.0509-0.99162.73280.86234.9930.0172-0.24840.0880.26320.0185-0.0595-0.19930.1038-0.03570.3052-0.06690.02330.1292-0.02370.244235.573117.58623.562
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 84
2X-RAY DIFFRACTION2A85 - 90
3X-RAY DIFFRACTION3A91 - 95
4X-RAY DIFFRACTION4A96 - 107
5X-RAY DIFFRACTION5A108 - 114
6X-RAY DIFFRACTION6A115 - 124
7X-RAY DIFFRACTION7A125 - 134
8X-RAY DIFFRACTION8A135 - 140
9X-RAY DIFFRACTION9A141 - 147
10X-RAY DIFFRACTION10A148 - 154
11X-RAY DIFFRACTION11B1 - 45
12X-RAY DIFFRACTION12B46 - 62
13X-RAY DIFFRACTION13B63 - 69
14X-RAY DIFFRACTION14B70 - 107
15X-RAY DIFFRACTION15B108 - 169
16X-RAY DIFFRACTION16B170 - 195
17X-RAY DIFFRACTION17B196 - 224
18X-RAY DIFFRACTION18B225 - 279
19X-RAY DIFFRACTION19B280 - 296
20X-RAY DIFFRACTION20B297 - 316
21X-RAY DIFFRACTION21C79 - 85
22X-RAY DIFFRACTION22C86 - 90
23X-RAY DIFFRACTION23C91 - 95
24X-RAY DIFFRACTION24C96 - 102
25X-RAY DIFFRACTION25C103 - 108
26X-RAY DIFFRACTION26C109 - 113
27X-RAY DIFFRACTION27C114 - 123
28X-RAY DIFFRACTION28C124 - 132
29X-RAY DIFFRACTION29C133 - 140
30X-RAY DIFFRACTION30C141 - 154
31X-RAY DIFFRACTION31D4 - 43
32X-RAY DIFFRACTION32D44 - 62
33X-RAY DIFFRACTION33D63 - 72
34X-RAY DIFFRACTION34D73 - 126
35X-RAY DIFFRACTION35D127 - 144
36X-RAY DIFFRACTION36D145 - 178
37X-RAY DIFFRACTION37D179 - 209
38X-RAY DIFFRACTION38D210 - 267
39X-RAY DIFFRACTION39D268 - 295
40X-RAY DIFFRACTION40D296 - 316

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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