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- PDB-6xlq: Crystal Structure of the Human BTN3A1 Ectodomain in Complex with ... -

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基本情報

登録情報
データベース: PDB / ID: 6xlq
タイトルCrystal Structure of the Human BTN3A1 Ectodomain in Complex with the CTX-2026 Fab
要素
  • Butyrophilin subfamily 3 member A1
  • CTX-2026 Heavy Chain
  • CTX-2026 Light Chain
キーワードIMMUNE SYSTEM / Gamma/Delta T cell Activation Alpha/Beta T cell Suppression
機能・相同性
機能・相同性情報


Butyrophilin (BTN) family interactions / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / signaling receptor binding / external side of plasma membrane / plasma membrane
類似検索 - 分子機能
Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Butyrophilin subfamily 3 member A1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3 Å
データ登録者Payne, K.K. / Mine, J.A. / Biswas, S. / Chaurio, R.A. / Perales-Puchalt, A. / Anadon, C.M. / Costich, T.L. / Harro, C.M. / Walrath, J. / Ming, Q. ...Payne, K.K. / Mine, J.A. / Biswas, S. / Chaurio, R.A. / Perales-Puchalt, A. / Anadon, C.M. / Costich, T.L. / Harro, C.M. / Walrath, J. / Ming, Q. / Tcyganov, E. / Buras, A.L. / Rigolizzo, K.E. / Mandal, G. / Lajoie, J. / Ophir, M. / Tchou, J. / Marchion, D. / Luca, V.C. / Bobrowicz, P. / McLaughlin, B. / Eskiocak, U. / Schmidt, M. / Cubillos-Ruiz, J.R. / Rodriguez, P.C. / Gabrilovich, D.I. / Conejo-Garcia, J.R.
資金援助 米国, 5件
組織認可番号
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA157664 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA124515 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA178687 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA211913 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)U01CA232758 米国
引用ジャーナル: Science / : 2020
タイトル: BTN3A1 governs antitumor responses by coordinating alpha beta and gamma delta T cells.
著者: Payne, K.K. / Mine, J.A. / Biswas, S. / Chaurio, R.A. / Perales-Puchalt, A. / Anadon, C.M. / Costich, T.L. / Harro, C.M. / Walrath, J. / Ming, Q. / Tcyganov, E. / Buras, A.L. / Rigolizzo, K.E. ...著者: Payne, K.K. / Mine, J.A. / Biswas, S. / Chaurio, R.A. / Perales-Puchalt, A. / Anadon, C.M. / Costich, T.L. / Harro, C.M. / Walrath, J. / Ming, Q. / Tcyganov, E. / Buras, A.L. / Rigolizzo, K.E. / Mandal, G. / Lajoie, J. / Ophir, M. / Tchou, J. / Marchion, D. / Luca, V.C. / Bobrowicz, P. / McLaughlin, B. / Eskiocak, U. / Schmidt, M. / Cubillos-Ruiz, J.R. / Rodriguez, P.C. / Gabrilovich, D.I. / Conejo-Garcia, J.R.
履歴
登録2020年6月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年9月2日Provider: repository / タイプ: Initial release
改定 1.12023年10月18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
改定 1.22024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Butyrophilin subfamily 3 member A1
B: CTX-2026 Heavy Chain
C: CTX-2026 Light Chain
D: Butyrophilin subfamily 3 member A1
E: CTX-2026 Heavy Chain
F: CTX-2026 Light Chain
G: Butyrophilin subfamily 3 member A1
H: CTX-2026 Heavy Chain
I: CTX-2026 Light Chain
J: Butyrophilin subfamily 3 member A1
K: CTX-2026 Heavy Chain
L: CTX-2026 Light Chain


分子量 (理論値)分子数
合計 (水以外)284,69912
ポリマ-284,69912
非ポリマー00
48627
1
A: Butyrophilin subfamily 3 member A1
B: CTX-2026 Heavy Chain
C: CTX-2026 Light Chain


分子量 (理論値)分子数
合計 (水以外)71,1753
ポリマ-71,1753
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
2
D: Butyrophilin subfamily 3 member A1
E: CTX-2026 Heavy Chain
F: CTX-2026 Light Chain


分子量 (理論値)分子数
合計 (水以外)71,1753
ポリマ-71,1753
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
3
G: Butyrophilin subfamily 3 member A1
H: CTX-2026 Heavy Chain
I: CTX-2026 Light Chain


分子量 (理論値)分子数
合計 (水以外)71,1753
ポリマ-71,1753
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
4
J: Butyrophilin subfamily 3 member A1
K: CTX-2026 Heavy Chain
L: CTX-2026 Light Chain


分子量 (理論値)分子数
合計 (水以外)71,1753
ポリマ-71,1753
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)111.309, 159.850, 188.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21chain D
31chain G
41chain J
12chain B
22chain E
32chain H
42chain K
13chain C
23chain F
33chain I
43chain L

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPHEPHEchain AAA1 - 2131 - 213
21GLNGLNPHEPHEchain DDD1 - 2131 - 213
31GLNGLNPHEPHEchain GGG1 - 2131 - 213
41GLNGLNPHEPHEchain JJJ1 - 2131 - 213
12PCAPCAPROPROchain BBB1 - 2231 - 223
22PCAPCAPROPROchain EEE1 - 2231 - 223
32PCAPCAPROPROchain HHH1 - 2231 - 223
42PCAPCAPROPROchain KKK1 - 2231 - 223
13ASPASPGLYGLYchain CCC1 - 2121 - 212
23ASPASPGLYGLYchain FFF1 - 2121 - 212
33ASPASPGLYGLYchain III1 - 2121 - 212
43ASPASPGLYGLYchain LLL1 - 2121 - 212

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質
Butyrophilin subfamily 3 member A1


分子量: 24282.447 Da / 分子数: 4 / 断片: ectodomain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BTN3A1, BTF5 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O00481
#2: 抗体
CTX-2026 Heavy Chain


分子量: 23979.969 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#3: 抗体
CTX-2026 Light Chain


分子量: 22912.400 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 27 / 由来タイプ: 天然 / : H2O
研究の焦点であるリガンドがあるかN
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: 3.04 Å3/Da / 溶媒含有率: 59.56 %
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: 7.1 / 詳細: 100 mM Bis-Tris pH 7.1, 0.2 M NaBr, 17% PEG 3350 / PH範囲: 7.1

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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: APS / ビームライン: 17-ID / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年10月13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: 3→38.2 Å / Num. obs: 67082 / % possible obs: 98.9 % / 冗長度: 4.5 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 5.4
反射 シェル解像度: 3→3.11 Å / Rmerge(I) obs: 0.124 / Num. unique obs: 6381 / Rpim(I) all: 0.124 / Rrim(I) all: 0.176 / % possible all: 98.7

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
PDB_EXTRACT3.25データ抽出
MOSFLMデータ削減
MOSFLMデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4F80
解像度: 3→38.174 Å / SU ML: 0.49 / 交差検証法: THROUGHOUT / σ(F): 1.97 / 位相誤差: 32.78 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2957 3329 4.98 %
Rwork0.246 63551 -
obs0.2485 66880 98.43 %
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: 183.04 Å2 / Biso mean: 77.094 Å2 / Biso min: 8.94 Å2
精密化ステップサイクル: final / 解像度: 3→38.174 Å
タンパク質核酸リガンド溶媒全体
原子数19360 0 0 27 19387
Biso mean---29.04 -
残基数----2552
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsタイプ
11A2524X-RAY DIFFRACTION8.253TORSIONAL
12D2524X-RAY DIFFRACTION8.253TORSIONAL
13G2524X-RAY DIFFRACTION8.253TORSIONAL
14J2524X-RAY DIFFRACTION8.253TORSIONAL
21B2604X-RAY DIFFRACTION8.253TORSIONAL
22E2604X-RAY DIFFRACTION8.253TORSIONAL
23H2604X-RAY DIFFRACTION8.253TORSIONAL
24K2604X-RAY DIFFRACTION8.253TORSIONAL
31C2556X-RAY DIFFRACTION8.253TORSIONAL
32F2556X-RAY DIFFRACTION8.253TORSIONAL
33I2556X-RAY DIFFRACTION8.253TORSIONAL
34L2556X-RAY DIFFRACTION8.253TORSIONAL
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 (%)
3-3.04290.40611200.3695252895
3.0429-3.08830.39581160.3565255596
3.0883-3.13650.41400.3369255597
3.1365-3.18790.38221300.3321260798
3.1879-3.24290.34651520.3219258298
3.2429-3.30180.38691340.3125262898
3.3018-3.36530.38041280.3065265099
3.3653-3.43390.32741340.3079265399
3.4339-3.50850.33141330.2828262499
3.5085-3.59010.32551330.26162688100
3.5901-3.67980.36531340.2738263599
3.6798-3.77920.30661310.2742266199
3.7792-3.89030.34531550.2669264099
3.8903-4.01570.31271600.2532259398
4.0157-4.15910.29491430.216267499
4.1591-4.32540.28711090.19972713100
4.3254-4.5220.23331370.18452690100
4.522-4.760.22361490.17582682100
4.76-5.05760.23991410.1753267199
5.0576-5.4470.26291340.1893269599
5.447-5.99330.22551380.2117268999
5.9933-6.85620.24961540.2247268198
6.8562-8.62160.24691800.2267271299
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)
13.98772.6893-0.38164.2251-1.81791.60530.19080.7052-0.36550.1073-0.389-0.93840.85410.27790.12640.83830.9555-0.1631.7038-0.24291.24871.2277-17.367627.8437
23.1825-0.40630.96210.0538-0.10140.6640.21690.9396-0.6163-0.14670.1422-0.27441.19350.4219-0.21190.64420.9747-0.15852.294-0.52731.220865.8751-19.63224.4846
33.35631.49680.45194.2611-0.74631.9480.30510.8607-0.5409-0.30990.1748-0.34650.39310.4008-0.48671.01990.6677-0.15311.4192-0.42770.91362.5973-16.432128.3577
43.31131.04370.85194.3617-1.48493.0210.17441.272-1.7848-0.83830.0556-1.57851.63891.0873-0.17241.15750.6475-0.15911.5348-0.54991.488867.3448-27.58824.0932
53.01650.1611.12358.5423-2.32484.1850.07610.1921-0.55320.20510.2250.79320.3620.5894-0.32240.38640.050.07380.774-0.05980.603235.6136-4.222330.0225
65.81410.1132-1.4434.49-1.97221.15680.77070.6315-1.39960.3891-0.315-0.23410.14890.3699-0.49571.18050.4405-0.30771.1972-0.27630.923364.1551-20.041441.9771
77.87390.6106-1.20851.6437-0.38020.95820.3575-0.7001-0.62250.2487-0.3707-0.208-0.0180.01090.01730.30760.0086-0.04430.8260.05450.3035-5.3144-24.8978-9.6613
82.00750.45911.58885.37661.3913.56450.42640.47381.0894-0.61610.24510.5925-0.2301-0.3619-0.4170.4274-0.00420.02120.85780.18460.4921-9.0852-12.1554-14.7702
98.99220.0306-1.57622.018-0.30851.05290.0751-0.06620.3625-0.0448-0.15950.10470.0009-0.2793-0.01640.3316-0.0345-0.06430.6301-0.00590.249-9.9259-19.064-10.2026
105.33121.7694-2.26681.3056-1.08611.16980.17940.47720.0049-0.29220.07860.14470.1636-0.168-0.25350.4394-0.0728-0.11170.7986-0.02650.315-23.3099-28.8169-11.4642
113.59190.13330.09170.8541-0.2270.19960.22290.6756-0.0188-1.12560.00830.5110.9485-1.01-0.16460.8231-0.3176-0.31491.90810.17290.3242-53.8314-36.7739-13.6776
123.59720.61830.72491.53190.18331.87910.26520.8504-0.5049-0.11920.1030.00120.8415-0.3423-0.30550.4997-0.1416-0.1590.97010.14590.4993-37.2333-36.268-11.66
138.17580.42410.01748.5897-3.12274.19070.10680.8248-0.9781-0.82420.31840.38890.2604-0.4328-0.44761.0379-0.3685-0.10911.33420.10150.5245-44.5183-46.5506-13.4029
147.76470.1399-0.85853.7144-2.75014.8640.33730.68750.7499-0.78340.61950.5929-0.3404-0.6221-0.58420.4838-0.06150.08331.33980.37130.5418-36.1266-25.1489-15.2377
154.9043-0.1551-1.36423.6077-0.62093.76010.14550.5286-0.8872-0.54570.06240.40511.2843-0.9953-0.13850.665-0.2125-0.12551.27540.09570.5223-45.7299-41.3851-10.7885
168.57031.5555-1.40373.2083-0.14381.70790.53750.2316-0.9544-0.332-0.05020.57151.0991-0.6346-0.20670.6175-0.4287-0.2171.16370.28770.5358-45.9746-41.1792-5.3008
173.03280.89230.43583.0712-0.45950.356-0.0363-0.72020.04480.2416-0.3537-0.5914-0.05490.84830.31160.3275-0.0874-0.08761.03960.08150.398322.9586-7.3316-16.0985
182.14410.9708-0.97032.123-0.49411.15750.0835-0.08110.09870.535-0.0313-0.2944-0.35680.4627-0.08690.3302-0.1452-0.10731.0770.07150.455724.09353.7082-22.5556
193.4094-1.28830.17922.9679-1.45852.55510.4495-1.10341.05830.5654-0.4101-0.6833-1.62180.9444-0.00161.0325-0.50510.07021.0899-0.23090.988137.261423.2447-26.126
204.1249-0.049-0.01677.4056-1.66773.3742-0.03140.45120.3928-0.21590.04960.7549-0.2182-0.6468-0.00480.23-0.023-0.03830.63570.03140.44876.85492.2041-29.9993
212.4113.5453-3.90225.6605-6.00186.47010.75710.21740.5107-0.32780.24520.6209-0.48040.109-0.9710.8324-0.03280.05920.64050.06670.598114.629921.1645-38.9022
227.3251-1.28881.44675.2659-1.08142.62640.35680.15910.1547-0.1365-0.0998-0.5406-0.6911.1753-0.10350.7092-0.31870.11550.802-0.1520.633536.482121.1833-40.7381
236.392-2.3811.50685.838-0.9911.3355-0.08720.0997-0.189-0.41120.20650.161-0.26250.4659-0.15610.6817-0.0869-0.00060.64070.01240.346629.209217.6958-39.4116
242.8788-0.63690.97683.7412-1.30951.82230.44911.37970.8969-0.5208-0.3486-0.7404-0.16660.6083-0.15370.8242-0.3080.21571.14410.14090.753539.64721.2039-46.9287
252.2538-1.0022.77344.929-1.35365.7826-0.0825-0.03140.11590.11770.0651-0.4156-0.30030.07920.04770.3591-0.0524-0.08090.85460.04470.4216-18.1556-47.003529.9618
263.5834-0.23262.26042.3797-0.6474.4069-0.4623-0.20740.4490.04050.4040.2196-0.2208-0.33170.01190.2729-0.0102-0.14120.90010.13520.5887-22.3201-44.290830.2444
274.34170.81361.88825.1673-1.63933.05770.0909-0.67030.83550.41470.27530.6222-0.5954-1.6348-0.27090.3989-0.00520.12091.27960.21680.5765-50.0679-35.54026.8394
280.8491-0.3216-0.2571.0693-0.57271.4725-0.0714-0.16340.3147-0.2709-0.5729-0.4418-0.160.20830.19140.25970.05780.15111.24030.20420.40556.0844-58.516150.3453
294.6881-0.7891.96673.57990.16960.880.2931-0.00090.26170.3383-0.20680.1802-0.2260.01490.08190.3477-0.03190.0320.9593-0.01160.35-3.1767-57.311356.893
301.2565-0.29230.44651.9827-1.2774.4082-0.1373-0.01670.9904-0.0166-0.1148-0.1084-0.6259-0.05640.42840.3918-0.0527-0.10080.9703-0.17780.3799-1.4421-47.090155.7551
312.08760.26610.69431.8392-0.68211.11650.0911-0.1110.7094-0.3068-0.46110.08480.11320.32940.27550.3225-0.0020.06721.06590.04730.25840.2427-56.512453.019
321.7140.93690.38163.92840.47361.20840.46360.4552-0.26750.1853-0.3641-1.01860.42740.3734-0.06830.43740.1981-0.1361.05770.0270.521814.7148-80.095174.8782
332.00580.7067-0.94484.5226-1.04822.511-0.3720.6224-0.3154-0.3393-0.1623-0.5730.99370.68460.2670.51230.4228-0.01031.3696-0.06060.354911.1309-84.310567.6828
341.50642.89831.06545.80382.40831.21290.16510.12170.05670.3454-0.1027-0.22840.23540.7631-0.18640.37580.19330.14210.82660.02830.29748.0325-73.011574.3378
355.08341.6885-0.44852.004-0.88584.81820.2470.0585-0.9127-0.1834-0.084-1.20881.65541.0574-0.09911.01420.4101-0.09921.07920.05610.721310.2944-96.830370.3692
361.60530.5415-0.52022.28440.09110.16880.29040.5154-0.5457-0.15860.2653-1.1310.81470.56350.0928-0.17231.09120.21751.65250.1470.735519.1028-84.149567.8242
372.10860.38020.65784.9863-1.36441.74860.0641-0.36970.0804-0.3339-0.10.51730.2534-0.50740.06460.3370.0078-0.00920.9228-0.08270.3571-16.3644-69.932355.497
384.62750.27584.83924.3235-0.39896.2031-0.1253-0.0912-0.00670.17850.07770.06850.04230.0970.06440.43680.16120.080.88350.08710.32971.5343-85.221382.0519
394.40981.5263-4.51313.0831-1.41867.2202-0.3531-0.8155-0.86910.01810.3974-0.35730.8713-0.04820.10490.7670.17620.25831.31720.20070.56338.025738.4934-27.2551
405.04271.2371-4.93425.3781-0.59497.2361-0.0892-0.33870.04380.54610.48010.1588-0.10230.0492-0.47180.47970.18150.06641.08810.10080.448910.279149.8155-30.4951
413.33831.1192-2.88231.673-1.19624.787-0.16450.1003-0.14970.3060.97860.58590.1458-0.6104-0.41580.6631-0.02190.27161.30480.45480.76684.355743.5449-31.4637
424.5351.4052-0.59218.1562-1.59744.8207-0.09481.29320.1615-0.13760.38760.48070.2614-1.4371-0.35120.6240.13360.10970.8760.19020.396-23.427836.7337-7.6177
436.95433.4216-2.85699.0312-1.04292.1308-0.25581.48170.1841-0.75730.85780.44580.0104-1.0421-0.56620.68160.03250.06071.39220.13720.6066-21.656636.0775-13.1571
447.4274-0.262-1.50767.0042-0.33234.71630.17170.7353-0.83510.40390.0710.77670.6656-1.02940.05020.58160.10090.16950.95060.10450.4674-23.372930.8764-4.4695
451.44820.0820.09880.4354-0.44070.5179-0.6257-0.5584-0.2195-0.19090.1327-0.6420.3204-0.00110.07790.2081-0.0327-0.23061.2999-0.12180.089832.474358.5312-50.9665
464.7760.72-1.06321.30740.37860.4634-0.15460.7072-0.5862-0.3924-0.1767-0.1919-0.1302-0.16530.3020.2911-0.16550.00710.9465-0.11340.332123.722257.1326-58.0646
472.3935-0.421.07542.1252-0.7573.4952-0.3915-0.6618-0.8010.3416-0.0807-0.0528-0.09140.01540.49770.49980.03030.04580.91480.0270.330731.161549.3786-51.6266
482.3477-1.8196-1.77492.15991.94391.8452-0.27630.076-0.01020.03720.10020.30530.6968-0.33340.09270.4008-0.05960.01150.8761-0.15770.298931.216557.8307-61.1186
493.73230.4114-1.50362.0852-0.96891.74250.1307-0.4556-0.30451.60910.47720.3396-0.35270.7093-0.31280.0315-0.051-0.26261.2885-0.14840.066621.460858.7622-49.1458
500.9313-0.7181.12936.61350.6382.5659-0.09990.32670.3546-0.6361-0.2249-1.0485-1.31620.14890.20480.4167-0.14140.01351.62280.17550.702142.253480.1495-74.7556
512.6988-0.7120.65948.53010.15861.6350.16350.05730.7274-0.0534-0.1579-0.4865-0.28210.6229-0.06160.5235-0.2080.01150.9380.00590.631737.91681.0146-69.3608
523.19-0.44110.49437.87430.69852.1315-0.0390.01781.4722-0.2438-0.1839-1.5327-0.81060.75820.04340.714-0.24380.06611.06630.08531.091842.840789.8862-68.874
533.65490.1721-0.034.8403-1.38761.0419-0.20720.02880.19870.10210.14230.4369-0.1216-0.55620.0190.35950.0152-0.02881.0518-0.12270.301611.207567.7841-53.6399
540.9013-0.041-0.03354.1768-1.42661.91180.06810.91730.4183-1.1282-0.1667-0.3341-0.29020.56060.06080.8902-0.1061-0.02361.18750.22710.552329.104986.741-75.9901
553.1616-1.4502-1.80434.0431-0.4293.25920.25371.74040.7818-1.5273-0.3723-0.1849-0.1021-0.41160.11571.09670.0957-0.02381.56470.2670.601826.299584.4881-81.9391
567.117-0.76452.9161.8633-1.21982.6954-0.45490.43040.3050.11040.0085-0.3116-0.62710.71820.43070.55110.0462-0.04811.08540.06960.430322.114224.94729.3563
579.8346-1.32852.17786.3495-0.65444.66650.2967-0.981-1.85510.56810.18530.3289-0.0179-0.2068-0.39930.4061-0.0701-0.10850.79310.19360.798418.857811.998413.9282
586.5970.4412.33572.29590.39981.2002-0.04810.7185-0.5881-0.1018-0.385-0.2770.00860.37060.28540.4895-0.09410.07621.1951-0.01150.564218.409717.33266.4092
596.8145-0.83843.0841.7423-0.77572.9509-0.159-0.7952-0.13630.1873-0.204-0.0528-0.12780.30080.3260.50110.11040.01850.74250.09510.383116.904220.791313.2107
602.0149-2.0281.93990.5968-0.65240.80540.1627-0.15580.01760.10920.0683-0.0536-0.38320.2225-0.11290.62490.18630.04530.79340.29270.49263.849828.163410.8482
614.9197-0.5788-0.54541.6691.00031.09180.0493-1.30310.41440.411-0.06990.0026-0.5659-0.82440.14860.88490.32960.2931.32390.11190.531-18.4834.856111.7791
626.794-0.63971.46645.8445-0.13395.1031-0.3192-1.20420.93340.23180.09240.0794-0.1202-0.19720.10921.66790.59970.48091.09230.14551.0253-17.615744.93712.9657
636.6431-3.7380.1763.23350.36041.8978-0.5515-1.2818-1.0010.89170.53490.52890.3463-0.29140.06210.97080.30570.11451.31430.38120.6266-13.721428.684813.8182
641.0704-0.5474-0.25794.39151.32974.3948-0.2729-0.73150.81580.6571-0.2994-0.0472-0.3754-0.72330.54930.79780.11240.12640.6229-0.01980.492-17.340441.57748.1899
658.897-1.78263.00631.97940.48541.7961-0.1392-0.15161.07980.4987-0.06070.0967-0.6252-0.31640.08790.74530.09820.2190.96760.1750.5852-19.072340.00264.6647
664.8044-0.24031.53753.1412-0.76460.6112-0.04760.96380.1033-0.7437-0.1875-0.70450.41471.04090.15740.6788-0.01410.21641.8408-0.10330.802255.40532.744912.4228
675.3515-0.79210.85012.4007-0.41080.1487-0.2641.2498-0.1447-0.2579-0.3842-0.12230.02270.4090.52830.48020.0011-0.0091.50520.06890.619243.49717.036513.4544
685.0629-1.312.0923.2622-1.23393.4731-0.83690.65720.6060.050.1675-0.6212-0.29240.67690.76430.5241-0.0997-0.10761.4740.26760.68947.524111.971620.4442
692.3689-1.05540.37323.5162-1.62171.2485-0.32671.5385-0.0785-0.1523-0.1011-0.44140.04370.84160.41930.5146-0.03360.03821.72410.14910.631848.46927.627116.8619
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 122 through 145 )E122 - 145
2X-RAY DIFFRACTION2chain 'E' and (resid 146 through 167 )E146 - 167
3X-RAY DIFFRACTION3chain 'E' and (resid 168 through 187 )E168 - 187
4X-RAY DIFFRACTION4chain 'E' and (resid 188 through 223 )E188 - 223
5X-RAY DIFFRACTION5chain 'F' and (resid 1 through 113 )F1 - 113
6X-RAY DIFFRACTION6chain 'F' and (resid 114 through 212 )F114 - 212
7X-RAY DIFFRACTION7chain 'G' and (resid 1 through 40 )G1 - 40
8X-RAY DIFFRACTION8chain 'G' and (resid 41 through 60 )G41 - 60
9X-RAY DIFFRACTION9chain 'G' and (resid 61 through 103 )G61 - 103
10X-RAY DIFFRACTION10chain 'G' and (resid 104 through 125 )G104 - 125
11X-RAY DIFFRACTION11chain 'G' and (resid 126 through 139 )G126 - 139
12X-RAY DIFFRACTION12chain 'G' and (resid 140 through 152 )G140 - 152
13X-RAY DIFFRACTION13chain 'G' and (resid 153 through 162 )G153 - 162
14X-RAY DIFFRACTION14chain 'G' and (resid 163 through 174 )G163 - 174
15X-RAY DIFFRACTION15chain 'G' and (resid 175 through 195 )G175 - 195
16X-RAY DIFFRACTION16chain 'G' and (resid 196 through 213 )G196 - 213
17X-RAY DIFFRACTION17chain 'H' and (resid 2 through 98 )H2 - 98
18X-RAY DIFFRACTION18chain 'H' and (resid 99 through 145 )H99 - 145
19X-RAY DIFFRACTION19chain 'H' and (resid 146 through 223 )H146 - 223
20X-RAY DIFFRACTION20chain 'I' and (resid 1 through 102 )I1 - 102
21X-RAY DIFFRACTION21chain 'I' and (resid 103 through 113 )I103 - 113
22X-RAY DIFFRACTION22chain 'I' and (resid 114 through 150 )I114 - 150
23X-RAY DIFFRACTION23chain 'I' and (resid 151 through 174 )I151 - 174
24X-RAY DIFFRACTION24chain 'I' and (resid 175 through 212 )I175 - 212
25X-RAY DIFFRACTION25chain 'J' and (resid 1 through 78 )J1 - 78
26X-RAY DIFFRACTION26chain 'J' and (resid 79 through 115 )J79 - 115
27X-RAY DIFFRACTION27chain 'J' and (resid 116 through 213 )J116 - 213
28X-RAY DIFFRACTION28chain 'K' and (resid 2 through 33 )K2 - 33
29X-RAY DIFFRACTION29chain 'K' and (resid 34 through 52 )K34 - 52
30X-RAY DIFFRACTION30chain 'K' and (resid 53 through 67 )K53 - 67
31X-RAY DIFFRACTION31chain 'K' and (resid 68 through 121 )K68 - 121
32X-RAY DIFFRACTION32chain 'K' and (resid 122 through 145 )K122 - 145
33X-RAY DIFFRACTION33chain 'K' and (resid 146 through 175 )K146 - 175
34X-RAY DIFFRACTION34chain 'K' and (resid 176 through 187 )K176 - 187
35X-RAY DIFFRACTION35chain 'K' and (resid 188 through 204 )K188 - 204
36X-RAY DIFFRACTION36chain 'K' and (resid 205 through 223 )K205 - 223
37X-RAY DIFFRACTION37chain 'L' and (resid 1 through 113 )L1 - 113
38X-RAY DIFFRACTION38chain 'L' and (resid 114 through 212 )L114 - 212
39X-RAY DIFFRACTION39chain 'A' and (resid 1 through 26 )A1 - 26
40X-RAY DIFFRACTION40chain 'A' and (resid 27 through 84 )A27 - 84
41X-RAY DIFFRACTION41chain 'A' and (resid 85 through 115 )A85 - 115
42X-RAY DIFFRACTION42chain 'A' and (resid 116 through 152 )A116 - 152
43X-RAY DIFFRACTION43chain 'A' and (resid 153 through 174 )A153 - 174
44X-RAY DIFFRACTION44chain 'A' and (resid 175 through 213 )A175 - 213
45X-RAY DIFFRACTION45chain 'B' and (resid 2 through 40 )B2 - 40
46X-RAY DIFFRACTION46chain 'B' and (resid 41 through 51 )B41 - 51
47X-RAY DIFFRACTION47chain 'B' and (resid 52 through 83 )B52 - 83
48X-RAY DIFFRACTION48chain 'B' and (resid 84 through 98 )B84 - 98
49X-RAY DIFFRACTION49chain 'B' and (resid 99 through 121 )B99 - 121
50X-RAY DIFFRACTION50chain 'B' and (resid 122 through 145 )B122 - 145
51X-RAY DIFFRACTION51chain 'B' and (resid 146 through 187 )B146 - 187
52X-RAY DIFFRACTION52chain 'B' and (resid 188 through 223 )B188 - 223
53X-RAY DIFFRACTION53chain 'C' and (resid 1 through 102 )C1 - 102
54X-RAY DIFFRACTION54chain 'C' and (resid 103 through 139 )C103 - 139
55X-RAY DIFFRACTION55chain 'C' and (resid 140 through 212 )C140 - 212
56X-RAY DIFFRACTION56chain 'D' and (resid 1 through 40 )D1 - 40
57X-RAY DIFFRACTION57chain 'D' and (resid 41 through 60 )D41 - 60
58X-RAY DIFFRACTION58chain 'D' and (resid 61 through 84 )D61 - 84
59X-RAY DIFFRACTION59chain 'D' and (resid 85 through 103 )D85 - 103
60X-RAY DIFFRACTION60chain 'D' and (resid 104 through 125 )D104 - 125
61X-RAY DIFFRACTION61chain 'D' and (resid 126 through 152 )D126 - 152
62X-RAY DIFFRACTION62chain 'D' and (resid 153 through 162 )D153 - 162
63X-RAY DIFFRACTION63chain 'D' and (resid 163 through 181 )D163 - 181
64X-RAY DIFFRACTION64chain 'D' and (resid 182 through 195 )D182 - 195
65X-RAY DIFFRACTION65chain 'D' and (resid 196 through 213 )D196 - 213
66X-RAY DIFFRACTION66chain 'E' and (resid 2 through 25 )E2 - 25
67X-RAY DIFFRACTION67chain 'E' and (resid 26 through 40 )E26 - 40
68X-RAY DIFFRACTION68chain 'E' and (resid 41 through 64 )E41 - 64
69X-RAY DIFFRACTION69chain 'E' and (resid 65 through 121 )E65 - 121

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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