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- PDB-7dkh: Crystal structure of the Ctr9/Paf1/Cdc73/Rtf1 quaternary complex -

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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: 7dkh

タイトル

Crystal structure of the Ctr9/Paf1/Cdc73/Rtf1 quaternary complex

要素

Cell division control protein 73
RNA polymerase II-associated protein 1
RNA polymerase-associated protein CTR9
RNA polymerase-associated protein RTF1

キーワード

GENE REGULATION / Paf1 complex / H2B mono-ubiquitination / Rad6/Bre1 / ubiquitin discharge

機能・相同性

機能・相同性情報

: / : / : / snoRNA transcription by RNA polymerase II / : / : / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / sno(s)RNA 3'-end processing / regulation of transcription initiation by RNA polymerase II ...
類似検索 - 分子機能

生物種

Saccharomyces cerevisiae (パン酵母)

手法

X線回折 /

シンクロトロン /

単波長異常分散 / 解像度: 2.9 Å

データ登録者

Chen, F.L. / Liu, B.B. / Guo, L. / Li, D.F. / Zhou, H. / Long, J.F.

資金援助

中国, 2件

引用

ジャーナル: J.Mol.Biol. / 年: 2021
タイトル: Crystal Structure of the Core Module of the Yeast Paf1 Complex.
著者: Chen, F.L. / Liu, B.B. / Zeng, J.W. / Guo, L. / Ge, X. / Feng, W. / Li, D.F. / Zhou, H. / Long, J.F.

履歴

登録	2020年11月24日	登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.0	2021年11月24日	Provider: repository / タイプ: Initial release
改定 1.1	2022年1月5日	Group: Database references / カテゴリ: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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	7dkh.cif.gz	1.5 MB	表示	PDBx/mmCIF形式
PDB形式	pdb7dkh.ent.gz	1.2 MB	表示	PDB形式
PDBx/mmJSON形式	7dkh.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

文書・要旨	7dkh_validation.pdf.gz	544.6 KB	表示	wwPDB検証レポート
文書・詳細版	7dkh_full_validation.pdf.gz	614.1 KB	表示
XML形式データ	7dkh_validation.xml.gz	112.8 KB	表示
CIF形式データ	7dkh_validation.cif.gz	152.7 KB	表示
アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/dk/7dkh ftp://data.pdbj.org/pub/pdb/validation_reports/dk/7dkh	HTTPS FTP

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関連構造データ

類似構造データ	7dkh-3 7dkh-2 1ahw-d 2bzd-d 1y8q-d 6z3m-1 4uih-d 1333 Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) 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	#230 - 2019年2月開始因子eIF4E (Initiation Factor eIF4E) 類似性 (6) #141 - 2011年9月 O-GlcNAc転移酵素 (O-GlcNAc Transferase) 類似性 (5) #166 - 2013年10月プロテアソーム (Proteasome) 類似性 (3)

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集合体

登録構造単位

A: RNA polymerase-associated protein CTR9

B: RNA polymerase II-associated protein 1

C: Cell division control protein 73

D: RNA polymerase-associated protein RTF1

E: RNA polymerase-associated protein CTR9

F: RNA polymerase II-associated protein 1

G: Cell division control protein 73

H: RNA polymerase-associated protein RTF1

I: RNA polymerase-associated protein CTR9

J: RNA polymerase II-associated protein 1

K: Cell division control protein 73

L: RNA polymerase-associated protein RTF1

421 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)

A: RNA polymerase-associated protein CTR9

B: RNA polymerase II-associated protein 1

C: Cell division control protein 73

D: RNA polymerase-associated protein RTF1

登録者・ソフトウェアが定義した集合体
根拠: gel filtration
140 kDa, 4 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)

E: RNA polymerase-associated protein CTR9

F: RNA polymerase II-associated protein 1

G: Cell division control protein 73

H: RNA polymerase-associated protein RTF1

登録者・ソフトウェアが定義した集合体
140 kDa, 4 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)

I: RNA polymerase-associated protein CTR9

J: RNA polymerase II-associated protein 1

K: Cell division control protein 73

L: RNA polymerase-associated protein RTF1

登録者・ソフトウェアが定義した集合体
140 kDa, 4 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)

単位格子

Length a, b, c (Å)	190.195, 190.195, 216.423
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

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要素

#1: タンパク質	RNA polymerase-associated protein CTR9 / Centromere-binding factor 1-dependent protein 1 / Cln three-requiring protein 9 分子量: 113746.820 Da / 分子数: 3 / 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) 遺伝子: CTR9, CDP1, YOL145C / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P89105
#2: タンパク質	RNA polymerase II-associated protein 1 / Protein PAF1 分子量: 11956.307 Da / 分子数: 3 / 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) 遺伝子: PAF1, YBR279W, YBR2016 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P38351
#3: タンパク質	Cell division control protein 73 / RNA polymerase-associated protein CDC73 分子量: 6333.072 Da / 分子数: 3 / 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) 遺伝子: CDC73, YLR418C / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q06697
#4: タンパク質	RNA polymerase-associated protein RTF1 分子量: 8207.274 Da / 分子数: 3 / 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) 遺伝子: RTF1, CSL3, YGL244W, HRA458 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P53064
研究の焦点であるリガンドがあるか	Y

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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: 2.71 Å³/Da / 溶媒含有率: 54.57 %
結晶化	温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 8% tascimate, pH 6.0, 12% PEG 3350

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データ収集

回折	平均測定温度: 97 K / Serial crystal experiment: N
放射光源	由来: シンクロトロン / サイト: SSRF / ビームライン: BL19U1 / 波長: 0.97791 Å
検出器	タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2018年11月3日
放射	プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長	波長: 0.97791 Å / 相対比: 1
反射	解像度: 2.9→48.96 Å / Num. obs: 100181 / % possible obs: 99.9 % / 冗長度: 31.2 % / B_iso Wilson estimate: 73.48 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.173 / R_pim(I) all: 0.044 / R_rim(I) all: 0.178 / Net I/σ(I): 17
反射シェル	解像度: 2.9→3.004 Å / R_merge(I) obs: 1.756 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9841 / CC_1/2: 0.794 / R_pim(I) all: 0.455 / R_rim(I) all: 1.815

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.14_3260	精密化
XDS		データ削減
XDS		データスケーリング
PHENIX		位相決定

精密化

構造決定の手法:

単波長異常分散 / 解像度: 2.9→48.96 Å / SU ML: 0.4021 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.0631 / 立体化学のターゲット値: CDL v1.2

	R_factor	反射数	%反射
R_free	0.2478	5119	5.11 %
R_work	0.1926	95013	-
obs	0.1954	100132	99.81 %

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: 90.01 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.9→48.96 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	27198	0	0	0	27198

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0043	27674
X-RAY DIFFRACTION	f_angle_d	0.9361	37277
X-RAY DIFFRACTION	f_chiral_restr	0.0491	4167
X-RAY DIFFRACTION	f_plane_restr	0.0062	4768
X-RAY DIFFRACTION	f_dihedral_angle_d	23.6889	10648

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 (%)
2.9-2.93	0.3672	162	0.3101	3065	X-RAY DIFFRACTION	96.76
2.93-2.97	0.3248	166	0.2698	3150	X-RAY DIFFRACTION	100
2.97-3	0.3342	161	0.2702	3136	X-RAY DIFFRACTION	100
3-3.04	0.3373	167	0.2746	3126	X-RAY DIFFRACTION	100
3.04-3.08	0.3549	182	0.2779	3127	X-RAY DIFFRACTION	100
3.08-3.12	0.3947	189	0.2658	3128	X-RAY DIFFRACTION	100
3.12-3.17	0.3193	212	0.2686	3143	X-RAY DIFFRACTION	100
3.17-3.22	0.3652	158	0.2684	3112	X-RAY DIFFRACTION	100
3.22-3.27	0.2875	131	0.254	3181	X-RAY DIFFRACTION	100
3.27-3.32	0.3022	155	0.2462	3171	X-RAY DIFFRACTION	100
3.32-3.38	0.3409	177	0.2445	3142	X-RAY DIFFRACTION	100
3.38-3.44	0.269	169	0.2272	3153	X-RAY DIFFRACTION	99.97
3.44-3.5	0.2912	167	0.2295	3145	X-RAY DIFFRACTION	99.85
3.5-3.58	0.3035	154	0.2142	3164	X-RAY DIFFRACTION	99.91
3.58-3.65	0.2706	186	0.2143	3174	X-RAY DIFFRACTION	99.97
3.65-3.74	0.2666	169	0.2055	3130	X-RAY DIFFRACTION	99.94
3.74-3.83	0.2807	164	0.1916	3164	X-RAY DIFFRACTION	99.97
3.83-3.94	0.2187	152	0.1813	3178	X-RAY DIFFRACTION	100
3.94-4.05	0.2343	194	0.178	3149	X-RAY DIFFRACTION	100
4.05-4.18	0.2218	164	0.1713	3178	X-RAY DIFFRACTION	99.97
4.18-4.33	0.1977	178	0.1717	3167	X-RAY DIFFRACTION	99.97
4.33-4.5	0.2521	199	0.169	3146	X-RAY DIFFRACTION	99.94
4.5-4.71	0.2118	181	0.1547	3151	X-RAY DIFFRACTION	100
4.71-4.96	0.2033	189	0.1513	3159	X-RAY DIFFRACTION	100
4.96-5.27	0.232	187	0.1709	3193	X-RAY DIFFRACTION	100
5.27-5.67	0.274	161	0.1946	3194	X-RAY DIFFRACTION	99.97
5.67-6.24	0.2562	137	0.2048	3251	X-RAY DIFFRACTION	99.97
6.24-7.15	0.2539	162	0.1816	3243	X-RAY DIFFRACTION	99.97
7.15-8.99	0.1749	180	0.1526	3259	X-RAY DIFFRACTION	99.88
8.99-48.96	0.187	166	0.1587	3334	X-RAY DIFFRACTION	98.29

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	5.27674820412	-1.81129239866	-0.68748803334	4.24484030097	3.58945935602	7.66243930609	0.139319962336	0.375373310054	0.0478272712054	0.252222911284	-0.462190158772	0.82754178417	0.504833776002	-1.25737058276	0.293479155417	0.621066969984	-0.102606769023	0.122038679169	0.721419750149	-0.157544940401	1.31079788277	-15.6635856757	71.5472070904	15.6300989559
2	2.04717782305	0.38762486615	0.179973805335	3.18629767604	0.81679599773	1.23175843728	0.0180456899666	0.194451302997	-0.546129716046	0.132831454584	-0.12178641355	0.357183480314	0.199740228392	-0.0643642238118	0.0975071270499	0.38172197749	0.0334207677124	0.039876371696	0.438316014343	-0.0651790371477	0.41232937671	8.80373369221	96.2657188772	25.8377960083
3	2.78317089107	2.09538630479	-0.0978363151225	4.95275496867	0.476608237945	1.44748031148	-0.127372441786	0.434003567721	0.439733871215	-0.293075419293	0.218730120736	-0.263104642467	-0.29463796012	0.267990515641	-0.106987552415	0.341505552333	-0.0419189229222	-0.052310079309	0.554225707695	0.153877891773	0.542864043945	40.926425327	138.072177069	33.9792462851
4	8.49273777088	0.35890514215	1.06465662422	1.00919428013	0.524028209773	1.00223370859	-0.0149315391509	-0.295411653639	0.564379551403	0.43017889569	0.164722305965	-0.314459045169	0.151725923372	0.181304850905	-0.161351653456	0.609007471363	-0.0697015091465	-0.115715143326	0.510178767527	-0.0435874878465	0.552792378805	61.540177901	140.053171649	59.8822140824
5	1.24025909786	-0.841972556918	-1.57960290036	4.60308211689	1.54336404263	2.3616000515	-0.418505103952	-0.522674449209	0.61447483795	0.511826528492	0.833580086561	-0.827440519776	0.155422995282	0.453166645373	-0.407360675594	0.72404101279	0.116823798618	-0.414970893679	0.933594934566	-0.387308426227	1.01555402116	94.8007855669	141.89307906	66.3439746946
6	5.10324711306	5.29639165832	3.29776872055	8.79228832134	2.30370087462	2.42227030345	-1.00033702737	-1.20138988119	2.60016016127	0.457113503836	0.123636208804	0.370109726385	-0.272023299139	-0.239195243423	0.621123415451	0.716491881525	-0.168442769805	0.0265718060768	0.79431451406	-0.213701793786	0.761706837477	65.8096705466	143.053803043	63.6867935236
7	2.75462434556	2.54293215005	5.00437019372	2.27902436343	4.45167871031	8.8954942839	-0.734639382621	0.417210369713	0.233949574365	-0.0311708181864	0.103899279573	0.666645151124	-0.140783169538	1.31446795404	0.413518965706	0.405826035684	-0.138216813588	-0.0776120341619	0.69451467334	0.135817084288	0.806688747925	46.506503314	141.766008507	42.9296743555
8	2.01234470096	2.1647494468	-0.830608782234	2.13673847707	-0.922332013591	0.347865542577	-0.947472465871	0.62957212592	1.10266246202	-1.41703697268	0.501318435416	0.881240638837	-0.113561987352	0.0494659547242	0.316305502428	0.531242855335	-0.0827195074879	-0.127725125095	0.549551338501	0.125303976312	0.482141106412	26.56922077	127.602492859	25.8298470902
9	7.51526807496	5.42560102573	2.56354188847	7.04116902581	2.67880995392	1.36257498216	0.425748655355	0.603610289797	-0.567596613217	0.976298800896	-0.0433238162426	0.275334369625	0.378124643828	0.126798389345	-0.36325420073	0.442430357629	-0.00153344515669	0.0176831368214	0.499549828663	-0.126278277819	0.385371321496	11.5353260291	98.8084645007	23.0688721079
10	4.45980488372	5.25592931302	2.83301564188	6.08775469185	3.30657349369	2.08286327926	0.497922551249	0.290435290263	-1.01226302561	-0.28853924179	-0.447429088932	-0.272207067742	0.505147478164	0.0519552052959	-0.0277575181071	0.799935539874	-0.0517353439535	0.13462839786	0.59338540131	-0.112366885815	1.26830961898	-3.54483163193	67.8839203181	20.8276853704
11	5.63177180321	-0.768276322168	-0.967273335712	7.31651016545	0.905424502275	8.77259697863	-0.434885576649	0.377105877427	-2.07166430463	-0.304161794355	1.02048462442	-1.46574651365	0.845468208755	1.09685846716	-0.643865439328	0.649552323629	0.224920026498	-0.0892190499234	0.767897066714	-0.337495911792	1.35260560869	19.6069938028	73.2405368837	19.780541494
12	5.03998257513	3.61977912517	-2.57748762913	3.19734887577	-2.21707291221	7.15145908761	0.910313563322	-0.056189140907	1.80548700246	-1.69242356539	0.371392883051	0.999345748223	-0.246121842877	-1.43516399788	-1.03813330935	1.20472737734	0.16121176442	0.0565356891886	1.13514886762	0.772744514374	2.04213306893	30.2408673742	157.935296411	32.35315584
13	3.44324032574	4.03005826853	-3.80044162669	4.72390891202	-4.44128490945	4.17897168067	0.126015154446	0.707205110754	-0.830836781677	0.544391143808	0.0805400692087	0.0973614754414	-1.28038937609	-0.68654675854	-0.397263098866	0.914362254736	-0.00902474670126	-0.138052461083	0.925773308191	0.25198231133	0.968778690696	29.6726554628	146.315803096	26.6811288233
14	7.75354270623	-0.643590247987	4.75895961284	1.1162002361	-0.772159644	3.05238709167	0.0486168317366	0.323501017107	0.677078634248	0.298837054414	-0.306732729158	0.243279688794	-0.0118650836646	0.23551295917	0.15272966846	0.477099761472	-0.0935246003012	-0.00632854261605	0.452650304354	-0.016506822112	0.570872783419	40.0327985076	133.637089941	42.534237668
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18	5.22624876298	-7.41176733944	0.587725006982	2.0194098551	-0.849580018747	0.574699452647	0.656317384476	-2.65562697769	0.222173692638	-0.877901788683	0.346485624789	-0.868154067963	0.348740401826	1.76664226141	-0.817922461906	0.70276526446	0.0805743218099	0.0242849565903	1.37369370441	-0.0619293926529	1.09748864641	41.847659038	100.290832416	11.9161389152
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25	3.68283453369	-0.162902363543	0.738380803953	2.20602733515	-1.27698974151	0.878784534816	0.159977432274	0.273003633072	-0.474474522339	0.0408546787192	0.209704686973	-0.184017315487	-0.528608479596	0.32381227065	-0.398348351701	1.05444025077	0.0767032506111	-0.0904824920895	0.617653187216	-0.0911156637757	0.611517099878	87.9589008629	94.9085601223	62.6211537941
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28	6.61594450036	-4.83329869318	-5.29400558721	3.76827951252	4.22666144136	4.78078134388	-0.612010707023	-0.376187172806	0.727706624526	-0.688006129044	0.483998379344	1.10036014859	-0.580668723545	0.377445840705	-0.0272922613598	0.513759760211	-0.0371364765442	-0.10278243296	0.570848735441	0.198174016332	0.689653567625	72.7648240633	172.028172113	25.4735520249
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31	6.75180951169	4.04517445893	-0.541134626992	6.43931256739	-4.38445523575	4.13737580082	-0.381282611669	-0.664555569154	1.51199571455	-1.11377421707	-0.4522065483	2.85245196528	-1.62548394802	-2.79308520982	0.874476541683	0.756769651294	0.281099994243	-0.442455563174	0.957678918406	-0.196569722183	1.71079668901	50.3303840287	186.619448946	27.9650452435
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34	6.75415585624	-0.783879090328	-4.99846458368	2.94346632783	1.64823323358	9.12487536036	-0.45598009854	1.26599101489	-0.0421092203855	-0.672072059665	-0.0469593314843	-0.76104769529	0.50264161028	0.588587978427	0.596565651306	1.07100813665	-0.21976498369	0.556973724604	0.939198478011	0.081992899973	1.19336616533	109.836073498	122.761038146	24.9098016986
35	7.38311675687	6.93097133887	-6.93257134011	6.42449520201	-6.51594397051	6.53145454836	-0.652952959523	-0.216891603363	-0.572604759532	-1.69733984676	-0.101012914815	-1.42322428434	1.2522287674	0.912356180638	0.714391893455	0.908435931294	0.00714422542881	0.216475804456	0.519820741505	0.0340822188813	0.831832608783	99.5883957456	121.875036613	34.2886901194
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52	5.37515280401	-6.81634689441	-1.37985870035	9.02687572153	1.05226971176	2.44279984302	0.325455682013	-0.733180311477	1.32755218565	-0.212764048367	-0.274951014742	-1.93974731185	-0.21408882281	1.22027313148	0.0137269556807	0.516449154978	-0.103724813137	0.0722819617315	0.654200011637	0.0450017395139	0.924455843899	135.796299093	78.7783747956	23.3084596382
53	6.55204357062	-0.176942396529	0.456624985564	2.64182916854	-0.621772214581	7.89667795327	0.745771476393	0.480027356482	2.5976185391	0.12575839865	-0.282207279277	-0.619886392037	-1.35347223544	-0.0662244915385	-0.438518195266	0.774727337107	-0.137117008517	0.238689897213	0.443790782352	-0.0459724720773	1.14598097723	117.708437335	95.1773931056	21.2895400309
54	3.00232461017	-1.22134457358	2.20293885798	3.41383936028	-2.99376476429	3.13428723858	-0.403932448067	0.145648108973	-0.803701251709	-0.848507569971	0.592472406115	0.997412793116	0.658939471023	-0.139446804395	-0.268332244357	0.657186214411	-0.0263844507321	-0.132545100486	0.652758372215	-0.222952530487	1.41967220336	43.4824741063	64.4598552002	26.5577579808
55	1.89307436036	-1.09245204181	-2.8639692854	2.48309526943	1.8079940877	7.1300464333	0.350315430523	0.623667612241	-0.5401608843	0.0272828386669	-0.132754773514	-0.407277422375	0.769764766017	-0.391950651065	-0.163602291763	0.622134338541	0.12893544762	-0.100537706025	0.635780987111	0.0573234384566	1.22986416911	51.6105748246	75.0083298624	33.8010785345
56	1.89050193835	-0.299265344676	0.0935410264261	2.74106627322	1.07539052453	2.79751858191	-0.43261274712	-0.374438902283	-0.0790568631656	1.23194671643	-0.517139218749	-1.08327626142	-0.107274743357	1.35394513989	0.764544472919	1.05222727269	-0.0313796983259	-0.537981832821	0.727617843714	0.225263765499	1.21661203416	52.8603868901	85.4697029499	61.259091973
57	-0.0767442387603	0.0897426172546	-0.0638205123133	0.0490225040201	-0.0900143384985	-0.160030975242	-0.0650324074006	-0.380142851388	-0.0796639410827	-2.05525446684	-0.234119690099	0.736356417131	-0.21543764403	-0.17717275106	0.275967757395	1.44722373764	-0.00810772959594	-0.15634370391	1.24667813642	0.234243476894	0.902243146434	83.8363212738	108.082495274	10.7916191893
58	2.57406317008	-3.39231965563	-1.4495445815	7.69959599632	-2.81065833659	8.90679537831	0.206998064601	1.02233402052	-1.00628800552	-1.87470281124	-0.354427215776	0.293927122283	0.22601261082	-0.441676118309	0.193176647377	0.792168345499	-0.109578092451	0.0507119673265	0.885078031527	-0.110837851798	0.56228053847	86.7276963052	75.1031018582	9.23037191249

精密化 TLSグループ

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 133 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 134 through 430 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 431 through 646 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 647 through 834 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 835 through 922 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 5 through 14 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 15 through 24 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 25 through 39 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 65 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 66 through 84 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 85 through 103 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 7 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 8 through 15 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 16 through 35 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 36 through 45 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 46 through 53 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 18 through 26 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 27 through 43 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 44 through 68 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 10 through 233 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 234 through 454 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 455 through 600 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 601 through 646 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 647 through 922 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 5 through 15 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 16 through 39 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 40 through 55 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 56 through 60 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 61 through 65 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 66 through 80 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 81 through 85 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 86 through 103 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 3 through 7 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 8 through 12 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 13 through 24 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 25 through 45 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 46 through 53 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 18 through 26 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 27 through 43 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 44 through 59 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 60 through 68 )
42	X-RAY DIFFRACTION	42	chain 'I' and (resid 10 through 133 )
43	X-RAY DIFFRACTION	43	chain 'I' and (resid 134 through 430 )
44	X-RAY DIFFRACTION	44	chain 'I' and (resid 431 through 600 )
45	X-RAY DIFFRACTION	45	chain 'I' and (resid 601 through 730 )
46	X-RAY DIFFRACTION	46	chain 'I' and (resid 731 through 875 )
47	X-RAY DIFFRACTION	47	chain 'I' and (resid 876 through 923 )
48	X-RAY DIFFRACTION	48	chain 'J' and (resid 5 through 14 )
49	X-RAY DIFFRACTION	49	chain 'J' and (resid 15 through 29 )
50	X-RAY DIFFRACTION	50	chain 'J' and (resid 30 through 39 )
51	X-RAY DIFFRACTION	51	chain 'J' and (resid 40 through 70 )
52	X-RAY DIFFRACTION	52	chain 'J' and (resid 71 through 84 )
53	X-RAY DIFFRACTION	53	chain 'J' and (resid 85 through 103 )
54	X-RAY DIFFRACTION	54	chain 'K' and (resid 3 through 12 )
55	X-RAY DIFFRACTION	55	chain 'K' and (resid 13 through 24 )
56	X-RAY DIFFRACTION	56	chain 'K' and (resid 25 through 53 )
57	X-RAY DIFFRACTION	57	chain 'L' and (resid 18 through 43 )
58	X-RAY DIFFRACTION	58	chain 'L' and (resid 44 through 68 )

+
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://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

+
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)