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万見

- PDB-6x04: Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN5 -

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データを開く

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基本情報

登録情報

データベース: PDB / ID: 6x04

タイトル

Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN5

要素

Nucleoporin NUP133
VHH-SAN5

キーワード

STRUCTURAL PROTEIN (タンパク質) /

Nucleoporin (ヌクレオポリン) /

Nanobody (ナノボディ)

機能・相同性

機能・相同性情報

mRNA export from nucleus in response to heat stress / nuclear pore localization / telomere tethering at nuclear periphery / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation ...
類似検索 - 分子機能

生物種

Saccharomyces cerevisiae (パン酵母)

Vicugna pacos (アルパカ)

手法

X線回折 /

シンクロトロン /

分子置換 / 解像度: 2.68 Å

データ登録者

Nordeen, S.A. / Schwartz, T.U.

資金援助

米国, 1件

引用

ジャーナル: Nat Commun / 年: 2020
タイトル: Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif.
著者: Nordeen, S.A. / Turman, D.L. / Schwartz, T.U.

履歴

登録	2020年5月15日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2020年12月9日	Provider: repository / タイプ: Initial release
改定 1.1	2023年10月18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

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ダウンロードとリンク

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ダウンロード

PDBx/mmCIF形式	6x04.cif.gz	1.2 MB	表示	PDBx/mmCIF形式
PDB形式	pdb6x04.ent.gz	864.2 KB	表示	PDB形式
PDBx/mmJSON形式	6x04.json.gz		ツリー表示	PDBx/mmJSON形式
その他	その他のダウンロード

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検証レポート

アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/x0/6x04 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/6x04	HTTPS FTP

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関連構造データ

関連構造データ	6x02C 6x03C 6x05C 4q9tS S: 精密化の開始モデル C: 同じ文献を引用 (文献)
類似構造データ	5x1h-d 5fkv-d 20034 2539 6d03-d 20033 Omokage検索で類似形状データを探す (詳細) 類似検索 - 機能・相同性F&H 検索類似検索 - 機能F&H 検索類似検索 - 相同性F&H 検索

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リンク

PDBのページ	PDBj / wwPDB / NCBI
「今月の分子」の関連する項目	#205 - 2017年1月核膜孔複合体 (Nuclear Pore Complex) 類似性 (5) #136 - 2011年4月ナノボディ (Nanobodies) 類似性 (1) #21 - 2001年9月抗体 (Antibodies) 類似性 (1) #256 - 2021年4月 SARSコロナウイルス2型のスパイクと抗体 (SARS-CoV-2 Spike and Antibodies) 類似性 (1)

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集合体

登録構造単位

A: Nucleoporin NUP133

B: VHH-SAN5

C: Nucleoporin NUP133

D: VHH-SAN5

E: Nucleoporin NUP133

F: VHH-SAN5

G: Nucleoporin NUP133

H: VHH-SAN5

I: Nucleoporin NUP133

J: VHH-SAN5

K: Nucleoporin NUP133

L: VHH-SAN5

367 kDa, 12 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

登録構造と同一
登録者が定義した集合体
根拠: gel filtration

単位格子

Length a, b, c (Å)	85.799, 204.761, 205.833
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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要素

#1: タンパク質	Nucleoporin NUP133 / Nuclear pore protein NUP133 分子量: 48493.730 Da / 分子数: 6 / 由来タイプ: 組換発現由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 株: ATCC 204508 / S288c / 遺伝子: NUP133, RAT3, YKR082W, YKR402 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P36161
#2: 抗体	VHH-SAN5 分子量: 12754.293 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli (大腸菌)
#3: 水	ChemComp-HOH / water / 水分子量: 18.015 Da / 分子数: 15 / 由来タイプ: 天然 / 式: H₂O

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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: 2.51 Å³/Da / 溶媒含有率: 51 %
結晶化	温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法詳細: 15% PEG MME 2,000, 0.1M potassium chloride, 0.1M Tris/HCl pH 8

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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: APS / ビームライン: 24-ID-C / 波長: 0.9791 Å
検出器	タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2017年6月17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: 0.9791 Å / 相対比: 1
反射	解像度: 2.68→49.68 Å / Num. obs: 100374 / % possible obs: 98.7 % / 冗長度: 8.6 % / B_iso Wilson estimate: 72.6 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.035 / Net I/σ(I): 29.1
反射シェル	解像度: 2.68→2.8 Å / 冗長度: 8.3 % / Mean I/σ(I) obs: 1.49 / Num. unique obs: 9937 / CC_1/2: 0.567 / R_pim(I) all: 0.684 / % possible all: 99.1

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.18_3845	精密化
HKL-2000		データ削減
HKL-2000		データスケーリング
PHENIX		位相決定

精密化

構造決定の手法:

分子置換
開始モデル: 4Q9T

4q9t

解像度: 2.68→49.68 Å / SU ML: 0.4285 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 29.6567
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2

	R_factor	反射数	%反射
R_free	0.2614	1999	1.99 %
R_work	0.2435	98267	-
obs	0.2439	100266	98.06 %

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

B_iso mean: 88.69 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.68→49.68 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	20000	0	0	15	20015

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0047	20356
X-RAY DIFFRACTION	f_angle_d	0.6472	27693
X-RAY DIFFRACTION	f_chiral_restr	0.0497	3285
X-RAY DIFFRACTION	f_plane_restr	0.0035	3481
X-RAY DIFFRACTION	f_dihedral_angle_d	17.4361	6833

LS精密化シェル

解像度 (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.68-2.75	0.4169	135	0.3807	6306	X-RAY DIFFRACTION	89.8
2.75-2.82	0.3217	140	0.3449	6799	X-RAY DIFFRACTION	96.32
2.82-2.91	0.3532	137	0.3146	7024	X-RAY DIFFRACTION	99.13
2.91-3	0.3408	146	0.3024	7018	X-RAY DIFFRACTION	99.11
3-3.11	0.3253	142	0.291	7020	X-RAY DIFFRACTION	99.16
3.11-3.23	0.3164	143	0.2864	7074	X-RAY DIFFRACTION	99.42
3.23-3.38	0.2955	143	0.2802	7080	X-RAY DIFFRACTION	99.34
3.38-3.56	0.2922	139	0.2529	6940	X-RAY DIFFRACTION	97.52
3.56-3.78	0.2677	145	0.2439	7114	X-RAY DIFFRACTION	99.53
3.78-4.07	0.2743	142	0.2483	7114	X-RAY DIFFRACTION	99.56
4.07-4.48	0.2343	147	0.2034	7139	X-RAY DIFFRACTION	99.43
4.48-5.13	0.1774	143	0.1888	7042	X-RAY DIFFRACTION	97.58
5.13-6.46	0.2749	147	0.2274	7258	X-RAY DIFFRACTION	99.72
6.46-49.68	0.2374	150	0.2453	7339	X-RAY DIFFRACTION	97.12

精密化 TLS

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

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.35648278661	-0.0843070487864	-0.949816160684	7.51014701225	-3.76541232677	6.92005657668	-0.190841167888	0.906022936838	0.420107608835	-1.47204522537	-0.446430845372	0.124984907364	-0.727227264851	-0.127120877587	0.354150492098	1.53218549948	0.197185326864	-0.333519297704	0.983917796164	0.220438433843	0.829731670132	9.99989220393	40.71575877	30.0136382696
2	4.12614212663	1.56009138047	-0.910491104707	3.63266825212	-1.81712695107	6.21227154121	-0.0552210953889	0.82681360195	-0.216526656638	-1.03662861305	0.132566289262	-0.0417725338788	0.302089126826	-0.276218995501	-0.0588128936418	0.741400949857	0.271123959741	0.0330472534611	0.64621475366	-0.0387865878329	0.321979108685	13.8964389501	22.086225517	39.3293762927
3	4.76294957062	0.279427944888	0.535391408974	8.08329265208	2.18300245104	1.70877670661	0.0297438161313	0.421955780651	-0.10662916717	-0.715078945213	-0.254258572691	-0.473727296041	-0.0724199748659	0.253937045533	0.208842492883	0.58785713679	0.158840199995	-0.0563100098576	0.553202727613	0.136223247071	0.408217270722	17.0555752241	22.0834628586	48.2346459187
4	2.02426120467	3.09434428016	0.143415770616	8.20793491732	-1.80094191268	9.22026420303	-0.0299919441748	-0.092921788019	0.38262844586	-0.269399954022	-0.201213361932	-0.0964945547726	-0.125044570481	0.271137575256	0.180957469078	0.485320732043	0.154680087004	-0.0675649088795	0.46617902761	0.0689416875437	0.453887453673	17.9524094505	37.6194979242	55.3181326749
5	4.8142209242	1.50925247713	0.984793571895	7.91519282608	2.79914146226	6.11376280015	-0.209178242328	0.135390067096	-0.262751721598	-0.52506255041	0.0266477196369	0.380536651548	-0.230955493327	0.111947595341	0.163496157583	0.500766560963	0.150764814991	-0.0123997648005	0.496011964353	0.00361024420386	0.452652656504	13.7916874838	-2.01548624866	55.8260076611
6	3.81006818174	4.43992108795	-4.92370826619	9.24716394672	-2.61222507289	8.77666542346	0.910037280841	-1.96268748977	-0.666979620332	0.999012512463	-0.879268253252	-0.758333539478	-0.467198551422	1.44307480822	-0.173316088175	0.455149838061	0.142990636557	-0.057144686181	0.971377657234	-0.0788034511299	0.54042022795	14.2660426084	-1.29960333329	64.9193238051
7	2.16856794832	0.462401389178	-0.178400445468	3.80145682419	-0.445109970369	1.64677827287	-0.0679788530048	0.0484632588097	-0.107772920122	-0.456245648787	-0.216850084949	-0.261507176169	0.18045504957	0.140755565271	0.273795339799	0.589796851051	0.163300459598	-0.0684293509632	0.541239171243	-0.0547035737539	0.601397929301	16.5393594092	-1.89399717313	54.1623789658
8	2.96522115456	1.49426590161	2.88008390582	4.77943872629	0.431554768715	6.42002222633	0.948158582584	-0.478373669003	-0.721806959003	1.39624440747	-0.390844298289	-0.583412589145	1.39398136827	0.615465021179	-0.398948609238	1.1151791601	0.0327551527865	-0.248108901015	1.07635736918	0.166667633899	0.674653044658	42.9495077961	4.49648889063	119.590786024
9	0.267975625773	0.218089100847	-1.15691095842	6.15888110264	-4.34538972459	6.79742811679	1.48701264435	-0.940615365516	-1.15420854621	0.501606426591	-0.704311956087	-0.785010971769	1.19095116275	-0.881611943331	-0.329123790257	1.14993256389	-0.31722602661	-0.574568303213	1.3477873191	0.208184742663	0.68306005716	48.9925930041	14.1538687371	128.027012115
10	2.55458611461	-1.93563658971	-1.39439588152	3.59537441538	-0.55538132425	4.07104651609	0.126161401266	-1.25866353717	0.401662423867	2.13600320366	0.102410302272	-0.857715953258	-0.314830821757	0.636952551486	-0.20679191109	0.83164669237	-0.237099196254	-0.261619351495	1.13062921952	0.0849934744812	0.496379980636	48.6105329105	24.4135394619	131.267042535
11	1.26092311806	0.445741577658	0.104084456482	7.29471539987	1.37804148658	6.28361650878	0.255494052151	-0.881344280738	0.459331008905	0.539574225909	-0.121106871071	-0.0742239264796	0.0289617180511	-0.105261401552	-0.104725593694	0.416224864416	-0.0531075686541	-0.0830525138755	0.893871543538	-0.0417143848171	0.452708968458	44.2554203526	28.5519092307	118.522631753
12	4.04422614815	1.8304362578	1.61835840541	1.88558561188	1.80896198138	2.11657012219	-0.0479104017662	-0.388508709013	-0.0265504872343	-0.161336186019	0.0317925608443	-0.122657167027	-0.265384516325	-0.0421519508542	0.032341385455	0.22308241202	-0.0275040359722	-0.048818638796	0.496370098585	0.0457630201267	0.387089151634	37.4119616821	26.6354056476	101.799652094
13	4.73131735959	-0.41748940502	1.18909830985	5.91417859261	0.0724356682015	7.32032445602	-0.064681316228	-0.506814129749	0.470418417157	0.209456504074	-0.0186128034495	-0.561418133885	0.165020626433	0.212355795836	0.0815828809313	0.207053144	0.0208378610238	-0.0741003872698	0.322625292129	0.0457168914338	0.424360388238	34.5743167214	17.0219132141	101.102597948
14	0.570082629851	-1.44657396236	-0.366172152709	4.06469112282	0.194489278381	5.85821241351	-0.0383808389434	0.137753603184	-0.0747083381244	-0.136879465389	0.191056877042	-0.452964487744	-0.112892352214	0.292447242917	-0.15326654534	0.202411134514	0.014307451346	-0.103445814768	0.520050782692	-0.0192553996843	0.412145871176	37.1180707644	19.6222656906	94.8786517962
15	0.911822054823	0.631492197525	1.69015275681	2.35887178336	1.6650582422	5.90540311256	0.141455961516	-0.314871080147	-0.672760723722	-0.0845790434472	0.00965527885981	-0.692334627604	0.447577025773	-0.524618920956	-0.0786933196495	0.509533278438	-0.0679327849428	-0.172743339617	0.588738498375	0.116709091969	0.825466083145	35.8181974095	9.18185571364	105.831238226
16	9.49183738617	3.02539941796	4.19357703489	9.01270372673	-0.457290215479	4.15629460798	-0.694355717811	1.96887269139	-1.3285736761	-1.8977738582	0.261416875745	-1.24146458702	0.246977138392	1.61934679202	0.239650231897	0.677513526122	-0.0807794867056	0.00600900183962	0.902854844154	-0.0904417010169	0.801199937803	41.7629732592	6.63133832983	94.9821605406
17	4.93315705666	3.11744259541	5.4815227588	6.60021487254	3.90205692769	6.97882183781	0.595915532179	-0.173965892782	-0.855274378543	1.49332289145	-0.375740233356	-0.68920229178	1.09048211456	0.365346083614	-0.215714411793	0.904161189135	-0.0290333469736	-0.443590650513	0.873358329597	0.148057692557	0.91095391	39.9407862341	2.56527213453	113.378435499
18	3.83226382056	-1.7088087614	0.725748963815	9.71358680716	-0.378448243519	5.85811450978	-0.240145623108	0.703473142947	-0.124035054963	-0.405035649434	0.153652257698	0.187151359523	0.440515496732	0.0391968465596	0.0749608473752	0.373308162342	-0.0781411128701	-0.0304390265383	0.625165241092	0.0324975814619	0.298783393859	21.1462665245	27.1294994249	70.3905424336
19	6.38979376133	3.58174539269	3.13798709772	7.72010865776	-4.09903405006	7.55057551879	-0.396641891888	-0.610374958128	-1.25612628732	-2.38711499308	-0.47185965502	-1.25085510124	2.35385134298	2.26814067956	0.700199095644	0.71504742543	0.0662624564833	0.114576418082	0.597760103452	-0.0254379189219	0.770025572552	27.482042924	9.58870892222	77.5840707124
20	0.989419742124	-1.77107793345	0.717410464857	4.96239297842	-2.1040833904	3.74006513995	-0.107758390271	-0.225036321885	0.0906911398884	0.864358463099	0.0358692407292	0.337461129449	-0.335659488947	-0.00135226519507	0.0494417065154	0.145763289655	-0.0403287259646	-0.092059313467	0.446368946143	-0.0194094036543	0.489885174654	20.0213601844	26.974247985	84.2291351113
21	2.74452739277	-1.66648328043	-2.61190059986	2.05518258345	-0.412076023515	6.54868891615	0.141134196153	0.114118510012	-1.12448525566	-0.277007774673	-0.818865123111	0.908738617567	0.469473592197	-0.127449691447	0.768299576928	0.366398090575	-0.049444429508	-0.101827784391	0.458550732295	0.0469468089065	0.751026508228	16.7351409057	17.4851042771	76.7171968514
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58	1.64943149563	0.61480588693	0.0836699569303	6.2667097267	-0.470769738047	6.27677920713	0.255663946209	-0.133558604146	0.0840399722286	0.852535870342	-0.0563040776015	-0.864938272072	-0.315630414387	-0.381691353773	-0.148687810399	0.259099707139	0.0890167332442	-0.0587350570054	0.791730509559	-0.158387740151	0.492572979994	-6.17702188862	29.4062818799	84.920861018
59	5.28845796801	-0.145679172801	2.7474028387	6.84262066355	2.59853151828	6.64722935824	0.0177171216024	0.425710867693	-0.102882637305	-0.500426170489	0.0448717547702	0.754227525828	0.547498668639	-0.684101089	-0.130205676867	0.250560929334	-0.0731436899538	-0.000332323052531	0.779485915492	-0.0199210414642	0.443251330828	-9.40799993537	21.9861798818	75.5338160232
60	4.35512313418	2.88539031869	2.35673778503	2.91674729376	3.07423530356	3.62804461742	-0.0396836081245	0.660491732262	-0.446865225439	-0.498298179001	0.195389736707	0.00702751515865	0.307060848545	0.135118812743	-0.113244334232	0.438891785281	0.00491853461047	0.0558837730598	0.612847460941	-0.0423530091239	0.539214333355	0.127537435674	21.9259938203	74.475030266
61	2.91718623962	3.05256697582	2.02984585362	3.17159370365	2.41368883563	3.15350371675	0.0193662622759	0.221533054132	0.0330636625737	-0.414383898641	-0.0507475111521	-0.496471696192	-0.0960454492994	-0.159574269572	0.100695258344	0.31775458274	0.0400739371659	-0.000654956778721	0.639301715339	-0.0807570823688	0.465151604494	-6.17439626476	26.6572212581	77.4830575096
62	4.49366520265	3.89725704352	2.88487611425	3.95746208412	4.09016449282	5.32878984132	-0.109460414529	-0.639822616425	0.804572840122	-0.208525488175	-0.487471887282	1.80155731601	0.0478752958134	-1.19446308137	0.505168398163	0.409036073157	-0.0215413283945	-0.0626472482367	0.787045726173	-0.0638229974566	0.449148105045	-13.3862289206	22.6708939176	78.0185846961
63	2.81375668698	0.535162701871	-0.189815460654	5.61901221978	-1.60123278673	3.4275363996	0.13853267144	-0.474158465182	-0.917403082476	-0.369150498683	-0.53415359517	-0.3347436789	1.08206828198	-0.297417649375	0.350192077909	1.54530874998	-0.160538633673	0.0717139453033	0.82006865553	0.256911748763	0.802545488368	-0.355077412932	-45.2522031033	112.204928288
64	8.75424986143	4.4085820784	-2.60153443525	5.98622272188	-4.09765282314	2.94834232111	-0.456990616224	-0.100029214449	-1.83608210989	-0.786204823592	0.363821610061	1.24308734299	1.65197797042	-0.0919189864548	0.067001886896	2.04986355176	-0.379317164367	0.182526055999	0.712084915338	0.0564665632182	1.43049611086	-6.22071473847	-52.4231034159	99.2538326
65	2.82251036996	1.6350011742	-0.532421045743	6.62862914174	-2.05006273715	3.2862271433	-0.0189142549399	-0.071673101268	0.183368894907	-0.309136927599	0.160019672315	0.972249207231	1.17121635491	-0.49444780361	-0.0628403567446	1.09285736582	-0.287361006113	-0.357178352758	0.55365327052	0.083657258475	0.996208598285	-6.15892176985	-32.736795858	91.3818467078
66	6.900391817	0.0820979708693	-1.80918469083	5.72099819227	-0.259366113727	5.31623578265	-0.133944720717	0.393255762907	-0.134325670401	-0.231202247675	-0.118098497175	-0.131692971104	0.568300461328	-0.231457797834	0.207546285005	0.836917310321	-0.158931931105	-0.237140538791	0.543367099321	0.0656069730703	0.663041122205	-3.09589066352	-25.3370259971	96.7567185682
67	8.06113710477	0.529126557457	-3.3109096526	2.84135389392	-4.01698981404	6.70020211056	0.0500654426663	-0.999935055684	0.0442481856409	1.22845874601	-0.0510455242168	-0.00419555241121	-0.0790893784152	0.210605024868	-0.0416275122908	1.16527438798	0.0217128663582	-0.0896262268708	0.621839919719	0.0634904726262	0.825981235501	1.32311527373	-26.1800436056	112.00570083
68	4.58686561899	0.716848301461	0.496257975843	2.90367190671	-0.795770455695	0.354709767451	-0.14789589322	0.706966964398	0.448393726773	-0.595027031175	0.231158224971	0.240782647917	-0.0972446685293	-0.217100817242	0.034248418125	0.729794445129	0.16995778756	-0.273241322321	0.833491666819	0.10655264417	0.979011198351	-13.2574749231	-10.3732732984	63.5291803203
69	3.19086463087	-1.93260222123	-0.399651847564	2.4346602567	-1.57052210589	5.86623011767	0.15504740378	-0.130383455978	0.286502354463	0.18719347265	0.146232721692	0.0531940695577	0.390770856479	-0.90591469128	-0.25155839573	0.784670644147	-0.0695768004059	-0.387266211689	0.696263102018	0.0926356958461	0.853336476811	-7.71023356038	-13.5678305485	72.7534861263
70	9.03566844971	0.685153279358	4.77844294102	4.41341112622	-2.92003139674	7.04504850265	0.573051242371	-0.460358013575	-0.704421144199	0.586667722443	-0.356890065948	-0.952130399276	1.13000748827	0.717387480362	0.0932101722778	0.720247396691	0.114757532458	-0.328533882986	0.678418478291	-0.0209859335522	1.1627885433	4.01872652312	-14.0745581772	75.8093658817
71	2.92667300511	0.227978556663	-2.65147862231	0.979354442593	0.121350952445	5.45272844545	0.344334641834	-0.19538722554	0.511591953491	-0.264620235999	0.252601424526	-0.381543388813	0.555106426641	0.521975919161	-0.666172625493	0.683170703665	0.103287668093	-0.364232990855	0.755624454654	0.0839090393925	0.967552766696	-1.70360468142	-10.9870265788	67.6292895872
72	5.58636426641	-2.70058761396	-1.66118547013	2.36509603034	-1.07187569754	4.00785897474	0.119585164514	0.576325345752	-0.0614162348232	-0.169491874677	0.163527377824	-0.465139544454	0.547250153403	0.248614771505	-0.135089388072	0.960829362231	0.00577403450341	-0.147246675274	0.926776744083	-0.0449747768219	0.938191492431	-6.44301642974	-19.3748652267	57.1828818453
73	2.91793107216	-2.016543884	-2.64616542506	4.52190572481	-1.295507361	5.83753640286	-0.217206604368	-0.354985767133	0.108343505082	0.77778323721	0.384804088436	-0.130346243268	0.386026824224	0.947344997272	-0.203919651516	0.899552974211	0.074490184416	-0.437922974512	0.843553882228	-0.0572176259086	0.954093950439	-9.41595893271	-13.8345148192	77.2181979572
74	3.43928443448	-1.88019481542	2.56095032054	1.12015606906	-1.98877995522	7.89553613192	-0.639491911528	-0.559672899891	-0.17309508936	0.753489458702	0.291483429668	0.672163087322	0.00999570273228	-1.89285136751	0.359080211226	1.04905127817	0.0981098902399	-0.375060754276	0.733838860338	-0.0928640902859	0.793584857868	-9.81786228899	-13.957821935	85.7792291539
75	6.99982570127	-4.66238319377	-6.1950088658	5.67931608886	5.05659317171	5.81066388404	-0.226419061732	1.58555325662	0.231324963875	-0.0119470723293	-0.54918382258	0.0630754811686	1.11971660375	-3.44375192894	0.79354830036	0.985033501364	-0.213422853466	-0.487055689436	1.33835896332	0.104427556259	1.01729905912	-15.839431869	-15.828275087	63.1330354905
76	3.13732874196	2.04275976455	-0.196280542924	1.38287503563	0.63435808219	6.21318750831	0.172173027502	0.262524976202	1.20983909677	-0.937254044206	-0.248905293371	0.354216230344	-0.755063256577	-0.697311729218	0.143328524985	1.38731980892	0.23948985747	-0.235096843341	0.667751765107	0.20956038582	1.02521170698	14.1057017937	50.4298094753	45.9993954307

精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'G' and (resid 169 through 279 )	G	G	169 - 279	65 - 152
2	2	chain 'G' and (resid 280 through 331 )	G	G	280 - 331	153 - 204
3	3	chain 'G' and (resid 332 through 382 )	G	G	332 - 382	205 - 255
4	4	chain 'G' and (resid 383 through 481 )	G	G	383 - 481	256 - 334
5	5	chain 'H' and (resid 2 through 65 )	H	H	2 - 65	1 - 64
6	6	chain 'H' and (resid 66 through 75 )	H	H	66 - 75	65 - 74
7	7	chain 'H' and (resid 76 through 117 )	H	H	76 - 117	75 - 116
8	8	chain 'I' and (resid 61 through 103 )	I	I	61 - 103	1 - 36
9	9	chain 'I' and (resid 104 through 163 )	I	I	104 - 163	37 - 62
10	10	chain 'I' and (resid 164 through 197 )	I	I	164 - 197	63 - 84
11	11	chain 'I' and (resid 198 through 279 )	I	I	198 - 279	85 - 153
12	12	chain 'I' and (resid 280 through 331 )	I	I	280 - 331	154 - 204
13	13	chain 'I' and (resid 332 through 357 )	I	I	332 - 357	205 - 230
14	14	chain 'I' and (resid 358 through 382 )	I	I	358 - 382	231 - 255
15	15	chain 'I' and (resid 383 through 420 )	I	I	383 - 420	256 - 285
16	16	chain 'I' and (resid 421 through 443 )	I	I	421 - 443	286 - 308
17	17	chain 'I' and (resid 444 through 481 )	I	I	444 - 481	309 - 346
18	18	chain 'J' and (resid 2 through 25 )	J	J	2 - 25	1 - 24
19	19	chain 'J' and (resid 26 through 32 )	J	J	26 - 32	25 - 31
20	20	chain 'J' and (resid 33 through 65 )	J	J	33 - 65	32 - 64
21	21	chain 'J' and (resid 66 through 75 )	J	J	66 - 75	65 - 74
22	22	chain 'J' and (resid 76 through 100 )	J	J	76 - 100	75 - 99
23	23	chain 'J' and (resid 101 through 117 )	J	J	101 - 117	100 - 116
24	24	chain 'K' and (resid 61 through 140 )	K	K	61 - 140	1 - 54
25	25	chain 'K' and (resid 141 through 312 )	K	K	141 - 312	55 - 177
26	26	chain 'K' and (resid 313 through 357 )	K	K	313 - 357	178 - 222
27	27	chain 'K' and (resid 358 through 481 )	K	K	358 - 481	223 - 328
28	28	chain 'L' and (resid 2 through 22 )	L	L	2 - 22	1 - 21
29	29	chain 'L' and (resid 23 through 45 )	L	L	23 - 45	22 - 44
30	30	chain 'L' and (resid 46 through 76 )	L	L	46 - 76	45 - 75
31	31	chain 'L' and (resid 77 through 117 )	L	L	77 - 117	76 - 116
32	32	chain 'A' and (resid 61 through 163 )	A	A	61 - 163	1 - 66
33	33	chain 'A' and (resid 164 through 192 )	A	A	164 - 192	67 - 91
34	34	chain 'A' and (resid 193 through 266 )	A	A	193 - 266	92 - 152
35	35	chain 'A' and (resid 267 through 331 )	A	A	267 - 331	153 - 217
36	36	chain 'A' and (resid 332 through 481 )	A	A	332 - 481	218 - 367
37	37	chain 'B' and (resid 2 through 9 )	B	B	2 - 9	1 - 8
38	38	chain 'B' and (resid 10 through 22 )	B	B	10 - 22	9 - 21
39	39	chain 'B' and (resid 23 through 32 )	B	B	23 - 32	22 - 31
40	40	chain 'B' and (resid 33 through 40 )	B	B	33 - 40	32 - 39
41	41	chain 'B' and (resid 41 through 58 )	B	B	41 - 58	40 - 57
42	42	chain 'B' and (resid 59 through 65 )	B	B	59 - 65	58 - 64
43	43	chain 'B' and (resid 66 through 76 )	B	B	66 - 76	65 - 75
44	44	chain 'B' and (resid 77 through 100 )	B	B	77 - 100	76 - 99
45	45	chain 'B' and (resid 101 through 117 )	B	B	101 - 117	100 - 116
46	46	chain 'C' and (resid 61 through 86 )	C	C	61 - 86	1 - 21
47	47	chain 'C' and (resid 87 through 140 )	C	C	87 - 140	22 - 55
48	48	chain 'C' and (resid 141 through 200 )	C	C	141 - 200	56 - 83
49	49	chain 'C' and (resid 201 through 227 )	C	C	201 - 227	84 - 110
50	50	chain 'C' and (resid 228 through 266 )	C	C	228 - 266	111 - 130
51	51	chain 'C' and (resid 267 through 298 )	C	C	267 - 298	131 - 160
52	52	chain 'C' and (resid 299 through 331 )	C	C	299 - 331	161 - 190
53	53	chain 'C' and (resid 332 through 357 )	C	C	332 - 357	191 - 216
54	54	chain 'C' and (resid 358 through 382 )	C	C	358 - 382	217 - 241
55	55	chain 'C' and (resid 383 through 412 )	C	C	383 - 412	242 - 268
56	56	chain 'C' and (resid 413 through 454 )	C	C	413 - 454	269 - 310
57	57	chain 'C' and (resid 455 through 481 )	C	C	455 - 481	311 - 337
58	58	chain 'D' and (resid 2 through 22 )	D	D	2 - 22	1 - 21
59	59	chain 'D' and (resid 23 through 52 )	D	D	23 - 52	22 - 51
60	60	chain 'D' and (resid 53 through 76 )	D	D	53 - 76	52 - 75
61	61	chain 'D' and (resid 77 through 100 )	D	D	77 - 100	76 - 99
62	62	chain 'D' and (resid 101 through 117 )	D	D	101 - 117	100 - 116
63	63	chain 'E' and (resid 60 through 218 )	E	E	60 - 218	1 - 98
64	64	chain 'E' and (resid 219 through 266 )	E	E	219 - 266	99 - 132
65	65	chain 'E' and (resid 267 through 357 )	E	E	267 - 357	133 - 215
66	66	chain 'E' and (resid 358 through 427 )	E	E	358 - 427	216 - 274
67	67	chain 'E' and (resid 428 through 481 )	E	E	428 - 481	275 - 315
68	68	chain 'F' and (resid 2 through 17 )	F	F	2 - 17	1 - 16
69	69	chain 'F' and (resid 18 through 52 )	F	F	18 - 52	17 - 51
70	70	chain 'F' and (resid 53 through 58 )	F	F	53 - 58	52 - 57
71	71	chain 'F' and (resid 59 through 81 )	F	F	59 - 81	58 - 80
72	72	chain 'F' and (resid 82 through 89 )	F	F	82 - 89	81 - 88
73	73	chain 'F' and (resid 90 through 100 )	F	F	90 - 100	89 - 99
74	74	chain 'F' and (resid 101 through 108 )	F	F	101 - 108	100 - 107
75	75	chain 'F' and (resid 109 through 117 )	F	F	109 - 117	108 - 116
76	76	chain 'G' and (resid 59 through 168 )	G	G	59 - 168	1 - 64

+
万見について

-
お知らせ

-
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

-
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

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

すべてのお知らせ

-
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

-
ムービー

-
構造ビューア

+
ビューアのログ

-
このページ

-
このウェブサイト

-
オプション

+
データを開く

-
基本情報

-
構造の表示

-
ダウンロードとリンク

-
ダウンロード

-
検証レポート

-
関連構造データ

-
リンク

-
集合体

-
要素

-
実験情報

-
実験

-
試料調製

-
データ収集

-
解析

+
万見について

-
お知らせ

-
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

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)

-ムービー

-構造ビューア

+ビューアのログ

-このページ

-このウェブサイト

-オプション

+データを開く

-基本情報

-構造の表示

-ダウンロードとリンク

-ダウンロード

-検証レポート

-関連構造データ

-リンク

-集合体

-要素

-実験情報

-実験

-試料調製

-データ収集

-解析

+万見について

-お知らせ

-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

-2020年8月12日: 新型コロナ情報

+2020年3月5日: 新型コロナウイルスの構造データ

+2019年1月31日: EMDBのIDの桁数の変更

+2017年7月12日: PDB大規模アップデート

-万見 (Yorodumi)

-
ムービー

-
構造ビューア

+
ビューアのログ

-
このページ

-
このウェブサイト

-
オプション

+
データを開く

-
基本情報

-
構造の表示

-
ダウンロードとリンク

-
ダウンロード

-
検証レポート

-
関連構造データ

-
リンク

-
集合体

-
要素

-
実験情報

-
実験

-
試料調製

-
データ収集

-
解析

+
万見について

-
お知らせ

-
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

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)