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- PDB-5nt2: Complex of influenza A NS1 with TRIM25 coiled coil domain -

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基本情報

登録情報
データベース: PDB / ID: 5nt2
タイトルComplex of influenza A NS1 with TRIM25 coiled coil domain
要素
  • E3 ubiquitin/ISG15 ligase TRIM25
  • Non-structural protein 1
キーワードLIGASE / Viral protein/host protein/E3 ligase/TRIM protein
機能・相同性
機能・相同性情報


: / Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / regulation of viral entry into host cell / RIG-I binding / symbiont-mediated suppression of host mRNA processing / suppression of viral release by host / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling ...: / Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / regulation of viral entry into host cell / RIG-I binding / symbiont-mediated suppression of host mRNA processing / suppression of viral release by host / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / host-mediated suppression of symbiont invasion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / NS1 Mediated Effects on Host Pathways / response to vitamin D / protein serine/threonine kinase inhibitor activity / Modulation of host responses by IFN-stimulated genes / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / ligase activity / RSV-host interactions / TRAF6 mediated NF-kB activation / viral release from host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / Viral mRNA Translation / protein monoubiquitination / protein K48-linked ubiquitination / ERAD pathway / antiviral innate immune response / cellular response to leukemia inhibitory factor / positive regulation of DNA-binding transcription factor activity / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / RING-type E3 ubiquitin transferase / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / response to estrogen / cytoplasmic stress granule / Interferon gamma signaling / positive regulation of NF-kappaB transcription factor activity / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / regulation of protein localization / TRAF3-dependent IRF activation pathway / ubiquitin-dependent protein catabolic process / response to oxidative stress / positive regulation of canonical NF-kappaB signal transduction / host cell cytoplasm / transcription coactivator activity / nuclear body / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / symbiont-mediated suppression of host gene expression / innate immune response / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm
類似検索 - 分子機能
TRIM25, PRY/SPRY domain / : / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated ...TRIM25, PRY/SPRY domain / : / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / S15/NS1, RNA-binding / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
類似検索 - ドメイン・相同性
Non-structural protein 1 / E3 ubiquitin/ISG15 ligase TRIM25
類似検索 - 構成要素
生物種Influenza A virus (A型インフルエンザウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4.259 Å
データ登録者Koliopoulos, M.G. / Rittinger, K.
資金援助 英国, 1件
組織認可番号国
The Francis Crick InstituteFC001142 英国
引用ジャーナル: Nat Commun / 年: 2018
タイトル: Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition.
著者: Koliopoulos, M.G. / Lethier, M. / van der Veen, A.G. / Haubrich, K. / Hennig, J. / Kowalinski, E. / Stevens, R.V. / Martin, S.R. / Reis E Sousa, C. / Cusack, S. / Rittinger, K.
履歴
登録2017年4月27日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年5月23日Provider: repository / タイプ: Initial release
改定 1.12024年1月17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

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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
F: Non-structural protein 1
C: Non-structural protein 1
D: Non-structural protein 1
E: Non-structural protein 1
I: E3 ubiquitin/ISG15 ligase TRIM25
A: E3 ubiquitin/ISG15 ligase TRIM25
V: E3 ubiquitin/ISG15 ligase TRIM25
N: E3 ubiquitin/ISG15 ligase TRIM25


分子量 (理論値)分子数
合計 (水以外)191,5188
ポリマ－191,5188
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration, SEC-MALLS analysis shows that full-length NS1 is a dimer., gel filtration, SEC-MALLS analysis shows that TRIM25 coiled-coil is dimeric. Additional structural data show that it ...根拠: gel filtration, SEC-MALLS analysis shows that full-length NS1 is a dimer., gel filtration, SEC-MALLS analysis shows that TRIM25 coiled-coil is dimeric. Additional structural data show that it is an antiparallel dimer (see 4LTB in PDB).
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area32560 Å2
ΔGint-203 kcal/mol
Surface area69220 Å2
手法PISA
単位格子
Length a, b, c (Å)73.257, 76.296, 92.072
Angle α, β, γ (deg.)100.04, 93.71, 111.14
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Non-structural protein 1 / NS1 / NS1A


分子量: 25867.648 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) (A型インフルエンザウイルス)
株: A/Puerto Rico/8/1934 H1N1 / 遺伝子: NS / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P03496
#2: タンパク質
E3 ubiquitin/ISG15 ligase TRIM25 / Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / ...Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / RING-type E3 ubiquitin transferase TRIM25 / Tripartite motif-containing protein 25 / Ubiquitin/ISG15-conjugating enzyme TRIM25 / Zinc finger protein 147


分子量: 22011.930 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRIM25, EFP, RNF147, ZNF147 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q14258, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ（ペプチド合成）, RING-type E3 ubiquitin transferase

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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: 2.44 Å3/Da / 溶媒含有率: 49.67 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 / 詳細: 100 mM sodium citrate pH 6.5, 24% PEG 3350

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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: Diamond / ビームライン: I04 / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年7月10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: 0.9795 Å / 相対比: 1
反射解像度: 4.259→61.51 Å / Num. obs: 12516 / % possible obs: 98.6 % / 冗長度: 2.6 % / CC1/2: 0.985 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.14 / Net I/σ(I): 5.7
反射 シェル解像度: 4.26→4.33 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 630 / CC1/2: 0.8 / % possible all: 98.6

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829: ???)精密化
XDSデータ削減
Aimless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: 4LTB

4ltb


解像度: 4.259→61.684 Å / SU ML: 0.78 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 38.03 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3088 635 5.1 %
Rwork0.2702 --
obs0.2721 12451 98.07 %
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
精密化ステップサイクル: LAST / 解像度: 4.259→61.684 Å
タンパク質核酸リガンド溶媒全体
原子数10516 0 0 0 10516
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00410633
X-RAY DIFFRACTIONf_angle_d0.814298
X-RAY DIFFRACTIONf_dihedral_angle_d12.9076705
X-RAY DIFFRACTIONf_chiral_restr0.0451678
X-RAY DIFFRACTIONf_plane_restr0.0051834
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2585-4.58730.39431280.30972341X-RAY DIFFRACTION97
4.5873-5.04870.30691340.29752355X-RAY DIFFRACTION98
5.0487-5.77880.37191240.32452377X-RAY DIFFRACTION99
5.7788-7.27880.40851260.34262396X-RAY DIFFRACTION99
7.2788-61.69070.22131230.20042347X-RAY DIFFRACTION98
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)
16.32522.838-4.06467.80844.09318.43251.50640.46181.9186-0.054-1.1066-0.641-0.7840.5151-0.11531.70290.3645-0.26021.3278-0.35681.6546-136.6101-75.8288-197.6639
21.96071.5648-0.39514.96725.23755.81781.5373-4.30631.53831.2681.94120.5509-0.23560.70950.87142.20730.54870.33042.39370.57840.3712-150.0506-76.7036-210.8737
37.3227-0.0759-0.23152.81312.0976.99220.14141.4032-2.1823-0.5447-0.68550.99111.1438-1.4199-0.13641.80240.1083-0.37521.19710.35930.894-145.0457-85.0576-214.1167
47.57180.6272-0.10385.39411.51278.60890.1153-1.9804-0.71440.81230.5651-2.4040.7367-0.3229-0.23421.20920.4275-0.28461.3608-0.14471.2888-131.0545-83.2523-201.3731
54.36680.4689-2.64694.07580.54427.3246-1.69580.53680.27520.37460.80750.76270.46352.6412-0.00291.21180.03570.18850.88110.08490.9333-139.448-80.1826-204.363
66.0275-0.73190.86023.73163.46777.8374-0.148-0.63541.92040.52950.4318-1.65-0.0987-0.26060.17361.3770.5066-0.181.8835-0.22331.4581-142.0312-77.4693-209.7861
75.6473-2.0888-1.44221.08730.96490.9033-2.4663-1.0161-0.48970.41540.0239-0.43951.0996-0.38770.25741.84810.46690.05430.9099-0.34961.3646-142.9369-93.1775-198.3719
85.8151.2753-2.57875.60293.09077.03550.3593-0.7366-0.86030.94050.1952-3.24491.86372.68850.47651.80910.09280.33870.57630.50961.7136-136.1873-88.3846-213.0649
95.5197-1.1633-1.3973.891-1.37633.2249-0.30211.19481.36880.57581.0449-0.1846-0.80850.5488-0.21351.00510.08830.11711.2671-0.10191.2336-133.261-78.3855-217.0923
104.63612.8047-2.07935.43171.29672.7752-1.5696-0.28-0.3414-0.01070.9133-0.5-0.27813.1539-0.27661.15210.0074-0.33951.2505-0.12021.533-126.3161-81.8527-204.492
118.9438-3.454-2.03576.4919-0.66065.1326-0.9015-1.0249-2.88771.27823.05960.64141.89051.1658-0.01861.61050.06950.47832.0554-0.59950.9021-102.5399-36.5781-78.8204
125.20983.13262.30794.78861.28995.2568-1.70980.28930.3827-1.19151.1342.0237-2.57090.1562-0.44991.20760.37640.26511.42170.02521.7581-107.0707-23.0074-67.016
132.011-2.3319-3.28692.2789-1.29853.2154-0.93340.00531.78270.7683-0.30880.1582-0.88110.3845-1.4729-1.18460.05393.19742.07490.3666-0.455-93.5674-20.2828-64.3732
142.89681.45992.64413.3560.93085.0659-3.39670.6668-0.472-0.65281.4451-0.2927-0.94381.8833-1.8771-0.05471.02771.75751.8345-1.0799-0.975-98.6333-25.6719-62.0294
151.64652.7040.76777.0761-2.59926.3062-1.02561.8195-1.206-2.0951-0.3659-0.97820.7154-1.1171-0.691.31880.5091-0.02891.7844-0.59591.5231-93.6625-37.9821-75.2851
162.11910.59592.03795.52250.35126.5964-0.307-0.8221-1.1857-0.506-0.1916-0.41121.51812.236-0.46771.22190.33960.20341.4174-0.01390.7401-101.5647-30.6278-69.5343
173.7377-4.5949-1.3626.23631.86110.5301-0.9943-0.0201-0.6794-0.7444-1.5849-0.517-0.23573.5081-0.441.57230.0865-0.09312.88510.02571.4569-88.7898-23.8872-78.7356
182.49980.49721.14565.28360.81616.01050.33270.2934-0.01040.62191.048-1.13891.6799-0.0328-0.38430.92130.07790.14322.113-0.21491.2808-93.2867-33.2441-62.4961
195.0459-0.69040.70882.9541-1.87542.69920.25431.4801-1.4123-0.33512.1862-1.29363.46620.12550.40042.14960.69630.64091.1526-0.33431.3278-92.938-43.0208-71.9975
202.5302-2.9977-1.82984.58340.62221.94870.34440.5045-2.6994-1.0272-0.17170.2680.2008-0.222-0.33141.5434-0.0314-0.14141.8303-0.38392.5404-131.9299-53.7667-138.9206
214.79690.37450.65082.7587-2.0071.07130.35720.915-1.4106-1.6139-3.6836-0.17582.6134-0.4019-0.36452.5052-0.30020.02441.817-1.33012.3965-123.0518-59.6382-147.2425
226.3666-1.79543.03240.6106-1.13627.7218-0.0447-0.21593.062-0.7591-0.2820.74150.26861.15040.04722.1081-0.00770.78462.6498-1.30432.9986-107.0087-54.3323-138.2643
235.3895-1.1242-2.77098.30670.42021.35570.1435-0.2086-0.1213-2.463-0.09131.499-0.2261-0.50630.06341.7322-0.2159-0.34260.98480.18951.3433-102.8189-91.5188-150.0916
245.0159-2.06722.93136.2297-1.54651.28040.63630.5202-1.1102-0.8175-1.25430.49410.16960.7529-0.44781.43110.2759-0.06211.5325-0.02381.7565-119.9987-48.248-140.6156
255.1114-2.1826-1.08646.0743-0.32364.06150.5649-0.90380.81450.9497-0.2286-0.5398-0.03360.5454-0.08061.2402-0.04120.07191.0551-0.19021.2691-81.8887-53.5412-128.58
262.4352-3.9089-3.51543.92374.35535.65360.5560.13060.6621-0.15170.4029-1.4341-0.3229-0.00770.2841.1781-0.24910.37751.4545-0.04791.4102-92.6875-57.7482-109.8755
27-0.03970.17570.03920.51010.32790.12051.73510.36570.7573-1.93730.471-0.21260.962-3.50730.29012.43910.68290.02943.3013-0.15671.9515-69.8115-111.334-159.6486
282.0634-2.3824-1.79386.42991.48662.118-0.6623-0.3609-1.10060.8763-0.25661.42550.14160.21271.19461.0839-0.27650.19941.9731-0.30721.5389-101.9007-78.4512-118.5277
292.9726-0.91082.4657-0.1015-1.18913.37751.0730.5806-1.52820.18390.15840.14881.00870.31320.00251.18950.0841-0.26531.14680.00721.2954-115.7147-77.0707-170.1752
303.06391.0859-0.91151.88421.29471.5738-1.9193-0.0363-0.2172.018-1.7865-0.3392-0.25761.8318-0.46032.67580.8582-0.51443.4860.32992.1306-54.2418-78.7691-115.8427
314.20830.92872.05780.2598-0.31482.0243-1.3147-0.4882.12980.12240.0871-0.135-1.6616-0.06960.43231.3462-0.114-0.24121.5153-0.09131.5146-96.1621-61.4091-158.7691
324.06560.3662.2740.96070.1142.0356-0.7709-0.42010.65840.16750.0961-0.18-0.9004-0.34030.74021.055-0.02980.11141.45-0.25621.0037-109.1192-70.1499-156.9016
332.8109-0.2463.04280.0357-0.07893.4791-1.1837-3.48491.9769-1.2504-3.21541.329-2.6829-0.31190.77522.7226-0.0558-0.31312.7861-0.70683.3481-176.2499-80.2189-202.1172
344.9703-0.38423.80752.14191.45013.2359-1.61752.629-0.03850.22280.7083-0.6468-0.94742.0760.88751.0239-0.20440.06541.97420.51940.978-118.516-66.5406-182.3212
350.7603-0.3770.02375.62852.77161.66630.16750.23670.0295-0.6417-0.14420.0757-0.3008-0.18810.30821.31670.0611-0.17821.26220.00390.7927-97.8843-62.7646-120.1335
363.9278-4.3112-2.29084.74942.4981.3296-2.8602-1.05582.00240.0559-1.16380.0646-1.67460.5275-0.19562.03640.38330.32732.35350.07813.6568-108.10465.9517-74.4916
373.8017-0.6429-0.21743.45533.01313.6384-0.0596-0.71550.36590.8418-1.07050.0663-0.73380.31780.13773.8476-0.7967-2.61672.33061.87148.0441-116.17714.2732-73.0675
386.2223-1.9414-0.08033.9115-0.11280.57470.86870.37172.2258-0.63550.04220.5187-1.011-0.1716-0.0820.7171-0.21262.1373.95233.03816.5511-116.6642-5.1908-73.3309
392.9296-0.7564-0.26939.75973.96943.5292-0.09970.28571.35330.89-1.14790.1935-0.0153-1.04860.24641.52950.08760.36191.8713-0.12372.0875-114.1942-30.773-81.1462
403.2477-2.0538-3.32334.94511.06665.1174-0.8737-0.0898-0.31472.6368-0.61110.07142.1255-0.69890.4491.90630.11180.38421.4429-0.13891.1582-100.7412-67.6295-100.0697
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 87 through 99 )
2X-RAY DIFFRACTION2chain 'F' and (resid 100 through 106 )
3X-RAY DIFFRACTION3chain 'F' and (resid 107 through 126 )
4X-RAY DIFFRACTION4chain 'F' and (resid 127 through 142 )
5X-RAY DIFFRACTION5chain 'F' and (resid 143 through 151 )
6X-RAY DIFFRACTION6chain 'F' and (resid 152 through 162 )
7X-RAY DIFFRACTION7chain 'F' and (resid 163 through 170 )
8X-RAY DIFFRACTION8chain 'F' and (resid 171 through 188 )
9X-RAY DIFFRACTION9chain 'F' and (resid 189 through 195 )
10X-RAY DIFFRACTION10chain 'F' and (resid 196 through 201 )
11X-RAY DIFFRACTION11chain 'C' and (resid 87 through 98 )
12X-RAY DIFFRACTION12chain 'C' and (resid 99 through 106 )
13X-RAY DIFFRACTION13chain 'C' and (resid 107 through 112 )
14X-RAY DIFFRACTION14chain 'C' and (resid 113 through 126 )
15X-RAY DIFFRACTION15chain 'C' and (resid 127 through 142 )
16X-RAY DIFFRACTION16chain 'C' and (resid 143 through 162 )
17X-RAY DIFFRACTION17chain 'C' and (resid 163 through 170 )
18X-RAY DIFFRACTION18chain 'C' and (resid 171 through 195 )
19X-RAY DIFFRACTION19chain 'C' and (resid 196 through 201 )
20X-RAY DIFFRACTION20chain 'D' and (resid 4 through 50 )
21X-RAY DIFFRACTION21chain 'D' and (resid 51 through 74 )
22X-RAY DIFFRACTION22chain 'D' and (resid 75 through 84 )
23X-RAY DIFFRACTION23chain 'D' and (resid 85 through 203 )
24X-RAY DIFFRACTION24chain 'E' and (resid 3 through 85 )
25X-RAY DIFFRACTION25chain 'E' and (resid 86 through 203 )
26X-RAY DIFFRACTION26chain 'I' and (resid 190 through 304 )
27X-RAY DIFFRACTION27chain 'I' and (resid 305 through 316 )
28X-RAY DIFFRACTION28chain 'I' and (resid 317 through 362 )
29X-RAY DIFFRACTION29chain 'A' and (resid 190 through 298 )
30X-RAY DIFFRACTION30chain 'A' and (resid 299 through 316 )
31X-RAY DIFFRACTION31chain 'A' and (resid 317 through 362 )
32X-RAY DIFFRACTION32chain 'V' and (resid 190 through 298 )
33X-RAY DIFFRACTION33chain 'V' and (resid 299 through 316 )
34X-RAY DIFFRACTION34chain 'V' and (resid 317 through 362 )
35X-RAY DIFFRACTION35chain 'N' and (resid 190 through 298 )
36X-RAY DIFFRACTION36chain 'N' and (resid 299 through 304 )
37X-RAY DIFFRACTION37chain 'N' and (resid 305 through 311 )
38X-RAY DIFFRACTION38chain 'N' and (resid 312 through 316 )
39X-RAY DIFFRACTION39chain 'N' and (resid 317 through 330 )
40X-RAY DIFFRACTION40chain 'N' and (resid 331 through 362 )

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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