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- PDB-6hc2: Crystal structure of NuMA/LGN hetero-hexamers -

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基本情報

登録情報
データベース: PDB / ID: 6hc2
タイトルCrystal structure of NuMA/LGN hetero-hexamers
要素
  • G-protein-signaling modulator 2
  • Nuclear mitotic apparatus protein 1
キーワードCELL CYCLE / Cell division Asymmetric cell division Spindle orientation Force generator
機能・相同性
機能・相同性情報


anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / microtubule minus-end / cortical microtubule / Mitotic Prophase / microtubule bundle / lateral cell cortex ...anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / microtubule minus-end / cortical microtubule / Mitotic Prophase / microtubule bundle / lateral cell cortex / positive regulation of chromosome segregation / cell cortex region / mitotic spindle astral microtubule / maintenance of centrosome location / microtubule minus-end binding / mitotic spindle midzone / positive regulation of hair follicle development / astral microtubule organization / microtubule plus-end / positive regulation of intracellular transport / regulation of metaphase plate congression / positive regulation of spindle assembly / spindle pole centrosome / microtubule plus-end binding / positive regulation of BMP signaling pathway / microtubule bundle formation / positive regulation of keratinocyte differentiation / response to light intensity / GDP-dissociation inhibitor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / mitotic spindle pole / nucleus organization / dynein complex binding / establishment of mitotic spindle orientation / G-protein alpha-subunit binding / lateral plasma membrane / positive regulation of protein localization to cell cortex / positive regulation of microtubule polymerization / phosphatidylinositol binding / tubulin binding / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic spindle organization / mitotic spindle organization / meiotic cell cycle / spindle microtubule / spindle / nuclear matrix / spindle pole / disordered domain specific binding / mitotic spindle / chromosome / cell cortex / microtubule binding / G alpha (i) signalling events / postsynaptic density / G protein-coupled receptor signaling pathway / protein domain specific binding / cell division / nucleotide binding / neuronal cell body / centrosome / dendrite / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
: / : / NuMA N-terminal hook domain / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat ...: / : / NuMA N-terminal hook domain / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
類似検索 - ドメイン・相同性
G-protein-signaling modulator 2 / Nuclear mitotic apparatus protein 1
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: 4.31 Å
データ登録者Pasqualato, S. / Culurgioni, S. / Foadi, J. / Alfieri, A. / Mapelli, M.
資金援助 イタリア, 2件
組織認可番号国
Italian Association for Cancer ResearchIG 18629 イタリア
RF-2013-02357254 イタリア
引用ジャーナル: Nat Commun / 年: 2019
タイトル: Hexameric NuMA:LGN structures promote multivalent interactions required for planar epithelial divisions.
著者: Pirovano, L. / Culurgioni, S. / Carminati, M. / Alfieri, A. / Monzani, S. / Cecatiello, V. / Gaddoni, C. / Rizzelli, F. / Foadi, J. / Pasqualato, S. / Mapelli, M.
履歴
登録2018年8月13日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年5月29日Provider: repository / タイプ: Initial release
改定 1.12024年1月17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: G-protein-signaling modulator 2
B: Nuclear mitotic apparatus protein 1
C: G-protein-signaling modulator 2
D: Nuclear mitotic apparatus protein 1
E: G-protein-signaling modulator 2
F: Nuclear mitotic apparatus protein 1
G: G-protein-signaling modulator 2
H: Nuclear mitotic apparatus protein 1
I: G-protein-signaling modulator 2
J: Nuclear mitotic apparatus protein 1
K: G-protein-signaling modulator 2
L: Nuclear mitotic apparatus protein 1
M: G-protein-signaling modulator 2
N: Nuclear mitotic apparatus protein 1
O: G-protein-signaling modulator 2
P: Nuclear mitotic apparatus protein 1
Q: G-protein-signaling modulator 2
R: Nuclear mitotic apparatus protein 1
S: G-protein-signaling modulator 2
T: Nuclear mitotic apparatus protein 1
U: G-protein-signaling modulator 2
V: Nuclear mitotic apparatus protein 1
W: G-protein-signaling modulator 2
X: Nuclear mitotic apparatus protein 1


分子量 (理論値)分子数
合計 (水以外)582,03624
ポリマ－582,03624
非ポリマー00
水00
1
A: G-protein-signaling modulator 2
B: Nuclear mitotic apparatus protein 1
C: G-protein-signaling modulator 2
D: Nuclear mitotic apparatus protein 1
E: G-protein-signaling modulator 2
F: Nuclear mitotic apparatus protein 1


分子量 (理論値)分子数
合計 (水以外)145,5096
ポリマ－145,5096
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15580 Å2
ΔGint-96 kcal/mol
Surface area58280 Å2
手法PISA
2
G: G-protein-signaling modulator 2
H: Nuclear mitotic apparatus protein 1
I: G-protein-signaling modulator 2
J: Nuclear mitotic apparatus protein 1
K: G-protein-signaling modulator 2
L: Nuclear mitotic apparatus protein 1


分子量 (理論値)分子数
合計 (水以外)145,5096
ポリマ－145,5096
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15490 Å2
ΔGint-93 kcal/mol
Surface area58120 Å2
手法PISA
3
M: G-protein-signaling modulator 2
N: Nuclear mitotic apparatus protein 1
O: G-protein-signaling modulator 2
P: Nuclear mitotic apparatus protein 1
Q: G-protein-signaling modulator 2
R: Nuclear mitotic apparatus protein 1


分子量 (理論値)分子数
合計 (水以外)145,5096
ポリマ－145,5096
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-92 kcal/mol
Surface area57750 Å2
手法PISA
4
S: G-protein-signaling modulator 2
T: Nuclear mitotic apparatus protein 1
U: G-protein-signaling modulator 2
V: Nuclear mitotic apparatus protein 1
W: G-protein-signaling modulator 2
X: Nuclear mitotic apparatus protein 1


分子量 (理論値)分子数
合計 (水以外)145,5096
ポリマ－145,5096
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15760 Å2
ΔGint-83 kcal/mol
Surface area57910 Å2
手法PISA
単位格子
Length a, b, c (Å)153.940, 153.940, 732.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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要素

#1: タンパク質
G-protein-signaling modulator 2 / Mosaic protein LGN


分子量: 40755.629 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GPSM2, LGN / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P81274
#2: タンパク質
Nuclear mitotic apparatus protein 1 / Nuclear matrix protein-22 / NMP-22 / Nuclear mitotic apparatus protein / NuMA protein / SP-H antigen


分子量: 7747.409 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NUMA1, NMP22, NUMA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q14980

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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: 3.73 Å3/Da / 溶媒含有率: 67.03 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 10% PEG3350, 0.05M Bis-Tris propane and 0.1M Na-formate or 0.1M Na-acetate trihydrate

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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: Diamond / ビームライン: I04 / 波長: 0.9698 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2015年6月25日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9698 Å / 相対比: 1
反射解像度: 4.29→243.48 Å / Num. obs: 61354 / % possible obs: 99.9 % / 冗長度: 98.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.343 / Net I/σ(I): 19.1
反射 シェル解像度: 4.29→4.4 Å / 冗長度: 88.7 % / Rmerge(I) obs: 7.028 / Mean I/σ(I) obs: 2.1 / % possible all: 98.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.13_2998: ???)精密化
xia2データ削減
xia2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: pdb entries 3SF4 and 3RO2

3sf4

3ro2


解像度: 4.31→150.653 Å / SU ML: 0.58 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 26.85 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2341 3058 5.02 %
Rwork0.1816 --
obs0.1842 60924 99.77 %
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: 4.31→150.653 Å
タンパク質核酸リガンド溶媒全体
原子数37562 0 0 0 37562
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00538247
X-RAY DIFFRACTIONf_angle_d1.00351693
X-RAY DIFFRACTIONf_dihedral_angle_d6.95822609
X-RAY DIFFRACTIONf_chiral_restr0.0655587
X-RAY DIFFRACTIONf_plane_restr0.0066878
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)
1-0.1227-0.0502-0.5447-0.0042-0.3594-0.0875-0.05840.04250.10430.39440.01070.0115-0.0949-0.070501.9563-0.0006-0.05982.261-0.40332.148828.3038114.3531-97.7578
20.0335-0.00170.040.1767-0.00090.11760.01710.0733-0.59590.04370.0292-0.5088-0.0608-0.1091-02.665-0.277-0.15112.3157-0.27942.673914.011135.0002-106.2694
30.1489-0.1376-0.18950.123-0.32670.1816-0.4211-0.6486-0.1519-0.61210.51220.40840.12620.341701.9277-0.03920.10912.08620.02051.9235-7.5022120.8516-118.9431
40.0157-0.01680.050.0311-0.06780.1576-0.1191-0.0294-0.097-0.0345-0.07330.0203-0.0140.05380.00022.9916-0.2504-0.42593.6472-0.23112.8405-3.4915123.5824-74.3029
50.01340.00570.0057-0.00150.00050.00510.20430.1802-0.02650.02150.06950.10010.00680.142901.9873-0.41720.22042.1885-0.14212.3129-4.3387119.2778-84.1014
6-0.00630.0046-0.01120.0287-0.0050.0653-0.3842-0.2031-0.0037-0.1131-0.05920.1938-0.03490.046703.14750.36130.39142.84180.3322.8043-9.6452135.2083-95.3145
70.00120.00340.00510.00050.00420.00290.0644-0.0886-0.06730.0202-0.0629-0.03930.1354-0.009702.865-0.7363-0.28772.946-0.07043.3674-8.9494130.7638-108.3116
80.113-0.0373-0.00540.00480.0172-0.00090.09170.0009-0.0767-0.05580.28670.01520.09920.04060.00012.7554-0.54140.10172.4881-0.3092.7463.1147126.5026-109.3393
90.0346-0.01450.01030.01580.0048-0.001-0.1113-0.0812-0.03450.0085-0.16460.082-0.09410.0786-02.99490.1377-0.41982.7248-0.32273.178918.6617123.9274-107.0874
100.00350-0.00050.0045-0.00170.0018-0.06760.0359-0.0547-0.0356-0.09960.00730.06680.041502.2268-0.1971-0.31312.22620.10592.436430.9907116.5293-107.694
110.00820.00040.00050.01240.00490.0050.16810.01590.0303-0.18350.28-0.1216-0.0806-0.0763-0.00012.26660.34080.02531.76680.03542.364541.6521114.2446-104.0242
120.0880.24280.04820.6110.86230.55020.4357-0.02980.08340.2263-0.04470.2829-0.24880.415202.0366-0.0850.01241.9375-0.05371.8076-13.4599103.075-82.7787
130.32530.8136-0.6360.436-0.2783-0.4837-2.2377-0.09060.81412.45130.3663-0.5085-2.9880.43430-11.2625-0.82654.21620.57220.5093-1.1501-19.353469.8617-81.3076
140.0527-0.005-0.06210.03040.02760.0042-0.1963-0.0677-0.3811-0.0364-0.34250.42550.17240.214102.4749-0.01530.40332.7556-0.4833.56230.178972.2458-68.1458
15-0.0142-0.02080.01670.00480.0063-0.00690.147-0.1577-0.25940.18550.21020.01950.30750.3855-02.1614-0.01280.13982.34070.21542.3785-20.233887.3546-81.0359
160.00610.0115-0.00280.00390.0012-0.0095-0.103-0.09480.06090.0105-0.180.0276-0.10520.229401.43380.1929-0.07942.0559-0.0913.1742-23.4915108.7861-88.7461
170.19-0.2138-0.42410.32840.2327-0.3881-0.0541-0.8586-0.04950.05010.0632-0.066-0.1483-0.023401.3111-0.2404-0.1291.9583-0.01571.436525.612672.489-75.1123
180.71650.14870.86620.39830.2311-0.09580.5644-0.0257-0.3352-2.1065-0.84620.2297-0.8893-0.0021-0-0.7317-0.4143-0.09180.48520.24870.289946.160775.1174-101.9642
190.03320.0190.03520.02290.02110.0553-0.04690.1194-0.01470.04790.18410.13370.0631-0.1573-0.00042.4564-0.1557-0.00822.5994-0.04932.204337.0173105.263-85.0772
20-0.0265-0.0082-0.00720.00420.025-0.001-0.016-0.03230.25720.01050.20250.0027-0.2515-0.0702-0.00013.25910.2218-0.61173.065-0.37322.288343.9072101.2519-90.5829
210.01790.0037-0.00830.0015-0.00260.0038-0.04910.06540.08020.038-0.0088-0.00670.0138-0.03260.00022.30290.52010.27183.59720.05922.433645.418581.2011-98.8981
220.0114-0.0018-0.00940.0229-0.00840.01980.0428-0.084-0.071-0.10720.02070.1002-0.0612-0.11102.4252-0.0158-0.6662.59240.42.809140.075671.9685-87.9786
230.01510.001-0.00570.01680.00040.01140.1541-0.08290.1521-0.05990.0744-0.1172-0.11520.0569-02.33740.09970.35652.58780.22832.329627.955865.3351-80.5715
240.0080.0366-0.02440.7396-0.51190.35760.0386-0.0417-0.05080.0180.0834-0.01520.03270.0685-0.00222.43030.01130.18962.8760.54012.942921.240861.0565-80.2125
250.00260.002-0.00050.0018-0.0020.00280.0052-0.0838-0.1250.12060.0375-0.00650.0716-0.0057-01.79850.2223-0.05392.65520.57442.256217.654558.7266-72.9029
260.01030.01340.01830.05740.02340.0371-0.0914-0.08360.02530.05150.0004-0.01910.0128-0.0581-0.00022.56920.1428-0.40772.72580.00282.48813.331452.0959-69.2613
27-0.0651-0.19160.12490.0938-0.0029-0.3542-0.40180.4037-0.6043-0.4710.2579-0.39040.1669-0.5933-01.54270.08320.25781.93490.21122.3062-37.828639.2485-71.2092
280.1159-0.0165-0.0388-0.0506-0.25580.07550.376-0.04460.038-0.0318-0.10870.6473-0.38030.181801.59210.14150.15341.60350.1632.154-48.932660.4629-73.9407
290.01440.12780.06820.01340.28460.10440.42710.1246-0.3456-0.43990.32270.15010.09910.6476-01.81910.1378-0.01621.5443-0.0432.017-67.475965.6936-79.9508
30-0.0908-0.13310.03810.033-0.2310.07520.08830.80510.3282-0.23550.130.3326-0.1529-0.260701.48320.0042-0.14162.16870.38722.1778-67.226962.6528-90.8759
31-0.0065-0.011-0.11540.1135-0.1850.2863-0.07860.1270.66480.2252-0.0949-0.41540.4201-0.171301.5024-0.0180.05912.05620.37162.1977-83.684545.2535-85.066
320.0186-0.049-0.05530.06260.00750.05660.04010.45040.02250.1595-0.4842-0.03750.3785-0.786300.3726-0.25830.16320.62160.29370.7888-95.860144.6007-66.9142
330.0047-0.00340.00250.0068-0.0079-0.0046-0.0931-0.0054-0.0143-0.2921-0.0101-0.0842-0.1060.026702.5719-0.0573-0.0681.98890.32852.9671-79.660272.7996-62.7178
340.01580.03970.00920.0245-0.04180.0175-0.13790.23590.3665-0.39090.1024-0.3585-0.0457-0.2224-02.22660.0684-0.18023.03030.24442.1435-81.206657.9074-79.5945
350.0066-0.02070.0225-0.0192-0.0109-0.0010.067-0.235-0.00510.1133-0.1427-0.0263-0.17940.5225-02.0904-0.2971-0.20842.40040.08841.4767-54.157949.836-82.3575
360.00750.00920.0108-0.00520.00060.01020.0683-0.01120.1937-0.02760.13130.1435-0.2327-0.151802.2096-0.3906-0.75692.4935-0.151.6309-37.524547.2508-81.9057
37-0.00150.06160.087-0.1980.1374-0.09930.12170.77360.63780.6180.1519-0.01840.1013-0.377102.21620.1754-0.54692.11390.27482.1417-92.625857.4854-60.1512
380.03290.01940.02810.02680.08880.0534-0.0467-0.0166-0.16620.1863-0.3608-0.28730.13850.388502.4398-0.3239-0.26332.05130.22962.193-81.355567.1685-49.0645
390.0359-0.0908-0.07670.00580.02550.05880.07460.28810.0002-0.4032-0.39130.1694-0.0801-0.053802.9806-0.2352-0.73262.0526-0.09782.5482-80.967977.3289-39.8848
400.0406-0.0869-0.01650.02560.09630.0356-0.5805-0.33120.1175-0.62080.2016-0.09780.0950.354602.7738-0.0849-0.28262.2432-0.14922.2761-77.023670.6899-24.9578
410.0039-0.0284-0.0315-0.08910.05730.07750.1837-0.3128-0.743-0.327-0.4753-0.3673-0.7223-0.1086-02.5111-0.1286-0.37742.17420.03762.7759-84.937673.3928-22.2567
420.07590.1564-0.23070.1868-0.0874-0.0376-0.3264-0.21540.003-0.177-0.0971-0.0048-0.35580.0497-01.91810.138-0.38131.83780.01072.1906-87.537852.9087-13.2593
430.1097-0.0709-0.101-0.04740.11240.0602-1.31630.37020.0325-0.31820.7414-0.28880.34850.432701.2448-0.0483-0.36611.28480.17691.5587-67.905837.951-12.0391
440.018-0.042-0.0804-0.01460.0836-0.09040.0561-0.1658-0.3922-0.38090.06940.73610.01830.2945-01.35840.2281-0.08371.65510.07711.6331-61.784363.8126-18.6022
45-0.0126-0.0552-0.0017-0.00030.00380.00940.22210.05270.566-0.19280.5040.0811-0.00060.123902.87070.11830.00662.06720.18341.7712-88.771762.3189-34.4446
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570.06680.08120.04260.0217-0.0064-0.01380.26490.1734-0.5012-0.0391-0.23280.3938-0.0525-0.7547-03.0488-0.37150.04782.5450.01232.0435-51.761497.042616.2064
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590.0103-0.01840.0327-0.0213-0.00160.014-0.04770.5120.2704-0.3108-0.35620.1815-0.08070.0551-02.098-0.35560.03661.6727-0.04221.7975-21.464271.2289-9.8388
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660.02620.01440.00040.0185-0.00160.0002-0.14940.11470.06610.0299-0.229-0.0798-0.088-0.07402.48970.272-0.04512.39360.0372.0154-36.2302119.034834.7926
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680.7523-0.30770.56590.3485-0.17160.367-0.1440.31430.1830.1680.0957-0.1063-0.0896-0.1342-01.4567-0.0624-0.18931.4513-0.02561.49460.1181120.48621.1655
691.52570.66720.4329-0.1219-0.84040.33070.0636-0.13920.0747-0.1313-0.3162-0.0326-0.00960.2073-00.4297-0.0666-0.07560.07220.05450.584714.058392.2017-8.5187
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74-0.0149-0.0175-0.09620.03040.1208-0.0563-0.07580.1730.6039-0.2730.2101-0.51310.51220.337201.686-0.21050.34971.4383-0.14771.607733.2183-19.9402-25.5978
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76-0.00080.01740.20220.0740.07850.02110.3557-0.73630.2687-0.0854-0.38340.2710.3374-0.219-01.84120.02110.09031.4124-0.01271.356523.89974.2603-2.2339
770.4737-0.37570.22360.1833-0.07690.2262-0.06780.44140.13030.1567-0.20270.14820.33210.0994-01.5196-0.03830.03331.7779-0.1381.749544.90189.47862.261
780.1145-0.32410.1030.0966-0.0280.11321.1497-0.36240.63520.3913-0.34470.2866-1.29311.84980-0.70450.42060.00750.5996-0.19630.659552.519427.7926-14.9763
79-0.00360.0048-0.01460.0042-0.012-0.00770.0936-0.258-0.07450.1070.1654-0.18880.0751-0.5133-01.92320.04670.39821.8158-0.06951.947917.053823.9387-18.0316
800.0070.0576-0.01020.0472-0.0933-0.0402-0.180.05730.1361-0.6107-0.18550.0189-0.3028-0.219602.4346-0.11540.17541.77130.15021.709626.305829.1586-7.7588
810.0030.00740.0010.01860.01430.0078-0.0709-0.1375-0.0053-0.01190.0361-0.00430.01140.1121-02.1751-0.5157-0.0152.6478-0.32122.597241.438417.2573-5.6301
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850.2004-0.17940.0461-0.0999-0.04720.01250.4006-0.42250.04720.42420.1235-0.2623-0.23240.809701.9511-0.13830.16072.2378-0.37941.790837.824232.8693-20.9914
86-0.03710.2788-0.0385-0.1254-0.0240.1334-0.1050.28880.57750.0446-0.12080.16220.13620.248401.6312-0.07810.00582.7045-0.04721.859115.927231.9728-42.4427
87-0.2961-0.34750.2420.1688-0.1790.19260.35990.6572-0.6756-0.54180.14290.3889-0.6261-0.2289-0-0.86240.2357-1.83980.79291.631-4.840834.051431.4927-68.7814
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890.0041-0.00210.00780.0065-0.00420.0165-0.05410.02950.1146-0.1710.04890.00630.00660.010402.49750.0998-0.1442.4215-0.66572.480412.41559.0365-64.6306
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970.0547-0.2161-0.0623-0.13020.06740.1927-0.1761-0.2438-0.4125-0.30160.4703-0.27910.1335-0.236501.7937-0.05950.03132.02390.04552.202337.7196-37.228-53.7904
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102-0.0288-0.06-0.07630.0118-0.0421-0.01080.17610.2108-0.10750.25410.3195-0.10440.00330.12102.63750.3843-0.48891.0812-0.05573.094731.6731-35.3511-42.2225
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 164 )
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 248 )
3X-RAY DIFFRACTION3chain 'A' and (resid 249 through 367 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1864 through 1868 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1869 through 1877 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1878 through 1898 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1899 through 1903 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1904 through 1908 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1909 through 1913 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1914 through 1918 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1919 through 1924 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 164 )
13X-RAY DIFFRACTION13chain 'C' and (resid 165 through 367 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1867 through 1905 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1906 through 1915 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1916 through 1925 )
17X-RAY DIFFRACTION17chain 'E' and (resid 2 through 188 )
18X-RAY DIFFRACTION18chain 'E' and (resid 189 through 367 )
19X-RAY DIFFRACTION19chain 'F' and (resid 1870 through 1874 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1875 through 1901 )
21X-RAY DIFFRACTION21chain 'F' and (resid 1902 through 1906 )
22X-RAY DIFFRACTION22chain 'F' and (resid 1907 through 1911 )
23X-RAY DIFFRACTION23chain 'F' and (resid 1912 through 1916 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1917 through 1918 )
25X-RAY DIFFRACTION25chain 'F' and (resid 1919 through 1923 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1924 through 1928 )
27X-RAY DIFFRACTION27chain 'G' and (resid 1 through 50 )
28X-RAY DIFFRACTION28chain 'G' and (resid 51 through 130 )
29X-RAY DIFFRACTION29chain 'G' and (resid 131 through 164 )
30X-RAY DIFFRACTION30chain 'G' and (resid 165 through 228 )
31X-RAY DIFFRACTION31chain 'G' and (resid 229 through 328 )
32X-RAY DIFFRACTION32chain 'G' and (resid 329 through 367 )
33X-RAY DIFFRACTION33chain 'H' and (resid 1869 through 1878 )
34X-RAY DIFFRACTION34chain 'H' and (resid 1879 through 1909 )
35X-RAY DIFFRACTION35chain 'H' and (resid 1910 through 1918 )
36X-RAY DIFFRACTION36chain 'H' and (resid 1919 through 1925 )
37X-RAY DIFFRACTION37chain 'I' and (resid 1 through 50 )
38X-RAY DIFFRACTION38chain 'I' and (resid 51 through 87 )
39X-RAY DIFFRACTION39chain 'I' and (resid 88 through 130 )
40X-RAY DIFFRACTION40chain 'I' and (resid 131 through 164 )
41X-RAY DIFFRACTION41chain 'I' and (resid 165 through 208 )
42X-RAY DIFFRACTION42chain 'I' and (resid 209 through 307 )
43X-RAY DIFFRACTION43chain 'I' and (resid 308 through 367 )
44X-RAY DIFFRACTION44chain 'J' and (resid 1866 through 1907 )
45X-RAY DIFFRACTION45chain 'J' and (resid 1908 through 1917 )
46X-RAY DIFFRACTION46chain 'J' and (resid 1918 through 1925 )
47X-RAY DIFFRACTION47chain 'K' and (resid 2 through 50 )
48X-RAY DIFFRACTION48chain 'K' and (resid 51 through 130 )
49X-RAY DIFFRACTION49chain 'K' and (resid 131 through 165 )
50X-RAY DIFFRACTION50chain 'K' and (resid 166 through 328 )
51X-RAY DIFFRACTION51chain 'K' and (resid 329 through 367 )
52X-RAY DIFFRACTION52chain 'L' and (resid 1864 through 1877 )
53X-RAY DIFFRACTION53chain 'L' and (resid 1878 through 1913 )
54X-RAY DIFFRACTION54chain 'L' and (resid 1914 through 1928 )
55X-RAY DIFFRACTION55chain 'M' and (resid 2 through 188 )
56X-RAY DIFFRACTION56chain 'M' and (resid 189 through 367 )
57X-RAY DIFFRACTION57chain 'N' and (resid 1867 through 1903 )
58X-RAY DIFFRACTION58chain 'N' and (resid 1904 through 1913 )
59X-RAY DIFFRACTION59chain 'N' and (resid 1914 through 1927 )
60X-RAY DIFFRACTION60chain 'O' and (resid 3 through 208 )
61X-RAY DIFFRACTION61chain 'O' and (resid 209 through 367 )
62X-RAY DIFFRACTION62chain 'P' and (resid 1867 through 1872 )
63X-RAY DIFFRACTION63chain 'P' and (resid 1873 through 1877 )
64X-RAY DIFFRACTION64chain 'P' and (resid 1878 through 1900 )
65X-RAY DIFFRACTION65chain 'P' and (resid 1901 through 1910 )
66X-RAY DIFFRACTION66chain 'P' and (resid 1911 through 1915 )
67X-RAY DIFFRACTION67chain 'P' and (resid 1916 through 1927 )
68X-RAY DIFFRACTION68chain 'Q' and (resid 1 through 164 )
69X-RAY DIFFRACTION69chain 'Q' and (resid 165 through 367 )
70X-RAY DIFFRACTION70chain 'R' and (resid 1867 through 1880 )
71X-RAY DIFFRACTION71chain 'R' and (resid 1902 through 1916 )
72X-RAY DIFFRACTION72chain 'R' and (resid 1917 through 1927 )
73X-RAY DIFFRACTION73chain 'S' and (resid 2 through 30 )
74X-RAY DIFFRACTION74chain 'S' and (resid 31 through 50 )
75X-RAY DIFFRACTION75chain 'S' and (resid 51 through 130 )
76X-RAY DIFFRACTION76chain 'S' and (resid 131 through 188 )
77X-RAY DIFFRACTION77chain 'S' and (resid 189 through 307 )
78X-RAY DIFFRACTION78chain 'S' and (resid 308 through 367 )
79X-RAY DIFFRACTION79chain 'T' and (resid 1866 through 1875 )
80X-RAY DIFFRACTION80chain 'T' and (resid 1876 through 1901 )
81X-RAY DIFFRACTION81chain 'T' and (resid 1902 through 1906 )
82X-RAY DIFFRACTION82chain 'T' and (resid 1907 through 1916 )
83X-RAY DIFFRACTION83chain 'T' and (resid 1917 through 1921 )
84X-RAY DIFFRACTION84chain 'T' and (resid 1922 through 1926 )
85X-RAY DIFFRACTION85chain 'U' and (resid 2 through 50 )
86X-RAY DIFFRACTION86chain 'U' and (resid 51 through 188 )
87X-RAY DIFFRACTION87chain 'U' and (resid 189 through 367 )
88X-RAY DIFFRACTION88chain 'V' and (resid 1867 through 1871 )
89X-RAY DIFFRACTION89chain 'V' and (resid 1872 through 1876 )
90X-RAY DIFFRACTION90chain 'V' and (resid 1877 through 1902 )
91X-RAY DIFFRACTION91chain 'V' and (resid 1903 through 1907 )
92X-RAY DIFFRACTION92chain 'V' and (resid 1908 through 1912 )
93X-RAY DIFFRACTION93chain 'V' and (resid 1913 through 1917 )
94X-RAY DIFFRACTION94chain 'V' and (resid 1918 through 1926 )
95X-RAY DIFFRACTION95chain 'W' and (resid 2 through 130 )
96X-RAY DIFFRACTION96chain 'W' and (resid 131 through 208 )
97X-RAY DIFFRACTION97chain 'W' and (resid 209 through 328 )
98X-RAY DIFFRACTION98chain 'W' and (resid 329 through 367 )
99X-RAY DIFFRACTION99chain 'X' and (resid 1866 through 1870 )
100X-RAY DIFFRACTION100chain 'X' and (resid 1871 through 1875 )
101X-RAY DIFFRACTION101chain 'X' and (resid 1876 through 1880 )
102X-RAY DIFFRACTION102chain 'X' and (resid 1881 through 1905 )
103X-RAY DIFFRACTION103chain 'X' and (resid 1906 through 1915 )
104X-RAY DIFFRACTION104chain 'X' and (resid 1916 through 1925 )

+
万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://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

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