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- PDB-6f5p: A mechanism for the activation of the influenza virus transcriptase -

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基本情報

登録情報
データベース: PDB / ID: 6f5p
タイトルA mechanism for the activation of the influenza virus transcriptase
要素
  • ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
  • DNA-directed RNA polymerase subunit
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA-directed RNA polymerase catalytic subunit
キーワードREPLICATION / influenza virus RNA polymerase / Pol II / transcription
機能・相同性
機能・相同性情報


microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex ...microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / cap snatching / mRNA Splicing - Minor Pathway / PIWI-interacting RNA (piRNA) biogenesis / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / 7-methylguanosine mRNA capping / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / : / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / DNA-directed RNA polymerase activity / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / DNA-templated transcription termination / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / virion component / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / : / : / : / : / : / : / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / 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 / endonuclease activity / Estrogen-dependent gene expression / transcription by RNA polymerase II / 加水分解酵素; エステル加水分解酵素 / host cell cytoplasm / hydrolase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / nucleotide binding / DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / host cell nucleus / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus
類似検索 - 分子機能
Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : ...Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus
類似検索 - ドメイン・相同性
DNA-directed RNA polymerase II subunit RPB1 / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
類似検索 - 構成要素
生物種Influenza C virus (インフルエンザウイルス)
Fopius arisanus (昆虫)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 解像度: 4.14 Å
データ登録者Serna Martin, I. / Grimes, J.M.
資金援助 英国, 3件
組織認可番号国
Medical Research Council (United Kingdom)MR/K000241/1 英国
Wellcome Trust200835/Z/16/Z 英国
Wellcome Trust092931/Z/10/Z 英国
引用ジャーナル: Mol Cell / 年: 2018
タイトル: A Mechanism for the Activation of the Influenza Virus Transcriptase.
著者: Itziar Serna Martin / Narin Hengrung / Max Renner / Jane Sharps / Mónica Martínez-Alonso / Simonas Masiulis / Jonathan M Grimes / Ervin Fodor /
要旨: Influenza virus RNA polymerase (FluPol), a heterotrimer composed of PB1, PB2, and PA subunits (P3 in influenza C), performs both transcription and replication of the viral RNA genome. For ...Influenza virus RNA polymerase (FluPol), a heterotrimer composed of PB1, PB2, and PA subunits (P3 in influenza C), performs both transcription and replication of the viral RNA genome. For transcription, FluPol interacts with the C-terminal domain (CTD) of RNA polymerase II (Pol II), which enables FluPol to snatch capped RNA primers from nascent host RNAs. Here, we describe the co-crystal structure of influenza C virus polymerase (FluPol) bound to a Ser5-phosphorylated CTD (pS-CTD) peptide. The position of the CTD-binding site at the interface of PB1, P3, and the flexible PB2 C-terminal domains suggests that CTD binding stabilizes the transcription-competent conformation of FluPol. In agreement, both cap snatching and capped primer-dependent transcription initiation by FluPol are enhanced in the presence of pS-CTD. Mutations of amino acids in the CTD-binding site reduce viral mRNA synthesis. We propose a model for the activation of the influenza virus transcriptase through its association with pS-CTD of Pol II.
履歴
登録2017年12月2日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年9月19日Provider: repository / タイプ: Initial release
改定 1.12024年10月16日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type
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 / _struct_conn_type.id

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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: Polymerase acidic protein
D: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: RNA-directed RNA polymerase catalytic subunit
E: Polymerase basic protein 2
F: Polymerase basic protein 2
G: DNA-directed RNA polymerase subunit
H: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)516,28512
ポリマ－516,1878
非ポリマー974
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: homology, SAXS, gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area77730 Å2
ΔGint-443 kcal/mol
Surface area182040 Å2
手法PISA
単位格子
Length a, b, c (Å)185.700, 185.700, 597.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and (resseq 1:47 or (resid 48 and (name...
211(chain D and (resseq 1:47 or (resid 48 and (name...
112(chain B and (resseq 1:191 or resseq 203:230 or resseq...
212(chain C and (resseq 1:191 or resseq 203:230 or resseq...
113(chain F and (resseq 1:49 or resseq 51:249 or resseq 251:771))
213(chain E and (resseq 1:49 or resseq 51:249 or resseq 251:771))

NCSアンサンブル:
ID
1
2
3

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要素

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タンパク質 , 3種, 6分子 ADBCEF

#1: タンパク質 Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


分子量: 82025.531 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Influenza C virus (strain C/Johannesburg/1/1966) (インフルエンザウイルス)
株: C/Johannesburg/1/1966 / 遺伝子: PA, P3
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9IMP5, 加水分解酵素; エステル加水分解酵素
#2: タンパク質 RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


分子量: 86145.945 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Influenza C virus (strain C/Johannesburg/1/1966) (インフルエンザウイルス)
株: C/Johannesburg/1/1966 / 遺伝子: PB1
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9IMP4, RNA-directed RNA polymerase
#3: タンパク質 Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


分子量: 87949.422 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Influenza C virus (strain C/Johannesburg/1/1966) (インフルエンザウイルス)
株: C/Johannesburg/1/1966 / 遺伝子: PB2
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9IMP3

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タンパク質・ペプチド , 2種, 2分子 GH

#4: タンパク質・ペプチド DNA-directed RNA polymerase subunit


分子量: 3216.893 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Fopius arisanus (昆虫) / 遺伝子: RpII215_0, g.45518 / 発現宿主: synthetic construct (人工物) / 参照: UniProt: P24928*PLUS, DNA-directed RNA polymerase
#5: タンパク質・ペプチド ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


分子量: 728.793 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)

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非ポリマー , 1種, 4分子

#6: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mg

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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: 4.99 Å3/Da / 溶媒含有率: 75.35 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 70% (v/v) Morpheus G2 (Molecular Dimensions) and 7.5% (v/v) glycerol

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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: 0.9763 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年7月7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: 0.9763 Å / 相対比: 1
反射解像度: 4.1→132.4 Å / Num. obs: 75524 / % possible obs: 100 % / 冗長度: 13.5 % / CC1/2: 0.998 / Rpim(I) all: 0.055 / Net I/σ(I): 7.9
反射 シェル解像度: 4.14→4.21 Å / 冗長度: 2.1 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.733 / Rpim(I) all: 0.568 / % possible all: 60.6

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155: ???)精密化
xia2データ削減
xia2データスケーリング
PHENIX位相決定
精密化解像度: 4.14→131.31 Å / SU ML: 0.64 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 31.93
Rfactor反射数%反射
Rfree0.2958 2816 5.06 %
Rwork0.26 --
obs0.2618 55611 68.9 %
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: 4.14→131.31 Å
タンパク質核酸リガンド溶媒全体
原子数35282 0 0 0 35282
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00535891
X-RAY DIFFRACTIONf_angle_d0.81248264
X-RAY DIFFRACTIONf_dihedral_angle_d16.88322148
X-RAY DIFFRACTIONf_chiral_restr0.055302
X-RAY DIFFRACTIONf_plane_restr0.0056176
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A5622X-RAY DIFFRACTIONPOSITIONAL
12D5622X-RAY DIFFRACTIONPOSITIONAL0.067
21B5636X-RAY DIFFRACTIONPOSITIONAL
22C5636X-RAY DIFFRACTIONPOSITIONAL0.057
31F6120X-RAY DIFFRACTIONPOSITIONAL
32E6120X-RAY DIFFRACTIONPOSITIONAL0.041
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)
16.26890.46391.04094.9626-0.24362.83320.09960.3430.1464-0.0954-0.0737-0.0619-0.55251.0157-0.00981.2621-0.2696-0.19811.2916-0.26820.831226.5964-28.44487.7486
20.84690.4720.24181.64070.631.2949-0.19640.1640.1594-0.48680.1888-0.0217-0.14460.10480.12250.8606-0.1402-0.18911.13450.14040.7974-4.7957-77.2638-26.9135
34.9645-2.5896-1.50475.72072.40073.2741-0.1836-0.20890.1026-0.31730.30830.36780.6293-0.0256-0.1150.7438-0.3576-0.19650.84540.2040.703-15.0044-90.1109-20.3334
46.2489-0.58950.84852.6398-1.62333.2083-0.34660.1356-0.5493-0.23980.2736-0.71081.36130.73240.07481.73560.63550.24791.40780.42321.487114.5107-154.8666-60.1149
51.3026-0.48520.45273.5301-1.29642.86270.55290.6794-0.0638-0.7411-1.0117-1.00250.24891.57740.29870.48190.01190.28271.96080.23590.641518.9817-115.1242-95.4539
64.45872.9814-1.26726.3235-0.61417.2876-0.46220.9727-1.517-1.04560.42680.67881.1202-1.3460.05441.2354-0.40810.0861.3563-0.12851.0919-20.2236-87.92-112.9827
70.8377-0.5285-2.31743.59930.99824.11920.29450.17030.1186-0.9067-0.4566-0.1549-1.41270.13120.11121.2256-0.1119-0.03060.85110.03750.8137-0.072-92.5993-100.1314
86.77561.04024.43082.2731-0.55996.0991-0.1180.01050.4511-0.0042-0.0452-0.1901-1.37370.24340.07581.1442-0.30130.140.80160.01140.6774-4.4691-83.2624-95.1976
95.386-2.28730.25453.935-1.04583.78770.3140.41410.35530.00550.0524-0.8495-0.68360.8952-0.00371.0231-0.46060.13841.35880.23790.990922.3711-89.3646-98.604
105.54579.6858-3.95843.5081-9.4415.14210.5864-0.0069-0.68140.5525-0.4441-0.2569-1.44480.2857-0.08541.2885-0.23110.16611.1250.08641.537-14.4874-71.8848-24.4477
115.9174-0.8786-2.6192.170.58965.0133-0.1186-0.1357-0.3046-0.35570.1757-0.1595-0.060.3752-0.13360.931-0.3877-0.29280.7436-0.1040.92749.2452-49.0683-25.5375
121.4744-0.705-0.81721.7609-0.83012.7846-0.3390.13410.31660.03860.1799-0.0182-0.2199-0.59950.23440.5679-0.1794-0.18380.8106-0.04850.7128-5.8022-52.9596-22.2225
134.561-1.9181-2.59575.36114.45941.9713-0.18390.7181-0.6493-0.8394-0.27650.55260.1294-0.25250.18581.0531-0.3657-0.24040.74760.18911.035-0.5289-56.0544-43.718
147.8533-3.24951.72674.6516-0.28944.1929-0.3002-0.3642-0.59450.04610.36971.4817-0.4482-0.7209-0.00120.7520.0659-0.11540.8148-0.02140.9235-18.663-55.2669-13.7068
158.1318-1.4941-0.59729.51924.11848.57640.8197-0.4834-0.6159-0.80490.5272-1.34390.69570.3217-1.25090.83180.00690.00950.78080.05030.7216.1574-89.49191.2211
164.22453.7954-3.45139.4122-1.81144.9066-0.39050.6859-1.7438-0.576-0.3595-1.58021.12010.18610.53340.94890.12170.00731.2054-0.05861.55334.1267-68.8491-6.1967
17-1.4942-0.7722-0.61137.78137.14672.1278-0.04440.11570.212-0.9318-0.0057-0.3371-1.01881.26680.15331.377-0.3412-0.06381.33790.18031.104315.1462-98.6349-98.6611
185.67782.766-0.59626.0088-0.10293.80730.48580.51120.019-0.165-0.4749-0.0750.70540.49580.07520.90440.26250.07870.91260.2090.745713.5835-132.4994-96.9733
19-2.10251.46030.10154.72622.82953.8377-0.11980.11520.20590.2751-0.29160.1907-0.31781.5210.37980.94760.06070.09962.05450.33891.028721.9534-113.8849-87.8564
205.8238-3.16612.91612.3444-1.25056.22830.1292-0.16140.032-0.113-0.2834-0.3260.25911.02010.01780.73920.1280.0361.01750.16770.829415.7993-124.4026-108.7753
210.8485-1.295-0.23522.4925-0.56591.95320.37160.15410.9919-0.0011-0.417-0.8256-0.28371.42790.02411.1066-0.42450.11452.22840.28291.29329.5302-106.5063-86.8248
227.6314-0.10643.8694.5365-1.980711.03450.7867-0.168-0.31870.337-0.31720.97330.582-0.5924-0.39921.1946-0.5304-0.07750.81820.10220.8195-12.1885-97.2751-73.2404
230.6644-3.87790.31658.63033.45983.7142-0.16280.5089-0.1519-0.4707-0.6762.0082-0.1722-0.4390.73911.1792-0.4674-0.14131.4484-0.05341.3877-18.1301-132.1405-76.8395
241.31971.7768-0.9998.5008-2.2844-0.3696-0.58410.4465-0.1767-0.17410.6148-0.15270.6523-0.24840.16660.9914-0.04330.03622.0726-0.23451.242528.8939-71.5539-12.4663
251.3753-0.0303-0.71448.40333.61426.4882-0.14140.27060.2931-1.47270.6856-1.8564-0.57920.8732-0.35281.1666-0.13610.24311.101-0.00980.901613.5767-80.96524.6727
263.86773.56811.10689.77053.57298.0128-0.49410.2085-0.9415-0.90351.05240.0438-0.57291.4373-0.74320.7192-0.0644-0.35691.3620.26711.421823.9963-63.265111.8385
273.18854.2582.49378.97283.46513.2570.3279-1.6751.02460.0347-0.72260.8956-0.3418-0.69990.48190.94070.25070.12291.1073-0.17890.9453-4.503-70.485613.0198
287.6459-0.57282.55543.7057-2.4295.8534-0.8277-0.55430.22461.1520.66190.0209-0.70970.05240.23921.16890.10130.04070.8471-0.20720.9338-1.2109-43.855521.3914
296.8779-1.64932.16938.54741.12016.3129-0.5725-0.44560.29231.20140.15651.015-0.739-0.75540.33621.2130.24790.11111.19730.07771.0114-23.3549-46.035219.1712
302.85970.30893.12830.2301-1.79714.8655-0.0328-0.54820.98020.3061-0.3954-0.3308-0.09550.46010.55511.60360.4265-0.14621.5175-0.46691.4637.8173-44.346628.6648
31-0.7242-1.4295-1.58497.3053-4.46744.8220.45-1.0449-0.12532.46960.2335-0.76280.09492.9542-0.56331.9256-0.2719-0.50062.4257-0.21571.748735.2566-55.373939.6338
322.7873-1.84150.89779.1137-0.83162.6060.5991-0.3806-0.11540.9275-0.3366-1.63080.06351.0302-0.26691.0536-0.2761-0.42262.17450.17731.199735.6328-44.964414.023
331.8922-0.6213-0.29884.30180.61331.205-0.47160.36110.5782-0.75310.32540.66610.174-0.1290.17711.5712-0.5957-0.09631.5024-0.00761.0186-16.2666-126.9327-83.795
342.9563-0.76191.5872.2969-1.20035.99980.58720.3878-0.3174-0.4178-0.19890.93080.8269-0.0841-0.17520.9983-0.26850.01750.83720.04251.2074-11.5203-107.9535-68.5228
351.53493.1756-1.25934.9602-3.70287.3796-0.0622-0.4582-0.38040.35840.2153-0.16380.19960.8234-0.23840.93680.14220.01881.32260.03970.9882-0.4361-116.8669-59.9147
363.3957-0.1072-1.4813.02380.11995.7291-0.4531-0.7602-0.0870.1409-0.0214-0.79480.62161.78960.34880.97580.1436-0.30871.50380.25281.035228.0553-118.401-52.904
371.8006-0.01720.56580.15980.10941.59770.1929-0.5338-0.12750.4718-0.1302-0.1547-0.08071.43340.01571.45920.0524-0.08222.34160.22711.440430.8823-115.9722-47.181
383.65032.6453.17586.89774.5724.6622-0.0236-0.4705-0.03160.3558-0.3429-0.49060.4745-0.88040.44371.3088-0.22130.15031.20760.42631.2739-10.0176-137.7539-30.3537
397.3856-2.036-1.70784.5064-0.20446.72340.2607-0.2784-0.80360.35470.16140.681.02510.8966-0.41911.8293-0.25150.23761.08340.06890.8754-3.1343-148.17-55.0216
402.3222-5.12450.78749.9115-2.34210.71090.59450.14742.20441.89051.43941.4015-0.8598-0.1206-0.97691.422-0.4585-0.0031.87580.01632.8819-41.2895-60.046-15.6557
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 167 )
2X-RAY DIFFRACTION2chain 'A' and (resid 168 through 429 )
3X-RAY DIFFRACTION3chain 'A' and (resid 430 through 708 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 167 )
5X-RAY DIFFRACTION5chain 'D' and (resid 168 through 284 )
6X-RAY DIFFRACTION6chain 'D' and (resid 285 through 343 )
7X-RAY DIFFRACTION7chain 'D' and (resid 344 through 429 )
8X-RAY DIFFRACTION8chain 'D' and (resid 430 through 633 )
9X-RAY DIFFRACTION9chain 'D' and (resid 634 through 708 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 49 )
11X-RAY DIFFRACTION11chain 'B' and (resid 50 through 267 )
12X-RAY DIFFRACTION12chain 'B' and (resid 268 through 374 )
13X-RAY DIFFRACTION13chain 'B' and (resid 375 through 413 )
14X-RAY DIFFRACTION14chain 'B' and (resid 414 through 519 )
15X-RAY DIFFRACTION15chain 'B' and (resid 520 through 618 )
16X-RAY DIFFRACTION16chain 'B' and (resid 619 through 753 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 49 )
18X-RAY DIFFRACTION18chain 'C' and (resid 50 through 223 )
19X-RAY DIFFRACTION19chain 'C' and (resid 224 through 316 )
20X-RAY DIFFRACTION20chain 'C' and (resid 317 through 413 )
21X-RAY DIFFRACTION21chain 'C' and (resid 414 through 519 )
22X-RAY DIFFRACTION22chain 'C' and (resid 520 through 618 )
23X-RAY DIFFRACTION23chain 'C' and (resid 619 through 753 )
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 71 )
25X-RAY DIFFRACTION25chain 'E' and (resid 72 through 162 )
26X-RAY DIFFRACTION26chain 'E' and (resid 163 through 217 )
27X-RAY DIFFRACTION27chain 'E' and (resid 218 through 258 )
28X-RAY DIFFRACTION28chain 'E' and (resid 259 through 370 )
29X-RAY DIFFRACTION29chain 'E' and (resid 371 through 506 )
30X-RAY DIFFRACTION30chain 'E' and (resid 507 through 574 )
31X-RAY DIFFRACTION31chain 'E' and (resid 575 through 716 )
32X-RAY DIFFRACTION32chain 'E' and (resid 717 through 771 )
33X-RAY DIFFRACTION33chain 'F' and (resid 1 through 71 )
34X-RAY DIFFRACTION34chain 'F' and (resid 72 through 162 )
35X-RAY DIFFRACTION35chain 'F' and (resid 163 through 258 )
36X-RAY DIFFRACTION36chain 'F' and (resid 259 through 417 )
37X-RAY DIFFRACTION37chain 'F' and (resid 418 through 574 )
38X-RAY DIFFRACTION38chain 'F' and (resid 575 through 716 )
39X-RAY DIFFRACTION39chain 'F' and (resid 717 through 771 )
40X-RAY DIFFRACTION40chain 'G' and (resid 104 through 115 )

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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