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- PDB-3zrt: Crystal structure of human PSD-95 PDZ1-2 -

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基本情報

登録情報
データベース: PDB / ID: 3zrt
タイトルCrystal structure of human PSD-95 PDZ1-2
要素DISKS LARGE HOMOLOG 4
キーワードSIGNALING PROTEIN
機能・相同性
機能・相同性情報


LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior / cerebellar mossy fiber / neuron spine / Synaptic adhesion-like molecules / AMPA glutamate receptor clustering / establishment or maintenance of epithelial cell apical/basal polarity / protein localization to synapse / cellular response to potassium ion / dendritic spine morphogenesis / Trafficking of AMPA receptors / negative regulation of receptor internalization / juxtaparanode region of axon / acetylcholine receptor binding / neuron projection terminus / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / NMDA selective glutamate receptor signaling pathway / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / social behavior / locomotory exploration behavior / AMPA glutamate receptor complex / Long-term potentiation / Signaling by ERBB4 / neuromuscular process controlling balance / excitatory synapse / positive regulation of excitatory postsynaptic potential / D1 dopamine receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / learning / PDZ domain binding / adherens junction / establishment of protein localization / synaptic membrane / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / neuromuscular junction / cell-cell adhesion / kinase binding / endocytic vesicle membrane / cell junction / synaptic vesicle / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / synapse / protein-containing complex binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / signal transduction / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
Rhinovirus 14, subunit 4 - #60 / Rhinovirus 14, subunit 4 / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site ...Rhinovirus 14, subunit 4 - #60 / Rhinovirus 14, subunit 4 / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / Other non-globular / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Special / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
類似検索 - ドメイン・相同性
Disks large homolog 4
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: 3.398 Å
データ登録者Sorensen, P.L. / Kastrup, J.S. / Gajhede, M.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2012
タイトル: A High-Affinity, Dimeric Inhibitor of Psd-95 Bivalently Interacts with Pdz1-2 and Protects Against Ischemic Brain Damage.
著者: Bach, A. / Clausen, B.H. / Moller, M. / Vestergaard, B. / Chi, C.N. / Round, A. / Sorensen, P.L. / Nissen, K.B. / Kastrup, J.S. / Gajhede, M. / Jemth, P. / Kristensen, A.S. / Lundstrom, P. / ...著者: Bach, A. / Clausen, B.H. / Moller, M. / Vestergaard, B. / Chi, C.N. / Round, A. / Sorensen, P.L. / Nissen, K.B. / Kastrup, J.S. / Gajhede, M. / Jemth, P. / Kristensen, A.S. / Lundstrom, P. / Lambertsen, K.L. / Stromgaard, K.
履歴
登録2011年6月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02012年3月21日Provider: repository / タイプ: Initial release
改定 1.12019年12月18日Group: Derived calculations / Other
カテゴリ: pdbx_database_status / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list
改定 1.22023年12月20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: DISKS LARGE HOMOLOG 4
B: DISKS LARGE HOMOLOG 4
C: DISKS LARGE HOMOLOG 4
D: DISKS LARGE HOMOLOG 4


分子量 (理論値)分子数
合計 (水以外)85,3894
ポリマ－85,3894
非ポリマー00
水00
1
A: DISKS LARGE HOMOLOG 4
C: DISKS LARGE HOMOLOG 4


分子量 (理論値)分子数
合計 (水以外)42,6952
ポリマ－42,6952
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: DISKS LARGE HOMOLOG 4
D: DISKS LARGE HOMOLOG 4


分子量 (理論値)分子数
合計 (水以外)42,6952
ポリマ－42,6952
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)112.150, 112.150, 196.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
32
42
13
23
33
14
24
34
44
15
25
35
16
26
36
46
17
27
18
28
38
48
19
29
110
210
310
410

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ -7:3 )
211CHAIN B AND (RESSEQ -7:3 )
112CHAIN A AND (RESSEQ 4:9 )
212CHAIN B AND (RESSEQ 4:9 )
312CHAIN C AND (RESSEQ 4:9 )
412CHAIN D AND (RESSEQ 4:9 )
113CHAIN A AND (RESSEQ 10:57 )
213CHAIN B AND (RESSEQ 10:57 )
313CHAIN C AND (RESSEQ 10:57 )
114CHAIN A AND (RESSEQ 58:66 )
214CHAIN B AND (RESSEQ 58:66 )
314CHAIN C AND (RESSEQ 58:66 )
414CHAIN D AND (RESSEQ 58:66 )
115CHAIN A AND (RESSEQ 67:86 )
215CHAIN B AND (RESSEQ 67:86 )
315CHAIN C AND (RESSEQ 67:86 )
116CHAIN A AND (RESSEQ 88:92 )
216CHAIN B AND (RESSEQ 88:92 )
316CHAIN C AND (RESSEQ 88:92 )
416CHAIN D AND (RESSEQ 88:92 )
117CHAIN A AND (RESSEQ 93:99 )
217CHAIN B AND (RESSEQ 93:99 )
118CHAIN A AND (RESSEQ 100:178 )
218CHAIN B AND (RESSEQ 100:178 )
318CHAIN C AND (RESSEQ 100:178 )
418CHAIN D AND (RESSEQ 100:178 )
119CHAIN A AND (RESSEQ 179:179 )
219CHAIN B AND (RESSEQ 179:179 )
1110CHAIN A AND (RESSEQ 180:187 )
2110CHAIN B AND (RESSEQ 180:187 )
3110CHAIN C AND (RESSEQ 180:187 )
4110CHAIN D AND (RESSEQ 180:187 )

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixベクター
1given(0.878148, 0.478117, 0.016137), (0.478046, -0.878296, 0.008278), (0.018131, 0.000445, -0.999836)-6.83139, 26.5973, 19.8615
2given(0.878148, 0.478117, 0.016137), (0.478046, -0.878296, 0.008278), (0.018131, 0.000445, -0.999836)-6.83139, 26.5973, 19.8615
3given(-0.513938, -0.686193, 0.514788), (-0.751825, 0.071339, -0.655492), (0.41307, -0.723913, -0.552561)-61.815, -11.3248, 46.1599
4given(-0.663541, 0.568581, -0.486239), (-0.72147, -0.314325, 0.616993), (0.197973, 0.760207, 0.618782)-65.4018, -22.5045, 22.1794
5given(0.888485, 0.458901, -0.002092), (0.458886, -0.88848, -0.005197), (-0.004244, 0.003658, -0.999984)-6.51625, 26.1868, 19.6697
6given(-0.437725, -0.739458, 0.511467), (-0.785329, 0.03746, -0.617944), (0.437784, -0.67216, -0.597115)-59.0497, -14.5356, 49.8447
7given(0.891557, 0.452828, 0.008548), (0.452651, -0.891528, 0.016904), (0.015276, -0.011202, -0.999821)-6.44304, 26.3939, 19.8307
8given(-0.527988, -0.662466, 0.531383), (-0.745032, 0.060991, -0.664235), (0.407623, -0.746605, -0.525761)-62.5621, -11.0456, 44.9251
9given(-0.676752, 0.58235, -0.450418), (-0.712288, -0.363225, 0.600595), (0.186153, 0.72728, 0.660613)-67.5719, -20.6265, 22.1949
10given(0.88002, 0.474751, 0.0133), (0.474447, -0.880038, 0.02079), (0.021574, -0.011986, -0.999695)-6.64562, 26.46, 19.9407
11given(-0.530087, -0.677758, 0.50956), (-0.737147, 0.071337, -0.671957), (0.419074, -0.731816, -0.537422)-62.4819, -10.5939, 45.8882
12given(0.888876, 0.457748, -0.019138), (0.456291, -0.888258, -0.05289), (-0.04121, 0.03828, -0.998417)-6.40826, 26.3994, 18.8313
13given(-0.519313, -0.6834, 0.513107), (-0.72424, 0.033226, -0.688747), (0.453641, -0.729288, -0.5122)-62.0343, -9.64369, 47.3374
14given(-0.696348, 0.604936, -0.386202), (-0.694786, -0.433295, 0.574045), (0.179921, 0.668063, 0.722025)-67.8071, -18.9254, 22.4473
15given(0.87939, 0.475936, -0.012566), (0.476073, -0.879321, 0.012195), (-0.005246, -0.016706, -0.999847)-6.79841, 26.4852, 19.7844
16given(-0.533114, -0.678428, 0.505495), (-0.706477, 0.028243, -0.707172), (0.465489, -0.734124, -0.49435)-62.5783, -8.0902, 47.7177
17given(-0.660206, 0.596066, -0.456984), (-0.732926, -0.378295, 0.565432), (0.16416, 0.708236, 0.686624)-66.4658, -21.6446, 21.0095
18given(0.879072, 0.476685, 0.002073), (0.476572, -0.878943, 0.01839), (0.010588, -0.015178, -0.999829)-6.70362, 26.5083, 19.8291
19given(-0.527852, -0.665354, 0.527899), (-0.747427, 0.068691, -0.660783), (0.403393, -0.743361, -0.533562)-62.4399, -11.1566, 44.9243
20given(-0.665914, 0.575722, -0.474451), (-0.721833, -0.336573, 0.604712), (0.188458, 0.74516, 0.639703)-66.008, -22.0293, 21.9513
21given(0.89639, 0.442406, 0.027609), (0.442401, -0.896793, 0.006606), (0.027682, 0.006293, -0.999597)-5.78042, 26.022, 19.8424
22given(-0.583085, -0.55817, 0.590304), (-0.750745, 0.092519, -0.654081), (0.310474, -0.824552, -0.47299)-64.3678, -11.1633, 38.0664
23given(-0.729671, 0.476449, -0.490486), (-0.663912, -0.321896, 0.674985), (0.16371, 0.818156, 0.551198)-67.1497, -19.3767, 18.943
24given(0.877441, 0.479642, -0.006334), (0.479573, -0.877445, -0.009969), (-0.01034, 0.005709, -0.99993)-6.89592, 26.6827, 19.2049
25given(0.88505, 0.465022, 0.021008), (0.465222, -0.885176, -0.005643), (0.015971, 0.014768, -0.999763)-6.55451, 26.4844, 19.6421
26given(-0.337578, -0.76012, 0.55521), (-0.834373, -0.031402, -0.550305), (0.435733, -0.649024, -0.623623)-58.3193, -17.0808, 50.0395
27given(-0.63193, 0.522624, -0.572301), (-0.771007, -0.348825, 0.532794), (0.078818, 0.777937, 0.62338)-64.857, -23.8943, 17.8998

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要素

#1: タンパク質
DISKS LARGE HOMOLOG 4 / POSTSYNAPTIC DENSITY PROTEIN 95 / PSD-95 / SYNAPSE-ASSOCIATED PROTEIN 90 / SAP-90 / SAP90


分子量: 21347.328 Da / 分子数: 4 / 断片: PDZ1-2, REISDUES 61-249 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P78352

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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: 51 % / 解説: NONE
結晶化pH: 4.5
詳細: 0.1 M SODIUM ACETATE TRIHYDRATE PH 6.0, 2.0 M SODIUM FORMATE AND 5 % PEG 4000 (DROP SIZE: 1 UL SAMPLE AND 1UL RESERVOIR SOLUTION)

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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: ESRF / ビームライン: ID23-2 / 波長: 1.03
検出器タイプ: MARRESEARCH / 検出器: CCD / 日付: 2008年10月3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: 1.03 Å / 相対比: 1
反射解像度: 3.4→50 Å / Num. obs: 16900 / % possible obs: 95 % / Observed criterion σ(I): 2 / 冗長度: 3.6 % / Biso Wilson estimate: 49.14 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.3
反射 シェル解像度: 3.4→3.58 Å / 冗長度: 3.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.6 / % possible all: 97

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
MOSFLMデータ削減
SCALA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 ENTRY 2I1N

2i1n


解像度: 3.398→48.679 Å / SU ML: 0.62 / σ(F): 1.35 / 位相誤差: 23.21 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2638 861 5.1 %
Rwork0.2192 --
obs0.2214 16881 94.23 %
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 / Bsol: 20.003 Å2 / ksol: 0.325 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1-3.9291 Å20 Å20 Å2
2--3.9291 Å20 Å2
3----9.5579 Å2
精密化ステップサイクル: LAST / 解像度: 3.398→48.679 Å
タンパク質核酸リガンド溶媒全体
原子数5311 0 0 0 5311
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0075398
X-RAY DIFFRACTIONf_angle_d0.9857284
X-RAY DIFFRACTIONf_dihedral_angle_d16.2861996
X-RAY DIFFRACTIONf_chiral_restr0.056825
X-RAY DIFFRACTIONf_plane_restr0.006954
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A94X-RAY DIFFRACTIONPOSITIONAL
12B94X-RAY DIFFRACTIONPOSITIONAL0.032
21A54X-RAY DIFFRACTIONPOSITIONAL
22B54X-RAY DIFFRACTIONPOSITIONAL0.031
23C54X-RAY DIFFRACTIONPOSITIONAL0.038
24D54X-RAY DIFFRACTIONPOSITIONAL0.029
31A344X-RAY DIFFRACTIONPOSITIONAL
32B344X-RAY DIFFRACTIONPOSITIONAL0.031
33C344X-RAY DIFFRACTIONPOSITIONAL0.032
41A72X-RAY DIFFRACTIONPOSITIONAL
42B72X-RAY DIFFRACTIONPOSITIONAL0.034
43C72X-RAY DIFFRACTIONPOSITIONAL0.029
44D72X-RAY DIFFRACTIONPOSITIONAL0.037
51A144X-RAY DIFFRACTIONPOSITIONAL
52B144X-RAY DIFFRACTIONPOSITIONAL0.03
53C144X-RAY DIFFRACTIONPOSITIONAL0.033
61A46X-RAY DIFFRACTIONPOSITIONAL
62B46X-RAY DIFFRACTIONPOSITIONAL0.036
63C46X-RAY DIFFRACTIONPOSITIONAL0.057
64D46X-RAY DIFFRACTIONPOSITIONAL0.047
71A57X-RAY DIFFRACTIONPOSITIONAL
72B57X-RAY DIFFRACTIONPOSITIONAL0.036
81A579X-RAY DIFFRACTIONPOSITIONAL
82B579X-RAY DIFFRACTIONPOSITIONAL0.041
83C579X-RAY DIFFRACTIONPOSITIONAL0.051
84D579X-RAY DIFFRACTIONPOSITIONAL0.046
91A8X-RAY DIFFRACTIONPOSITIONAL
92B8X-RAY DIFFRACTIONPOSITIONAL0.023
101A64X-RAY DIFFRACTIONPOSITIONAL
102B64X-RAY DIFFRACTIONPOSITIONAL0.04
103C64X-RAY DIFFRACTIONPOSITIONAL0.045
104D64X-RAY DIFFRACTIONPOSITIONAL0.047
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.398-3.61080.31471370.27082653X-RAY DIFFRACTION95
3.6108-3.88950.27441620.23412622X-RAY DIFFRACTION95
3.8895-4.28070.26991570.20442636X-RAY DIFFRACTION95
4.2807-4.89970.22831400.17772654X-RAY DIFFRACTION94
4.8997-6.17110.2431290.20292686X-RAY DIFFRACTION94
6.1711-48.68360.25871360.23372769X-RAY DIFFRACTION91
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)
10.6281-0.48470.38952.15021.3569-0.745-0.04540.69230.08150.0820.34430.02580.6898-0.5039-0.09490.34190.08210.06530.52940.01390.2667-30.191912.564818.6235
21.34980.38880.4271.5747-0.926-0.8586-0.4055-0.54470.1983-1.03910.1377-0.11580.2514-0.22350.2840.36210.10.13910.2027-0.02750.3021-27.27141.16530.6359
30.0277-0.00030.00380.1073-0.0240.1014-0.1317-0.21970.21980.03320.36390.13630.23580.0740.04940.35390.07910.11380.21980.07270.1636-17.15016.279528.2277
4-0.00440.032-0.05350.0836-0.11580.12050.0653-0.1073-0.0427-0.1569-0.0496-0.14-0.0399-0.05480.11340.2679-0.04750.04530.22340.25010.2542-18.708812.7224-8.9046
50.93320.2388-0.80710.14410.090.40970.252-0.7136-0.0915-0.16340.12390.092-0.2990.1298-0.06680.17380.0520.04230.27930.06090.4405-43.6045-16.527521.306
60.4882-0.4658-1.19321.09980.3522-1.8623-0.08980.4380.35890.2197-0.2054-0.0357-0.0278-0.11650.19770.9739-0.2471-0.25661.13210.27810.6637-51.573823.0891-2.0249
7-0.44080.5481-0.35290.66920.32290.2532-0.0036-0.0379-0.0142-0.19050.186-0.2984-0.06420.2045-0.07710.0835-0.05050.06340.1497-0.14840.2944-11.211415.540221.819
80.3272-0.40050.1172-0.55090.19861.4298-0.225-0.11730.194-0.0308-0.1731-0.3373-0.94860.1268-0.60080.144-0.13680.15710.134-0.08850.265-9.17967.3976-2.2696
91.3790.3426-0.17541.3424-0.46980.56390.3249-0.47880.2410.613-0.26750.5485-0.1345-0.2619-0.28860.2351-0.11310.15330.33690.04550.3919-56.3023-15.148521.6987
100.42730.22070.40110.51121.08340.94010.1977-0.505-0.10730.13450.2137-0.21750.2199-0.1715-0.13850.3304-0.10770.05520.1123-0.02860.1344-20.673916.323329.7174
110.28240.1865-0.09620.233-0.24991.08820.35330.27060.4314-0.52470.27060.2965-0.71090.1108-0.23630.4478-0.20240.1548-0.01930.1791-0.02-16.97912.1032-10.1386
12-0.39920.7209-0.71230.4194-0.09510.77260.19020.4607-0.12330.19070.13890.39180.0694-0.2718-0.14110.08820.0781-0.07390.2454-0.06240.2458-48.793-14.710512.0245
13-0.6964-1.5504-0.95030.8109-0.61390.1856-0.0587-0.3442-0.7969-0.19790.34120.58550.1-1.1493-0.1921-0.6527-0.2166-0.39261.8168-0.03010.3299-56.375819.00556.7116
14-0.3564-0.16550.0268-0.2266-1.03670.83360.6043-0.2410.5678-0.01050.01970.0406-0.1035-0.22870.0969-0.3212-0.4701-0.0270.0244-0.11880.3482-16.309222.715228.1548
150.5477-0.06140.49761.2483-0.64620.49920.5474-0.1653-0.5209-0.29770.0233-0.6853-0.1739-0.0507-0.0252-0.2043-0.11120.27970.0588-0.0180.2874-10.1736-1.3262-8.5512
160.54070.7423-0.62760.4252-0.73110.84960.23590.66260.6322-0.07110.44610.8567-0.195-0.6685-0.3527-0.4033-0.1010.0250.37810.18580.2171-56.3552-16.029610.8446
17-3.8655-0.9556-1.812-1.972-3.9471-1.01860.0669-0.42890.5599-0.21770.198-0.16780.5838-0.22140.05650.2210.04550.0710.3946-0.08440.2012-18.42028.919925.3333
18-1.5132-3.77641.20892.1792-3.6034-0.4572-0.67660.3851-0.73150.17190.42-0.51560.1054-0.37480.2970.4762-0.20160.18730.1549-0.00780.3305-18.69669.7785-5.9676
19-0.3399-0.3028-1.6715-1.7946-1.4443-2.4367-0.05611.26120.3961-0.7296-0.0109-0.10550.41640.1603-0.28860.1085-0.0067-0.51690.3879-0.0458-0.8607-46.1408-13.29220.4249
202.86932.2244-3.4688-9.0253-2.28151.1127-0.5675-1.50830.47530.72220.6834-0.2697-1.2394-0.7843-0.25921.25770.0847-0.3321.30180.1410.7179-53.343419.4629-1.5946
21-0.15130.1724-0.09480.42840.18620.0001-0.1892-0.19490.4565-0.0965-0.64450.37350.27760.0341-0.03590.1825-0.1706-0.1131-0.4989-0.8914-0.6281-17.4778-3.37212.8736
220.3380.1578-0.04190.0179-0.3883-0.005-0.38730.2637-0.53710.2059-0.24430.2236-0.3067-0.432-0.0528-0.04540.07920.20020.2485-0.05630.0261-23.60521.36256.62
230.1966-0.1108-0.0120.29530.07290.64720.0605-0.17180.12310.09090.0390.05350.18110.03910.30820.2052-0.040.01510.00870.0480.0369-31.4378-14.07179.8097
240.368-0.2681-0.28180.3637-0.00860.890.7629-0.93440.25520.2649-0.2868-0.2414-0.2222-0.51240.3489-0.30420.7367-0.1793-0.4740.29270.018-41.05924.18839.4598
250.6218-0.8359-0.25822.6530.52480.6674-0.1934-0.10570.14190.89380.5825-0.17240.2464-0.5210.04730.09370.0347-0.0678-0.0588-0.15220.0923-29.0945.596338.2925
261.04410.6529-1.0454.00581.01980.9315-0.13080.39550.138-0.91280.3495-0.4567-0.6741-0.3023-0.00910.3102-0.06650.01030.17730.03130.0794-29.32837.7317-18.9379
277.17451.99895.28341.99952.00067.6769-0.2347-0.08780.0733-0.139-0.32750.4407-0.3083-0.33190.51690.03650.0428-0.59520.31950.0049-0.0117-37.0569-22.0086-3.1914
289.50031.9964-3.90152.00741.99957.2738-0.1131-0.1737-0.07930.15370.11450.0626-0.0849-0.4591-0.030.2008-0.12480.19720.76620.43291.0185-49.792428.346122.5455
292.90350.95921.8192.94542.14763.5045-0.88630.10520.3543-0.43970.90880.282-0.06330.03090.07840.98350.2269-0.34420.5264-0.04780.3232-24.864918.20746.9812
303.65031.88324.46479.73730.27515.4540.48360.5153-1.3119-1.35190.26440.3011-0.06040.1137-0.72771.07510.3030.170.5817-0.3180.5264-19.3961-1.9222-26.914
310.1387-0.10750.0584-0.0755-0.1980.7713-0.2462-0.1104-0.3957-0.4166-0.19730.19660.1535-0.0779-0.0584-0.2107-0.0321-0.14450.15260.0107-0.0044-27.2188-13.7292.891
32-0.61160.20121.04350.1598-0.37580.719-0.2854-0.19380.0454-0.103-0.30120.01750.0637-0.2453-0.2764-0.3492-0.00610.68330.13490.2297-0.5907-37.124725.656416.5002
330.2643-0.30490.7551.3568-1.1918-1.0271-0.4409-0.54940.02310.24170.4562-0.0710.3566-0.2571-0.06050.38590.01630.07510.19670.03740.0926-33.96986.976944.7697
341.3715-1.7353-0.08633.2981-2.1566-5.68660.0630.4506-0.2684-0.78951.12930.2198-0.1637-0.37650.00840.71190.0139-0.4840.3680.0057-0.2319-32.74094.2297-25.5025
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID -7:3
2X-RAY DIFFRACTION2CHAIN B AND RESID -7:3
3X-RAY DIFFRACTION3CHAIN A AND RESID 4:9
4X-RAY DIFFRACTION4CHAIN B AND RESID 4:9
5X-RAY DIFFRACTION5CHAIN C AND RESID 4:9
6X-RAY DIFFRACTION6CHAIN D AND RESID 4:9
7X-RAY DIFFRACTION7CHAIN A AND RESID 10:57
8X-RAY DIFFRACTION8CHAIN B AND RESID 10:57
9X-RAY DIFFRACTION9CHAIN C AND RESID 10:57
10X-RAY DIFFRACTION10CHAIN A AND RESID 58:66
11X-RAY DIFFRACTION11CHAIN B AND RESID 58:66
12X-RAY DIFFRACTION12CHAIN C AND RESID 58:66
13X-RAY DIFFRACTION13CHAIN D AND RESID 58:66
14X-RAY DIFFRACTION14CHAIN A AND RESID 67:86
15X-RAY DIFFRACTION15CHAIN B AND RESID 67:86
16X-RAY DIFFRACTION16CHAIN C AND RESID 67:86
17X-RAY DIFFRACTION17CHAIN A AND RESID 88:92
18X-RAY DIFFRACTION18CHAIN B AND RESID 88:92
19X-RAY DIFFRACTION19CHAIN C AND RESID 88:92
20X-RAY DIFFRACTION20CHAIN D AND RESID 88:92
21X-RAY DIFFRACTION21CHAIN A AND RESID 93:99
22X-RAY DIFFRACTION22CHAIN B AND RESID 93:99
23X-RAY DIFFRACTION23CHAIN A AND RESID 100:178
24X-RAY DIFFRACTION24CHAIN B AND RESID 100:178
25X-RAY DIFFRACTION25CHAIN C AND RESID 100:178
26X-RAY DIFFRACTION26CHAIN D AND RESID 100:178
27X-RAY DIFFRACTION27CHAIN A AND RESID 179
28X-RAY DIFFRACTION28CHAIN B AND RESID 179
29X-RAY DIFFRACTION29CHAIN C AND RESID 179
30X-RAY DIFFRACTION30CHAIN D AND RESID 179
31X-RAY DIFFRACTION31CHAIN A AND RESID 180:187
32X-RAY DIFFRACTION32CHAIN B AND RESID 180:187
33X-RAY DIFFRACTION33CHAIN C AND RESID 180:187
34X-RAY DIFFRACTION34CHAIN D AND RESID 180:187

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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