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- PDB-6ryi: WUS-HD bound to G-Box DNA -

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基本情報

登録情報
データベース: PDB / ID: 6ryi
タイトルWUS-HD bound to G-Box DNA
要素
  • DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*CP*GP*TP*GP*AP*CP*GP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3')
  • Protein WUSCHEL
キーワードDNA BINDING PROTEIN / Homeodomain Transcription factor
機能・相同性
機能・相同性情報


stomium development / anther development / axillary shoot meristem initiation / stem cell population maintenance / transcription cis-regulatory region binding / cell differentiation / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus
類似検索 - 分子機能
Protein WUSCHEL-like / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Protein WUSCHEL
類似検索 - 構成要素
生物種Arabidopsis thaliana (シロイヌナズナ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.691 Å
データ登録者Sloan, J.J. / Wild, K. / Sinning, I.
資金援助 ドイツ, 1件
組織認可番号国
German Research Foundation ドイツ
引用ジャーナル: Nat Commun / 年: 2020
タイトル: Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL.
著者: Sloan, J. / Hakenjos, J.P. / Gebert, M. / Ermakova, O. / Gumiero, A. / Stier, G. / Wild, K. / Sinning, I. / Lohmann, J.U.
履歴
登録2019年6月10日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年4月29日Provider: repository / タイプ: Initial release
改定 1.12020年5月20日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22024年1月24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

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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: Protein WUSCHEL
B: Protein WUSCHEL
C: Protein WUSCHEL
D: Protein WUSCHEL
E: Protein WUSCHEL
F: DNA (5'-D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3')
G: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*CP*GP*TP*GP*AP*CP*GP*AP*C)-3')
H: DNA (5'-D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3')
I: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*CP*GP*TP*GP*AP*CP*GP*AP*C)-3')


分子量 (理論値)分子数
合計 (水以外)64,3439
ポリマ－64,3439
非ポリマー00
水00
1
A: Protein WUSCHEL
B: Protein WUSCHEL
F: DNA (5'-D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3')
G: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*CP*GP*TP*GP*AP*CP*GP*AP*C)-3')


分子量 (理論値)分子数
合計 (水以外)27,6974
ポリマ－27,6974
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Protein WUSCHEL
D: Protein WUSCHEL
E: Protein WUSCHEL
H: DNA (5'-D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3')
I: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*CP*GP*TP*GP*AP*CP*GP*AP*C)-3')


分子量 (理論値)分子数
合計 (水以外)36,6465
ポリマ－36,6465
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)123.434, 83.068, 85.651
Angle α, β, γ (deg.)90.000, 112.950, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain I and ((resid 3 and (name P or name...
21(chain G and ((resid 3 and (name P or name...
12(chain A and (resseq 37:43 or resseq 45:46 or resseq...
22(chain B and (resseq 37:43 or resseq 45:46 or resseq...
32(chain C and (resseq 37:43 or resseq 45:46 or resseq...
42(chain D and (resseq 37:43 or resseq 45:46 or resseq...
52(chain E and (resseq 37:43 or resseq 45:46 or resseq...
13(chain H and ((resid 2 and (name P or name...
23(chain F and ((resid 2 and (name P or name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DCDCDCDC(chain I and ((resid 3 and (name P or name...II33
121DCDCDCDC(chain I and ((resid 3 and (name P or name...II3 - 163 - 16
131DCDCDCDC(chain I and ((resid 3 and (name P or name...II3 - 163 - 16
141DCDCDCDC(chain I and ((resid 3 and (name P or name...II3 - 163 - 16
151DCDCDCDC(chain I and ((resid 3 and (name P or name...II3 - 163 - 16
161DCDCDCDC(chain I and ((resid 3 and (name P or name...II3 - 163 - 16
171DCDCDCDC(chain I and ((resid 3 and (name P or name...II3 - 163 - 16
181DCDCDCDC(chain I and ((resid 3 and (name P or name...II3 - 163 - 16
191DCDCDCDC(chain I and ((resid 3 and (name P or name...II3 - 163 - 16
211DCDCDCDC(chain G and ((resid 3 and (name P or name...GG33
221DCDCDCDC(chain G and ((resid 3 and (name P or name...GG1 - 161 - 16
231DCDCDCDC(chain G and ((resid 3 and (name P or name...GG1 - 161 - 16
241DCDCDCDC(chain G and ((resid 3 and (name P or name...GG1 - 161 - 16
251DCDCDCDC(chain G and ((resid 3 and (name P or name...GG1 - 161 - 16
261DCDCDCDC(chain G and ((resid 3 and (name P or name...GG1 - 161 - 16
271DCDCDCDC(chain G and ((resid 3 and (name P or name...GG1 - 161 - 16
281DCDCDCDC(chain G and ((resid 3 and (name P or name...GG1 - 161 - 16
291DCDCDCDC(chain G and ((resid 3 and (name P or name...GG1 - 161 - 16
112THRTHRTHRTHR(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA37 - 438 - 14
122GLNGLNILEILE(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA45 - 4616 - 17
132ILEILELEULEU(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA48 - 5219 - 23
142TYRTYRTYRTYR(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA5324
152THRTHRGLUGLU(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA37 - 958 - 66
162THRTHRGLUGLU(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA37 - 958 - 66
172THRTHRGLUGLU(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA37 - 958 - 66
182THRTHRGLUGLU(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA37 - 958 - 66
192THRTHRGLUGLU(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA37 - 958 - 66
1102THRTHRGLUGLU(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA37 - 958 - 66
1112THRTHRGLUGLU(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA37 - 958 - 66
1122THRTHRGLUGLU(chain A and (resseq 37:43 or resseq 45:46 or resseq...AA37 - 958 - 66
212THRTHRTHRTHR(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB37 - 438 - 14
222GLNGLNILEILE(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB45 - 4616 - 17
232ILEILELEULEU(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB48 - 5219 - 23
242THRTHRGLUGLU(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB37 - 958 - 66
252THRTHRGLUGLU(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB37 - 958 - 66
262THRTHRGLUGLU(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB37 - 958 - 66
272THRTHRGLUGLU(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB37 - 958 - 66
282THRTHRGLUGLU(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB37 - 958 - 66
292THRTHRGLUGLU(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB37 - 958 - 66
2102THRTHRGLUGLU(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB37 - 958 - 66
2112THRTHRGLUGLU(chain B and (resseq 37:43 or resseq 45:46 or resseq...BB37 - 958 - 66
312THRTHRTHRTHR(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC37 - 438 - 14
322GLNGLNILEILE(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC45 - 4616 - 17
332ILEILELEULEU(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC48 - 5219 - 23
342THRTHRARGARG(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC37 - 968 - 67
352THRTHRARGARG(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC37 - 968 - 67
362THRTHRARGARG(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC37 - 968 - 67
372THRTHRARGARG(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC37 - 968 - 67
382THRTHRARGARG(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC37 - 968 - 67
392THRTHRARGARG(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC37 - 968 - 67
3102THRTHRARGARG(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC37 - 968 - 67
3112THRTHRARGARG(chain C and (resseq 37:43 or resseq 45:46 or resseq...CC37 - 968 - 67
412THRTHRTHRTHR(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD37 - 438 - 14
422GLNGLNILEILE(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD45 - 4616 - 17
432ILEILELEULEU(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD48 - 5219 - 23
442THRTHRARGARG(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD37 - 968 - 67
452THRTHRARGARG(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD37 - 968 - 67
462THRTHRARGARG(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD37 - 968 - 67
472THRTHRARGARG(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD37 - 968 - 67
482THRTHRARGARG(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD37 - 968 - 67
492THRTHRARGARG(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD37 - 968 - 67
4102THRTHRARGARG(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD37 - 968 - 67
4112THRTHRARGARG(chain D and (resseq 37:43 or resseq 45:46 or resseq...DD37 - 968 - 67
512THRTHRTHRTHR(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE37 - 438 - 14
522GLNGLNILEILE(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE45 - 4616 - 17
532ILEILELEULEU(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE48 - 5219 - 23
542THRTHRARGARG(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE37 - 968 - 67
552THRTHRARGARG(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE37 - 968 - 67
562THRTHRARGARG(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE37 - 968 - 67
572THRTHRARGARG(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE37 - 968 - 67
582THRTHRARGARG(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE37 - 968 - 67
592THRTHRARGARG(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE37 - 968 - 67
5102THRTHRARGARG(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE37 - 968 - 67
5112THRTHRARGARG(chain E and (resseq 37:43 or resseq 45:46 or resseq...EE37 - 968 - 67
113DTDTDTDT(chain H and ((resid 2 and (name P or name...HH22
123DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
133DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
143DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
153DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
163DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
173DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
183DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
193DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
1103DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
1113DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
1123DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
1133DGDGDGDG(chain H and ((resid 2 and (name P or name...HH1 - 151 - 15
213DTDTDTDT(chain F and ((resid 2 and (name P or name...FF22
223DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
233DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
243DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
253DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
263DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
273DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
283DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
293DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
2103DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
2113DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
2123DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16
2133DGDGDGDG(chain F and ((resid 2 and (name P or name...FF1 - 161 - 16

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質
Protein WUSCHEL / AtWUS / Plant growth activator 6


分子量: 8949.188 Da / 分子数: 5 / 由来タイプ: 組換発現
由来: (組換発現) Arabidopsis thaliana (シロイヌナズナ)
遺伝子: WUS, PGA6, At2g17950, T27K22.18 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9SB92
#2: DNA鎖 DNA (5'-D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3')


分子量: 4970.214 Da / 分子数: 2 / 由来タイプ: 合成
由来: (合成) Arabidopsis thaliana (シロイヌナズナ)
#3: DNA鎖 DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*CP*GP*TP*GP*AP*CP*GP*AP*C)-3')


分子量: 4828.145 Da / 分子数: 2 / 由来タイプ: 合成
由来: (合成) Arabidopsis thaliana (シロイヌナズナ)

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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: 3.66 Å3/Da / 溶媒含有率: 66.39 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.2 M lithium acetate, 20% PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: MASSIF-3 / 波長: 0.96769 Å
検出器タイプ: DECTRIS EIGER X 4M / 検出器: PIXEL / 日付: 2016年6月8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: 0.96769 Å / 相対比: 1
反射解像度: 2.69→40.67 Å / Num. obs: 21967 / % possible obs: 98.11 % / 冗長度: 4.8 % / Rpim(I) all: 0.0521 / Net I/σ(I): 10.97
反射 シェル解像度: 2.691→2.788 Å / Num. unique obs: 2053 / CC1/2: 0.458

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
PDB_EXTRACT3.24データ抽出
XDSデータ削減
Aimless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: 6RY3

6ry3


解像度: 2.691→40.667 Å / SU ML: 0.49 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 33.46
Rfactor反射数%反射
Rfree0.2511 1033 4.73 %
Rwork0.1944 --
obs0.1971 21855 98.14 %
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: 248.29 Å2 / Biso mean: 94.4824 Å2 / Biso min: 40.64 Å2
精密化ステップサイクル: final / 解像度: 2.691→40.667 Å
タンパク質核酸リガンド溶媒全体
原子数2563 1252 0 0 3815
残基数----359
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.014024
X-RAY DIFFRACTIONf_angle_d1.1055685
X-RAY DIFFRACTIONf_chiral_restr0.063612
X-RAY DIFFRACTIONf_plane_restr0.007507
X-RAY DIFFRACTIONf_dihedral_angle_d21.4482177
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11I240X-RAY DIFFRACTION15.313TORSIONAL
12G240X-RAY DIFFRACTION15.313TORSIONAL
21A1063X-RAY DIFFRACTION15.313TORSIONAL
22B1063X-RAY DIFFRACTION15.313TORSIONAL
23C1063X-RAY DIFFRACTION15.313TORSIONAL
24D1063X-RAY DIFFRACTION15.313TORSIONAL
25E1063X-RAY DIFFRACTION15.313TORSIONAL
31H234X-RAY DIFFRACTION15.313TORSIONAL
32F234X-RAY DIFFRACTION15.313TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6913-2.83320.43821410.4072886302795
2.8332-3.01070.43951590.32932940309999
3.0107-3.2430.26391420.24953023316599
3.243-3.56920.24751440.21082963310799
3.5692-4.08530.24081540.1832978313298
4.0853-5.14540.23451330.16032943307697
5.1454-40.67130.21341600.1630893249100
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)
11.2198-2.32310.82545.1261-0.48049.79040.1881-0.38970.64070.1444-0.375-0.41620.0940.4062-0.05550.3287-0.07840.04370.6444-0.07580.668132.8761-20.8803-10.5961
24.84450.2629-2.21985.86820.44657.41730.5233-0.22380.2750.3213-0.5384-0.03470.84930.0511-0.05850.3336-0.1190.05140.5515-0.05180.681231.5561-26.8645-9.1406
36.77433.8062-5.16395.363-1.07035.0117-0.89360.14550.6338-0.3295-0.13230.60841.1636-1.22660.70161.08350.105-0.390.8482-0.12790.570129.3272-6.7982-0.1377
42.80421.6757-0.64173.8332.78293.7381-0.07170.0683-0.67210.9618-0.5428-1.58031.65480.93180.27630.64350.1157-0.09910.6959-0.021.011238.7383-10.889411.3277
52.10930.52971.70947.98667.67588.22280.9739-0.0655-0.11750.384-0.45560.1262-0.1957-1.1562-0.39980.815-0.0067-0.09720.6233-0.05890.513634.8473-3.152618.8711
63.4926-2.4189-1.91274.28761.97867.4175-0.56440.9953-0.0973-0.5132-0.06110.0628-1.82810.74540.49370.2949-0.0124-0.03240.7057-0.03440.761538.80770.27725.9201
72.86540.8310.22552.5532.3147.63140.49490.1556-0.34070.3172-0.89192.24510.7672-0.64360.46250.6643-0.02920.02650.6543-0.20140.899128.1669-5.283512.1629
84.35261.9678-1.74624.8228-1.09642.03850.44220.720.1272-0.21-0.40091.22840.1837-1.6576-0.23570.42240.16770.02660.8145-0.00460.768913.001215.597828.6334
94.61153.44173.71897.39240.47844.1404-1.3810.5586-0.2313-0.53970.2286-1.55780.55410.79120.05420.73660.01620.2140.7423-0.03620.779524.790111.346424.1016
109.56710.6125-2.52122.1111-0.94892.70530.15490.35970.98910.33820.281-0.1343-1.8941-0.0273-0.32850.91370.02820.07950.6171-0.0370.621520.264423.217830.133
118.18823.56551.6199.09921.63268.91890.1107-0.1998-0.8503-0.0516-0.12110.13470.4764-0.4202-0.03130.80190.00980.10020.6646-0.00010.561719.26099.383433.333
127.5850.81710.67489.7864-3.35661.9499-0.9907-0.02580.4210.30080.9123-0.89971.13520.3872-0.30411.2969-0.420.14411.2987-0.23080.780520.89375.688954.8042
133.80241.82430.81547.20230.24736.58490.5874-1.2954-1.53211.4094-0.41270.43461.30150.9690.1931.2079-0.21270.21490.96960.08290.758916.1307-7.834457.6903
146.76572.08730.82059.01320.68635.2856-0.1699-0.63940.2282.21070.16610.9982-0.01780.2267-0.20911.5727-0.19830.38780.9908-0.01130.862711.1114-0.420663.1149
156.7786-1.3872-2.48267.6695-0.18746.44170.35230.37270.41141.0949-0.5250.2517-0.6299-0.08860.24391.0217-0.1920.22250.63990.00050.85829.87540.054150.7466
164.4633-5.20023.45926.4667-4.47723.18510.74440.6225-0.1550.8763-0.75970.57391.468-1.33260.48641.3599-0.4768-0.30351.0455-0.10911.096730.0376-5.631848.4838
172.65812.47042.42092.37312.24062.1977-0.0338-1.71120.10810.11590.60561.24992.3724-1.0183-0.12311.0042-0.1511-0.0351.05790.06190.667336.582-3.589860.2587
183.6506-2.6986-3.10137.96980.54393.38840.43-0.57220.8893-0.2993-0.20640.07030.4161-0.4816-0.4010.5383-0.0612-0.00650.84340.12690.789145.48071.691759.2738
192.15981.07280.79536.26130.33299.59860.49370.466-1.3623-0.15250.13310.03583.32290.1275-0.49681.62430.0861-0.39570.8721-0.07980.864641.8343-10.849352.7015
206.5817-2.14061.13289.913-1.884.66190.0414-0.02870.02420.0794-0.3153-0.24330.16880.10390.31231.0697-0.1209-0.10970.68230.1240.583439.48123.419350.4599
215.6599-4.2353-4.25376.10654.60383.9669-0.0034-0.6110.5255-1.6689-1.29981.3588-1.3591-2.28150.91480.96130.1696-0.03881.3627-0.50491.333713.8854-25.5747-13.2145
222.2861-0.3455-0.09580.0240.26096.8979-0.1882-0.69930.68010.5151-0.63870.4829-0.116-2.30030.68650.61250.0021-0.05561.1672-0.48351.095418.0649-8.31777.7267
230.6361-1.129-0.91718.1263-1.90187.0374-0.0421-0.5541-0.88171.0511-0.96990.08181.3157-2.48171.05261.174-0.36340.0251.2874-0.36551.159617.8088-3.973717.7423
244.26370.60462.84531.2909-1.89816.8484-0.0978-0.4932-0.15550.1558-0.64210.58120.8606-2.81380.54790.6086-0.27650.08611.3153-0.39260.990416.6808-20.9129-3.3152
254.9242-1.99823.28246.20890.25215.6336-0.0847-0.1378-0.09790.06580.17610.80790.6911-0.2890.05650.8193-0.20740.06650.89320.08390.801821.10015.878942.2471
268.18752.0194-2.52373.81840.31976.7312-0.37710.62931.09120.45210.32270.4628-0.1398-0.31020.10140.812-0.01110.05340.7230.03680.753420.00098.430743.1969
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 62 )A37 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 95 )A63 - 95
3X-RAY DIFFRACTION3chain 'B' and (resid 37 through 42 )B37 - 42
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 56 )B43 - 56
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 62 )B57 - 62
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 80 )B63 - 80
7X-RAY DIFFRACTION7chain 'B' and (resid 81 through 95 )B81 - 95
8X-RAY DIFFRACTION8chain 'C' and (resid 37 through 55 )C37 - 55
9X-RAY DIFFRACTION9chain 'C' and (resid 56 through 62 )C56 - 62
10X-RAY DIFFRACTION10chain 'C' and (resid 63 through 80 )C63 - 80
11X-RAY DIFFRACTION11chain 'C' and (resid 81 through 96 )C81 - 96
12X-RAY DIFFRACTION12chain 'D' and (resid 37 through 42 )D37 - 42
13X-RAY DIFFRACTION13chain 'D' and (resid 43 through 55 )D43 - 55
14X-RAY DIFFRACTION14chain 'D' and (resid 56 through 80 )D56 - 80
15X-RAY DIFFRACTION15chain 'D' and (resid 81 through 96 )D81 - 96
16X-RAY DIFFRACTION16chain 'E' and (resid 37 through 42 )E37 - 42
17X-RAY DIFFRACTION17chain 'E' and (resid 43 through 53 )E43 - 53
18X-RAY DIFFRACTION18chain 'E' and (resid 54 through 62 )E54 - 62
19X-RAY DIFFRACTION19chain 'E' and (resid 63 through 80 )E63 - 80
20X-RAY DIFFRACTION20chain 'E' and (resid 81 through 96 )E81 - 96
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 5 )F1 - 5
22X-RAY DIFFRACTION22chain 'F' and (resid 6 through 16 )F6 - 16
23X-RAY DIFFRACTION23chain 'G' and (resid 1 through 5 )G1 - 5
24X-RAY DIFFRACTION24chain 'G' and (resid 6 through 16 )G6 - 16
25X-RAY DIFFRACTION25chain 'H' and (resid 1 through 15 )H1 - 15
26X-RAY DIFFRACTION26chain 'I' and (resid 3 through 16 )I3 - 16

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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://pdbjlvh1.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