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- PDB-5wfi: X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in comp... -

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基本情報

登録情報
データベース: PDB / ID: 5wfi
タイトルX-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin
要素
  • Ubiquitin
  • papain-like protease
キーワードVIRAL PROTEIN / ubiquitin specific protease / USP / papain-like protease / MHV / Mouse Hepatitis Virus / coronavirus / PLP / PLP2 / DUB / deubiquitinase
機能・相同性
機能・相同性情報


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / host cell membrane ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / host cell membrane / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / positive regulation of protein ubiquitination / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Deactivation of the beta-catenin transactivating complex / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53
類似検索 - 分子機能
RNA-dependent RNA polymerase, coronavirus HKU1-like / Coronavirus Nsp3 DPUP domain / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / NSP3, DPUP domain, murine hepatitis virus-like / Non-structural protein 2, MHV-like / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / Jelly Rolls - #1680 / AAA domain ...RNA-dependent RNA polymerase, coronavirus HKU1-like / Coronavirus Nsp3 DPUP domain / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / NSP3, DPUP domain, murine hepatitis virus-like / Non-structural protein 2, MHV-like / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / Jelly Rolls - #1680 / AAA domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Ubiquitin domain profile. / 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 / Ubiquitin-like domain / 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. / 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 (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 / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto 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.
類似検索 - ドメイン・相同性
FORMIC ACID / Replicase polyprotein 1ab / Polyubiquitin-B
類似検索 - 構成要素
生物種Murine coronavirus (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.851 Å
データ登録者Mesecar, A.D. / Chen, Y.
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)R01AI085089 米国
引用ジャーナル: To Be Published
タイトル: X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin
著者: Mesecar, A.D. / Chen, Y.
履歴
登録2017年7月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年8月1日Provider: repository / タイプ: Initial release
改定 1.12019年9月25日Group: Data collection / カテゴリ: reflns
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all
改定 1.22019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
B: papain-like protease
C: Ubiquitin
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)86,07818
ポリマ－84,9344
非ポリマー1,14414
水11,494638
1
A: papain-like protease
C: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,0399
ポリマ－42,4672
非ポリマー5727
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-9 kcal/mol
Surface area17340 Å2
手法PISA
2
B: papain-like protease
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,0399
ポリマ－42,4672
非ポリマー5727
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-7 kcal/mol
Surface area17310 Å2
手法PISA
単位格子
Length a, b, c (Å)199.515, 43.388, 110.159
Angle α, β, γ (deg.)90.00, 114.85, 90.00
Int Tables number5
Space group name H-MC121

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要素

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タンパク質 , 2種, 4分子 ABCD

#1: タンパク質 papain-like protease / pp1ab / ORF1ab polyprotein


分子量: 33890.113 Da / 分子数: 2 / 断片: UNP residues 1609-1911 / 変異: C1716S / 由来タイプ: 組換発現
由来: (組換発現) Murine coronavirus (strain A59) (ウイルス)
株: A59 / 遺伝子: rep, 1a-1b / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P0C6X9, 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: タンパク質 Ubiquitin


分子量: 8576.831 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / 発現宿主: Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0CG47

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非ポリマー , 4種, 652分子

#3: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物 ChemComp-FMT / FORMIC ACID


分子量: 46.025 Da / 分子数: 2 / 由来タイプ: 合成 / 式: CH2O2
#5: 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
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 638 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.55 Å3/Da / 溶媒含有率: 51.71 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
Temp details: Room Temperature

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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: 0.98 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2015年7月15日
放射モノクロメーター: diamond(111) / 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: 0.98 Å / 相対比: 1
反射解像度: 1.85→100 Å / Num. obs: 73615 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.7 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.952 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Rrim(I) all: 0.061 / Net I/σ(I): 25.3
反射 シェル最高解像度: 1.85 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10_2155: ???)精密化
HKL-2000データ削減
SCALEPACKデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 4YPT

4ypt


解像度: 1.851→37.576 Å / SU ML: 0.18 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 20.13
Rfactor反射数%反射
Rfree0.1973 1999 2.72 %
Rwork0.1571 --
obs0.1582 73602 99.81 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 1.851→37.576 Å
タンパク質核酸リガンド溶媒全体
原子数5931 0 68 638 6637
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0066182
X-RAY DIFFRACTIONf_angle_d0.7388350
X-RAY DIFFRACTIONf_dihedral_angle_d10.4933733
X-RAY DIFFRACTIONf_chiral_restr0.051927
X-RAY DIFFRACTIONf_plane_restr0.0051065
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.851-1.89730.28271410.22525055X-RAY DIFFRACTION99
1.8973-1.94860.27861400.20575034X-RAY DIFFRACTION100
1.9486-2.00590.2411430.18885090X-RAY DIFFRACTION100
2.0059-2.07060.24391420.18255084X-RAY DIFFRACTION100
2.0706-2.14460.2211410.1725062X-RAY DIFFRACTION100
2.1446-2.23050.20881420.16745083X-RAY DIFFRACTION100
2.2305-2.3320.22721430.16235098X-RAY DIFFRACTION100
2.332-2.45490.24381420.16925101X-RAY DIFFRACTION100
2.4549-2.60870.2181430.16995101X-RAY DIFFRACTION100
2.6087-2.810.23111430.17695133X-RAY DIFFRACTION100
2.81-3.09270.20951430.17025136X-RAY DIFFRACTION100
3.0927-3.53990.21571440.15385139X-RAY DIFFRACTION100
3.5399-4.45880.14591450.12435198X-RAY DIFFRACTION100
4.4588-37.58410.15581470.14135289X-RAY DIFFRACTION99
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)
12.5311.4748-1.16372.037-1.62342.3664-0.26540.32270.1423-0.55080.2636-0.15870.33090.06460.00990.3271-0.0280.0170.31440.0430.2616-9.73231.48249.1752
21.9453-0.07981.22081.4174-0.86173.4093-0.00510.17210.0253-0.1155-0.0394-0.072-0.08990.25130.03530.20340.01980.00790.2126-0.03140.1495-2.978223.936130.9192
31.68780.3261-0.34191.74-0.05423.3389-0.0074-0.0995-0.06770.2556-0.0229-0.130.49180.16490.02960.32550.0132-0.07240.218-0.00040.2228-0.191214.617251.2815
41.5965-0.0644-0.03323.64130.262.7648-0.00220.1053-0.2647-0.3213-0.12950.34090.1445-0.17460.11260.2015-0.03070.00510.2115-0.06430.267523.016711.3686-7.1721
51.80220.62420.20582.0926-0.32972.5203-0.0687-0.0994-0.02720.00490.11190.20620.0157-0.3578-0.03330.15010.02220.00760.21360.0130.22829.553715.415114.8839
62.04531.0280.47161.15150.33980.9726-0.0171-0.22940.10870.0199-0.02540.0267-0.13890.03710.03720.21770.04610.0130.1905-0.010.188746.313525.232326.3747
72.45260.67930.02780.90810.01472.16440.029-0.68240.03320.34710.00260.2733-0.0854-0.3327-0.01570.27010.05310.06280.43090.02160.256331.766317.810932.9857
85.9809-0.6377-1.80712.6607-0.38591.336-0.3661-0.39520.17860.24740.0581-0.1643-0.4364-0.30570.26440.32430.0733-0.04640.43-0.14710.2728-5.31933.510663.6911
95.0819-1.63464.7626.9288-2.99927.5766-0.1853-0.2310.24790.0459-0.01370.5451-0.7229-0.19960.17580.4050.1042-0.05680.3576-0.14070.331-8.654137.816264.4114
102.1428-0.10151.23370.4752-0.41221.10020.0803-0.18860.1039-0.1405-0.09190.2549-0.1106-0.24840.1140.12730.5393-0.42390.6917-0.33650.6463-18.905337.377756.9207
114.72911.2884-1.155.16440.44362.1151-0.0129-0.29770.9339-0.3519-0.08910.1255-0.688-0.1183-0.01040.59170.1305-0.15610.3643-0.15990.4338-7.995540.312654.8865
121.81390.29640.46174.52561.58621.7348-0.3962-0.04230.4545-0.43930.2669-0.4276-0.78460.24940.15760.4983-0.038-0.04960.2918-0.0710.3291-2.653835.221151.0046
134.8004-2.3909-0.90364.79-1.29962.61490.00280.09520.1433-0.606-0.4760.7252-0.5212-0.52660.38190.36070.0364-0.13730.4056-0.10030.305-12.795127.911651.8286
140.90480.3440.24943.61451.18244.1429-0.1788-0.2014-0.20160.0524-0.4030.954-0.0102-0.83880.40490.2739-0.0084-0.0730.7746-0.24090.3964-17.817428.648760.2195
152.8405-1.0318-2.83840.90670.97485.236-0.0327-0.06840.256-0.09960.0209-0.0669-0.51420.28020.04810.3234-0.0527-0.04350.3338-0.06540.25030.380630.302851.7721
162.46531.6958-2.35272.797-2.64634.78760.0276-0.1999-0.1268-0.0379-0.1592-0.19630.24910.31870.08340.21530.04870.02820.24140.09570.232962.968215.315221.5412
173.0997-1.48570.49564.48960.44511.97980.17670.1707-0.22580.2157-0.1757-0.5310.12630.416-0.1320.20410.06510.04060.24860.07170.254166.425714.43717.1793
183.623-0.30091.12470.6947-0.5561.02720.45240.75530.1264-0.5535-0.2848-0.43070.12080.2046-0.10190.2760.0680.07180.28470.08330.271362.978820.52296.4842
193.5421-1.2237-1.30257.0941-1.17682.41380.13970.2799-0.4529-0.2187-0.11480.05070.15310.0636-0.01860.23210.06390.03420.1624-0.00610.216459.502210.616411.382
202.631-1.1376-0.8262.86980.26152.21020.00160.0096-0.5908-0.0429-0.1210.61190.27780.05230.15920.21620.05160.02650.169-0.01730.266752.349810.075315.5508
215.1091-2.30981.77172.80341.04886.56260.098-0.0477-0.201-0.11380.00390.0939-0.29970.0203-0.12320.20420.01220.01470.16770.01440.202452.076323.867518.7866
227.92370.6436-1.97555.48682.69362.3304-0.1050.74190.2918-0.1227-0.33250.1578-0.0581-0.34630.45350.2040.021-0.03750.20480.03110.226951.087720.5199.0933
233.2579-0.9001-0.35192.05370.26191.60980.0730.27710.9384-0.43760.0112-0.4829-0.22560.2343-0.01430.26490.06180.02960.18840.07850.315956.713825.41379.0037
246.34530.3782-1.58372.0259-1.34068.20120.2678-0.0460.2984-0.1498-0.11490.3116-0.23140.5929-0.03720.20580.00830.02510.20460.03090.280564.416626.47215.5764
254.35810.9125-0.25832.17590.02672.87280.2426-0.0371-0.12950.1026-0.27690.0723-0.05490.22110.01340.18410.00510.01230.17490.02390.181855.755915.772821.2193
264.89295.3844-4.00927.0962-3.52254.0131-0.09120.6287-0.2844-0.52350.13870.34430.5071-0.2355-0.06080.24820.02010.00480.20320.04680.318942.34156.888919.6272
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1609 through 1668 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1669 through 1780 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1781 through 1909 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1609 through 1695 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1696 through 1780 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1781 through 1878 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1879 through 1911 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 11 )
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 16 )
10X-RAY DIFFRACTION10chain 'C' and (resid 17 through 22 )
11X-RAY DIFFRACTION11chain 'C' and (resid 23 through 34 )
12X-RAY DIFFRACTION12chain 'C' and (resid 35 through 44 )
13X-RAY DIFFRACTION13chain 'C' and (resid 45 through 56 )
14X-RAY DIFFRACTION14chain 'C' and (resid 57 through 65 )
15X-RAY DIFFRACTION15chain 'C' and (resid 66 through 76 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 11 )
17X-RAY DIFFRACTION17chain 'D' and (resid 12 through 16 )
18X-RAY DIFFRACTION18chain 'D' and (resid 17 through 22 )
19X-RAY DIFFRACTION19chain 'D' and (resid 23 through 34 )
20X-RAY DIFFRACTION20chain 'D' and (resid 35 through 44 )
21X-RAY DIFFRACTION21chain 'D' and (resid 45 through 49 )
22X-RAY DIFFRACTION22chain 'D' and (resid 50 through 54 )
23X-RAY DIFFRACTION23chain 'D' and (resid 55 through 59 )
24X-RAY DIFFRACTION24chain 'D' and (resid 60 through 65 )
25X-RAY DIFFRACTION25chain 'D' and (resid 66 through 71 )
26X-RAY DIFFRACTION26chain 'D' and (resid 72 through 76 )

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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