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- PDB-4plk: Hepatitis E Virus E2s domain (Genotype I) in complex with a neutr... -

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基本情報

登録情報
データベース: PDB / ID: 4plk
タイトルHepatitis E Virus E2s domain (Genotype I) in complex with a neutralizing antibody 8G12
要素
  • 8G12 heavy chain
  • 8G12 light chain
  • Capsid protein
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / Complex / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性: / Structural protein 2 C-terminal domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Capsid protein
機能・相同性情報
生物種Hepatitis E virus (E 型肝炎ウイルス)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4 Å
データ登録者Tang, X.H. / Li, S.W. / Sivaraman, J.
引用ジャーナル: Cell Res. / : 2015
タイトル: Structural basis for the neutralization of hepatitis E virus by a cross-genotype antibody
著者: Gu, Y. / Tang, X. / Zhang, X. / Song, C. / Zheng, M. / Wang, K. / Zhang, J. / Ng, M.H. / Hew, C.L. / Li, S. / Xia, N. / Sivaraman, J.
履歴
登録2014年5月18日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02015年4月8日Provider: repository / タイプ: Initial release
改定 1.12015年5月13日Group: Database references
改定 1.22024年11月6日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / entity_src_nat / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation

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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: Capsid protein
B: Capsid protein
L: 8G12 light chain
H: 8G12 heavy chain
C: 8G12 light chain
D: 8G12 heavy chain
E: Capsid protein
F: Capsid protein
K: 8G12 light chain
J: 8G12 heavy chain
G: 8G12 light chain
I: 8G12 heavy chain


分子量 (理論値)分子数
合計 (水以外)255,24812
ポリマ-255,24812
非ポリマー00
00
1
A: Capsid protein
B: Capsid protein
L: 8G12 light chain
H: 8G12 heavy chain
C: 8G12 light chain
D: 8G12 heavy chain


分子量 (理論値)分子数
合計 (水以外)127,6246
ポリマ-127,6246
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
2
E: Capsid protein
F: Capsid protein
K: 8G12 light chain
J: 8G12 heavy chain
G: 8G12 light chain
I: 8G12 heavy chain


分子量 (理論値)分子数
合計 (水以外)127,6246
ポリマ-127,6246
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)54.196, 191.993, 192.584
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Capsid protein


分子量: 15607.430 Da / 分子数: 4 / 断片: E2s domain, UNP residues 8-152 / 由来タイプ: 組換発現
由来: (組換発現) Hepatitis E virus (E 型肝炎ウイルス)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: L0L7P5
#2: 抗体
8G12 light chain


分子量: 23415.779 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
#3: 抗体
8G12 heavy chain


分子量: 24788.795 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
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: 3.98 Å3/Da / 溶媒含有率: 69.11 %
結晶化温度: 294 K / 手法: 蒸気拡散法 / 詳細: 12% PEG 5000, 0.05M NaH2PO4

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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: SSRF / ビームライン: BL17U / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2011年12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: 1 Å / 相対比: 1
反射解像度: 4→33.992 Å / Num. obs: 31821 / % possible obs: 90.5 % / 冗長度: 3.2 % / Net I/σ(I): 5.8

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.9_1692)精密化
HKL-2000data processing
精密化構造決定の手法: 分子置換 / 解像度: 4→33.992 Å / SU ML: 0.55 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.14 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2961 1879 6.2 %Random
Rwork0.264 ---
obs0.2662 30302 91.18 %-
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→33.992 Å
タンパク質核酸リガンド溶媒全体
原子数17368 0 0 0 17368
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00617803
X-RAY DIFFRACTIONf_angle_d1.5824286
X-RAY DIFFRACTIONf_dihedral_angle_d14.9496268
X-RAY DIFFRACTIONf_chiral_restr0.0652748
X-RAY DIFFRACTIONf_plane_restr0.0063086
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.1080.35981280.34471959X-RAY DIFFRACTION83
4.108-4.22870.33091350.32481959X-RAY DIFFRACTION82
4.2287-4.36490.34651340.30751991X-RAY DIFFRACTION84
4.3649-4.52050.28121510.27182077X-RAY DIFFRACTION85
4.5205-4.70110.32281400.28652018X-RAY DIFFRACTION87
4.7011-4.91440.28721410.27852137X-RAY DIFFRACTION88
4.9144-5.17270.31251430.26722138X-RAY DIFFRACTION91
5.1727-5.49550.32691550.25222251X-RAY DIFFRACTION93
5.4955-5.91780.34531410.2722341X-RAY DIFFRACTION97
5.9178-6.50960.34091450.27942362X-RAY DIFFRACTION98
6.5096-7.44290.24181630.27692367X-RAY DIFFRACTION99
7.4429-9.34490.26951590.24342403X-RAY DIFFRACTION99
9.3449-33.99320.25011440.20092420X-RAY DIFFRACTION98
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.6388-1.14920.46732.3615-2.26893.9346-0.7501-0.27331.8063-0.2546-0.6929-0.3401-1.0944-0.14530.151.2846-0.06350.38850.4658-0.5652.866413.3927-3.870891.4268
24.79391.14392.44262.38870.72544.41290.8541-1.26280.2042-0.51450.3160.50930.709-0.88810.23070.2735-0.09150.09720.86940.10231.73077.5585-23.008689.6853
32.88590.040.52963.6505-1.54950.8650.9325-0.33840.3891-0.29210.17921.34620.48490.0095-0.08280.5239-0.3048-0.09651.16390.40451.38273.5113-24.278683.2285
42.65562.28560.52692.2933-0.37222.17850.2248-1.80311.27620.7263-0.57351.1742-1.0501-0.2127-0.1931.5509-0.0840.37581.06090.16691.58911.0717-9.754896.5659
52.3873-1.6340.43653.5549-1.28182.4654-0.0279-0.1160.73940.99530.58221.11290.3248-0.7775-0.38971.42320.36130.18350.24830.15132.44922.0848-6.980588.6657
64.92970.75080.55115.6239-0.60733.3441-0.58140.05811.7043-1.0177-0.2291.5048-0.3377-0.6096-0.05511.44070.49410.1111.65060.49121.39645.6195-7.371877.5897
75.08060.30550.32473.1068-1.10482.60790.0306-0.24680.51-0.96110.37680.86981.135-0.3258-0.34090.72970.06120.28061.11370.42941.144310.5863-20.565484.1921
84.8009-0.01960.70322.179-1.00093.64180.47740.59910.686-0.6862-0.16890.40430.77570.1564-0.3594-0.2909-1.0094-0.09211.53980.65570.996816.9562-27.529276.3281
91.65580.42990.55482.352-0.06972.88650.67160.71480.5139-0.93320.681.56370.91581.82320.35480.249-0.6780.20050.03240.97511.61385.9002-23.199383.7432
100.70260.9024-1.28811.0145-1.79356.62110.0278-0.2270.97830.29360.29561.283-1.34450.5376-0.12680.78150.060.10.80320.24561.544114.8066-13.791784.336
112.92291.00070.21580.9979-0.57550.67440.178-1.43781.14720.82-0.2990.254-0.7921-0.62810.24721.2313-0.845-0.13752.9395-0.62910.854626.9585-15.7052102.6287
122.9144-1.7509-1.27071.13580.91010.71010.6222-0.5707-0.3297-0.1616-1.7677-0.98420.63040.2469-0.0342-1.60950.22421.06141.99450.24670.564835.2678-22.922381.8112
136.827-1.14731.48862.3954-1.27342.55460.1294-2.09430.92770.3726-0.0698-0.9703-1.39221.40120.13380.8935-0.31610.00531.9060.31450.896834.7353-13.85592.0083
140.63420.41520.38915.7353-2.4723.5263-0.2839-0.3105-0.81620.84150.48540.2990.5686-0.5376-0.10381.2467-0.32860.14791.48370.03331.00734.0763-22.3041103.8585
151.15821.54230.07622.40380.13440.12260.357-0.0114-0.6201-0.0441-0.3303-1.04051.20980.31030.31530.7973-0.0493-0.08461.71160.42921.085134.4833-28.862192.2887
166.14841.20751.08010.8328-0.08832.04230.14011.36660.00860.6806-0.7289-0.02610.46580.66490.60840.4409-0.17020.27641.61370.10061.115624.5205-22.483378.3521
171.8197-1.7819-1.23051.73410.79732.46421.1754-1.4670.8533-0.26750.1858-1.0219-0.43561.37960.4927-1.8741.0239-1.93141.55911.6405-0.841835.3539-24.703289.3306
181.42840.6668-0.83212.19390.0740.69130.1862-0.8382-0.2472-0.2344-0.2161-0.47320.15420.2598-0.24910.4987-0.01020.05111.4050.2030.823329.1295-21.839183.1578
191.6882-1.7242.67944.8428-4.21475.41291.11350.5750.094-1.2916-0.91790.44240.92821.20430.14941.40970.39020.42891.30210.12671.361114.282-59.647493.0345
200.72051.3818-0.14424.6038-0.65150.5439-0.40450.5118-0.0672-1.5659-0.4408-0.13830.53910.8161-0.14320.94030.90630.0173-0.11221.80890.352218.4822-48.386290.8363
211.88972.3044-2.11853.1544-3.32364.0625-0.5252-0.2646-0.95321.13880.15010.1261.10690.44570.92840.92320.07110.30821.00550.84262.491111.0757-54.2985105.2847
220.23570.2219-1.23342.4826-0.75438.8698-0.0194-0.6855-0.31330.92030.17250.4885-1.17511.32930.36441.21470.99530.61371.81511.52612.026322.9995-52.8297100.1658
231.76110.7680.36683.395-1.72422.39610.7258-1.9399-1.6457-0.05660.169-1.24051.16150.95040.28952.14350.84080.58961.3941.53361.1415.1663-62.1211103.5892
241.9238-1.61960.05565.03560.68043.1315-0.8673-0.70880.0479-1.1811.0623-1.1520.92350.80450.41720.44630.09160.15790.92580.46811.266611.0522-43.928594.1911
250.81310.95490.6873.24250.80930.4966-1.003-0.5658-0.6879-0.2789-0.4652-0.42562.15930.56260.26032.45120.32680.52411.12570.76812.29710.2737-73.2649102.2175
261.1471-0.0988-0.92341.14621.19421.8051-1.01140.55850.17541.1993-0.4728-0.4581-0.1670.64481.13251.1895-0.05520.0241.38560.39021.584-16.9266-77.9051115.8672
272.1968-0.3965-0.96530.74650.48052.9928-0.46310.3259-1.9989-0.266-0.3124-1.59641.1168-0.35850.29442.3448-0.09510.56951.57030.84692.2514-9.4311-77.6248104.9419
282.23950.9766-0.94370.4877-0.52120.56290.4497-0.1853-0.252-0.8264-0.4363-0.21150.38850.35730.31823.5739-0.48431.9999-0.52091.13133.7728-13.9302-88.1883107.917
293.69821.3793-2.15683.0522-1.47922.1090.2619-1.8357-0.25010.69010.40170.77560.46920.9825-0.23120.6571-0.17320.31451.39480.22591.2623-1.3915-42.795107.6794
304.4182-0.2121-2.35884.4306-1.62553.46770.3367-0.70131.75241.2707-0.43150.05170.00270.38090.26370.5483-0.23860.46270.23630.26132.28753.6071-34.2704101.1702
312.80792.0807-1.54412.1137-1.2552.27090.3396-1.4080.3878-0.0186-0.41480.27090.53240.339-0.0380.77020.10570.16571.29660.43541.676-2.9819-46.2703105.6329
326.8738-5.64875.04639.0732-4.29748.4110.24080.0038-0.4338-0.22640.0211-0.7140.36450.8665-0.15841.3769-0.01110.18081.44450.27561.4784-10.105-72.3532116.1179
336.0783-3.30065.03734.3746-1.72125.54990.6625-0.30920.84160.9175-0.2298-0.90670.45930.4555-0.24381.1096-0.14830.2761.38910.49961.7765-5.1027-64.474117.7693
341.14961.01762.21647.8729-4.17049.63360.303-0.36360.5671-1.1566-0.682-1.07060.94321.40480.42131.1140.0850.27091.26990.10071.675-10.6179-69.2276119.0745
350.4489-0.31770.23280.4292-0.98564.3531-0.4110.9670.1775-0.8756-0.19880.40640.93240.31960.3121.4682-0.49-0.31951.6520.20730.931624.468-15.387152.3901
363.95313.6339-4.193.3549-3.78574.85720.23151.69890.9644-0.8430.23910.455-0.5706-0.9137-0.34710.2949-0.68970.21142.75561.17591.227228.5359-2.187753.3913
371.5617-0.6863-1.90493.2167-1.69664.60940.38990.53490.6845-1.22910.40851.4533-0.3808-0.5447-0.7010.9771-0.5381-0.42511.87810.68961.526622.8537-7.653.5622
380.21330.1301-0.27770.0123-0.50470.2339-1.0884-0.6295-0.9742-0.90110.2001-0.68810.3630.10680.23772.0074-0.5252-0.08582.51890.86341.560546.13222.423730
391.28810.41091.59541.87290.24961.836-0.29260.36-1.2729-1.54430.77810.49830.8033-0.4974-0.59432.5943-0.8072-0.08872.35080.72131.77150.4285-3.606229.3341
40-0.0115-0.131-0.01842.86320.3126-0.0571-0.14530.9372-0.5364-1.93690.079-1.01770.51450.9257-0.14282.708-0.6650.30542.6088-0.08730.942558.36581.117617.799
414.90512.3282-2.12623.5817-2.27085.51520.4668-1.19750.7631-0.2103-0.20990.5011-0.64620.8879-0.23550.7611-0.2249-0.00891.39410.31571.11640.3049-2.377266.1557
420.37680.4933-0.27993.28570.48691.01450.99780.3136-0.7917-0.69880.51240.1537-0.56220.3642-0.94851.2154-0.20370.17742.06910.25971.582654.38968.686736.1352
430.35580.6345-1.15223.8556-3.03286.7147-0.2080.31560.356-0.56280.59750.8370.4053-1.9325-0.10811.4455-0.33760.03912.03820.52091.187650.112311.275638.5301
443.92240.89961.98586.1601-2.4612.40680.58011.6435-0.9594-2.34890.17550.7351-0.83460.24580.58721.3790.61240.01312.2628-0.2420.814454.543-100.901-6.6568
456.03510.09333.73733.07360.40233.64480.30340.5278-0.62551.217-1.4671-0.9484-0.81440.4404-0.2017-0.47130.3782-0.22951.96880.16080.741160.1587-99.856212.4132
462.6689-0.9712-1.08911.2336-0.68181.79970.4920.2813-0.19030.9174-1.052-0.2290.1581.63820.07110.52440.1736-0.32761.33660.35920.9364.2236-93.407513.81
474.44993.18385.24954.55344.5397.18250.5951.4269-2.2617-0.991-0.11271.33850.50660.1464-0.88521.33890.3261-0.47361.3623-0.21291.373956.8908-106.7021-0.856
481.02081.10951.93925.75943.39644.2084-0.44361.6384-0.4415-0.0352-0.0275-0.65290.5845-0.371-0.33940.90860.35270.05162.663-0.07480.745465.9044-98.7453-3.8089
494.6195-0.0565-2.21843.6980.52773.3841-0.3241.8530.3512-0.49780.6968-0.3985-1.28010.7636-0.37881.29980.28410.42.51120.42831.527162.4928-87.1002-2.7672
503.368-0.9138-0.06741.2608-0.29053.62510.07951.25450.0909-1.1797-0.622-0.5893-0.66031.9704-0.4576-2.52090.836-0.66032.02980.64521.068157.0997-94.329510.1989
510.137-0.2432-0.14693.7976-1.61922.09810.51360.85090.591-0.0187-0.03981.1883-0.55670.1164-0.18080.85620.0061-0.27751.27410.47131.437450.7045-86.647317.1764
520.20070.41550.00170.8268-0.2291.19960.41221.35271.04240.439-0.20650.8591-0.58240.8240.59270.06050.3096-0.59552.12450.75071.025261.7458-93.874212.6003
531.7523-1.51240.58125.44411.461.8881-0.37171.0634-0.6999-0.9812-0.54930.01870.02450.35270.86820.5888-0.0036-0.07871.90850.18180.558552.9156-94.19413.4169
540.55670.8484-0.15492.9441-1.30130.72650.370.8694-1.2605-0.17680.1772-1.57851.9811.1353-0.69811.00090.5316-0.74121.2813-0.75912.351140.5222-113.14595.4836
550.9618-0.5652-0.6450.32110.27790.61560.3971-0.1119-0.67121.07511.03361.129-0.7548-0.7333-0.43690.2910.28490.21111.19990.39741.958732.4646-91.91612.3606
565.5426-0.40211.88163.0875-2.54473.8067-0.09880.9567-1.8851-0.81940.99441.72741.0579-1.2921-0.53360.66740.0956-0.12071.10270.12761.287332.9065-102.23883.3578
570.395-0.15620.05341.3023-1.30081.41070.405-0.1678-1.3392-0.09250.336-0.55210.24920.37760.11091.0195-0.1227-0.16541.20180.22652.702433.6243-113.907112.2089
586.3716-1.1054-0.10182.8065-0.43513.51170.5944-0.9238-0.98041.16150.4331.1853-0.7803-1.451-0.43450.6289-0.038-0.23921.16570.55931.745133.207-102.259218.3943
593.26980.16940.21663.27970.45787.62690.17440.4830.69470.36951.16321.55290.02380.3478-0.80510.50960.24020.1781.07620.11171.247943.1428-88.529612.0166
601.3149-1.1725-0.39851.0650.5070.74810.5815-1.0156-1.18280.5815-0.23911.4698-0.06-0.2145-0.38680.6119-0.0171-0.00280.98260.26261.563635.7258-96.270412.7617
613.48921.637-0.17035.1179-3.20193.65070.2648-0.71660.5555-0.29510.27420.9401-0.15140.515-0.32981.55120.32690.14781.0455-0.00751.336953.2934-103.002849.2231
623.8803-2.19481.01564.5294-0.96031.7089-0.0775-2.43510.46790.5680.7448-0.6039-0.18940.1027-0.66191.04360.37720.25811.65490.56481.022552.9684-107.844240.9634
634.2786-1.15980.39535.2562-1.56872.7057-0.4542-1.0345-1.16950.54330.91432.11950.70360.0574-0.57571.25430.44230.68861.24221.292.070544.6182-110.42142.4423
643.087-3.35823.89385.5508-2.96395.78870.6503-0.9713-1.94650.0339-0.3790.08470.809-0.9895-0.29771.49270.32920.03781.64310.91831.362752.3121-113.461551.8632
651.96710.6517-1.45240.3298-0.25063.1724-0.4374-0.62690.10740.84-0.51220.3379-0.41610.0209-0.43640.78690.23240.49411.4640.70511.994757.3368-104.247833.8148
660.97860.10651.27950.1003-0.2222.5121-1.5227-0.1294-0.82661.69660.69840.2064-0.62260.39970.44072.73180.36740.57922.44120.87820.958356.972-112.180663.1485
674.7362-1.7456-0.03641.23790.73820.8861-0.57150.10220.03640.47410.95480.3815-0.87930.71320.2911.6499-0.3714-0.43632.76880.64651.586984.6897-126.236267.3446
681.8951-0.4226-0.2522.14550.60470.35060.7254-1.81940.19230.03040.0737-0.251-0.5269-0.90510.24712.9530.5466-0.25222.40590.87231.309876.741-115.180367.0917
695.7562-2.32212.19621.7689-0.49171.36030.1668-1.1935-0.9571.28360.020.3965-1.04890.8121-0.92322.98930.7189-0.35552.74090.49981.220481.2797-117.669177.6353
704.3677-1.70131.68092.4049-1.01381.96130.1017-0.116-1.7382-0.0153-0.05670.0985-0.06160.6802-0.19340.86680.41440.04571.37370.60941.209769.0302-117.778132.3427
712.4245-1.21270.57161.7392-0.25391.30050.36281.32730.1193-0.4505-0.0670.65130.791-0.105-0.30140.61370.46390.0791.67550.37151.34664.1352-111.229723.9148
722.3017-0.65021.67722.8451-1.61873.99880.02810.3728-0.6799-0.02570.23670.41740.41450.2845-0.32380.7390.1770.10031.41450.52821.229670.6524-115.790335.7343
738.375.7198-7.68897.254-4.7867.75570.4479-0.5231-0.465-0.4336-0.05251.2381-0.0776-0.6846-0.3031.885-0.0072-0.15281.52640.59071.495877.8191-126.258661.7713
744.08844.0696-0.70345.966-2.1324.35970.1862-0.5445-1.18311.0364-0.0480.31560.1227-0.7177-0.66751.26450.3627-0.26732.00330.59781.595972.8075-128.083454.0859
750.8162-0.87322.39234.0658-0.89627.82110.0988-0.1744-1.33770.31710.34080.4333-0.0335-0.427-0.37971.24370.403-0.0781.79850.62071.618778.3829-129.200358.7336
760.77470.71730.23274.6601-0.62142.7538-0.22020.39920.63560.4874-0.0631-0.9263-0.42720.36350.31651.3937-0.3248-0.37881.33860.1821.593542.9989-62.46354.8126
772.6403-0.01740.94233.9691-1.11133.2399-0.3731-0.19961.2036-0.6273-0.4052-0.2774-0.89710.27850.42390.8809-0.1488-0.25961.17210.77871.744439.3412-63.6123-8.2127
785.14032.3622-3.41163.3854-1.60912.06370.0521.57781.0661-0.1149-0.6515-0.4604-1.03581.65330.27661.0019-0.3995-0.47391.78960.8211.530744.8397-63.6789-2.8408
790.0789-0.1410.14160.1501-0.01940.1927-0.56470.70.45810.41490.1987-0.0769-0.96640.2360.35111.9167-0.0818-0.56911.22360.71882.74221.4632-40.5251-13.1353
800.66980.65160.73910.90021.15032.32850.1077-1.8309-0.81981.21670.2727-0.6736-1.0526-0.17260.0922.4611-0.0568-0.36491.39030.5292.286715.7035-36.9629-8.0944
815.0089-2.04681.44994.5788-1.44273.05930.44791.2355-0.6024-0.6564-0.2110.4509-0.18020.27330.00990.77840.0614-0.33441.41440.26961.319127.39-76.4202-8.2358
821.45710.3004-1.50490.83831.60454.87190.76120.31250.0718-0.4854-0.462-0.0257-0.9629-0.1520.49191.27130.2063-0.381.36650.75882.03913.3021-46.462-19.4489
83-0.0460.0615-0.00016.6562-3.8791.90430.29020.68-0.06010.2562-0.8525-0.8336-0.39311.07570.30261.26530.0266-0.26731.45680.58041.946517.696-48.797-21.8042
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 459 through 469 )
2X-RAY DIFFRACTION2chain 'A' and (resid 470 through 481 )
3X-RAY DIFFRACTION3chain 'A' and (resid 482 through 501 )
4X-RAY DIFFRACTION4chain 'A' and (resid 502 through 511 )
5X-RAY DIFFRACTION5chain 'A' and (resid 512 through 521 )
6X-RAY DIFFRACTION6chain 'A' and (resid 522 through 531 )
7X-RAY DIFFRACTION7chain 'A' and (resid 532 through 554 )
8X-RAY DIFFRACTION8chain 'A' and (resid 555 through 564 )
9X-RAY DIFFRACTION9chain 'A' and (resid 565 through 594 )
10X-RAY DIFFRACTION10chain 'A' and (resid 595 through 605 )
11X-RAY DIFFRACTION11chain 'B' and (resid 459 through 469 )
12X-RAY DIFFRACTION12chain 'B' and (resid 470 through 491 )
13X-RAY DIFFRACTION13chain 'B' and (resid 492 through 515 )
14X-RAY DIFFRACTION14chain 'B' and (resid 516 through 525 )
15X-RAY DIFFRACTION15chain 'B' and (resid 526 through 545 )
16X-RAY DIFFRACTION16chain 'B' and (resid 546 through 563 )
17X-RAY DIFFRACTION17chain 'B' and (resid 564 through 582 )
18X-RAY DIFFRACTION18chain 'B' and (resid 583 through 605 )
19X-RAY DIFFRACTION19chain 'L' and (resid 1 through 18 )
20X-RAY DIFFRACTION20chain 'L' and (resid 19 through 34 )
21X-RAY DIFFRACTION21chain 'L' and (resid 35 through 48 )
22X-RAY DIFFRACTION22chain 'L' and (resid 49 through 75 )
23X-RAY DIFFRACTION23chain 'L' and (resid 76 through 88 )
24X-RAY DIFFRACTION24chain 'L' and (resid 89 through 101 )
25X-RAY DIFFRACTION25chain 'L' and (resid 102 through 113 )
26X-RAY DIFFRACTION26chain 'L' and (resid 114 through 128 )
27X-RAY DIFFRACTION27chain 'L' and (resid 129 through 187 )
28X-RAY DIFFRACTION28chain 'L' and (resid 188 through 212 )
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 42 )
30X-RAY DIFFRACTION30chain 'H' and (resid 43 through 58 )
31X-RAY DIFFRACTION31chain 'H' and (resid 59 through 144 )
32X-RAY DIFFRACTION32chain 'H' and (resid 145 through 155 )
33X-RAY DIFFRACTION33chain 'H' and (resid 156 through 175 )
34X-RAY DIFFRACTION34chain 'H' and (resid 176 through 223 )
35X-RAY DIFFRACTION35chain 'C' and (resid 1 through 33 )
36X-RAY DIFFRACTION36chain 'C' and (resid 34 through 49 )
37X-RAY DIFFRACTION37chain 'C' and (resid 50 through 101 )
38X-RAY DIFFRACTION38chain 'C' and (resid 102 through 139 )
39X-RAY DIFFRACTION39chain 'C' and (resid 140 through 186 )
40X-RAY DIFFRACTION40chain 'C' and (resid 187 through 211 )
41X-RAY DIFFRACTION41chain 'D' and (resid 1 through 119 )
42X-RAY DIFFRACTION42chain 'D' and (resid 120 through 145 )
43X-RAY DIFFRACTION43chain 'D' and (resid 146 through 223 )
44X-RAY DIFFRACTION44chain 'E' and (resid 459 through 469 )
45X-RAY DIFFRACTION45chain 'E' and (resid 470 through 481 )
46X-RAY DIFFRACTION46chain 'E' and (resid 482 through 501 )
47X-RAY DIFFRACTION47chain 'E' and (resid 502 through 511 )
48X-RAY DIFFRACTION48chain 'E' and (resid 512 through 521 )
49X-RAY DIFFRACTION49chain 'E' and (resid 522 through 531 )
50X-RAY DIFFRACTION50chain 'E' and (resid 532 through 554 )
51X-RAY DIFFRACTION51chain 'E' and (resid 555 through 564 )
52X-RAY DIFFRACTION52chain 'E' and (resid 565 through 594 )
53X-RAY DIFFRACTION53chain 'E' and (resid 595 through 605 )
54X-RAY DIFFRACTION54chain 'F' and (resid 459 through 469 )
55X-RAY DIFFRACTION55chain 'F' and (resid 470 through 491 )
56X-RAY DIFFRACTION56chain 'F' and (resid 492 through 515 )
57X-RAY DIFFRACTION57chain 'F' and (resid 516 through 525 )
58X-RAY DIFFRACTION58chain 'F' and (resid 526 through 545 )
59X-RAY DIFFRACTION59chain 'F' and (resid 546 through 563 )
60X-RAY DIFFRACTION60chain 'F' and (resid 564 through 605 )
61X-RAY DIFFRACTION61chain 'K' and (resid 1 through 18 )
62X-RAY DIFFRACTION62chain 'K' and (resid 19 through 48 )
63X-RAY DIFFRACTION63chain 'K' and (resid 49 through 75 )
64X-RAY DIFFRACTION64chain 'K' and (resid 76 through 88 )
65X-RAY DIFFRACTION65chain 'K' and (resid 89 through 101 )
66X-RAY DIFFRACTION66chain 'K' and (resid 102 through 113 )
67X-RAY DIFFRACTION67chain 'K' and (resid 114 through 128 )
68X-RAY DIFFRACTION68chain 'K' and (resid 129 through 187 )
69X-RAY DIFFRACTION69chain 'K' and (resid 188 through 212 )
70X-RAY DIFFRACTION70chain 'J' and (resid 1 through 42 )
71X-RAY DIFFRACTION71chain 'J' and (resid 43 through 58 )
72X-RAY DIFFRACTION72chain 'J' and (resid 59 through 144 )
73X-RAY DIFFRACTION73chain 'J' and (resid 145 through 155 )
74X-RAY DIFFRACTION74chain 'J' and (resid 156 through 175 )
75X-RAY DIFFRACTION75chain 'J' and (resid 176 through 223 )
76X-RAY DIFFRACTION76chain 'G' and (resid 1 through 33 )
77X-RAY DIFFRACTION77chain 'G' and (resid 34 through 49 )
78X-RAY DIFFRACTION78chain 'G' and (resid 50 through 101 )
79X-RAY DIFFRACTION79chain 'G' and (resid 102 through 139 )
80X-RAY DIFFRACTION80chain 'G' and (resid 140 through 211 )
81X-RAY DIFFRACTION81chain 'I' and (resid 1 through 119 )
82X-RAY DIFFRACTION82chain 'I' and (resid 120 through 145 )
83X-RAY DIFFRACTION83chain 'I' and (resid 146 through 223 )

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万見について

-
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