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- PDB-5f9h: Crystal structure of RIG-I helicase-RD in complex with 24-mer 5' ... -

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基本情報

登録情報
データベース: PDB / ID: 5f9h
タイトルCrystal structure of RIG-I helicase-RD in complex with 24-mer 5' triphosphate hairpin RNA
要素
  • Probable ATP-dependent RNA helicase DDX58
  • RNA (5'-R(P*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
キーワードhydrolase/rna / Complex / RIG-I / capped RNA / self versus non-self / innate immunity / hydrolase-rna complex
機能・相同性
機能・相同性情報


regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / cellular response to exogenous dsRNA ...regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / cellular response to exogenous dsRNA / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / RSV-host interactions / response to exogenous dsRNA / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / bicellular tight junction / positive regulation of defense response to virus by host / antiviral innate immune response / positive regulation of interferon-beta production / regulation of cell migration / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / double-stranded RNA binding / Ovarian tumor domain proteases / actin cytoskeleton / TRAF3-dependent IRF activation pathway / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
類似検索 - 分子機能
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / RIG-I, CARD domain repeat 2 / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / RIG-I, CARD domain repeat 2 / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Beta Complex / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Antiviral innate immune response receptor RIG-I
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å
データ登録者Wang, C. / Marcotrigiano, J. / Miller, M. / Jiang, F.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2016
タイトル: Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I.
著者: Devarkar, S.C. / Wang, C. / Miller, M.T. / Ramanathan, A. / Jiang, F. / Khan, A.G. / Patel, S.S. / Marcotrigiano, J.
履歴
登録2015年12月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年1月13日Provider: repository / タイプ: Initial release
改定 1.12016年1月20日Group: Database references / Structure summary
改定 1.22016年1月27日Group: Database references
改定 1.32016年4月6日Group: Other
改定 1.42023年9月27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 / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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集合体

登録構造単位
A: Probable ATP-dependent RNA helicase DDX58
B: RNA (5'-R(P*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
C: Probable ATP-dependent RNA helicase DDX58
D: RNA (5'-R(P*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
E: Probable ATP-dependent RNA helicase DDX58
F: RNA (5'-R(P*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
G: Probable ATP-dependent RNA helicase DDX58
H: RNA (5'-R(P*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
I: Probable ATP-dependent RNA helicase DDX58
J: RNA (5'-R(P*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
K: Probable ATP-dependent RNA helicase DDX58
L: RNA (5'-R(P*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)525,12032
ポリマ－521,39512
非ポリマー3,72620
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
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area35330 Å2
ΔGint-303 kcal/mol
Surface area182590 Å2
手法PISA
単位格子
Length a, b, c (Å)111.180, 174.810, 309.280
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
Probable ATP-dependent RNA helicase DDX58 / DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG- ...DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


分子量: 79594.734 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DDX58 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O95786, RNA helicase
#2: RNA鎖
RNA (5'-R(P*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')


分子量: 7304.353 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn
#4: 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: 8 / 由来タイプ: 合成 / 式: Mg
#5: 化合物
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 2.87 Å3/Da / 溶媒含有率: 57.08 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 23% (w/v) PEG 3350, 0.25 M KSCN, 100 mM MOPS (pH 7.8)

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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: NSLS / ビームライン: X25 / 波長: 1.1 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2012年7月22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: 1.1 Å / 相対比: 1
反射解像度: 3.1→49.664 Å / Num. obs: 109315 / % possible obs: 99.5 % / 冗長度: 11.1 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 9.6
反射 シェル解像度: 3.2→3.4 Å / 冗長度: 10.6 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1690精密化
iMOSFLMデータ削減
Aimless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: 5E3H

5e3h


解像度: 3.1→49.442 Å / SU ML: 0.39 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 26.13 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2656 5451 4.99 %
Rwork0.2135 --
obs0.216 109315 99.41 %
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: 3.1→49.442 Å
タンパク質核酸リガンド溶媒全体
原子数30480 3108 15 0 33603
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00434556
X-RAY DIFFRACTIONf_angle_d0.73747390
X-RAY DIFFRACTIONf_dihedral_angle_d12.0613230
X-RAY DIFFRACTIONf_chiral_restr0.0315473
X-RAY DIFFRACTIONf_plane_restr0.0035523
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13520.36081850.3073414X-RAY DIFFRACTION99
3.1352-3.17210.35971860.29873441X-RAY DIFFRACTION100
3.1721-3.21080.34321740.29333383X-RAY DIFFRACTION100
3.2108-3.25140.33711890.28593438X-RAY DIFFRACTION99
3.2514-3.29420.35771720.28993461X-RAY DIFFRACTION100
3.2942-3.33930.28671770.27633389X-RAY DIFFRACTION100
3.3393-3.3870.36821930.26783428X-RAY DIFFRACTION99
3.387-3.43750.3391860.2573382X-RAY DIFFRACTION99
3.4375-3.49120.29771820.25543470X-RAY DIFFRACTION99
3.4912-3.54850.31931760.25383404X-RAY DIFFRACTION100
3.5485-3.60960.3011810.24653436X-RAY DIFFRACTION99
3.6096-3.67530.26641850.23643415X-RAY DIFFRACTION99
3.6753-3.74590.28081620.22543454X-RAY DIFFRACTION99
3.7459-3.82240.27441700.2273456X-RAY DIFFRACTION99
3.8224-3.90540.22561910.21153399X-RAY DIFFRACTION99
3.9054-3.99620.24671810.20653451X-RAY DIFFRACTION99
3.9962-4.09610.23261570.20253453X-RAY DIFFRACTION99
4.0961-4.20680.2411670.20173430X-RAY DIFFRACTION99
4.2068-4.33060.26121570.19763470X-RAY DIFFRACTION99
4.3306-4.47020.23552020.17743423X-RAY DIFFRACTION99
4.4702-4.62990.23051840.16073450X-RAY DIFFRACTION99
4.6299-4.81510.2271860.16743436X-RAY DIFFRACTION99
4.8151-5.03410.23061810.16973490X-RAY DIFFRACTION100
5.0341-5.29920.20911970.1753500X-RAY DIFFRACTION100
5.2992-5.63080.24811800.19623490X-RAY DIFFRACTION100
5.6308-6.06480.26921660.2093522X-RAY DIFFRACTION100
6.0648-6.67380.26552000.2093524X-RAY DIFFRACTION100
6.6738-7.63650.24021920.1933553X-RAY DIFFRACTION100
7.6365-9.60960.21031810.17013584X-RAY DIFFRACTION100
9.6096-49.44820.2672110.20953718X-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)
10.61020.37620.00610.4330.13540.33480.01740.12920.05360.06840.1011-0.01320.0470.1527-0.00010.29410.0579-0.00790.3164-0.05990.2875-48.1572-29.584871.4589
20.59930.19430.16760.80850.25090.81480.2541-0.02310.31130.5035-0.111-0.06960.276-0.0313-0.05780.5971-0.11510.01810.1615-0.10790.1411-57.1174-29.0914101.1531
30.36040.0302-0.07190.0837-0.0680.15830.56970.39630.04040.7944-0.46770.46130.6487-0.31530.10051.2877-0.3070.0670.27820.02630.5542-70.3782-55.51989.9774
40.02110.0091-0.03130.0002-0.00310.0184-0.1496-0.1795-0.12450.1971-0.0350.06690.193-0.149900.6789-0.057-0.04890.33350.01170.3936-53.3295-39.617689.7959
5-0.0032-0.00610.00180.0028-0.00080.0001-0.06330.0073-0.12580.0077-0.0589-0.08880.0033-0.005-01.429-0.0097-0.46431.47720.36951.2611-42.3819-45.0415101.861
6-0.00660.00820.0003-0.01580.01760.0220.11340.1109-0.0790.51650.02340.05130.01290.036500.6706-0.01690.00510.3266-0.01970.3836-56.8604-39.290491.8479
70.0226-0.00880.0313-0.00960.00980.0286-0.1173-0.1445-0.18960.36340.0098-0.0819-0.0857-0.002100.30710.01560.03650.3720.0040.4356-86.8186-21.814667.481
80.1987-0.003-0.11550.22760.0240.13410.02850.0179-0.1120.0128-0.04890.2667-0.00040.065800.31460.0211-0.02040.3652-0.04480.4593-76.6338-28.437954.36
90.2446-0.0094-0.19580.1907-0.08940.19030.27640.06490.1110.0312-0.17210.1245-0.1237-0.25180.02860.31260.0466-0.00360.3334-0.0170.5859-90.8943-8.618755.6154
100.02650.03610.0220.00840.02730.06740.19430.20140.1772-0.06850.14370.34190.04580.09370.0241.29510.48120.50440.83570.47970.7606-68.9239.20621.6028
110.18440.01530.1294-0.08170.09730.10350.3669-0.05850.587-0.2294-0.0714-0.3381-0.21960.1281-0.050.96160.08030.55160.53370.10561.1612-64.447714.598938.595
120.1367-0.06510.18880.0409-0.06120.45720.3874-0.18930.1319-0.37730.0193-0.4047-0.11990.15130.10.4748-0.00220.23050.4264-0.11520.7654-72.57124.204957.4053
130.1364-0.30850.11360.2846-0.30240.13240.25160.30870.1385-0.3078-0.18120.3386-0.2816-0.3381-0.00410.49790.08190.00080.5332-0.03630.5691-87.442-10.757543.1298
140.17160.0177-0.11520.1276-0.06550.06150.54120.2801-0.106-0.1862-0.2898-0.1975-0.19350.05650.0020.67650.16440.10640.6256-0.00760.468-60.066-16.817527.1393
150.01570.0232-0.01870.0056-0.00020.00750.15240.16370.1509-0.09620.16140.0923-0.11310.1355-00.59310.20920.11290.47380.0440.6442-77.9725-9.379739.7574
16-0.003-0.00020.005-0.00050.00510.0041-0.02970.112-0.0299-0.06430.05910.03540.0444-0.107901.31750.5038-0.14031.52770.23091.3906-89.1752-1.642529.329
17-0.0165-0.012-0.0040.0085-0.0216-0.01710.18150.25670.0144-0.17970.1014-0.132-0.326-0.1088-00.45810.07480.07140.40620.08650.4385-74.5185-7.408839.0234
180.5998-0.22830.01210.32230.10660.47640.05120.03750.1296-0.00140.02150.00590.02060.0898-00.3542-0.0145-0.01140.3776-0.0230.5203-27.773414.187397.8486
19-0.0488-0.04410.0498-0.02770.0284-0.00480.0567-0.1376-0.3286-0.10370.21720.00550.24980.21270.1139-0.01190.6959-1.71450.39890.3612-1.0975-13.1946-18.3336129.3668
200.10490.07520.12790.19820.18710.15440.08270.1708-0.03790.1593-0.00070.00650.16830.10650.00010.58710.0587-0.14420.505-0.11510.6124-24.3191-13.185699.3431
210.25370.2988-0.05290.5649-0.34860.41350.0264-0.13970.37610.2456-0.0338-0.150.00740.32920.24940.56170.1443-0.14470.8501-0.2030.5339-13.869511.3039126.9599
220.0048-0.01650.0110.00850.00990.02290.0611-0.3573-0.03820.05350.3113-0.00410.1609-0.0277-00.541-0.0177-0.13970.6877-0.08980.5724-25.92730.2244117.2073
23-0.0103-0.01950.00350.06480.01180.03160.1047-0.35730.11540.08780.07350.0499-0.0005-0.274-00.54260.0952-0.12330.6374-0.03880.5802-26.12340.1774119.7126
240.12820.1566-0.09170.1494-0.06810.21030.1028-0.3618-0.2256-0.1535-0.08310.0515-0.00870.3876-0.00020.3955-0.0854-0.08530.71370.01470.3728-15.4435-41.462329.9547
250.2108-0.0093-0.10310.14680.03120.1460.2457-0.15470.0802-0.0857-0.072-0.0125-0.20850.2592-0.00250.4803-0.09830.00690.799-0.05160.4583-3.6703-29.230616.7347
260.004-0.00560.04270.02940.01420.01350.0793-0.01670.1660.1609-0.0858-0.0388-0.25040.08101.2442-0.00670.4020.5001-0.07820.8163-24.65768.540919.9824
270.26240.00880.04760.10320.03460.16410.58360.47960.5272-0.02850.00560.1056-0.41070.08880.37150.77730.28020.49040.3979-0.22080.3815-29.7995-4.27047.7131
280.01040.0123-0.01580.02620.02520.00610.1959-0.3089-0.11340.0032-0.06120.2646-0.1695-0.248800.55470.0064-0.01420.6883-0.04620.5309-26.0106-26.44064.9342
290.26960.12870.05140.307-0.19720.10390.3335-0.10610.1276-0.0042-0.1528-0.2143-0.37420.39440.04760.5758-0.17570.08350.7132-0.09910.3593-8.5584-20.300922.6786
300.5081-0.23720.3040.1923-0.14310.24950.5178-0.40890.01460.1411-0.16540.1755-0.24920.15040.11420.7921-0.18310.23010.5924-0.19660.4912-34.6266-10.337139.8522
310.007-0.01740.0040.0112-0.00330.0037-0.0120.0890.154-0.22-0.0994-0.0597-0.2322-0.0937-00.8219-0.34540.32350.8482-0.2770.5699-16.7106-16.515526.5924
32-0.0010.0021-0.001-0.00060.00530.0048-0.0781-0.11610.01050.0784-0.0289-0.099-0.02860.051901.3906-0.56730.40231.5317-0.41871.4642-5.4754-3.553426.4759
330.0379-0.05290.07840.0533-0.11760.08630.3252-0.2230.2079-0.17090.1768-0.137-0.25540.11190.02820.5119-0.13720.20950.5417-0.22730.5001-20.2288-14.745125.379
340.2339-0.0126-0.00540.29710.15690.2880.0924-0.31340.0276-0.03830.0591-0.07980.01930.08730.00010.3398-0.01980.04120.5415-0.08680.64928.092923.032587.2837
350.68820.1984-0.08620.0695-0.10350.25031.5197-1.161-1.2702-0.2966-0.68790.0143-0.6252-0.27910.3454-1.72912.88490.6828-1.8538-0.905-0.1952-4.787222.85648.481
360.1577-0.0995-0.25360.30360.26490.67890.52820.01120.1912-0.5357-0.2398-0.2282-0.2642-0.0390.06240.60640.10550.18490.3986-0.02720.7324-0.401237.650467.8657
370.0072-0.01650.01540.0123-0.01940.01050.02030.08750.2535-0.18-0.24850.257-0.00790.1343-00.69150.19710.26460.40350.01720.81734.105532.898866.2894
38-0.00580.0026-0.0040.00380.0048-0.0038-0.1251-0.10640.10940.0648-0.0961-0.093-0.10540.058101.3450.08150.48341.30770.24761.500515.926439.093855.5845
390.00540.0135-0.0037-0.01510.02590.0080.2498-0.01790.1269-0.3835-0.1862-0.2063-0.04060.010900.57660.11180.15320.33240.01280.60110.700832.859164.1256
400.6247-0.213-0.17970.42340.11970.5334-0.04120.01670.0467-0.0237-0.08440.0665-0.01330.0897-00.38830.0018-0.05140.4413-0.04520.3163-47.2224-53.59425.2392
410.23540.0689-0.08120.07740.02790.0268-0.03290.3749-0.2659-0.3815-0.3555-0.12140.52010.3412-0.00440.88840.33860.04790.7124-0.03780.6739-32.7885-92.22486.8787
420.3306-0.10940.15290.25580.04980.2922-0.01290.0641-0.2981-0.1355-0.08970.20450.14260.172-0.00030.54260.1273-0.05970.6268-0.06490.4608-45.5989-68.841513.4388
430.0742-0.04010.01350.08640.08960.1141-0.0227-0.28120.1626-0.1289-0.1598-0.52650.1970.413400.56790.16790.02920.73150.16250.7608-25.6852-83.105335.369
440.0175-0.0251-0.01480.0092-0.01680.02470.1015-0.1943-0.2522-0.2320.00790.14270.11750.1664-00.56590.0868-0.10460.491-0.04890.5588-44.9631-77.147221.4006
45-0.00480.00290.03990.006-0.0060.0089-0.08040.0929-0.3154-0.0241-0.01750.36970.21340.012600.6130.07030.05550.4876-0.00490.6371-45.0558-79.476722.5102
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 241 through 470 )
2X-RAY DIFFRACTION2chain 'A' and (resid 471 through 793 )
3X-RAY DIFFRACTION3chain 'A' and (resid 794 through 922 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 8 )
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 14 )
6X-RAY DIFFRACTION6chain 'B' and (resid 15 through 24 )
7X-RAY DIFFRACTION7chain 'C' and (resid 241 through 283 )
8X-RAY DIFFRACTION8chain 'C' and (resid 284 through 395 )
9X-RAY DIFFRACTION9chain 'C' and (resid 396 through 470 )
10X-RAY DIFFRACTION10chain 'C' and (resid 471 through 530 )
11X-RAY DIFFRACTION11chain 'C' and (resid 531 through 624 )
12X-RAY DIFFRACTION12chain 'C' and (resid 625 through 731 )
13X-RAY DIFFRACTION13chain 'C' and (resid 732 through 819 )
14X-RAY DIFFRACTION14chain 'C' and (resid 820 through 922 )
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 8 )
16X-RAY DIFFRACTION16chain 'D' and (resid 9 through 14 )
17X-RAY DIFFRACTION17chain 'D' and (resid 15 through 24 )
18X-RAY DIFFRACTION18chain 'E' and (resid 242 through 470 )
19X-RAY DIFFRACTION19chain 'E' and (resid 471 through 601 )
20X-RAY DIFFRACTION20chain 'E' and (resid 602 through 770 )
21X-RAY DIFFRACTION21chain 'E' and (resid 771 through 922 )
22X-RAY DIFFRACTION22chain 'F' and (resid 2 through 10 )
23X-RAY DIFFRACTION23chain 'F' and (resid 11 through 24 )
24X-RAY DIFFRACTION24chain 'G' and (resid 240 through 395 )
25X-RAY DIFFRACTION25chain 'G' and (resid 396 through 469 )
26X-RAY DIFFRACTION26chain 'G' and (resid 470 through 527 )
27X-RAY DIFFRACTION27chain 'G' and (resid 528 through 648 )
28X-RAY DIFFRACTION28chain 'G' and (resid 649 through 710 )
29X-RAY DIFFRACTION29chain 'G' and (resid 711 through 819 )
30X-RAY DIFFRACTION30chain 'G' and (resid 820 through 922 )
31X-RAY DIFFRACTION31chain 'H' and (resid 2 through 8 )
32X-RAY DIFFRACTION32chain 'H' and (resid 9 through 14 )
33X-RAY DIFFRACTION33chain 'H' and (resid 15 through 24 )
34X-RAY DIFFRACTION34chain 'I' and (resid 240 through 451 )
35X-RAY DIFFRACTION35chain 'I' and (resid 452 through 710 )
36X-RAY DIFFRACTION36chain 'I' and (resid 711 through 923 )
37X-RAY DIFFRACTION37chain 'J' and (resid 2 through 8 )
38X-RAY DIFFRACTION38chain 'J' and (resid 9 through 14 )
39X-RAY DIFFRACTION39chain 'J' and (resid 15 through 24 )
40X-RAY DIFFRACTION40chain 'K' and (resid 242 through 470 )
41X-RAY DIFFRACTION41chain 'K' and (resid 471 through 624 )
42X-RAY DIFFRACTION42chain 'K' and (resid 625 through 819 )
43X-RAY DIFFRACTION43chain 'K' and (resid 820 through 922 )
44X-RAY DIFFRACTION44chain 'L' and (resid 2 through 10 )
45X-RAY DIFFRACTION45chain 'L' and (resid 11 through 24 )

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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