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- PDB-5y3d: Structural insight into the interaction between RNA polymerase an... -

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基本情報

登録情報
データベース: PDB / ID: 5y3d
タイトルStructural insight into the interaction between RNA polymerase and VPg for norovirus replication
要素
  • RNA-dependent RNA polymerase
  • viral protein genome-linked (VPg)
キーワードVIRAL PROTEIN / norovirus / RNA-dependent RNA polymerase / VPg / interaction / viral replication
機能・相同性
機能・相同性情報


calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
類似検索 - 分子機能
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Helix non-globular / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Genome polyprotein
類似検索 - 構成要素
生物種Murine norovirus 1 (マウスノロウイルス 1)
Murine norovirus (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.14 Å
データ登録者Kim, K.H. / Lee, J.-H. / Seok, J.H.
資金援助 韓国, 1件
組織認可番号国
National Research FoundationNRF-2013R1A1A2064940 韓国
引用ジャーナル: Front Microbiol / 年: 2018
タイトル: Insight Into the Interaction Between RNA Polymerase and VPg for Murine Norovirus Replication.
著者: Lee, J.H. / Park, B.S. / Han, K.R. / Biering, S.B. / Kim, S.J. / Choi, J. / Seok, J.H. / Alam, I. / Chung, M.S. / Kim, H.M. / Hwang, S. / Kim, K.H.
履歴
登録2017年7月28日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02018年7月18日Provider: repository / タイプ: Initial release
改定 1.12018年8月8日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22018年9月19日Group: Data collection / Database references / カテゴリ: pdbx_related_exp_data_set
改定 1.32023年11月22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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
C: RNA-dependent RNA polymerase
D: RNA-dependent RNA polymerase
E: RNA-dependent RNA polymerase
F: RNA-dependent RNA polymerase
G: viral protein genome-linked (VPg)
H: viral protein genome-linked (VPg)


分子量 (理論値)分子数
合計 (水以外)357,1118
ポリマ－357,1118
非ポリマー00
水32418
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)109.172, 159.729, 121.704
Angle α, β, γ (deg.)90.000, 97.240, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain G and (resid 22 through 36 or resid 40 through 56))
21chain H
12(chain A and (resid 8 through 124 or resid 126...
22(chain B and (resid 8 through 124 or resid 126...
32(chain C and (resid 8 through 124 or resid 126...
42(chain D and (resid 8 through 124 or resid 126...
52(chain E and (resid 8 through 124 or resid 126...
62(chain F and (resid 8 through 124 or resid 126...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111UNKUNKUNKUNK(chain G and (resid 22 through 36 or resid 40 through 56))GG22 - 361 - 15
121UNKUNKUNKUNK(chain G and (resid 22 through 36 or resid 40 through 56))GG40 - 5619 - 35
211UNKUNKUNKUNKchain HHH22 - 561 - 35
112PROPROTYRTYR(chain A and (resid 8 through 124 or resid 126...AA8 - 1245 - 121
122TYRTYRPROPRO(chain A and (resid 8 through 124 or resid 126...AA126 - 434123 - 431
132SERSERSERSER(chain A and (resid 8 through 124 or resid 126...AA441438
142LEULEULYSLYS(chain A and (resid 8 through 124 or resid 126...AA443 - 467440 - 464
152ALAALAGLYGLY(chain A and (resid 8 through 124 or resid 126...AA469 - 473466 - 470
162VALVALGLYGLY(chain A and (resid 8 through 124 or resid 126...AA478 - 491475 - 488
212PROPROTYRTYR(chain B and (resid 8 through 124 or resid 126...BB8 - 1245 - 121
222TYRTYRPROPRO(chain B and (resid 8 through 124 or resid 126...BB126 - 434123 - 431
232SERSERSERSER(chain B and (resid 8 through 124 or resid 126...BB441438
242LEULEULYSLYS(chain B and (resid 8 through 124 or resid 126...BB443 - 467440 - 464
252ALAALAGLYGLY(chain B and (resid 8 through 124 or resid 126...BB469 - 473466 - 470
262VALVALGLYGLY(chain B and (resid 8 through 124 or resid 126...BB478 - 491475 - 488
312PROPROTYRTYR(chain C and (resid 8 through 124 or resid 126...CC8 - 1245 - 121
322TYRTYRPROPRO(chain C and (resid 8 through 124 or resid 126...CC126 - 434123 - 431
332SERSERSERSER(chain C and (resid 8 through 124 or resid 126...CC441438
342LEULEULYSLYS(chain C and (resid 8 through 124 or resid 126...CC443 - 467440 - 464
352ALAALAGLYGLY(chain C and (resid 8 through 124 or resid 126...CC469 - 473466 - 470
362VALVALVALVAL(chain C and (resid 8 through 124 or resid 126...CC477474
372PROPROGLYGLY(chain C and (resid 8 through 124 or resid 126...CC479 - 491476 - 488
412PROPROTYRTYR(chain D and (resid 8 through 124 or resid 126...DD8 - 1245 - 121
422TYRTYRPROPRO(chain D and (resid 8 through 124 or resid 126...DD126 - 434123 - 431
432SERSERSERSER(chain D and (resid 8 through 124 or resid 126...DD441438
442LEULEULYSLYS(chain D and (resid 8 through 124 or resid 126...DD443 - 467440 - 464
452ALAALAGLYGLY(chain D and (resid 8 through 124 or resid 126...DD469 - 473466 - 470
462VALVALGLYGLY(chain D and (resid 8 through 124 or resid 126...DD478 - 491475 - 488
512PROPROTYRTYR(chain E and (resid 8 through 124 or resid 126...EE8 - 1245 - 121
522TYRTYRPROPRO(chain E and (resid 8 through 124 or resid 126...EE126 - 434123 - 431
532SERSERSERSER(chain E and (resid 8 through 124 or resid 126...EE441438
542LEULEULYSLYS(chain E and (resid 8 through 124 or resid 126...EE443 - 467440 - 464
552ALAALAGLYGLY(chain E and (resid 8 through 124 or resid 126...EE469 - 473466 - 470
562VALVALGLYGLY(chain E and (resid 8 through 124 or resid 126...EE478 - 491475 - 488
612PROPROTYRTYR(chain F and (resid 8 through 124 or resid 126...FF8 - 1245 - 121
622TYRTYRPROPRO(chain F and (resid 8 through 124 or resid 126...FF126 - 434123 - 431
632SERSERSERSER(chain F and (resid 8 through 124 or resid 126...FF441438
642LEULEULYSLYS(chain F and (resid 8 through 124 or resid 126...FF443 - 467440 - 464
652ALAALAGLYGLY(chain F and (resid 8 through 124 or resid 126...FF469 - 473466 - 470
662VALVALVALVAL(chain F and (resid 8 through 124 or resid 126...FF477474
672PROPROGLYGLY(chain F and (resid 8 through 124 or resid 126...FF479 - 491476 - 488

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
RNA-dependent RNA polymerase / RdRp


分子量: 58519.539 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Murine norovirus 1 (マウスノロウイルス 1)
プラスミド: pET22b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): DE3 / 参照: UniProt: Q80J95
#2: タンパク質・ペプチド viral protein genome-linked (VPg)


分子量: 2996.685 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Murine norovirus (ウイルス) / プラスミド: pET22b-VPg / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): DE3
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 18 / 由来タイプ: 天然 / 式: H2O
配列の詳細The author knows the sequence of chains G/H but is unsure of the alignment. The sequence is ...The author knows the sequence of chains G/H but is unsure of the alignment. The sequence is MGKKGKNKKGRGRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLKATRLEHHHHHH

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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: 3.18 Å3/Da / 溶媒含有率: 61.28 %
結晶化温度: 297.15 K / 手法: 蒸発脱水法 / pH: 6.5 / 詳細: 0.1 M cacodylate (pH 6.5), 1.0 M sodium citrate / Temp details: Room temp.

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データ収集

回折平均測定温度: 100 K / Ambient temp details: 100
放射光源由来: シンクロトロン / サイト: Photon Factory / ビームライン: BL-17A / 波長: 0.987 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2011年11月25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: 0.987 Å / 相対比: 1
反射解像度: 3.14→50 Å / Num. obs: 69820 / % possible obs: 96.3 % / 冗長度: 3.6 % / Biso Wilson estimate: 54.51 Å2 / Net I/σ(I): 5.2

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解析

ソフトウェア
名称バージョン分類
PHENIX1.12_2829精密化
HKL-2000データ収集
SCALEPACKデータスケーリング
PDB_EXTRACT3.22データ抽出
HKL-2000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3QID

3qid


解像度: 3.14→47.235 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 23 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2409 3518 5.06 %
Rwork0.2025 66042 -
obs0.2045 69560 96.3 %
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
原子変位パラメータBiso max: 164.32 Å2 / Biso mean: 54.55 Å2 / Biso min: 1.4 Å2
精密化ステップサイクル: final / 解像度: 3.14→47.235 Å
タンパク質核酸リガンド溶媒全体
原子数23143 0 0 18 23161
Biso mean---28.62 -
残基数----2946
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00423694
X-RAY DIFFRACTIONf_angle_d0.54532097
X-RAY DIFFRACTIONf_chiral_restr0.0393433
X-RAY DIFFRACTIONf_plane_restr0.0064191
X-RAY DIFFRACTIONf_dihedral_angle_d4.68814401
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11G180X-RAY DIFFRACTION7.894TORSIONAL
12H180X-RAY DIFFRACTION7.894TORSIONAL
21A13885X-RAY DIFFRACTION7.894TORSIONAL
22B13885X-RAY DIFFRACTION7.894TORSIONAL
23C13885X-RAY DIFFRACTION7.894TORSIONAL
24D13885X-RAY DIFFRACTION7.894TORSIONAL
25E13885X-RAY DIFFRACTION7.894TORSIONAL
26F13885X-RAY DIFFRACTION7.894TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1401-3.18310.31021050.3162465257089
3.1831-3.22850.40291130.30222447256089
3.2285-3.27670.30461330.30022511264492
3.2767-3.32790.31641230.2832519264292
3.3279-3.38240.33211130.2732551266492
3.3824-3.44080.34331380.27052523266194
3.4408-3.50330.31731620.25522562272494
3.5033-3.57070.26311510.25552616276795
3.5707-3.64350.28881280.23982634276296
3.6435-3.72270.28391460.22842663280998
3.7227-3.80930.29031190.21292685280497
3.8093-3.90450.24081430.20542655279897
3.9045-4.010.23781500.1952641279197
4.01-4.12790.22221380.18292692283098
4.1279-4.26110.22891270.16972688281598
4.2611-4.41330.2411420.17772714285699
4.4133-4.58980.2161440.15942686283098
4.5898-4.79850.19181580.15812698285698
4.7985-5.05130.18271260.15312716284299
5.0513-5.36730.20351720.16372700287299
5.3673-5.78110.22781690.19192691286099
5.7811-6.36160.22331430.18722736287999
6.3616-7.27920.23021500.17732742289299
7.2792-9.16010.18231540.15827492903100
9.1601-47.24080.19691710.18522758292999
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)
11.8495-0.11370.2241.91030.30530.08590.03020.0639-0.0358-0.21720.1097-0.423-0.14750.1847-0.12740.2887-0.03490.02320.2136-0.03630.2688-7.06714.1985264.7642
21.2599-0.228-0.11261.30370.04891.3787-0.0512-0.0115-0.04730.0090.13360.03660.07070.0974-0.08890.1842-0.00690.04040.1196-0.03090.2102-18.12447.5265274.7522
31.2249-0.9627-0.50411.77890.20640.16870.1583-0.22470.58260.09360.1488-0.9807-0.11010.0887-0.13080.2414-0.04560.00840.2779-0.0808-0.0561-13.661519.8856277.6371
40.8017-0.7012-0.14262.8061.1321.22170.11190.02950.1454-0.2912-0.0301-0.1342-0.17010.0136-0.07210.207-0.01430.03830.1942-0.00330.2025-23.969621.3912259.6219
54.3594-2.2056-2.51413.12222.00335.27210.28780.954-0.8508-0.3252-0.24121.2650.3582-0.46070.12290.39760.0618-0.17210.4604-0.12770.719-34.45692.6749246.8324
60.1868-0.05740.5411.46250.85253.4955-0.0317-0.2121-0.15850.491-0.44010.40740.0301-0.9339-0.79840.3937-0.0188-0.01970.23580.30480.0626-81.634415.5699282.9081
71.71720.5242-1.0221.0893-0.98051.359-0.08510.2099-0.15780.0119-0.0301-0.11650.0289-0.15550.10220.2201-0.0638-0.04510.21-0.06190.1073-70.41053.4163263.5776
80.025-0.5043-0.4814.15743.60314.8331-0.2409-0.0926-0.0924-0.34350.18940.4154-0.22810.2552-0.01030.05910.01450.06790.31050.03570.3091-77.781812.6848272.6894
92.7642.65911.15622.7370.82090.56640.0883-0.2901-0.3188-0.0183-0.262-0.32460.07360.06050.07130.31530.06040.07970.12680.03930.2553-54.95912.5087263.9429
101.9320.5461-0.35731.3157-0.26470.9758-0.12790.07810.2711-0.25750.5165-0.05220.067-0.0613-0.26630.1833-0.0301-0.0580.31460.01470.2059-73.355810.1669258.44
114.6073-0.2410.34233.5323-0.73563.4758-0.09330.10.98290.14660.15130.039-0.3813-0.0869-0.09590.20260.0311-0.04870.17010.03750.2773-60.992827.561257.6413
124.24112.343-2.83511.6999-1.51753.36150.26880.2954-0.13930.3576-0.0157-0.1774-0.2923-0.2834-0.21470.25910.04280.02870.2412-0.04190.2847-58.668219.9712284.7682
136.7034-1.2612-2.93022.8211.54983.4696-0.3587-1.1450.16410.92610.129-0.68840.69520.44340.31670.43330.1208-0.0310.48060.1790.5432-49.114218.9311293.8247
144.01842.0228-0.4083.4478-1.16641.69630.2848-0.286-0.79-0.3764-0.3935-0.72640.19730.4363-0.00750.22950.11860.05620.2654-0.02070.27115.184145.0878298.5691
151.51540.14960.15982.0057-0.47681.6287-0.0112-0.0335-0.01680.0173-0.0369-0.3308-0.07520.10950.06010.133-0.01340.05180.2593-0.0990.2205-4.248264.2593298.1326
164.2093.52423.99883.96343.91144.3378-0.09450.2913-0.0663-0.02130.16640.0851-0.23840.0754-0.040.2673-0.0630.10740.3892-0.09970.3152-21.692862.7025291.3825
172.6723-0.73910.79410.9864-0.29080.7641-0.04660.1814-0.12710.0863-0.02820.17230.15490.07070.07970.2624-0.01870.08450.2139-0.05220.2326-3.155868.869290.4274
184.12680.58670.56182.2926-0.62413.6929-0.24020.5219-0.2742-0.42610.0226-0.23340.28590.48740.09550.26020.01810.1060.265-0.15870.2814-15.837259.4304276.6091
197.9076-3.03576.09092.7995-1.55245.04780.2075-0.280.1611-0.0515-0.2092-0.08240.4241-0.1533-0.19840.2498-0.09140.11820.25650.0130.3485-15.60740.0111298.118
203.5168-1.81913.73738.169-2.83225.91850.1288-0.2587-0.04040.6198-0.10870.53320.0335-0.7341-0.01030.2831-0.03170.14060.5211-0.01820.324-26.90335.8235300.5993
210.9444-1.7932-1.18894.75233.89085.5638-0.7108-0.024-0.2204-0.13960.17080.36840.04930.12590.48020.249-0.04470.04360.44020.13450.3898-64.893143.2217219.449
221.1480.6633-1.14970.597-0.53274.7770.05990.4397-0.2118-0.2258-0.01710.3890.534-0.01820.0550.4626-0.1419-0.05690.305-0.04470.3336-53.775225.8657205.1194
231.41440.2986-0.41170.9191-0.96072.8254-0.0113-0.0439-0.11930.2576-0.10110.27960.349-0.12910.00310.31580.0178-0.0152-0.01150.2272-0.1615-48.155539.9862236.4791
241.66790.18920.36251.9964-0.47431.3557-0.05260.25280.2689-0.3240.0303-0.0856-0.28110.0707-0.04310.2556-0.0552-0.01240.30430.10990.2101-48.045455.8569217.8166
250.84720.4731-0.33141.57420.89051.2273-0.0260.2014-0.29740.41920.2185-0.25350.03360.01860.02990.1104-0.0103-0.00520.19560.19740.2308-48.028743.3856221.6227
264.233-2.3580.29463.3486-0.22314.8452-0.5111-0.1420.3650.09690.0347-0.5886-0.26540.3440.18720.208-0.0930.04070.31810.13730.3131-26.621635.8511228.7436
272.01270.12720.09280.0884-0.04680.02610.1020.184-0.2450.24810.05090.4152-0.11030.0752-0.10540.3344-0.03840.02840.19470.10380.1848-47.328344.6269233.538
283.4739-0.5648-0.39342.2241-0.03345.7669-0.26290.0385-0.2788-0.08180.33310.03740.36250.22460.00530.2010.00360.01520.14920.09250.2602-34.5527.7161233.8804
295.3065-3.22163.42624.8414-1.12013.89110.66740.134-0.3384-0.5418-0.6004-0.31430.39410.2966-0.08910.3510.0760.01640.48340.04980.3126-44.495729.9016202.3671
306.36891.60882.51473.33741.22684.0964-0.22391.6594-0.5705-1.0989-0.0392-0.0024-0.52680.95050.03840.58860.16540.07230.80890.02370.3829-26.557926.6269203.7584
312.094-0.19930.23442.2143-0.00330.2898-0.08590.0381-0.1341-0.08410.1710.4574-0.04270.0906-0.10770.28450.0241-0.00480.2737-0.07050.0963-69.395361.5053290.5143
320.8415-0.7584-0.16691.0242-0.04831.923-0.0966-0.1407-0.03670.13620.13860.1471-0.0770.1405-0.00630.2627-0.0150.04910.2236-0.06140.1201-63.245356.3602305.6099
332.38670.2328-1.18550.8689-0.18730.69290.08730.13510.44310.18240.0678-0.2030.08030.0829-0.17630.3740.0330.10560.294-0.08140.265-48.151455.8921285.2232
342.8313-0.1225-0.13270.7513-0.04420.54720.2048-0.13670.3114-0.23210.05660.10690.1267-0.1355-0.24610.27390.01350.0150.2296-0.01060.2096-62.816646.1406293.8993
355.42652.31180.38175.10291.2263.61050.030.17230.4157-0.35850.0127-0.06110.05270.1211-0.11590.21160.06340.05850.3044-0.06590.2476-52.183552.551275.9197
366.304-3.5662-4.4973.94022.94973.29360.0148-0.12220.1497-0.1515-0.1348-0.4046-0.2573-0.0909-0.07840.4109-0.0567-0.05730.29180.00610.1882-52.929377.0113290.7836
375.7398-4.88961.71837.31191.36844.3599-0.1295-0.4480.92490.93390.20830.0724-0.49170.6077-0.18160.4363-0.14040.17780.4025-0.1910.7459-41.974682.4513291.7927
384.0531-1.5057-2.08723.64292.85962.6573-0.0852-0.41590.57420.5730.4053-0.84380.31180.4833-0.35060.33030.0633-0.11510.33990.02720.282720.548250.9303232.8285
392.1591-0.19760.95594.831-0.7491.61090.3305-0.1279-0.8610.28310.106-0.41770.1655-0.1288-0.39040.21430.04360.10270.39630.0207-0.018610.39926.9589222.1241
403.41782.7576-1.58296.764-1.54033.18030.1799-0.26910.3334-0.06770.06680.2365-0.273-0.0131-0.23750.1828-0.0444-0.04720.2325-0.01980.12018.324149.6845206.136
411.80580.25230.37180.95480.84392.65360.36240.1506-0.1165-0.11090.153-0.51040.2866-0.0777-0.0347-0.00250.0638-0.11060.3860.02130.295516.590543.3998225.3745
422.26990.0235-1.62850.918-1.69894.00210.08150.01850.02250.09390.19750.2170.0625-0.6037-0.40970.2597-0.0110.02930.27270.07520.2772-6.03536.3302220.8751
431.25431.1510.03111.50310.36961.1794-0.0790.00150.38380.04660.1426-0.3187-0.0372-0.0189-0.16830.18640.0207-0.02750.3586-0.02660.415212.399232.1382216.1502
445.9070.662-0.24736.2078-0.61383.48-0.3762-0.2159-0.7812-0.47420.3252-0.48250.0538-0.3453-0.0280.3514-0.08360.07780.25440.1130.251-2.018624.2589223.7286
455.1144-2.36261.02195.57221.48452.2087-0.245-0.7743-0.11750.6510.2582-0.49880.6385-0.6493-0.05560.33010.01210.01260.46560.13970.35940.902221.4743233.3418
463.1309-2.0652-0.87893.4310.00560.7028-0.5604-0.92480.13341.24090.5043-0.0728-0.20430.14410.21020.4303-0.0439-0.04530.6331-0.09620.2087-1.402531.2106239.3963
476.79126.6343-2.25596.7193-2.0491.97510.10730.46360.18520.5340.24910.237-0.00280.018-0.35330.3790.14120.06860.3438-0.01330.3119-1.176354.6861237.7128
485.0756.08722.65099.01533.56592.56690.1108-0.4951.2973-0.31410.11521.1266-0.6261-0.2711-0.03520.4772-0.01850.24350.5008-0.12790.7849-12.407658.535240.9274
490.1327-0.1542-0.14680.30330.07430.20930.0010.4883-0.055-0.15830.2353-0.0183-0.18310.6460.03230.3914-0.3014-0.61870.4854-0.06150.3431-17.90738.6195217.0447
505.9023-0.7598-2.81322.2067-0.51883.9121-0.45690.3556-1.3221-0.0456-0.30880.01540.7148-0.18330.39590.0104-0.27240.14470.387-0.03690.6208-12.43896.457227.23
510.1267-0.0353-0.10940.1108-0.04210.1442-0.1788-0.21030.29950.26670.2104-0.1053-0.0997-0.0620.29120.14330.5844-0.1210.51370.18350.406-33.26879.6164269.9919
520.05350.0537-0.13710.2951-0.03740.3757-0.22550.22490.2075-0.0129-0.01090.0196-0.37250.16470.41960.11820.2337-0.43330.6449-0.0579-0.0478-27.764971.6221262.4201
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 100 )A8 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 242 )A101 - 242
3X-RAY DIFFRACTION3chain 'A' and (resid 243 through 328 )A243 - 328
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 439 )A329 - 439
5X-RAY DIFFRACTION5chain 'A' and (resid 440 through 491 )A440 - 491
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 61 )B8 - 61
7X-RAY DIFFRACTION7chain 'B' and (resid 62 through 155 )B62 - 155
8X-RAY DIFFRACTION8chain 'B' and (resid 156 through 191 )B156 - 191
9X-RAY DIFFRACTION9chain 'B' and (resid 192 through 242 )B192 - 242
10X-RAY DIFFRACTION10chain 'B' and (resid 243 through 307 )B243 - 307
11X-RAY DIFFRACTION11chain 'B' and (resid 308 through 388 )B308 - 388
12X-RAY DIFFRACTION12chain 'B' and (resid 389 through 454 )B389 - 454
13X-RAY DIFFRACTION13chain 'B' and (resid 455 through 491 )B455 - 491
14X-RAY DIFFRACTION14chain 'C' and (resid 8 through 61 )C8 - 61
15X-RAY DIFFRACTION15chain 'C' and (resid 62 through 191 )C62 - 191
16X-RAY DIFFRACTION16chain 'C' and (resid 192 through 242 )C192 - 242
17X-RAY DIFFRACTION17chain 'C' and (resid 243 through 305 )C243 - 305
18X-RAY DIFFRACTION18chain 'C' and (resid 306 through 395 )C306 - 395
19X-RAY DIFFRACTION19chain 'C' and (resid 396 through 440 )C396 - 440
20X-RAY DIFFRACTION20chain 'C' and (resid 441 through 491 )C441 - 491
21X-RAY DIFFRACTION21chain 'D' and (resid 8 through 31 )D8 - 31
22X-RAY DIFFRACTION22chain 'D' and (resid 32 through 61 )D32 - 61
23X-RAY DIFFRACTION23chain 'D' and (resid 62 through 100 )D62 - 100
24X-RAY DIFFRACTION24chain 'D' and (resid 101 through 174 )D101 - 174
25X-RAY DIFFRACTION25chain 'D' and (resid 175 through 210 )D175 - 210
26X-RAY DIFFRACTION26chain 'D' and (resid 211 through 242 )D211 - 242
27X-RAY DIFFRACTION27chain 'D' and (resid 243 through 328 )D243 - 328
28X-RAY DIFFRACTION28chain 'D' and (resid 329 through 410 )D329 - 410
29X-RAY DIFFRACTION29chain 'D' and (resid 411 through 439 )D411 - 439
30X-RAY DIFFRACTION30chain 'D' and (resid 440 through 491 )D440 - 491
31X-RAY DIFFRACTION31chain 'E' and (resid 8 through 100 )E8 - 100
32X-RAY DIFFRACTION32chain 'E' and (resid 101 through 211 )E101 - 211
33X-RAY DIFFRACTION33chain 'E' and (resid 212 through 254 )E212 - 254
34X-RAY DIFFRACTION34chain 'E' and (resid 255 through 328 )E255 - 328
35X-RAY DIFFRACTION35chain 'E' and (resid 329 through 395 )E329 - 395
36X-RAY DIFFRACTION36chain 'E' and (resid 396 through 441 )E396 - 441
37X-RAY DIFFRACTION37chain 'E' and (resid 442 through 492 )E442 - 492
38X-RAY DIFFRACTION38chain 'F' and (resid 8 through 61 )F8 - 61
39X-RAY DIFFRACTION39chain 'F' and (resid 62 through 100 )F62 - 100
40X-RAY DIFFRACTION40chain 'F' and (resid 101 through 155 )F101 - 155
41X-RAY DIFFRACTION41chain 'F' and (resid 156 through 191 )F156 - 191
42X-RAY DIFFRACTION42chain 'F' and (resid 192 through 242 )F192 - 242
43X-RAY DIFFRACTION43chain 'F' and (resid 243 through 305 )F243 - 305
44X-RAY DIFFRACTION44chain 'F' and (resid 306 through 344 )F306 - 344
45X-RAY DIFFRACTION45chain 'F' and (resid 345 through 368 )F345 - 368
46X-RAY DIFFRACTION46chain 'F' and (resid 369 through 401 )F369 - 401
47X-RAY DIFFRACTION47chain 'F' and (resid 402 through 454 )F402 - 454
48X-RAY DIFFRACTION48chain 'F' and (resid 455 through 492 )F455 - 492
49X-RAY DIFFRACTION49chain 'G' and (resid 22 through 41 )G22 - 41
50X-RAY DIFFRACTION50chain 'G' and (resid 42 through 56 )G42 - 56
51X-RAY DIFFRACTION51chain 'H' and (resid 22 through 41 )H22 - 41
52X-RAY DIFFRACTION52chain 'H' and (resid 42 through 56 )H42 - 56

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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://pdbjlvh1.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