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- PDB-5oew: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in c... -

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基本情報

登録情報
データベース: PDB / ID: 5oew
タイトルCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with glutamate and positive allosteric modulator BPAM538
要素Glutamate receptor 2
キーワードMEMBRANE PROTEIN / Ionotropic glutamate receptor GluA2. ligand-binding domain / positive allosteric modulator
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 / ligand-gated monoatomic cation channel activity / perisynaptic space / 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 / ligand-gated monoatomic cation channel activity / perisynaptic space / 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 / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor 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 / establishment of protein localization / synaptic transmission, glutamatergic / 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 / growth cone / presynapse / 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-9TE / ACETATE ION / GLUTAMIC ACID / 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: 2 Å
データ登録者Larsen, A.P. / 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.
#1: ジャーナル: J. Med. Chem. / 年: 2013
タイトル: Synthesis, pharmacological and structural characterization, and thermodynamic aspects of GluA2-positive allosteric modulators with a 3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide scaffold.
著者: Norholm, A.B. / Francotte, P. / Olsen, L. / Krintel, C. / Frydenvang, K. / Goffin, E. / Challal, S. / Danober, L. / Botez-Pop, I. / Lestage, P. / Pirotte, B. / Kastrup, J.S.
履歴
登録2017年7月10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 ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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11月13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
B: Glutamate receptor 2
C: Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)90,31929
ポリマ－87,8363
非ポリマー2,48226
水9,386521
1
A: Glutamate receptor 2
B: Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,90516
ポリマ－58,5572
非ポリマー1,34714
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-203 kcal/mol
Surface area23460 Å2
手法PISA
2
C: Glutamate receptor 2
ヘテロ分子

C: Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)60,82726
ポリマ－58,5572
非ポリマー2,27024
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area4090 Å2
ΔGint-337 kcal/mol
Surface area23720 Å2
手法PISA
単位格子
Length a, b, c (Å)114.702, 164.374, 47.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and ((resid 3 and (name O or name...
21(chain B and (resseq 3:18 or resseq 20 or resseq...
31(chain C and ((resid 3 and (name O or name...

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
11ASNASNASNASN(chain A and ((resid 3 and (name O or name...AA33
12GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
13GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
14GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
15GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
16GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
17GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
18GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
19GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
110GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
111GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
112GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
113GLYGLYCYSCYS(chain A and ((resid 3 and (name O or name...AA1 - 2611 - 261
21ASNASNMETMET(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 183 - 18
22LYSLYSLYSLYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB2020
23LEULEUASNASN(chain B and (resseq 3:18 or resseq 20 or resseq...BB26 - 2926 - 29
24ARGARGGLUGLU(chain B and (resseq 3:18 or resseq 20 or resseq...BB31 - 4231 - 42
25ALAALAALAALA(chain B and (resseq 3:18 or resseq 20 or resseq...BB4444
26HISHISHISHIS(chain B and (resseq 3:18 or resseq 20 or resseq...BB4646
27ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
28ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
29ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
210ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
211ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
212ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
213ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
214ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
215ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
216ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
217ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
218ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
219ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
220ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
221ASNASNCYSCYS(chain B and (resseq 3:18 or resseq 20 or resseq...BB3 - 2613 - 261
31ASNASNASNASN(chain C and ((resid 3 and (name O or name...CC33
32GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
33GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
34GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
35GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
36GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
37GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
38GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
39GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
310GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
311GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
312GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261
313GLYGLYCYSCYS(chain C and ((resid 3 and (name O or name...CC1 - 2611 - 261

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要素

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タンパク質 , 1種, 3分子 ABC

#1: タンパク質 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: 29278.732 Da / 分子数: 3 / 由来タイプ: 組換発現
詳細: Ligand-binding domain, UNP residues 413-527 and 653-797 connected by a GT linker (numbering including signal peptide)
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 , 5種, 547分子

#2: 化合物 ChemComp-GLU / GLUTAMIC ACID


タイプ: L-peptide linking / 分子量: 147.129 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C5H9NO4
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 17 / 由来タイプ: 合成 / 式: Zn
#4: 化合物
ChemComp-ACT / ACETATE ION


分子量: 59.044 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C2H3O2
#5: 化合物 ChemComp-9TE / 4-cyclopropyl-7-(3-methoxyphenoxy)-2,3-dihydro-1$l^{6},2,4-benzothiadiazine 1,1-dioxide


分子量: 346.401 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C17H18N2O4S / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 521 / 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: 2.54 Å3/Da / 溶媒含有率: 51.57 %
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, 0.23M lithium-sulfate, 0.1M phosphate-citrate

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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: 1 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2013年5月14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: 2→29.27 Å / Num. all: 61361 / Num. obs: 61361 / % possible obs: 99.8 % / 冗長度: 4.1 % / Biso Wilson estimate: 20.77 Å2 / Rpim(I) all: 0.046 / Rrim(I) all: 0.099 / Rsym value: 0.087 / Net I/av σ(I): 6.5 / Net I/σ(I): 10.3 / Num. measured all: 253105
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2-2.114.10.31320.1720.3590.313100
2.11-2.244.20.2183.20.1180.2490.218100
2.24-2.394.10.1753.90.0950.20.175100
2.39-2.584.20.13850.0750.1580.138100
2.58-2.834.10.1076.30.0570.1230.107100
2.83-3.164.10.0837.70.0430.0950.083100
3.16-3.654.10.0688.90.0350.0780.06899.9
3.65-4.474.10.05610.50.0290.0640.05699.7
4.47-6.324.10.05110.70.0260.0580.05199.2
6.32-28.5213.90.04513.20.0240.0510.04597.2

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位相決定

位相決定手法: 分子置換
Phasing MRModel details: Phaser MODE: MR_AUTO
最高解像度最低解像度
Rotation4.63 Å28.52 Å
Translation4.63 Å28.52 Å

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解析

ソフトウェア
名称バージョン分類
SCALA3.3.20データスケーリング
PHASER2.5.1位相決定
PHENIX1.1精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 3TDJ

3tdj


解像度: 2→28.521 Å / SU ML: 0.16 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 16.95
Rfactor反射数%反射
Rfree0.1889 3110 5.07 %
Rwork0.1673 --
obs0.1684 61325 99.74 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 113.83 Å2 / Biso mean: 26.8321 Å2 / Biso min: 7.13 Å2
精密化ステップサイクル: final / 解像度: 2→28.521 Å
タンパク質核酸リガンド溶媒全体
原子数6096 0 136 522 6754
Biso mean--29.97 34.43 -
残基数----781
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0036391
X-RAY DIFFRACTIONf_angle_d0.6068619
X-RAY DIFFRACTIONf_chiral_restr0.043944
X-RAY DIFFRACTIONf_plane_restr0.0031075
X-RAY DIFFRACTIONf_dihedral_angle_d13.133874
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3788X-RAY DIFFRACTION4.356TORSIONAL
12B3788X-RAY DIFFRACTION4.356TORSIONAL
13C3788X-RAY DIFFRACTION4.356TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03130.20861430.197526002743100
2.0313-2.06450.23291360.189826332769100
2.0645-2.10010.19181240.186225992723100
2.1001-2.13830.25051360.182526402776100
2.1383-2.17940.20631390.181125942733100
2.1794-2.22390.18941400.179126212761100
2.2239-2.27220.20871550.173226002755100
2.2722-2.32510.20871350.171326292764100
2.3251-2.38320.2071610.174726312792100
2.3832-2.44760.2211440.17825932737100
2.4476-2.51960.2161540.170226412795100
2.5196-2.60080.17281440.168726272771100
2.6008-2.69370.19111450.161526212766100
2.6937-2.80150.16991210.159326832804100
2.8015-2.92890.19291350.165526322767100
2.9289-3.08310.13631380.168426582796100
3.0831-3.2760.20171530.161826512804100
3.276-3.52850.19341320.158726602792100
3.5285-3.88280.16741470.154726912838100
3.8828-4.44290.17031430.13712686282999
4.4429-5.59060.15441350.1482713284899
5.5906-28.52420.21371500.20772812296297
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)
13.47920.06650.40083.3341-0.06223.16060.07620.00470.28370.09210.0001-0.0691-0.3350.2747-0.18220.1701-0.03360.01180.09070.02520.1587135.662142.180472.6076
28.53053.1631-2.39093.2158-1.94122.60390.2624-0.30230.4920.023-0.1253-0.114-0.51410.2986-0.08970.2153-0.05850.0110.13080.01390.1835132.500946.777571.6897
35.8568-2.1507-0.74416.01210.96453.48620.0876-0.07730.17240.2092-0.013-0.55550.02990.4097-0.10220.1065-0.0329-0.0290.19710.02610.0736137.361535.150476.6982
40.8187-0.2767-0.37950.90280.53973.4293-0.0468-0.0006-0.06780.05920.0122-0.06510.2610.22010.01360.13820.0051-0.0020.08140.01910.1526133.24725.996870.4333
54.50410.5306-0.78745.8047-0.83754.4261-0.3066-0.2549-0.60540.0676-0.0407-0.09170.47370.26870.28450.19770.0940.05590.15560.08240.3162137.40715.216459.0231
63.5837-3.4297-0.04543.39130.19182.1996-0.0744-0.0977-0.57880.0777-0.0617-0.14690.37360.32450.07480.22630.09850.05990.22260.08530.3014142.708514.333959.9412
75.6702-1.2945-1.31648.34522.29857.2164-0.20050.0432-0.0906-0.42050.0246-0.70140.02710.80680.11870.1640.01140.03030.21030.06310.2747145.288427.291351.8167
85.1843-0.3071-4.13787.19510.74894.2208-0.0142-0.1103-0.10530.01650.07620.29830.04130.1056-0.07670.13820.0328-0.04160.16070.01070.0979134.510829.223655.9197
95.73433.1118-3.47035.6096-2.98814.6719-0.15090.54050.093-0.31810.0580.01940.09870.06560.08130.20050.0322-0.05630.28530.01580.1584132.342828.375151.8838
104.1133-0.1425-0.37982.42940.01767.4759-0.1768-0.3110.02340.20420.09220.2691-0.1386-0.01030.06510.1035-0.01860.01190.06760.0220.1796121.81533.689176.6802
115.9892-1.8923-3.90893.49751.09032.62550.36920.71240.2097-0.33-0.2315-0.0626-0.407-0.3397-0.15050.22870.0028-0.03490.20280.06580.1839125.074641.435558.5515
123.04651.2385-0.39453.55910.07824.34630.10380.008-0.5139-0.0282-0.05570.15820.3787-0.1616-0.04750.1778-0.0194-0.02180.096-0.02990.2549104.34078.378670.9881
135.6582-3.9060.83967.3023-1.3922.3010.0203-0.1066-0.26970.16180.04980.4010.0338-0.2411-0.0940.113-0.0346-0.00940.1465-0.01250.0762100.971518.919376.57
141.4665-0.34770.02910.5581-0.18553.7954-0.00610.01190.0515-0.02320.00980-0.1594-0.139-0.00490.1352-0.0255-0.00620.0654-0.01330.1397105.271727.086770.2563
152.8411-0.0561-0.23035.1933-0.34253.75740.26340.04590.693-0.00040.01640.1942-0.7722-0.328-0.16340.31910.07930.10590.1937-0.00340.326298.937438.181959.4963
163.7872-1.31671.00239.4763-3.44477.77850.1370.46540.1927-0.53940.18230.6560.1093-1.02-0.27220.14520.0113-0.01830.390900.200593.216725.864751.7337
175.6989-0.70773.92836.8611-0.03663.4815-0.00970.0908-0.0099-0.19590.1771-0.242-0.03610.0725-0.18240.1756-0.02110.03320.21460.01250.1156104.073123.918455.4681
186.40843.88134.32965.03612.63895.8084-0.10850.6409-0.1493-0.29230.1299-0.02270.08770.0205-0.0270.17340.01830.03990.341-0.02010.1975105.939824.419351.4582
195.0432-0.2719-1.35773.1569-0.93257.1208-0.1452-0.4326-0.25280.30710.0229-0.41430.02250.18950.0580.1246-0.0388-0.05650.098-0.02070.2098116.583419.247376.6571
209.1335-0.80356.26974.3055-0.6266.30670.33590.9022-0.4176-0.6947-0.1262-0.250.46560.4104-0.27880.3125-0.01950.08130.2583-0.12570.2901113.503611.55458.4848
212.34080.4133-0.35341.904-0.05181.7389-0.0181-0.0845-0.14230.0816-0.0204-0.19230.17790.2260.01110.11110.0304-0.01110.1350.00530.1054131.701271.914484.4119
220.91760.1290.09291.92711.08561.5335-0.06510.0245-0.0382-0.0432-0.00810.11870.14140.04960.06810.11840.02080.02210.08340.03460.1404119.807669.257370.497
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 65 )A48 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 123 )A66 - 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 187 )A174 - 187
8X-RAY DIFFRACTION8chain 'A' and (resid 188 through 202 )A188 - 202
9X-RAY DIFFRACTION9chain 'A' and (resid 203 through 217 )A203 - 217
10X-RAY DIFFRACTION10chain 'A' and (resid 218 through 243 )A218 - 243
11X-RAY DIFFRACTION11chain 'A' and (resid 244 through 261 )A244 - 261
12X-RAY DIFFRACTION12chain 'B' and (resid 3 through 47 )B3 - 47
13X-RAY DIFFRACTION13chain 'B' and (resid 48 through 65 )B48 - 65
14X-RAY DIFFRACTION14chain 'B' and (resid 66 through 123 )B66 - 123
15X-RAY DIFFRACTION15chain 'B' and (resid 124 through 173 )B124 - 173
16X-RAY DIFFRACTION16chain 'B' and (resid 174 through 187 )B174 - 187
17X-RAY DIFFRACTION17chain 'B' and (resid 188 through 202 )B188 - 202
18X-RAY DIFFRACTION18chain 'B' and (resid 203 through 217 )B203 - 217
19X-RAY DIFFRACTION19chain 'B' and (resid 218 through 243 )B218 - 243
20X-RAY DIFFRACTION20chain 'B' and (resid 244 through 261 )B244 - 261
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 93 )C1 - 93
22X-RAY DIFFRACTION22chain 'C' and (resid 94 through 261 )C94 - 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