[日本語] English
- PDB-8coi: Human adenovirus-derived synthetic ADDobody binder -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 8coi
タイトルHuman adenovirus-derived synthetic ADDobody binder
要素ADDobody
キーワードVIRAL PROTEIN / penton base / crown domain / human adenovirus
生物種Human adenovirus sp. (ヒトアデノウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.17 Å
データ登録者Buzas, D. / Toelzer, C. / Gupta, K. / Berger-Schaffitzel, C. / Berger, I.
資金援助 英国, 1件
組織認可番号
Max Planck Bristol Centre for Minimal Biology - University of BristolU100572-102 英国
引用ジャーナル: Structure / : 2024
タイトル: Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders.
著者: Dora Buzas / Huan Sun / Christine Toelzer / Sathish K N Yadav / Ufuk Borucu / Gunjan Gautam / Kapil Gupta / Joshua C Bufton / Julien Capin / Richard B Sessions / Frederic Garzoni / Imre ...著者: Dora Buzas / Huan Sun / Christine Toelzer / Sathish K N Yadav / Ufuk Borucu / Gunjan Gautam / Kapil Gupta / Joshua C Bufton / Julien Capin / Richard B Sessions / Frederic Garzoni / Imre Berger / Christiane Schaffitzel /
要旨: Adenovirus-derived nanoparticles (ADDomer) comprise 60 copies of adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport, and deployment of ADDomer-based ...Adenovirus-derived nanoparticles (ADDomer) comprise 60 copies of adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport, and deployment of ADDomer-based therapeutics independent of a cold chain. To expand the scope of ADDomers for new applications, we engineered ADDobodies, representing PBP crown domain, genetically separated from PBP multimerization domain. We inserted heterologous sequences into hyper-variable loops, resulting in monomeric, thermostable ADDobodies expressed at high yields in Escherichia coli. The X-ray structure of an ADDobody prototype validated our design. ADDobodies can be used in ribosome display experiments to select a specific binder against a target, with an enrichment factor of ∼10-fold per round. ADDobodies can be re-converted into ADDomers by genetically reconnecting the selected ADDobody with the PBP multimerization domain from a different species, giving rise to a multivalent nanoparticle, called Chimera, confirmed by a 2.2 Å electron cryo-microscopy structure. Chimera comprises 60 binding sites, resulting in ultra-high, picomolar avidity to the target.
履歴
登録2023年2月28日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年12月27日Provider: repository / タイプ: Initial release
改定 1.12024年1月24日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年3月20日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first

-
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

-
集合体

登録構造単位
A: ADDobody
B: ADDobody
C: ADDobody
D: ADDobody
E: ADDobody
F: ADDobody
G: ADDobody
H: ADDobody
I: ADDobody
J: ADDobody
K: ADDobody
L: ADDobody
M: ADDobody
N: ADDobody
O: ADDobody
P: ADDobody
Q: ADDobody
R: ADDobody
S: ADDobody
T: ADDobody


分子量 (理論値)分子数
合計 (水以外)704,97020
ポリマ-704,97020
非ポリマー00
00
1
A: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
2
B: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
3
C: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
4
D: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
5
E: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
6
F: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
7
G: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
8
H: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
9
I: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
10
J: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
11
K: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
12
L: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
13
M: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
14
N: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
15
O: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
16
P: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
17
Q: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
18
R: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
19
S: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
20
T: ADDobody


分子量 (理論値)分子数
合計 (水以外)35,2491
ポリマ-35,2491
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)103.853, 104.629, 180.494
Angle α, β, γ (deg.)92.03, 95.65, 112.61
Int Tables number1
Space group name H-MP1

-
要素

#1: タンパク質
ADDobody


分子量: 35248.512 Da / 分子数: 20 / 由来タイプ: 組換発現
由来: (組換発現) Human adenovirus sp. (ヒトアデノウイルス)
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.22 Å3/Da / 溶媒含有率: 61.82 %
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: 5.5 / 詳細: 20 w/v % PEG 3350, 0.15 M citrate pH 5.5

-
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: Diamond / ビームライン: I03 / 波長: 0.9795 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2019年10月21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: 0.9795 Å / 相対比: 1
反射解像度: 3.17→96.41 Å / Num. obs: 116474 / % possible obs: 98.6 % / 冗長度: 3.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.88
反射 シェル解像度: 3.17→3.28 Å / Num. unique obs: 11604 / CC1/2: 0.723

-
解析

ソフトウェア
名称バージョン分類
PHENIX(1.19.2_4158: ???)精密化
XDSデータ削減
Cootモデル構築
PHASER位相決定
Aimlessデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 3.17→19.97 Å / SU ML: 0.44 / 交差検証法: FREE R-VALUE / σ(F): 1.93 / 位相誤差: 27.16 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2613 5851 5.02 %
Rwork0.213 --
obs0.2154 116437 98.6 %
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: 3.17→19.97 Å
タンパク質核酸リガンド溶媒全体
原子数37335 0 0 0 37335
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00238245
X-RAY DIFFRACTIONf_angle_d0.49151997
X-RAY DIFFRACTIONf_dihedral_angle_d13.00213760
X-RAY DIFFRACTIONf_chiral_restr0.0425665
X-RAY DIFFRACTIONf_plane_restr0.0046792
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.20.33331970.30923587X-RAY DIFFRACTION97
3.2-3.240.33172090.29833669X-RAY DIFFRACTION99
3.24-3.280.35511760.29373703X-RAY DIFFRACTION98
3.28-3.320.33021900.29063675X-RAY DIFFRACTION99
3.32-3.370.33161830.28773698X-RAY DIFFRACTION98
3.37-3.410.31922010.27863687X-RAY DIFFRACTION99
3.41-3.460.33831810.27583719X-RAY DIFFRACTION99
3.46-3.510.29171780.26323662X-RAY DIFFRACTION99
3.51-3.570.29972040.25483661X-RAY DIFFRACTION99
3.57-3.630.29591850.25093704X-RAY DIFFRACTION99
3.63-3.690.30471870.25013700X-RAY DIFFRACTION99
3.69-3.750.31122150.24873682X-RAY DIFFRACTION99
3.75-3.830.29991820.23333694X-RAY DIFFRACTION99
3.83-3.90.26941870.22143712X-RAY DIFFRACTION99
3.9-3.990.23951870.20383717X-RAY DIFFRACTION99
3.99-4.080.25571910.19283647X-RAY DIFFRACTION99
4.08-4.180.23291970.19133741X-RAY DIFFRACTION99
4.18-4.290.2451610.20013707X-RAY DIFFRACTION99
4.29-4.420.26142030.19433702X-RAY DIFFRACTION99
4.42-4.560.2292220.18113659X-RAY DIFFRACTION99
4.56-4.720.22221900.17463749X-RAY DIFFRACTION99
4.72-4.910.22111860.17163647X-RAY DIFFRACTION99
4.91-5.120.24371670.18183766X-RAY DIFFRACTION99
5.13-5.390.23791990.19423679X-RAY DIFFRACTION99
5.39-5.720.26781970.20253717X-RAY DIFFRACTION99
5.72-6.150.24741980.21053696X-RAY DIFFRACTION99
6.15-6.750.26882270.22563666X-RAY DIFFRACTION99
6.75-7.670.26262420.21683646X-RAY DIFFRACTION99
7.68-9.490.20872120.18163691X-RAY DIFFRACTION99
9.49-19.970.25011970.18933607X-RAY DIFFRACTION97
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)
15.6028-4.8105-3.23394.12772.88622.8309-0.5904-0.62543.0289-1.73370.015-0.7876-1.9193-0.91980.43281.14780.0984-0.22210.9737-0.01231.3092-20.91966.5922-2.1353
26.4543-3.3491-0.76834.56852.00663.5580.83740.24610.051-0.8854-0.1715-0.4333-0.11830.4704-0.43470.62820.08370.12990.7113-0.02630.557-0.3497-7.4833-13.5606
32.34981.48542.09142.2340.18962.4337-0.09220.2403-0.1006-0.2140.1842-0.20180.0130.2362-0.08670.4120.1760.20670.7865-0.01030.6112.2932-4.07571.17
43.24920.27211.39384.3988-1.08284.0556-0.05420.3780.3528-0.3457-0.2193-0.3973-0.08180.29530.19890.42560.14440.13620.70540.06140.55850.67317.4296-4.8514
50.24410.1987-0.46131.28921.26961.61820.01830.481-0.35560.0917-0.1437-0.30550.49360.61920.0940.54580.26420.18911.0325-0.05361.034813.5808-5.66681.9711
62.84112.0808-0.74285.91913.61563.9431-0.21170.1437-0.2571-1.0495-0.67951.3783-1.52030.19410.5760.3774-0.01060.08580.75610.04260.56282.317611.27820.027
74.72794.78122.67948.93463.4769.926-0.2085-0.6919-0.33651.1285-0.4320.34162.2256-0.47750.07160.63260.23340.21970.68170.0080.7974-1.7544-8.39265.8718
84.3211-0.6904-0.1954.0879-1.79152.8125-0.3013-0.17630.07540.5056-0.4725-0.7896-0.03820.86130.65080.4802-0.1185-0.1230.4804-0.02260.6521-10.091436.0751-8.5064
91.91681.1205-0.80616.7912-5.34614.1812-0.87790.77880.7152-1.48761.63372.4508-1.3360.4191-0.08611.0287-0.2321-0.14080.96720.08180.7851-18.361754.6827-37.65
102.82870.85132.45353.0842-1.82857.73970.337-0.13070.1699-0.07110.1505-0.33560.10590.7043-0.32410.37390.04910.07210.6083-0.01130.5232-14.383843.2462-13.6842
114.53941.3037-0.37823.9521-2.2221.96740.00710.1123-0.3702-0.3603-0.0292-0.059-0.388-0.220.18080.46320.01320.02170.5812-0.08290.3791-26.25744.0829-17.3169
126.853-2.4483-0.794.1868-0.87496.6882-0.2843-0.481-0.2089-0.00420.4337-0.1265-0.1957-0.466-0.45030.2995-0.0248-0.01150.4672-0.0320.4973-36.553940.2525-12.9749
139.458-0.3674-0.14463.48680.25244.4953-0.03360.3908-0.8964-0.1961-0.09490.09180.74970.16910.22480.3867-0.01970.07220.58540.00530.5308-17.378431.1438-12.2974
143.4473-0.99672.11814.48-6.12118.15650.25580.4325-0.8243-0.6392-0.6549-0.15531.21-0.13490.39040.5685-0.08160.14350.7711-0.1410.8003-18.524524.0877-17.5875
158.4736-0.83991.56094.2268-1.09115.9643-0.2380.25251.318-0.28070.15860.5748-0.532-1.05480.19110.46420.0715-0.060.6970.09230.5576-38.590848.9875-21.2997
163.97730.7862-0.28048.4963-1.60543.11630.25790.7908-0.0206-1.0472-0.16560.7220.11690.1025-0.12060.38520.1115-0.06870.5421-0.0740.3861-31.901537.647-20.6022
172.85531.560.87437.9057-0.60243.47750.0881-0.3097-0.09120.3645-0.506-0.1379-0.1331-0.41890.30690.20420.10390.06830.71810.0730.5488-26.442537.7758-10.8008
183.82530.95820.85393.85785.22167.89180.0632-0.1351-0.1319-1.3988-0.13790.2684-0.9516-0.37460.20130.460.0474-0.0840.55920.14680.5957-42.9081-15.06768.1593
192.1110.227-0.96492.4846-0.40551.98260.16020.03450.0699-0.32370.03080.1850.2235-0.1455-0.21820.4147-0.0106-0.05450.4837-0.07050.4734-32.0707-17.1026.085
203.74341.1165-1.0942.8751-0.80992.79030.01730.52320.0033-0.46630.0237-0.09140.3005-0.0811-0.04020.4429-0.0225-0.00710.6143-0.10140.4723-28.9438-13.4659-2.1978
212.58242.86830.62826.7141-1.63627.1620.9692-0.64260.29080.9289-0.3441-0.79740.01840.5349-0.59730.4466-0.01090.17560.5818-0.13150.6545-27.2859-13.865212.9357
227.76055.0063-2.51896.2785-0.97973.18870.14480.151-0.59710.8451-0.1614-0.52570.12130.2730.14540.47650.0746-0.11980.5866-0.09110.6691.279757.461321.3629
232.04190.42650.37711.570.10373.15450.0701-0.1210.01410.1604-0.0619-0.19980.08630.3744-0.06710.3044-0.02970.02240.47140.00760.5638-2.858854.044613.228
242.20730.41770.36711.45031.62285.11720.10570.18490.10840.1249-0.0185-0.0509-0.34210.2958-0.0430.375-0.06220.07070.51490.09780.5845-5.262557.3242.5757
256.3063.51720.97153.76194.13728.02160.8437-1.00950.17611.1093-0.8027-0.2850.4553-0.1784-0.26330.34310.03770.00330.44360.11410.5808-14.273858.268510.8196
265.35563.85153.22633.75-0.96136.4215-0.17430.42280.1059-0.17080.0793-0.1884-0.51540.09180.04540.4050.08730.12590.7430.06120.773616.722512.557518.7842
271.65450.7374-0.87461.3556-1.11212.84730.03080.03750.04310.4588-0.1287-0.6209-0.12040.29320.07650.41570.0616-0.17670.70110.09410.795412.53311.72935.2448
288.69966.9874-3.86619.2124-3.06254.66140.39960.48861.1760.79840.11870.4166-0.57440.5523-0.46340.59740.04840.00120.9321-0.00840.7459-38.12244.685846.6452
293.69112.04880.73456.15330.56551.95660.0272-0.71950.3750.2524-0.13621.36850.4159-0.53760.05860.5785-0.06310.22110.93760.00640.4737-42.0991-9.046150.4743
300.92910.35731.01733.07471.14362.2639-0.00360.0211-0.11540.29430.12310.31420.24720.1246-0.05230.4098-0.04940.04520.50630.05810.5841-36.4907-12.411338.4061
311.10230.4521-0.20775.8704-0.33145.541-0.21450.1653-0.0194-0.0629-0.11770.8077-0.2557-0.92440.31220.4380.04590.0710.8025-0.0540.7486-46.7922.151738.0007
322.7562-2.13010.5315.71711.4893.90940.25330.121-0.3587-0.26210.195-0.11820.58750.0976-0.52330.6125-0.1889-0.01470.53130.05160.6032-37.8497-27.828232.891
333.9008-0.9049-0.16228.2201-0.86877.63760.2375-0.1555-0.63621.3660.02810.85740.2508-1.0173-0.39490.4946-0.13680.00680.6660.01650.6914-44.144-16.588134.7452
349.0224-1.75725.46059.0305-0.24194.4748-0.4687-0.7645-0.4-0.4556-0.2290.5641-1.1182-0.57450.94920.48550.0223-0.02220.871-0.05140.4985-42.9197-1.594831.0132
355.40122.6328-4.18164.5889-5.25836.61960.0593-1.1436-0.5321.1215-1.2324-1.5836-0.99131.77040.66070.5786-0.00550.04870.5056-0.03930.4237-29.4485-13.603839.2556
360.80160.50331.54252.9484-0.59534.1276-0.175-0.31361.47160.44330.8209-1.31740.51050.4162-0.3230.4339-0.0740.05750.82280.29540.9214-63.35929.470829.87
373.1252-0.172-1.75125.210.87073.3647-0.09450.2204-0.38710.7145-0.08380.58760.3177-0.71-0.02250.50040.08090.13020.87580.06360.7362-62.184633.857428.3085
382.54520.03850.11173.09730.09851.75510.0563-0.1411-0.07650.26670.21650.1062-0.1543-0.5406-0.16490.44840.11110.23520.85350.09490.6504-53.189839.19535.546
399.3597-6.49213.05166.1653-2.17223.20640.0843-1.0135-1.69730.47710.63731.16540.3917-0.2265-0.59790.6744-0.06080.08960.79210.13710.8671-52.390823.947943.1644
402.81821.78190.61274.22621.73550.4617-0.1071-0.16080.12420.84750.03070.9441-0.4072-0.35180.02150.55520.12610.23780.7373-0.02860.5858-53.488346.258142.3386
414.45611.29390.84030.7597-0.82988.7235-0.1221.1282-0.070.0271-0.24670.3943-0.2606-0.21960.12050.41650.14810.17110.6966-0.02790.5782-52.627342.186726.1002
425.9257-2.30611.64063.2499-0.65053.46750.20430.1639-0.8178-0.4449-0.03270.450.1726-0.6034-0.17370.4533-0.08270.00360.7935-0.12010.6227-53.096928.6916-11.4029
430.4121-0.3869-1.46064.21361.40584.1884-0.0776-0.0833-0.33020.3503-0.00930.45630.1612-0.55580.04770.2484-0.0045-0.00790.7936-0.00030.6735-55.41729.10795.5796
448.0962-5.8947.53024.9376-5.40248.75030.09360.0723-1.5913-1.39420.68561.38351.829-1.0947-0.28380.4748-0.16340.01610.8932-0.02721.1484-55.263512.98021.7513
453.4159-2.44360.19442.01331.26231.31120.0280.19340.13370.11540.05480.9503-0.1815-0.4829-0.1060.42640.07710.02280.94070.03130.9202-66.305937.09664.4565
461.02890.67320.13396.9645-4.22966.10810.0964-0.34510.4427-0.2358-0.08920.70340.42250.55950.05220.39380.1618-0.03740.6596-0.17230.7342-53.00629.53513.8306
471.19891.174-0.81292.37650.70617.71610.0831-0.12940.45920.30760.0509-0.1268-0.74270.52420.15090.4435-0.0315-0.04850.56980.06380.8579-1.618213.61658.548
483.30811.2367-0.28393.2548-0.34521.48730.0633-0.338-0.00670.3594-0.0256-0.29190.0430.2063-0.06220.62870.0068-0.20110.59520.030.4127-9.04847.110354.9042
493.2593-0.50340.13816.8186-0.61721.3390.2725-0.4327-0.15670.9042-0.1824-0.02020.0924-0.2378-0.09060.8331-0.1059-0.10050.64780.05690.4207-17.00550.56259.7874
507.6648-0.9653-1.44752.47481.56441.11140.6999-1.1215-1.52670.3919-0.66260.50630.21650.48470.0050.9362-0.1055-0.16110.79650.24030.5495-13.5074-2.026363.7431
514.62951.91941.63688.9196-0.08769.29710.1063-0.53420.24570.0758-0.01311.0692-0.6954-0.3178-0.08140.6023-0.0348-0.01910.65050.1580.5704-26.264410.042656.6744
527.7627-3.8801-1.63886.34273.12141.47010.3270.81520.48210.1659-0.2703-0.169-0.06360.0195-0.03190.50370.0575-0.03710.61520.08740.4215-12.22476.665848.1348
533.52460.04270.38998.41273.4725.3229-0.1932-0.0781-0.32190.32690.7961-0.36380.41710.4737-0.50930.69090.0590.02630.77020.11490.6903-30.266749.44251.3142
543.94841.57430.80543.021-1.5433.1310.1447-0.1165-0.14420.370.1219-0.4045-0.36350.1313-0.25080.57810.00150.19610.7518-0.08570.442-30.022653.970150.7971
553.3862-0.5661-1.33654.07990.62743.6723-0.23270.10070.05490.62420.07280.16290.0702-0.41060.05290.41990.06150.02410.5134-0.03960.3765-25.158556.494738.8504
562.9503-0.094-0.84252.3390.77241.54530.2626-0.3413-0.44761.305-0.43280.43380.1659-0.09120.13450.70170.01350.04540.82120.07450.3649-21.884643.521245.9303
575.62250.2222-1.9664.52170.03830.8846-0.2815-1.2187-1.01941.0883-0.391-1.1464-1.23590.62520.1930.9762-0.0495-0.31530.6767-0.03010.41-13.874442.250649.6936
581.4212.9675-1.0677.53-3.88513.05680.39410.02970.49450.09780.46211.2997-0.2701-0.8105-0.58210.76740.07770.16260.5833-0.07260.8006-20.341470.883435.2009
594.8534-1.2785-0.34862.0552-0.43443.7042-0.3878-0.51760.23651.2225-0.48550.2772-0.19830.23920.65820.579-0.09860.01440.5736-0.04860.5865-16.085659.809441.3444
603.21071.02551.66315.09530.13622.5449-0.1648-0.1531-0.28680.1250.1798-0.23360.01710.1566-0.04440.5380.06020.10880.5466-0.00230.3368-21.358951.618837.6577
612.1754-0.7668-0.8472.14090.28682.1617-0.06780.2194-0.1038-0.30130.11520.3280.32570.0139-0.03470.8476-0.0596-0.24060.52440.05190.60765.603110.785395.9756
622.53240.3549-0.86193.14931.69572.73190.0509-0.05820.0857-0.1930.04330.40690.1259-0.2302-0.06110.7332-0.0097-0.20830.62630.06230.59952.881815.7469106.1931
635.3052.08330.97229.69690.45923.52290.505-0.5072-0.16441.7938-0.6108-0.1118-0.0992-0.7687-0.31540.80240.1584-0.14270.88140.06670.5355-37.140451.1432-42.3387
642.17551.2285-0.84344.4084-2.13252.11490.2763-0.29280.30210.0554-0.6713-0.4187-0.1610.05790.28370.88270.1753-0.19820.7734-0.17910.7009-37.02254.5572-44.2761
651.50640.6785-0.61142.82420.34874.026-0.0893-0.220.3517-0.2041-0.1315-0.2292-0.48840.00960.12370.886-0.0034-0.24470.575-0.06030.6127-32.794751.6142-55.4905
661.84670.8624-1.42534.8929-2.42181.3687-0.13590.13690.4677-0.4238-0.0395-0.6159-0.6899-0.2560.20221.24520.0021-0.19380.4456-0.17051.1425-31.75568.5171-61.5512
674.66223.6940.19265.34832.82342.89370.286-0.6512-0.0849-0.4906-0.8437-0.99090.5451.60390.1331.0096-0.0674-0.19730.82970.00230.7353-20.847447.7838-61.2625
684.7231-2.9295-1.47185.05333.13425.3083-0.24840.3817-0.18850.0146-0.27520.18980.1776-0.52760.41710.9736-0.0986-0.19730.42620.03870.6503-37.501749.441-59.226
693.7263-0.1275-3.12896.42945.24615.9232-0.068-0.4750.12320.57770.4711-1.06911.6077-0.08160.11881.11890.2757-0.11910.86810.04540.606-71.520725.2508-52.075
708.3189-1.1843-1.98314.15722.06344.58650.89320.8699-0.07121.207-1.89211.20310.1159-2.28770.38020.92920.21720.23471.0863-0.00660.757-84.768645.6664-34.5528
711.84280.8472-0.25754.064-0.15840.572-0.02140.03750.12120.359-0.02020.21590.0493-0.025-0.00510.79520.0635-0.09940.5421-0.09310.4843-67.465437.239-49.9322
726.29160.22112.25082.8961-1.66182.3448-0.7249-0.8253-0.76910.73540.90310.08770.7861-0.80350.03831.62610.10770.13710.94050.01570.5868-61.099825.8752-38.9536
732.4425-0.1831-0.58216.72220.99452.8832-0.13-0.36860.57710.6940.10350.504-0.5375-0.28830.11460.88830.1352-0.09680.7056-0.24520.7587-64.145352.5055-43.7109
743.1334-2.90520.39295.4796-3.07953.5608-0.9443-0.5796-0.1234-0.54880.0899-0.3707-0.4149-0.22631.08570.8604-0.0667-0.19480.62330.01330.6238-54.775232.8903-43.129
755.5537-2.7451-0.81572.96930.01013.1053-0.20620.90091.13730.32450.2887-0.72290.0617-0.1759-0.18171.07660.1018-0.20370.5447-0.09390.6974-68.973144.1992-57.4122
764.7699-1.9299-1.04040.61650.02973.147-0.3447-0.0469-0.84680.6610.33290.24560.1581-0.08030.19110.9928-0.09030.03650.5177-0.07630.9115-35.642836.04195.6947
773.62220.88472.3112.9810.98063.4865-0.03560.07520.247-0.32570.0876-0.04150.5568-0.0480.0450.9369-0.17670.02050.5360.12520.5903-46.307935.87291.3202
785.43412.5838-0.17058.7848-3.87977.49120.42170.2312-0.3337-0.4934-0.6588-0.5784-0.12571.58340.06760.8262-0.06060.11890.72930.03260.7837-37.078824.122290.6217
791.9943-1.16371.20123.07370.05113.3037-0.36540.41960.6173-0.47920.2015-0.1615-0.30780.10650.09921.2264-0.2226-0.07330.83230.22390.7299-50.14739.652378.2601
803.5687-2.091-0.55966.01034.4044.6955-0.03740.3489-0.1570.05280.04230.18910.4887-0.2675-0.05731.1918-0.2314-0.17810.6950.22610.6467-48.535130.004889.5297
813.46721.7206-3.70156.5005-2.82236.5551-1.2351-0.402-0.2445-0.42160.8726-1.91880.6068-0.61360.41581.3431-0.1266-0.18290.5617-0.1331.0616-59.82614.386772.2015
826.8193-1.48932.23741.628-0.08074.77761.1287-0.1428-0.8091-0.0060.13940.1892-0.21670.4765-0.49741.0964-0.27040.10470.86880.11720.5675-64.360618.983466.9203
834.4438-0.40870.47964.7096-2.02985.756-0.67350.68820.5086-0.88180.4849-0.202-1.1256-0.9290.25931.1716-0.2468-0.08851.01310.0250.4793-65.383924.734870.9524
845.7698-0.9211-0.83042.4818-1.7571.5116-0.2830.6468-0.2105-0.13170.0040.2058-0.4667-0.1680.28221.213-0.2054-0.30510.88760.05690.5993-82.539418.317678.4458
855.2384-2.1921-2.86395.5842-0.25783.8381-0.6122-0.0664-0.6286-1.23010.61070.55420.96930.1730.02441.2494-0.09970.01550.7772-0.0610.5611-66.80524.915274.9764
869.51-3.53792.33382.455-1.2110.86580.21382.05210.601-0.6292-0.7898-0.58730.15630.67230.6171.768-0.1887-0.21260.92790.17580.5971-86.049718.718172.5453
873.28972.10353.63297.19-0.45115.4498-0.1694-0.64960.3888-2.1067-0.57280.8076-0.69050.1960.49471.4045-0.1538-0.47160.76710.1981.0421-93.872531.66372.5879
883.8718-1.22270.02840.3338-0.84692.0383-0.46720.75430.0437-1.10710.47730.0892-0.0127-0.05350.1091.4317-0.2824-0.24180.86670.11290.5624-81.128512.935572.8051
894.92151.88851.85623.92871.0662.7597-0.4719-0.08740.2218-0.3857-0.7313-0.6761-0.61540.99440.85971.04060.0125-0.02920.81380.04110.4841-72.08725.193981.1692
904.36174.05942.31277.33846.49225.2377-0.8247-0.43370.5897-1.83730.35781.7029-1.2633-0.45380.42091.23170.1932-0.05310.86330.13930.892918.1451-34.1445110.0089
913.49570.7676-0.68072.83651.13112.4029-0.1262-0.2144-0.1375-0.54630.03730.1308-0.60540.0189-0.01841.4273-0.02540.0330.49590.08860.80126.5894-36.0997106.5721
920.8208-1.0092-0.22311.74580.84052.15750.02150.0770.0092-0.80930.2349-0.0873-0.3926-0.0973-0.3271.6578-0.23770.17740.70350.00070.811430.6107-30.1147100.8437
933.06190.9091-0.61220.5118-0.54640.4198-0.54190.4616-0.129-0.82510.21940.3357-0.0754-0.07580.22671.6747-0.13910.04150.6042-0.00560.779231.0089-36.181497.3102
941.76881.26041.17970.7598-2.24944.5949-0.41860.27480.1061-1.05040.22510.3966-0.0883-0.2296-0.04741.7626-0.01860.05310.706-0.10380.777431.7596-32.597298.739
953.8854.2392-2.9656.7325-2.65872.27540.10050.33810.97830.75620.53271.5912-0.1097-0.5292-0.06111.59870.16910.08271.0278-0.13650.804-47.25880.4935-35.511
963.35672.27053.25874.55782.26332.8267-0.0386-0.60970.07910.0805-0.18740.0671-0.0874-0.36380.22171.20650.04950.19030.6356-0.00330.5477-48.7287-12.0548-43.7492
971.45720.3990.65725.866-2.07562.4311-0.5449-0.19180.38291.14170.47131.12040.1682-0.33190.01331.39260.09230.17510.7028-0.09750.7876-57.0873-3.2343-42.6506
981.41190.2601-0.03063.79050.765-0.42870.0452-0.3881-0.03220.4017-0.23910.31370.126-0.04740.16291.50110.02020.21150.73980.02640.6432-52.7886-16.0539-45.5884
994.949-5.50755.53119.2121-6.85826.0445-0.71250.02411.1893-0.5105-0.2273-1.0832-0.137-0.55931.37631.47250.10230.22691.050.12921.09-13.279719.0899-49.9996
1003.81560.95652.61344.606-1.89666.8651-0.57590.38280.8339-0.5635-0.2278-0.6485-0.24540.80440.61931.10050.15350.20820.8135-0.00270.8446-10.459910.9668-46.759
1012.7612.4355-0.51924.5917-2.54472.889-0.2530.1875-0.1956-0.0087-0.01220.06680.12580.12110.2951.34150.17510.02010.7686-0.05050.6558-21.84597.2276-39.2246
1024.3309-1.27920.0783.4436-1.6719-0.1409-0.0086-0.75440.20040.9057-0.2204-0.2139-0.21980.24960.20361.32960.1139-0.01040.92050.04050.7378-23.37252.2091-34.6343
1035.3492-0.1221-1.35672.1418-0.46698.026-1.20911.5005-1.8518-1.47720.0835-0.02740.80790.13330.5491.9979-0.14940.14250.47890.10750.8938-17.8905-1.7641-48.043
1043.56470.1952.35162.7280.5676-0.20860.36190.2721-0.1632-0.1541-0.18750.11260.26040.1446-0.21541.743-0.10080.40140.77240.04120.7985-51.7264-25.896282.3251
1057.2261-1.53083.74423.4182-3.59333.6412-0.6376-0.01320.3101-0.48740.4354-0.7481-0.3177-0.40040.3132.2289-0.42950.40540.8269-0.10970.9738-46.2109-18.587685.4504
1064.67591.12191.6632-0.25220.83230.06160.03350.5587-0.2244-0.0094-0.1754-0.1485-0.11180.17870.09921.6774-0.11170.48110.9242-0.01770.8176-39.5747-23.386883.6741
1076.0505-3.29562.35994.4725-1.71964.23731.0887-1.5270.7347-0.1426-0.3237-1.32641.3188-0.082-0.28852.0928-0.18670.33830.488-0.00711.2448-22.0484-4.112192.5086
1080.3903-0.92160.6561.8169-1.31693.5433-0.28840.82350.1711-0.2503-0.104-0.3928-0.254-0.30050.3461.5556-0.11150.36811.05840.05091.1038-21.1918-6.946592.9783
1093.7849-1.62131.50211.79460.72522.516-0.18571.0109-0.2997-1.14-0.0041-1.26970.57170.31060.0041.9139-0.00880.45760.89830.17931.0983-27.1131-12.198795.2667
1108.51630.73646.42414.7853.70256.94092.1345-0.71930.25390.55741.0468-0.6577-0.23450.14570.06191.67990.00760.84381.18040.3861.129-14.371-14.943894.8788
1112.65880.34161.82110.01040.67754.4468-0.275-0.02910.0861-0.26540.0627-0.2926-0.27120.22760.36961.6686-0.01020.38860.7224-0.01281.1602-24.8769-5.6438110.064
1122.8995-0.0668-0.872.4797-1.59355.27230.3413-0.02750.3715-1.8515-0.60970.04170.79910.9930.20131.9456-0.21050.30070.85910.27131.2934-19.40310.262107.9804
1130.79680.08891.08455.0374-4.96126.6365-0.1928-0.1562-0.07741.312-0.90740.3147-0.8730.00170.8611.15640.01750.27021.001-0.25541.3714-12.4897-16.6626113.491
1143.50280.945-0.23152.24533.68527.6278-0.44920.04680.1351-1.71120.4416-0.4508-0.92770.2727-0.01451.4052-0.08910.3670.81340.15490.7922-26.75270.8143110.5217
1155.69360.22334.59861.72733.0868.069-1.65520.27390.0723-2.76130.5195-0.9062-0.1663-0.52740.43062.0809-0.5090.61530.65020.30451.0222-26.8353-17.8515105.0548
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 175 )
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 284 )
7X-RAY DIFFRACTION7chain 'A' and (resid 285 through 301 )
8X-RAY DIFFRACTION8chain 'B' and (resid 8 through 27 )
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 80 )
11X-RAY DIFFRACTION11chain 'B' and (resid 81 through 107 )
12X-RAY DIFFRACTION12chain 'B' and (resid 108 through 127 )
13X-RAY DIFFRACTION13chain 'B' and (resid 128 through 149 )
14X-RAY DIFFRACTION14chain 'B' and (resid 150 through 163 )
15X-RAY DIFFRACTION15chain 'B' and (resid 164 through 207 )
16X-RAY DIFFRACTION16chain 'B' and (resid 208 through 229 )
17X-RAY DIFFRACTION17chain 'B' and (resid 230 through 300 )
18X-RAY DIFFRACTION18chain 'C' and (resid 7 through 37 )
19X-RAY DIFFRACTION19chain 'C' and (resid 38 through 128 )
20X-RAY DIFFRACTION20chain 'C' and (resid 129 through 242 )
21X-RAY DIFFRACTION21chain 'C' and (resid 243 through 300 )
22X-RAY DIFFRACTION22chain 'D' and (resid 8 through 37 )
23X-RAY DIFFRACTION23chain 'D' and (resid 38 through 163 )
24X-RAY DIFFRACTION24chain 'D' and (resid 164 through 288 )
25X-RAY DIFFRACTION25chain 'D' and (resid 289 through 300 )
26X-RAY DIFFRACTION26chain 'E' and (resid 9 through 93 )
27X-RAY DIFFRACTION27chain 'E' and (resid 94 through 300 )
28X-RAY DIFFRACTION28chain 'F' and (resid 9 through 27 )
29X-RAY DIFFRACTION29chain 'F' and (resid 28 through 63 )
30X-RAY DIFFRACTION30chain 'F' and (resid 64 through 128 )
31X-RAY DIFFRACTION31chain 'F' and (resid 129 through 163 )
32X-RAY DIFFRACTION32chain 'F' and (resid 164 through 206 )
33X-RAY DIFFRACTION33chain 'F' and (resid 207 through 228 )
34X-RAY DIFFRACTION34chain 'F' and (resid 229 through 285 )
35X-RAY DIFFRACTION35chain 'F' and (resid 286 through 300 )
36X-RAY DIFFRACTION36chain 'G' and (resid 8 through 37 )
37X-RAY DIFFRACTION37chain 'G' and (resid 38 through 80 )
38X-RAY DIFFRACTION38chain 'G' and (resid 81 through 149 )
39X-RAY DIFFRACTION39chain 'G' and (resid 150 through 163 )
40X-RAY DIFFRACTION40chain 'G' and (resid 164 through 242 )
41X-RAY DIFFRACTION41chain 'G' and (resid 243 through 299 )
42X-RAY DIFFRACTION42chain 'H' and (resid 9 through 94 )
43X-RAY DIFFRACTION43chain 'H' and (resid 95 through 149 )
44X-RAY DIFFRACTION44chain 'H' and (resid 150 through 163 )
45X-RAY DIFFRACTION45chain 'H' and (resid 164 through 229 )
46X-RAY DIFFRACTION46chain 'H' and (resid 230 through 300 )
47X-RAY DIFFRACTION47chain 'I' and (resid 8 through 37 )
48X-RAY DIFFRACTION48chain 'I' and (resid 38 through 149 )
49X-RAY DIFFRACTION49chain 'I' and (resid 150 through 205 )
50X-RAY DIFFRACTION50chain 'I' and (resid 206 through 222 )
51X-RAY DIFFRACTION51chain 'I' and (resid 223 through 235 )
52X-RAY DIFFRACTION52chain 'I' and (resid 236 through 300 )
53X-RAY DIFFRACTION53chain 'J' and (resid 9 through 37 )
54X-RAY DIFFRACTION54chain 'J' and (resid 38 through 63 )
55X-RAY DIFFRACTION55chain 'J' and (resid 64 through 127 )
56X-RAY DIFFRACTION56chain 'J' and (resid 128 through 149 )
57X-RAY DIFFRACTION57chain 'J' and (resid 150 through 163 )
58X-RAY DIFFRACTION58chain 'J' and (resid 164 through 207 )
59X-RAY DIFFRACTION59chain 'J' and (resid 208 through 228 )
60X-RAY DIFFRACTION60chain 'J' and (resid 229 through 300 )
61X-RAY DIFFRACTION61chain 'K' and (resid 9 through 149 )
62X-RAY DIFFRACTION62chain 'K' and (resid 150 through 301 )
63X-RAY DIFFRACTION63chain 'L' and (resid 9 through 37 )
64X-RAY DIFFRACTION64chain 'L' and (resid 38 through 63 )
65X-RAY DIFFRACTION65chain 'L' and (resid 64 through 175 )
66X-RAY DIFFRACTION66chain 'L' and (resid 176 through 222 )
67X-RAY DIFFRACTION67chain 'L' and (resid 223 through 235 )
68X-RAY DIFFRACTION68chain 'L' and (resid 236 through 301 )
69X-RAY DIFFRACTION69chain 'M' and (resid 9 through 27 )
70X-RAY DIFFRACTION70chain 'M' and (resid 28 through 47 )
71X-RAY DIFFRACTION71chain 'M' and (resid 48 through 149 )
72X-RAY DIFFRACTION72chain 'M' and (resid 150 through 163 )
73X-RAY DIFFRACTION73chain 'M' and (resid 164 through 228 )
74X-RAY DIFFRACTION74chain 'M' and (resid 229 through 283 )
75X-RAY DIFFRACTION75chain 'M' and (resid 284 through 300 )
76X-RAY DIFFRACTION76chain 'N' and (resid 9 through 47 )
77X-RAY DIFFRACTION77chain 'N' and (resid 48 through 127 )
78X-RAY DIFFRACTION78chain 'N' and (resid 128 through 163 )
79X-RAY DIFFRACTION79chain 'N' and (resid 164 through 229 )
80X-RAY DIFFRACTION80chain 'N' and (resid 230 through 301 )
81X-RAY DIFFRACTION81chain 'O' and (resid 11 through 27 )
82X-RAY DIFFRACTION82chain 'O' and (resid 28 through 62 )
83X-RAY DIFFRACTION83chain 'O' and (resid 63 through 94 )
84X-RAY DIFFRACTION84chain 'O' and (resid 95 through 132 )
85X-RAY DIFFRACTION85chain 'O' and (resid 133 through 163 )
86X-RAY DIFFRACTION86chain 'O' and (resid 164 through 175 )
87X-RAY DIFFRACTION87chain 'O' and (resid 176 through 203 )
88X-RAY DIFFRACTION88chain 'O' and (resid 204 through 242 )
89X-RAY DIFFRACTION89chain 'O' and (resid 243 through 301 )
90X-RAY DIFFRACTION90chain 'P' and (resid 9 through 37 )
91X-RAY DIFFRACTION91chain 'P' and (resid 38 through 112 )
92X-RAY DIFFRACTION92chain 'P' and (resid 113 through 140 )
93X-RAY DIFFRACTION93chain 'P' and (resid 141 through 208 )
94X-RAY DIFFRACTION94chain 'P' and (resid 209 through 300 )
95X-RAY DIFFRACTION95chain 'Q' and (resid 8 through 63 )
96X-RAY DIFFRACTION96chain 'Q' and (resid 64 through 127 )
97X-RAY DIFFRACTION97chain 'Q' and (resid 128 through 175 )
98X-RAY DIFFRACTION98chain 'Q' and (resid 176 through 300 )
99X-RAY DIFFRACTION99chain 'R' and (resid 11 through 27 )
100X-RAY DIFFRACTION100chain 'R' and (resid 28 through 80 )
101X-RAY DIFFRACTION101chain 'R' and (resid 81 through 175 )
102X-RAY DIFFRACTION102chain 'R' and (resid 176 through 284 )
103X-RAY DIFFRACTION103chain 'R' and (resid 285 through 301 )
104X-RAY DIFFRACTION104chain 'S' and (resid 9 through 112 )
105X-RAY DIFFRACTION105chain 'S' and (resid 113 through 149 )
106X-RAY DIFFRACTION106chain 'S' and (resid 150 through 301 )
107X-RAY DIFFRACTION107chain 'T' and (resid 17 through 27 )
108X-RAY DIFFRACTION108chain 'T' and (resid 28 through 62 )
109X-RAY DIFFRACTION109chain 'T' and (resid 63 through 81 )
110X-RAY DIFFRACTION110chain 'T' and (resid 82 through 94 )
111X-RAY DIFFRACTION111chain 'T' and (resid 95 through 149 )
112X-RAY DIFFRACTION112chain 'T' and (resid 150 through 175 )
113X-RAY DIFFRACTION113chain 'T' and (resid 176 through 222 )
114X-RAY DIFFRACTION114chain 'T' and (resid 223 through 284 )
115X-RAY DIFFRACTION115chain 'T' and (resid 285 through 300 )

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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