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- PDB-7cvq: crystal structure of Arabidopsis CO CCT domain in complex with NF... -

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基本情報

登録情報
データベース: PDB / ID: 7cvq
タイトルcrystal structure of Arabidopsis CO CCT domain in complex with NF-YB2/YC3 and FT CORE1 DNA
要素
  • Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS
  • FT CORE1 DNA forward strand
  • FT CORE1 DNA reverse strand
  • Nuclear transcription factor Y subunit B-2
キーワードDNA BINDING PROTEIN/DNA / CONSTANS / transcription factor / DNA BINDING PROTEIN-DNA complex
機能・相同性
機能・相同性情報


far-red light signaling pathway / positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / regulation of flower development / gibberellic acid mediated signaling pathway / regulation of seed germination / flower development / response to far red light / response to water deprivation ...far-red light signaling pathway / positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / regulation of flower development / gibberellic acid mediated signaling pathway / regulation of seed germination / flower development / response to far red light / response to water deprivation / abscisic acid-activated signaling pathway / plastid / transcription coregulator activity / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity / protein heterodimerization activity / DNA binding / zinc ion binding / nucleus
類似検索 - 分子機能
CCT domain / Zinc finger protein CONSTANS-like / CCT motif / CCT domain profile. / : / Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : / Transcription factor CBF/NF-Y/archaeal histone domain ...CCT domain / Zinc finger protein CONSTANS-like / CCT motif / CCT domain profile. / : / Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Zinc finger protein CONSTANS / Nuclear transcription factor Y subunit B-2 / Nuclear transcription factor Y subunit C-3
類似検索 - 構成要素
生物種Arabidopsis thaliana (シロイヌナズナ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.3 Å
データ登録者Lv, X. / Du, J.
引用ジャーナル: Plant Cell / 年: 2021
タイトル: Structural insights into the multivalent binding of the Arabidopsis FLOWERING LOCUS T promoter by the CO-NF-Y master transcription factor complex.
著者: Lv, X. / Zeng, X. / Hu, H. / Chen, L. / Zhang, F. / Liu, R. / Liu, Y. / Zhou, X. / Wang, C. / Wu, Z. / Kim, C. / He, Y. / Du, J.
履歴
登録2020年8月26日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年6月16日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS
B: Nuclear transcription factor Y subunit B-2
D: FT CORE1 DNA forward strand
E: FT CORE1 DNA reverse strand
F: Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS
K: Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS
P: Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS
G: Nuclear transcription factor Y subunit B-2
L: Nuclear transcription factor Y subunit B-2
Q: Nuclear transcription factor Y subunit B-2
I: FT CORE1 DNA forward strand
N: FT CORE1 DNA forward strand
T: FT CORE1 DNA forward strand
J: FT CORE1 DNA reverse strand
O: FT CORE1 DNA reverse strand
U: FT CORE1 DNA reverse strand


分子量 (理論値)分子数
合計 (水以外)186,21116
ポリマ－186,21116
非ポリマー00
水00
1
A: Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS
B: Nuclear transcription factor Y subunit B-2
D: FT CORE1 DNA forward strand
E: FT CORE1 DNA reverse strand


分子量 (理論値)分子数
合計 (水以外)46,5534
ポリマ－46,5534
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-79 kcal/mol
Surface area17740 Å2
手法PISA
2
F: Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS
G: Nuclear transcription factor Y subunit B-2
I: FT CORE1 DNA forward strand
J: FT CORE1 DNA reverse strand


分子量 (理論値)分子数
合計 (水以外)46,5534
ポリマ－46,5534
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-80 kcal/mol
Surface area18140 Å2
手法PISA
3
K: Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS
L: Nuclear transcription factor Y subunit B-2
N: FT CORE1 DNA forward strand
O: FT CORE1 DNA reverse strand


分子量 (理論値)分子数
合計 (水以外)46,5534
ポリマ－46,5534
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-75 kcal/mol
Surface area18630 Å2
手法PISA
4
P: Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS
Q: Nuclear transcription factor Y subunit B-2
T: FT CORE1 DNA forward strand
U: FT CORE1 DNA reverse strand


分子量 (理論値)分子数
合計 (水以外)46,5534
ポリマ－46,5534
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-83 kcal/mol
Surface area18530 Å2
手法PISA
単位格子
Length a, b, c (Å)103.244, 65.273, 138.284
Angle α, β, γ (deg.)90.000, 91.170, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANS / AtNF-YC-3


分子量: 20021.914 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Arabidopsis thaliana (シロイヌナズナ)
遺伝子: NFYC3, At1g54830, F14C21.41, T22H22.22, CO, At5g15840, F14F8_220
プラスミド: pET-Sumo / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q9ZVL3, UniProt: Q39057
#2: タンパク質
Nuclear transcription factor Y subunit B-2 / AtNF-YB-2 / Transcriptional activator HAP3B


分子量: 11175.779 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Arabidopsis thaliana (シロイヌナズナ)
遺伝子: NFYB2, HAP3B, At5g47640, MNJ7.23 / プラスミド: pET-Sumo / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q9FGJ3
#3: DNA鎖
FT CORE1 DNA forward strand


分子量: 7762.034 Da / 分子数: 4 / 由来タイプ: 合成
由来: (合成) Arabidopsis thaliana (シロイヌナズナ)
#4: DNA鎖
FT CORE1 DNA reverse strand


分子量: 7592.922 Da / 分子数: 4 / 由来タイプ: 合成
由来: (合成) Arabidopsis thaliana (シロイヌナズナ)

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.5 Å3/Da / 溶媒含有率: 50.83 %
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 / pH: 9.5 / 詳細: 0.1 M CHES, pH 9.5 and 40% PEG 400

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL19U1 / 波長: 0.9792 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2019年12月16日
放射モノクロメーター: LN2-cooled DCM with Si(111) crystals
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: 0.9792 Å / 相対比: 1
反射解像度: 3.3→40 Å / Num. obs: 28108 / % possible obs: 99.2 % / 冗長度: 4.4 % / Biso Wilson estimate: 95.43 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.148 / Rsym value: 0.148 / Net I/σ(I): 7.7
反射 シェル解像度: 3.3→3.42 Å / 冗長度: 4.1 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 1 / Num. unique obs: 2727 / CC1/2: 0.872 / CC star: 0.965 / Rsym value: 0.811 / % possible all: 97.4

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
HKL-3000データスケーリング
PDB_EXTRACT3.25データ抽出
HKL-3000データ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7CVO

7cvo


解像度: 3.3→35.181 Å / SU ML: 0.5 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 31.25 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2642 1411 5.08 %
Rwork0.2412 26377 -
obs0.2425 27788 98.75 %
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: 272.9 Å2 / Biso mean: 127.4662 Å2 / Biso min: 36.28 Å2
精密化ステップサイクル: final / 解像度: 3.3→35.181 Å
タンパク質核酸リガンド溶媒全体
原子数6834 4076 0 0 10910
残基数----1031
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00611506
X-RAY DIFFRACTIONf_angle_d1.00816327
X-RAY DIFFRACTIONf_chiral_restr0.0431823
X-RAY DIFFRACTIONf_plane_restr0.0061382
X-RAY DIFFRACTIONf_dihedral_angle_d25.8114703
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3001-3.41790.30441290.3137255296
3.4179-3.55470.35921370.2941258598
3.5547-3.71630.28961380.2868262399
3.7163-3.9120.28761170.2709263399
3.912-4.15670.28221380.2659264899
4.1567-4.4770.25591380.23542645100
4.477-4.92650.26641440.2262674100
4.9265-5.63690.2671480.25262999
5.6369-7.09230.30141470.2592267799
7.0923-350.21891750.1933271198
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)
12.59710.376-0.83951.2408-1.27592.0395-0.28820.22550.8955-1.00290.22940.2175-0.47961.3154-0.08561.24850.26310.171.1074-0.27251.417764.00133.10344.267
20.0267-0.07910.09570.1259-0.5864.7392-0.08370.3521-0.205-0.34110.7912-0.40510.5495-1.20790.07471.799-0.27560.2666-0.05410.29370.646345.61324.78350.102
35.87770.9669-4.11010.2231-0.6652.8643-0.1843-0.78320.32240.1973-0.05190.91830.8428-1.11740.07731.551-0.1303-0.0551.4201-0.01420.934832.36525.42560.977
43.98372.41520.01862.9351.10680.8325-0.2004-0.2167-0.27420.78950.266-0.3710.1576-0.1337-0.07880.78120.05-0.00361.5547-0.01530.922423.31331.49954.723
53.7343-0.77340.76893.3482-1.21964.18990.3611-0.7847-0.2256-1.140.56030.2455-1.306-0.4185-0.03090.7630.14780.0410.65020.0710.51943.64439.53531.659
64.74591.2125-0.69522.15621.07021.49540.82490.6611.8308-0.58190.16330.66-0.5617-0.86570.27181.47350.09220.3167-0.09491.2534-0.276746.62847.23419.456
71.8536-0.27781.51041.4309-1.21653.15430.5924-0.1291-0.23440.24730.3813-0.57370.2046-0.0481-0.15541.070.06240.05340.4681-0.01680.573253.23936.40940.665
80.8263-1.19661.64961.9875-2.63773.6639-0.5015-0.4514-0.53360.33390.7791-0.3154-0.29560.22310.01471.3978-0.0236-0.14220.8508-0.10140.720752.14238.62860.009
91.7228-0.3479-1.37921.35430.4671.1245-0.1668-0.35390.08111.4922-0.1213-1.1918-0.02821.174-1.99882.2128-0.4865-0.31110.5328-0.5941-0.116456.82145.33649.095
102.3893-0.3191-0.47963.9802-1.55860.9194-0.6834-0.0269-0.0665-1.79510.3384-0.2571-0.8732-0.2581-2.43991.5792-0.0113-0.05250.3129-0.27370.730750.01452.79546.934
115.6003-1.15131.57892.45691.34291.72841.9611-0.0101-1.60530.7640.0960.3378-0.3358-0.72880.62851.133-0.07480.27080.49260.21390.229943.29736.94447.223
122.21870.836-0.85560.4161-1.12835.2492-0.44420.052-0.4499-0.4845-0.4418-0.5169-0.166-0.1038-0.09191.4940.1160.20450.43110.05150.631652.36946.36129.995
134.06541.69990.40562.6017-0.87227.19331.06870.8136-0.8205-0.2060.6887-1.5475-0.84991.11680.13331.29110.0130.2820.5741-0.17790.736861.638.4830.119
14-0.0350.3577-0.56751.26310.08282.91740.1284-0.18830.25790.9665-0.1515-0.0279-0.3975-0.70830.05781.46980.32650.10711.0074-0.02270.583742.639.08768.918
151.57190.306-0.5366-0.1831-0.53213.77140.44570.4983-0.0036-0.49980.35730.6417-0.3972-2.05720.00561.3831-0.04680.0411.22650.09060.829329.83432.66731.601
160.7632-0.0865-1.32750.3223-0.78744.36470.00110.15650.0529-0.61530.30630.25760.7776-1.5990.01011.53910.0604-0.0151.19020.03220.747731.81235.51129.695
171.6714-0.575-0.6810.00480.0531.2750.5971-1.261-0.03891.70820.02990.1662-0.3457-0.31820.08181.7760.3030.06110.84490.09590.807140.638.77167.409
184.7001-4.02841.63873.9451-0.10575.60611.21450.66190.046-0.3813-0.60280.33710.54140.992-0.01811.1787-0.07440.03740.4738-0.0640.886366.74920.94625.999
191.8425-0.6870.38330.6029-0.13122.4788-0.59590.1173-0.4081-1.16590.1281-0.3595-0.1851-1.981-0.0460.9960.4193-0.10930.8830.05320.77937.90817.8413.859
20-0.00330.04790.00170.0408-0.06130.12470.7546-0.33640.1758-0.36240.89330.621-0.5277-0.02560.05842.70740.3039-0.09021.427-0.13421.3937-16.44530.9349.955
21-0.0104-0.0180.02350.00090.0013-0.010.6265-0.17520.53020.57270.1676-0.9429-0.4899-0.78910.0612.2271-0.36130.06261.59840.21451.32183.34627.56457.021
224.91544.5308-3.31057.9736-4.1652.5716-1.2637-0.6472-1.0583-0.0964-0.311-1.63880.120.0265-0.85322.4787-0.1598-0.29183.0931-1.27731.283714.2118.42569.288
230.03620.0627-0.02450.07780.0934-0.0065-0.0735-0.03040.79960.6045-0.32951.9447-1.0908-0.79790.05741.8596-1.1081-0.00162.9909-0.15761.7086-3.51232.33218.862
241.5073-1.15940.20621.01570.59061.45340.3429-0.2711-0.6485-0.6008-0.3281-0.9973-0.35060.46940.04221.31840.004-0.00431.21620.01960.6722.99744.1916.704
252.97831.5375-0.56451.961-1.13222.927-0.4075-0.64230.1820.8912-0.0470.2943-1.0333-0.8981-0.01591.07480.0958-0.01630.5467-0.04820.520748.8397.63937.182
262.6571-0.1136-0.90221.52450.55223.7490.85910.5722-0.1333-0.2826-0.3074-0.0347-0.021-0.18850.28991.55940.46640.01750.43490.34830.406553.7520.77649.222
271.683-0.1839-0.44742.012-0.17133.68280.1907-0.07890.4247-0.28250.2077-0.198-0.56381.1652-0.02241.007-0.17250.1080.4456-0.00960.394357.68113.91928.659
284.18344.0018-5.50235.74-3.45079.0067-0.0810.58831.6459-1.57930.91370.098-0.54571.0160.14971.24630.0650.06620.74060.06930.62957.77612.2269.174
295.19220.05530.32722.4341-0.35551.24830.070.54350.0864-1.740.7212-0.3730.63661.63240.01670.93680.1178-0.05660.6505-0.17710.577163.8616.41620.013
306.67342.2002-1.34082.19750.1823.1692-0.61181.41340.22210.92660.2238-0.42781.4070.1926-0.18770.94090.23060.12770.32510.08610.770759.042-2.71120.999
311.14180.2441-0.7291.4488-0.63551.8717-0.1376-0.0418-0.21340.34440.37190.04070.4085-0.03070.00580.90280.07050.11581.6753-0.17210.763-6.65216.91342.334
320.54830.15830.11311.44211.21171.9256-0.2888-0.9977-0.3573-0.2526-0.06931.1058-0.8945-0.92680.10821.436-0.03690.4651.58810.12571.2573-15.38712.4658.054
330.09660.575-0.03714.56381.150.27180.1945-0.7250.3197-0.23970.9846-1.87950.1141-1.6220.21831.36160.4527-0.02581.67370.17460.59487.51253.11833.282
340.77220.03930.56151.104-0.13450.70120.2845-0.0961-0.5820.94220.09991.19790.1745-0.83781.53091.4447-1.197-1.23653.43460.0162-1.20733.24642.27517.196
350.5412-0.5137-0.06030.7180.29660.26230.85980.1197-1.3434-0.75790.4579-0.12340.7024-0.5250.39171.787-1.072-0.4733.709-0.4805-0.0413-5.23747.90112.564
363.5083-2.2112-1.94611.97031.64111.29970.95740.36593.3316-0.41570.2648-0.9393-0.2857-1.07670.1231.39410.8391-0.57432.1170.2731.0601-3.78257.88713.272
372.50542.28110.03082.89540.33322.78330.1378-1.03480.24380.6266-0.41021.09561.3287-2.1418-0.10140.57820.0644-0.24610.63040.11750.488146.4797.25225.171
384.72711.94551.93369.50747.21075.62780.0588-0.02950.4358-0.79620.5284-1.46570.5291-0.58620.1040.79190.0404-0.02270.50740.2160.570152.55817.67215.377
391.95180.45120.5580.185-0.60556.7527-0.3831-0.49120.25180.3143-0.2878-0.11130.5473-0.1197-0.00291.05560.13-0.04180.5266-0.06560.483459.2833.73539.133
403.86581.7596-0.94120.84380.15724.017-0.6445-0.3169-0.85810.23180.2588-1.06990.36510.9443-0.07331.2732-0.0439-0.07190.6588-0.02430.706266.31911.72739.375
414.937-2.1774-2.09195.3945-0.63679.9869-1.2502-0.46650.99420.2886-0.3108-0.2987-0.52810.4521-0.22030.61420.25260.57860.4057-0.3351.142764.57819.7940.083
422.3594-2.77382.01473.5782-2.4631.77950.84170.1623-0.42340.34180.33360.68670.2809-0.1950.04261.6411-0.21010.32882.01-0.37831.1133-1.2946.23748.522
431.0009-0.47660.38740.42740.03880.31880.6767-0.4190.2895-0.03690.37170.07030.52270.00611.16420.7776-0.2837-0.08922.4277-0.360.35370.06618.35252.79
441.979-0.1890.80821.537-0.31493.9763-0.0965-0.69970.1042-0.0758-0.22980.3340.43740.22050.12431.36160.02970.11321.5350.00170.7996-11.114.31845.81
454.1906-1.35912.62660.59-1.39364.1333-0.0958-0.06730.07960.33390.25010.2691-0.788-0.01010.12811.46340.3678-0.11641.78520.02730.7866-12.96313.44823.049
460.4330.68210.56242.9260.43370.8113-0.53391.1229-1.16530.4218-0.62980.91-0.0553-0.42060.16991.53990.2615-0.20911.34180.16221.4202-16.60820.77831.84
470.0275-0.05580.02861.7679-1.39581.6326-0.54290.52691.6484-0.15091.3211-0.1407-0.1352-0.23190.00611.90260.27150.23321.82850.0711.0211-16.57125.33738.864
483.5714-0.2597-0.40581.13080.19122.7675-0.6215-0.5159-0.8377-0.2348-0.09320.8403-0.7478-1.91370.00231.21180.169-0.00811.8970.00570.57144.00449.18921.739
490.2965-0.14230.5196-0.0189-0.14790.76040.798-0.9451-1.6735-0.6690.9772-0.28830.2626-1.64320.17191.6603-0.26140.01632.88430.0981.168-3.8442.36836.014
503.7368-4.53531.45535.4894-2.20218.58572.0998-0.6538-0.5245-0.67621.3341-2.80720.6201-02.34751.9205-0.41690.04050.7028-0.17151.35554.88.318-7.629
510.717-0.4877-1.35550.6658-0.24532.6387-0.304-0.5528-0.86240.22410.28910.70480.9708-0.60840.08651.0987-0.0972-0.00190.8103-0.07860.74639.25611.21812.276
521.9960.01230.51741.6661-0.22914.6806-0.3008-0.722-0.5310.54460.3810.88920.4264-2.78730.04791.3022-0.15410.10361.47880.02030.916834.6678.77441.699
533.99221.65560.44021.9690.57985.25980.5667-0.1526-1.2527-0.98141.47712.19830.9511-1.71290.07341.6718-0.00790.18332.71920.16241.5169-8.93419.0685.053
540.0253-0.16170.2671.536-2.05994.6121-0.35740.0044-0.97170.8611-0.7548-1.75880.00190.94040.27982.01270.29280.03262.20090.2671.0191-0.81711.51771.678
553.7893.81750.94873.85360.96740.2299-0.1846-0.3412-2.65120.01740.4238-2.02590.90750.4884-0.28413.0067-0.25340.08223.2410.00371.309315.69613.47858.167
566.82540.18551.06224.3255-0.56036.01060.0105-0.9761-0.15431.9690.7007-0.30521.98640.3555-0.03171.98370.2915-0.23992.8825-0.03731.124810.5016.78143.668
572.0132-0.04810.16070.8148-1.18811.7581-0.76611.0213-0.8988-0.6661-0.9496-1.14490.13020.3847-0.12141.758-0.34910.13793.95460.04841.305111.27111.24225.256
581.6044-1.39860.86581.322-0.08643.50130.38960.3868-0.39470.53770.53510.3711-0.7071-0.98660.13971.5602-0.0331-0.14861.49810.18320.95149.49948.173-7.726
591.2401-0.67060.23822.750.73485.49150.1702-0.79070.33850.32220.817-0.5563-0.40712.1155-0.08341.5752-0.061-0.18991.4885-0.26281.012924.07954.64128.986
605.2232-0.71221.32233.2123-1.96555.116-0.4925-1.09430.060.61890.71380.48071.1712-1.8334-0.01591.6062-0.08580.19891.2048-0.04080.871337.2177.12347.813
613.4175-0.232-0.16941.8644-1.31351.5112-0.25081.27670.48850.16580.43160.78740.82-1.22110.06981.0626-0.28420.02381.11550.04210.779935.5348.79322.709
620.9030.7288-0.11852.1591-0.78210.8064-0.4447-0.6446-0.1387-0.88880.4565-0.15431.3035-0.78880.14311.5385-0.1114-0.09080.86290.02380.554848.4328.570.743
631.76670.58320.50330.75131.17072.04641.23730.9548-0.84940.3578-0.42810.07431.41890.33130.09511.39340.0139-0.15323.1877-0.16421.1859.9519.37332.754
641.3791-1.14982.74721.8615-3.72729.2245-0.0858-1.3673-0.05891.98480.4022-1.3329-0.19490.28110.07212.37350.95650.0333.05590.151.64969.0548.05658.644
653.99421.2604-0.24452.7573-0.09390.00481.4443-0.43740.77250.19090.1120.96791.0941.1050.2362.62810.26810.1812.564-0.09150.5333-2.76215.00976.287
661.3597-0.5668-1.0950.17850.84223.56030.256-0.35950.5878-0.36510.4486-0.2986-1.80720.4267-0.02042.1532-0.0890.21021.3382-0.12730.951220.96955.68330.875
672.1351-0.36210.1751.03740.13711.1331.24672.9417-0.84660.0912-0.00990.0416-0.0862-0.10070.03411.82280.0582-0.05012.00230.06981.013311.58149.696-6.011
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 304:318 )A304 - 318
2X-RAY DIFFRACTION2( CHAIN A AND RESID 319:328 )A319 - 328
3X-RAY DIFFRACTION3( CHAIN A AND RESID 329:337 )A329 - 337
4X-RAY DIFFRACTION4( CHAIN A AND RESID 338:345 )A338 - 345
5X-RAY DIFFRACTION5( CHAIN B AND RESID 29:44 )B29 - 44
6X-RAY DIFFRACTION6( CHAIN B AND RESID 45:52 )B45 - 52
7X-RAY DIFFRACTION7( CHAIN B AND RESID 53:80 )B53 - 80
8X-RAY DIFFRACTION8( CHAIN B AND RESID 81:87 )B81 - 87
9X-RAY DIFFRACTION9( CHAIN B AND RESID 88:100 )B88 - 100
10X-RAY DIFFRACTION10( CHAIN B AND RESID 101:113 )B101 - 113
11X-RAY DIFFRACTION11( CHAIN A AND RESID 66:90 )A66 - 90
12X-RAY DIFFRACTION12( CHAIN A AND RESID 91:125 )A91 - 125
13X-RAY DIFFRACTION13( CHAIN A AND RESID 126:148 )A126 - 148
14X-RAY DIFFRACTION14( CHAIN D AND RESID 1:11 )D1 - 11
15X-RAY DIFFRACTION15( CHAIN D AND RESID 12:25 )D12 - 25
16X-RAY DIFFRACTION16( CHAIN E AND RESID 1:15 )E1 - 15
17X-RAY DIFFRACTION17( CHAIN E AND RESID 16:25 )E16 - 25
18X-RAY DIFFRACTION18( CHAIN F AND RESID 304:318 )F304 - 318
19X-RAY DIFFRACTION19( CHAIN F AND RESID 319:345 )F319 - 345
20X-RAY DIFFRACTION20( CHAIN K AND RESID 304:318 )K304 - 318
21X-RAY DIFFRACTION21( CHAIN K AND RESID 319:328 )K319 - 328
22X-RAY DIFFRACTION22( CHAIN K AND RESID 329:339 )K329 - 339
23X-RAY DIFFRACTION23( CHAIN P AND RESID 304:318 )P304 - 318
24X-RAY DIFFRACTION24( CHAIN P AND RESID 319:345 )P319 - 345
25X-RAY DIFFRACTION25( CHAIN G AND RESID 29:44 )G29 - 44
26X-RAY DIFFRACTION26( CHAIN G AND RESID 45:52 )G45 - 52
27X-RAY DIFFRACTION27( CHAIN G AND RESID 53:80 )G53 - 80
28X-RAY DIFFRACTION28( CHAIN G AND RESID 81:87 )G81 - 87
29X-RAY DIFFRACTION29( CHAIN G AND RESID 88:100 )G88 - 100
30X-RAY DIFFRACTION30( CHAIN G AND RESID 101:114 )G101 - 114
31X-RAY DIFFRACTION31( CHAIN L AND RESID 29:80 )L29 - 80
32X-RAY DIFFRACTION32( CHAIN L AND RESID 81:114 )L81 - 114
33X-RAY DIFFRACTION33( CHAIN Q AND RESID 29:52 )Q29 - 52
34X-RAY DIFFRACTION34( CHAIN Q AND RESID 53:87 )Q53 - 87
35X-RAY DIFFRACTION35( CHAIN Q AND RESID 88:100 )Q88 - 100
36X-RAY DIFFRACTION36( CHAIN Q AND RESID 101:114 )Q101 - 114
37X-RAY DIFFRACTION37( CHAIN F AND RESID 66:81 )F66 - 81
38X-RAY DIFFRACTION38( CHAIN F AND RESID 82:90 )F82 - 90
39X-RAY DIFFRACTION39( CHAIN F AND RESID 91:125 )F91 - 125
40X-RAY DIFFRACTION40( CHAIN F AND RESID 126:142 )F126 - 142
41X-RAY DIFFRACTION41( CHAIN F AND RESID 143:148 )F143 - 148
42X-RAY DIFFRACTION42( CHAIN K AND RESID 68:72 )K68 - 72
43X-RAY DIFFRACTION43( CHAIN K AND RESID 73:82 )K73 - 82
44X-RAY DIFFRACTION44( CHAIN K AND RESID 83:118 )K83 - 118
45X-RAY DIFFRACTION45( CHAIN K AND RESID 119:125 )K119 - 125
46X-RAY DIFFRACTION46( CHAIN K AND RESID 126:135 )K126 - 135
47X-RAY DIFFRACTION47( CHAIN K AND RESID 136:148 )K136 - 148
48X-RAY DIFFRACTION48( CHAIN P AND RESID 69:118 )P69 - 118
49X-RAY DIFFRACTION49( CHAIN P AND RESID 119:147 )P119 - 147
50X-RAY DIFFRACTION50( CHAIN I AND RESID 1:6 )I1 - 6
51X-RAY DIFFRACTION51( CHAIN I AND RESID 7:14 )I7 - 14
52X-RAY DIFFRACTION52( CHAIN I AND RESID 15:25 )I15 - 25
53X-RAY DIFFRACTION53( CHAIN N AND RESID 1:5 )N1 - 5
54X-RAY DIFFRACTION54( CHAIN N AND RESID 6:10 )N6 - 10
55X-RAY DIFFRACTION55( CHAIN N AND RESID 11:15 )N11 - 15
56X-RAY DIFFRACTION56( CHAIN N AND RESID 16:20 )N16 - 20
57X-RAY DIFFRACTION57( CHAIN N AND RESID 21:25 )N21 - 25
58X-RAY DIFFRACTION58( CHAIN T AND RESID 1:11 )T1 - 11
59X-RAY DIFFRACTION59( CHAIN T AND RESID 12:25 )T12 - 25
60X-RAY DIFFRACTION60( CHAIN J AND RESID 1:9 )J1 - 9
61X-RAY DIFFRACTION61( CHAIN J AND RESID 10:16 )J10 - 16
62X-RAY DIFFRACTION62( CHAIN J AND RESID 17:25 )J17 - 25
63X-RAY DIFFRACTION63( CHAIN O AND RESID 1:11 )O1 - 11
64X-RAY DIFFRACTION64( CHAIN O AND RESID 12:16 )O12 - 16
65X-RAY DIFFRACTION65( CHAIN O AND RESID 17:25 )O17 - 25
66X-RAY DIFFRACTION66( CHAIN U AND RESID 1:15 )U1 - 15
67X-RAY DIFFRACTION67( CHAIN U AND RESID 16:25 )U16 - 25

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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