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- PDB-5o9a: Crystal structure of the GluA2 ligand-binding domain (S1S2J-L504Y... -

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基本情報

登録情報
データベース: PDB / ID: 5o9a
タイトルCrystal structure of the GluA2 ligand-binding domain (S1S2J-L504Y-N775S) in complex with glutamate and BPAM121 at 1.78 A resolution
要素Glutamate receptor 2,Glutamate receptor 2
キーワードMEMBRANE PROTEIN / AMPA receptor / Ligand-binding domain / positive allosteric modulator / signaling protein / Ionotropic glutamate receptor / GLUA2 / GLUR2 / L504Y-N775S
機能・相同性
機能・相同性情報


spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion ...spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / kainate selective glutamate receptor activity / immunoglobulin binding / asymmetric synapse / AMPA glutamate receptor complex / regulation of receptor recycling / extracellularly glutamate-gated ion channel activity / cellular response to glycine / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / conditioned place preference / positive regulation of synaptic transmission / response to fungicide / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / extracellular ligand-gated monoatomic ion channel activity / cytoskeletal protein binding / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / ionotropic glutamate receptor signaling pathway / ionotropic glutamate receptor binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / positive regulation of excitatory postsynaptic potential / dendritic shaft / synaptic membrane / SNARE binding / PDZ domain binding / synaptic transmission, glutamatergic / establishment of protein localization / protein tetramerization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / receptor internalization / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / long-term synaptic potentiation / amyloid-beta binding / synaptic vesicle membrane / presynapse / growth cone / signaling receptor activity / presynaptic membrane / scaffold protein binding / dendritic spine / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / external side of plasma membrane / axon / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
類似検索 - 分子機能
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / Receptor, ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / Receptor, ligand binding region / Receptor family ligand binding region / D-Maltodextrin-Binding Protein; domain 2 / Periplasmic binding protein-like I / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-7M6 / CITRIC ACID / GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
類似検索 - 構成要素
生物種Rattus norvegicus (ドブネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.78 Å
データ登録者Laulumaa, S. / Rovinskaja, K. / Frydenvang, K.A. / Kastrup, J.S.
引用ジャーナル: J. Med. Chem. / 年: 2018
タイトル: 7-Phenoxy-Substituted 3,4-Dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides as Positive Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors ...タイトル: 7-Phenoxy-Substituted 3,4-Dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides as Positive Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors with Nanomolar Potency.
著者: Goffin, E. / Drapier, T. / Larsen, A.P. / Geubelle, P. / Ptak, C.P. / Laulumaa, S. / Rovinskaja, K. / Gilissen, J. / Tullio, P. / Olsen, L. / Frydenvang, K. / Pirotte, B. / Hanson, J. / ...著者: Goffin, E. / Drapier, T. / Larsen, A.P. / Geubelle, P. / Ptak, C.P. / Laulumaa, S. / Rovinskaja, K. / Gilissen, J. / Tullio, P. / Olsen, L. / Frydenvang, K. / Pirotte, B. / Hanson, J. / Oswald, R.E. / Kastrup, J.S. / Francotte, P.
履歴
登録2017年6月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年1月3日Provider: repository / タイプ: Initial release
改定 1.12018年1月24日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
改定 1.22024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 / 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 1.32024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
C: Glutamate receptor 2,Glutamate receptor 2
D: Glutamate receptor 2,Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)121,36842
ポリマ－117,2074
非ポリマー4,16138
水20,8971160
1
A: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)60,48420
ポリマ－58,6032
非ポリマー1,88018
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-112 kcal/mol
Surface area24850 Å2
手法PISA
2
C: Glutamate receptor 2,Glutamate receptor 2
D: Glutamate receptor 2,Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)60,88422
ポリマ－58,6032
非ポリマー2,28120
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-146 kcal/mol
Surface area24320 Å2
手法PISA
単位格子
Length a, b, c (Å)47.308, 98.408, 121.787
Angle α, β, γ (deg.)90.000, 90.530, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 5:15 or resseq 17:20 or (resid...
21(chain B and (resseq 5:15 or resseq 17:20 or (resid...
31(chain D and (resseq 5:15 or resseq 17:20 or (resid...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPRO(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA5 - 155 - 15
12VALVALLYSLYS(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA17 - 2017 - 20
13HISHISHISHIS(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA2323
14GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
15GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
16GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
17GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
18GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
19GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
110GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
111GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
112GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
113GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
114GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
115GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
116GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
117GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
118GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
21THRTHRPROPRO(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB5 - 155 - 15
22VALVALLYSLYS(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB17 - 2017 - 20
23HISHISHISHIS(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB2323
24GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
25GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
26GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
27GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
28GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
29GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
210GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
211GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
212GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
213GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
214GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
215GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
216GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
217GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
218GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
31THRTHRPROPRO(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD5 - 155 - 15
32VALVALLYSLYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD17 - 2017 - 20
33HISHISHISHIS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2323
34ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
35ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
36ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
37ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
38ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
39ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
310ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
311ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
312ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
313ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
314ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
315ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
316ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
317ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
318ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261

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要素

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タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Glutamate receptor 2,Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


分子量: 29301.729 Da / 分子数: 4 / 変異: L504Y,N775S / 由来タイプ: 組換発現
詳細: Native GluA2 is a membrane protein. The crystallized protein is a double mutant (L540Y, N775S) of the ligand-binding domain of GluA2. Transmembrane regions were replaced with a Gly-Thr linker ...詳細: Native GluA2 is a membrane protein. The crystallized protein is a double mutant (L540Y, N775S) of the ligand-binding domain of GluA2. Transmembrane regions were replaced with a Gly-Thr linker (residues 117-118). Gly1 is a cloning remnant. The sequence matches discontinuously with reference database (413-527, 653-797).
由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Gria2, Glur2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P19491

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非ポリマー , 9種, 1198分子

#2: 化合物
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 16 / 由来タイプ: 組換発現 / 式: SO4
#3: 化合物
ChemComp-7M6 / 7-chloro-4-(2-fluoroethyl)-2,3-dihydro-1,2,4-benzothiadiazine 1,1-dioxide


分子量: 264.704 Da / 分子数: 4 / 由来タイプ: 組換発現 / 式: C9H10ClFN2O2S
#4: 化合物
ChemComp-CL / CHLORIDE ION


分子量: 35.453 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Cl
#5: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C3H8O3
#6: 化合物
ChemComp-GLU / GLUTAMIC ACID


タイプ: L-peptide linking / 分子量: 147.129 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C5H9NO4
#7: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


分子量: 62.068 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6O2
#8: 化合物 ChemComp-CIT / CITRIC ACID


分子量: 192.124 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H8O7
#9: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER


分子量: 106.120 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H10O3
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1160 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.42 Å3/Da / 溶媒含有率: 49.14 %
結晶化温度: 279 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5
詳細: 18% PEG4000, 0.23 M lithium sulfate, 0.1 M phosphate citrate pH 4.5

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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: MAX II / ビームライン: I911-3 / 波長: 0.979 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2015年2月19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: 0.979 Å / 相対比: 1
反射解像度: 1.78→121.782 Å / Num. all: 106755 / Num. obs: 106755 / % possible obs: 100 % / 冗長度: 3.7 % / Biso Wilson estimate: 15.47 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Rsym value: 0.063 / Net I/av σ(I): 10.4 / Net I/σ(I): 14.7 / Num. measured all: 395853
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.78-1.883.60.377256042155820.2330.4450.3773.5100
1.88-1.993.70.249354342146820.1510.2920.2495.3100
1.99-2.133.70.1554.851284138090.0940.1820.1558100
2.13-2.33.70.1057.148006128750.0630.1230.10511.3100
2.3-2.523.70.082944383118740.050.0960.08213.7100
2.52-2.813.70.061240212107280.0360.070.0617.9100
2.81-3.253.80.04315.93553394560.0260.0510.04323.9100
3.25-3.983.70.03219.93016380580.0190.0380.03232.4100
3.98-5.633.70.02620.92323562100.0160.0310.02636.8100
5.63-49.2043.60.026201265334810.0160.0310.0263499.8

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解析

ソフトウェア
名称分類
PHENIX精密化
XDS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: 3TKD

3tkd


解像度: 1.78→49.204 Å / SU ML: 0.16 / 交差検証法: THROUGHOUT / σ(F): 1.38 / 位相誤差: 17.13 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1789 5325 4.99 %
Rwork0.1534 101384 -
obs0.1547 106709 99.98 %
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: 112.84 Å2 / Biso mean: 22.4654 Å2 / Biso min: 5.63 Å2
精密化ステップサイクル: final / 解像度: 1.78→49.204 Å
タンパク質核酸リガンド溶媒全体
原子数8178 0 199 1186 9563
Biso mean--41.23 29.23 -
残基数----1054
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0058868
X-RAY DIFFRACTIONf_angle_d0.78612010
X-RAY DIFFRACTIONf_chiral_restr0.0491304
X-RAY DIFFRACTIONf_plane_restr0.0051490
X-RAY DIFFRACTIONf_dihedral_angle_d15.8165450
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3712X-RAY DIFFRACTION4.403TORSIONAL
12B3712X-RAY DIFFRACTION4.403TORSIONAL
13D3712X-RAY DIFFRACTION4.403TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.80020.27311470.22634323579100
1.8002-1.82140.25011840.217834243608100
1.8214-1.84360.22281320.197833563488100
1.8436-1.8670.23641910.191633213512100
1.867-1.89150.20971820.190234223604100
1.8915-1.91740.19821520.186633313483100
1.9174-1.94480.19971730.189733873560100
1.9448-1.97390.21731780.184234063584100
1.9739-2.00470.20191760.176933293505100
2.0047-2.03760.21391860.169733603546100
2.0376-2.07270.18431720.157533673539100
2.0727-2.11040.19022030.154333223525100
2.1104-2.1510.18342250.1533793604100
2.151-2.19490.14971690.145233163485100
2.1949-2.24260.17691620.144934463608100
2.2426-2.29480.19021890.147433103499100
2.2948-2.35220.18041780.146933983576100
2.3522-2.41580.1751790.145733493528100
2.4158-2.48690.17621790.147834353614100
2.4869-2.56710.17241760.14833153491100
2.5671-2.65890.17621940.146833983592100
2.6589-2.76530.1931750.144733663541100
2.7653-2.89120.16141610.148433783539100
2.8912-3.04360.18192050.155633633568100
3.0436-3.23420.18361890.14533733562100
3.2342-3.48390.15371600.138634153575100
3.4839-3.83440.15311830.134433913574100
3.8344-4.38890.13471780.121234143592100
4.3889-5.52840.14661740.132534113585100
5.5284-49.22280.22391730.18923470364399
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1731-0.22920.0982.02630.27551.9456-0.05710.32230.1682-0.15370.04950.0294-0.05610.06760.02280.1313-0.0175-0.01730.10170.0130.06728.930926.540324.6711
22.3426-0.10210.59490.9970.46213.5005-0.11660.27290.1778-0.25460.16810.0268-0.3670.1871-0.01720.1849-0.0651-0.02140.14530.04430.11958.131931.686522.4919
32.88960.84580.01233.09270.55552.1461-0.0980.0193-0.3412-0.10910.0675-0.17360.27550.12940.0630.0897-0.00180.01930.1127-0.02340.088314.682616.850831.763
42.72390.63750.24510.68630.19480.6443-0.0261-0.074-0.03650.0154-0.0035-0.01540.01510.0540.03330.09720.012-0.00790.06520.00610.0463.909320.380639.4679
53.24210.5937-0.04872.8361-0.72433.87360.0463-0.285-0.22250.2671-0.0738-0.13340.2543-0.05190.02050.19970.0019-0.01250.06050.02570.1003-4.30188.240144.0692
62.03010.29450.50393.77750.81271.84270.0812-0.199-0.29310.019-0.0011-0.01480.6332-0.12480.00220.20840.001-0.00410.08050.02170.1254-3.27373.788641.5509
73.45530.60270.48543.7191-0.24552.776-0.03670.0882-0.0898-0.13770.0481-0.03490.1299-0.15060.00160.0964-0.007-0.00230.0787-0.010.0416-9.267915.953132.7976
86.06121.17934.61780.41961.20667.4588-0.0371-0.27880.2302-0.0165-0.11990.1173-0.2569-0.52810.09340.14990.0244-0.00650.0851-0.01530.1452-11.617120.528436.8308
93.51990.2456-0.14132.54110.32181.7461-0.00140.0070.18360.0509-0.0227-0.1453-0.16310.14650.02870.1109-0.0117-0.02080.0975-0.01210.047913.705832.428739.5142
106.0994.44651.72964.13311.26941.8442-0.19440.01480.5971-0.11160.0050.4834-0.1503-0.16640.19650.16960.0223-0.03690.1025-0.00830.1761-5.217534.780831.4429
111.9762-0.33740.14881.89020.0371.57880.0306-0.123-0.02890.1144-0.0402-0.06090.03040.23960.0030.0927-0.01270.00390.1871-0.00510.08098.910830.092970.5916
121.9016-0.3162-0.14711.809-0.40961.80310.0011-0.09530.25310.0396-0.018-0.0151-0.22490.11680.03170.1179-0.0317-0.01010.1297-0.02530.1098.795440.339157.1352
131.3679-0.351-0.52813.69760.50772.31380.2830.05710.4976-0.11620.00520.7486-0.4083-0.2505-0.22520.36940.02290.09570.1572-0.01680.4317-5.167652.155853.5174
144.0454-1.3164-1.22512.37260.15512.15170.0582-0.19560.2082-0.0027-0.04550.4935-0.0488-0.23730.00150.1468-0.0432-0.00910.1272-0.04640.2363-2.651837.678156.9725
154.9584-0.8075-1.64522.42930.18022.7186-0.092-0.1565-0.08430.05890.01480.3220.1567-0.25640.1030.1004-0.0117-0.00770.15380.00520.08570.603623.665559.111
162.1767-0.02320.39641.8329-0.02691.4685-0.10850.22-0.2024-0.18880.0728-0.0070.1736-0.15840.04840.1331-0.03380.0250.1257-0.01730.1012-9.570419.962484.6026
172.95240.72320.03993.5047-0.55592.4338-0.08760.0080.2912-0.09880.10520.1409-0.2729-0.14020.01740.06440.0179-0.01840.11270.03640.0857-15.840732.367592.4356
181.99470.8003-0.2270.81050.05860.98650.0318-0.09620.08120.053-0.02880.0163-0.05070.05590.00320.07860.0199-0.00210.07720.01150.057-2.025733.7527102.2695
191.75080.3499-0.90724.22850.09843.02610.0501-0.17970.2729-0.0560.01710.03-0.70840.1085-0.02170.13980.00340.01090.1031-0.02140.10631.888945.4827102.2621
203.08360.6237-0.45133.96980.24653.1232-0.05940.07040.0568-0.16480.08690.0201-0.08310.1373-0.01450.0567-0.0019-0.0050.10520.00850.04597.962533.480993.416
217.40850.8186-6.39940.1088-0.93258.3417-0.0142-0.2876-0.1844-0.0283-0.09-0.06420.1510.53680.07430.10910.0322-0.00350.09310.02090.143410.351628.613497.7008
223.2477-0.32630.99143.5911-0.72212.4886-0.0252-0.1226-0.3175-0.1520.03040.20790.256-0.2069-0.00590.1113-0.01510.02910.10240.01460.0733-14.699717.1572100.3095
234.44092.4896-1.30762.1311-0.56111.9774-0.3532-0.1688-0.8447-0.12370.025-0.56420.29260.23570.30450.19050.04970.07570.14410.02290.24724.073314.557592.28
242.00680.1572-0.33892.33820.36531.82730.0492-0.13190.04960.2085-0.02490.09910.0468-0.2363-0.00390.1076-0.01220.01330.17260.03380.0933-10.855916.0813131.105
253.8732-0.96011.74072.5041-1.86347.2532-0.0299-0.08080.08220.21610.04380.0555-0.2762-0.1825-0.00890.0937-0.0082-0.00220.0829-0.02370.0868-10.701921.7356131.3769
263.5876-0.59510.00534.86720.09672.3461-0.0654-0.0805-0.4271-0.01690.05670.22370.4935-0.28080.02920.13-0.06980.02620.16890.06620.1396-17.06986.9232122.1429
271.9463-0.44590.44782.76980.99510.6627-0.0353-0.2618-0.08380.0829-0.13530.27420.2197-0.31950.11830.102-0.04790.00740.17390.02560.1183-16.158711.8389119.5395
281.6903-0.61460.7011.0112-0.38431.2026-0.0431-0.0273-0.1375-0.2385-0.1038-0.19830.3350.13370.04230.17420.02330.06550.14310.06320.1641-1.78039.4835113.7569
291.417-0.28930.13741.28140.1580.35140.48820.2342-0.5633-1.0319-0.2603-0.15210.63930.15940.14720.74460.2523-0.0530.12260.10210.31862.1818-3.8374112.3432
307.7987-3.1817-0.47367.01712.53725.5346-0.0682-0.9925-0.40730.0414-0.002-0.43680.23790.17930.1060.1909-0.00840.00540.25340.11510.22918.0438-0.9217126.5183
312.2481-1.4065-0.12922.6612-0.92741.20210.0798-0.16060.1089-0.1201-0.1987-0.51410.10750.37630.090.16360.03520.06020.23680.0980.28167.42469.5175120.3405
323.05660.2251-0.2283.2886-0.55531.4711-0.0361-0.00330.031-0.13840.06530.3373-0.015-0.31920.00170.0884-0.0031-0.01850.14090.01360.0548-15.335122.0464114.5471
337.0824-2.25022.41563.2592-0.34272.8217-0.2217-0.18750.25720.07770.1043-0.5199-0.21140.50.20260.1066-0.0284-0.01420.2170.00590.15093.239824.3856123.7666
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )A1 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 47 )A23 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 79 )A48 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 123 )A80 - 123
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 152 )A124 - 152
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 173 )A153 - 173
7X-RAY DIFFRACTION7chain 'A' and (resid 174 through 202 )A174 - 202
8X-RAY DIFFRACTION8chain 'A' and (resid 203 through 217 )A203 - 217
9X-RAY DIFFRACTION9chain 'A' and (resid 218 through 243 )A218 - 243
10X-RAY DIFFRACTION10chain 'A' and (resid 244 through 263 )A244 - 263
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 47 )B1 - 47
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 123 )B48 - 123
13X-RAY DIFFRACTION13chain 'B' and (resid 124 through 187 )B124 - 187
14X-RAY DIFFRACTION14chain 'B' and (resid 188 through 230 )B188 - 230
15X-RAY DIFFRACTION15chain 'B' and (resid 231 through 264 )B231 - 264
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 47 )C1 - 47
17X-RAY DIFFRACTION17chain 'C' and (resid 48 through 79 )C48 - 79
18X-RAY DIFFRACTION18chain 'C' and (resid 80 through 152 )C80 - 152
19X-RAY DIFFRACTION19chain 'C' and (resid 153 through 173 )C153 - 173
20X-RAY DIFFRACTION20chain 'C' and (resid 174 through 202 )C174 - 202
21X-RAY DIFFRACTION21chain 'C' and (resid 203 through 217 )C203 - 217
22X-RAY DIFFRACTION22chain 'C' and (resid 218 through 243 )C218 - 243
23X-RAY DIFFRACTION23chain 'C' and (resid 244 through 263 )C244 - 263
24X-RAY DIFFRACTION24chain 'D' and (resid 2 through 22 )D2 - 22
25X-RAY DIFFRACTION25chain 'D' and (resid 23 through 47 )D23 - 47
26X-RAY DIFFRACTION26chain 'D' and (resid 48 through 79 )D48 - 79
27X-RAY DIFFRACTION27chain 'D' and (resid 80 through 93 )D80 - 93
28X-RAY DIFFRACTION28chain 'D' and (resid 94 through 123 )D94 - 123
29X-RAY DIFFRACTION29chain 'D' and (resid 124 through 173 )D124 - 173
30X-RAY DIFFRACTION30chain 'D' and (resid 174 through 187 )D174 - 187
31X-RAY DIFFRACTION31chain 'D' and (resid 188 through 217 )D188 - 217
32X-RAY DIFFRACTION32chain 'D' and (resid 218 through 243 )D218 - 243
33X-RAY DIFFRACTION33chain 'D' and (resid 244 through 261 )D244 - 261

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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

他の情報も見る