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万見

- PDB-7rdb: Crystal structure of Tspan15 large extracellular loop (Tspan15 LEL) -

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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: 7rdb

タイトル

Crystal structure of Tspan15 large extracellular loop (Tspan15 LEL)

要素

Tetraspanin-15

キーワード

CELL ADHESION / Tetraspanin / Membrane Protein / Protein Trafficking

機能・相同性

機能・相同性情報

regulation of membrane protein ectodomain proteolysis / tetraspanin-enriched microdomain / negative regulation of Notch signaling pathway / protein maturation / protein localization to plasma membrane / late endosome membrane / cell junction / nuclear body / Amyloid fiber formation / endoplasmic reticulum lumen ...
類似検索 - 分子機能

生物種

Homo sapiens (ヒト)

手法

X線回折 /

シンクロトロン /

分子置換 / 解像度: 2.52 Å

データ登録者

Lipper, C.H. / Gabriel, K.H. / Seegar, T.C.M. / Durr, K.L. / Tomlinson, M.G. / Blacklow, S.C.

資金援助

米国,

英国, 4件

組織	認可番号	国
National Institutes of Health/National Cancer Institute (NIH/NCI)	R35CA220340	米国
Other private	Edward B. Goodnow	米国
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/P00783X/1	英国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41GM103403	米国

引用

ジャーナル: Structure / 年: 2022
タイトル: Crystal structure of the Tspan15 LEL domain reveals a conserved ADAM10 binding site.
著者: Lipper, C.H. / Gabriel, K.H. / Seegar, T.C.M. / Durr, K.L. / Tomlinson, M.G. / Blacklow, S.C.

履歴

登録	2021年7月9日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2021年11月3日	Provider: repository / タイプ: Initial release
改定 1.1	2021年11月17日	Group: Database references / カテゴリ: citation Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.2	2022年2月16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 1.3	2023年10月18日	Group: Data collection / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.4	2024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

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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	7rdb.cif.gz	1.3 MB	表示	PDBx/mmCIF形式
PDB形式	pdb7rdb.ent.gz	977.4 KB	表示	PDB形式
PDBx/mmJSON形式	7rdb.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/rd/7rdb ftp://data.pdbj.org/pub/pdb/validation_reports/rd/7rdb	HTTPS FTP

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関連構造データ

関連構造データ	7rd5SC 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	7rdb-6 7rdb-13 7rdb-10 7rdb-14 7rdb-11 7rdb-8 7rdb-24 7rdb-3 7rdb-20 7rdb-16 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) 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) 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) 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) 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) 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) 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

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集合体

登録構造単位

B: Tetraspanin-15

A: Tetraspanin-15

C: Tetraspanin-15

D: Tetraspanin-15

E: Tetraspanin-15

F: Tetraspanin-15

G: Tetraspanin-15

H: Tetraspanin-15

I: Tetraspanin-15

J: Tetraspanin-15

K: Tetraspanin-15

L: Tetraspanin-15

M: Tetraspanin-15

N: Tetraspanin-15

O: Tetraspanin-15

P: Tetraspanin-15

Q: Tetraspanin-15

R: Tetraspanin-15

S: Tetraspanin-15

T: Tetraspanin-15

U: Tetraspanin-15

V: Tetraspanin-15

W: Tetraspanin-15

X: Tetraspanin-15

344 kDa, 24 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)

B: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

C: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

D: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

F: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

G: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

H: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

J: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

K: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

L: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

M: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

N: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

O: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

P: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

Q: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

R: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

S: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

T: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

U: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

V: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

W: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)

X: Tetraspanin-15

登録者が定義した集合体
14.3 kDa, 1 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)	83.570, 91.950, 112.380
Angle α, β, γ (deg.)	87.552, 86.519, 86.241
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

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要素

#1: タンパク質	... Tetraspanin-15 / Tspan-15 / Tetraspan NET-7 / Transmembrane 4 superfamily member 15 分子量: 14345.235 Da / 分子数: 24 / 変異: N118Q, N189D, 231-236 expression tag / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TSPAN15, NET7, TM4SF15, UNQ677/PRO1311 / 細胞株 (発現宿主): Expi293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O95858
#2: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 41 / 由来タイプ: 天然 / 式: H₂O
Has protein modification	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: 2.5 Å³/Da / 溶媒含有率: 50.73 %
結晶化	温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.9 / 詳細: 0.1 M MES pH 6.9, 34-35 % polyethylene p-400

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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-E / 波長: 0.979 Å
検出器	タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年10月11日
放射	プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長	波長: 0.979 Å / 相対比: 1
反射	解像度: 2.52→48.67 Å / Num. obs: 111846 / % possible obs: 99.38 % / 冗長度: 5.7 % / B_iso Wilson estimate: 76.66 Å² / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.1461 / R_pim(I) all: 0.06505 / R_rim(I) all: 0.1601 / Net I/σ(I): 6.85
反射シェル	解像度: 2.52→2.61 Å / 冗長度: 4.7 % / R_merge(I) obs: 1.29 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 11044 / CC_1/2: 0.441 / CC star: 0.782 / R_pim(I) all: 0.6453 / R_rim(I) all: 1.451 / % possible all: 97.51

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.19.1_4122+SVN	精密化
XDS		データ削減
XSCALE		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: 7RD5

7rd5

解像度: 2.52→48.67 Å / SU ML: 0.4657 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 35.0584
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	0.2734	1971	1.76 %
R_work	0.235	109832	-
obs	0.2356	111803	99.4 %

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: 95.75 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.52→48.67 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	22730	0	0	41	22771

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0122	23198
X-RAY DIFFRACTION	f_angle_d	1.4058	31523
X-RAY DIFFRACTION	f_chiral_restr	0.1004	3473
X-RAY DIFFRACTION	f_plane_restr	0.0091	4120
X-RAY DIFFRACTION	f_dihedral_angle_d	13.8739	8176

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 (%)
2.52-2.58	0.4109	139	0.3656	7659	X-RAY DIFFRACTION	97.09
2.58-2.65	0.4352	140	0.359	7808	X-RAY DIFFRACTION	98.78
2.65-2.73	0.3272	143	0.3456	7845	X-RAY DIFFRACTION	99.44
2.73-2.82	0.4774	143	0.3873	7841	X-RAY DIFFRACTION	99.79
2.82-2.92	0.3662	142	0.365	7865	X-RAY DIFFRACTION	99.74
2.92-3.04	0.3259	142	0.3157	7901	X-RAY DIFFRACTION	99.75
3.04-3.17	0.3778	140	0.3027	7863	X-RAY DIFFRACTION	99.43
3.17-3.34	0.3341	139	0.2825	7861	X-RAY DIFFRACTION	99.71
3.34-3.55	0.2867	145	0.2596	7867	X-RAY DIFFRACTION	99.71
3.55-3.83	0.3165	142	0.2342	7884	X-RAY DIFFRACTION	99.88
3.83-4.21	0.2529	137	0.2239	7873	X-RAY DIFFRACTION	99.78
4.21-4.82	0.2451	139	0.1956	7850	X-RAY DIFFRACTION	99.46
4.82-6.07	0.2503	137	0.2089	7879	X-RAY DIFFRACTION	99.73
6.07-48.67	0.2069	143	0.1864	7836	X-RAY DIFFRACTION	99.28

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	2.24820096164	7.35103762028	4.75970772353	8.54012890496	5.09329089619	7.26084551167	-0.299806654545	0.768902449397	1.7314787576	-0.456057235237	-0.177934253721	2.34896654737	0.898931932897	-0.309281671485	0.464335869947	0.697976431347	-0.0793965364295	-0.171888253704	0.991478439194	-0.0530582074522	0.899478672039	-39.6444612171	-4.91089550358	-6.90156009031
2	5.17597973606	0.835594846537	-0.539868235937	3.68062021818	0.923834697109	6.80446467982	0.132210080208	0.481372825654	0.549534018757	-0.615884834485	-0.00102953108544	0.713344016856	-0.339976178554	-0.169482013079	-0.100726508403	0.535159108094	0.0578966743951	-0.0502171491151	0.492987574226	0.0765324523465	0.554804693945	-27.8295499197	2.09176492468	-3.68864916521
3	5.01432530766	1.70227835384	0.276430342253	2.92611674998	0.842852935112	7.55777147478	0.0573653225193	0.659307593782	0.152971442568	-0.627706682536	0.13914247024	-0.15493464732	-0.215273318726	0.169349203445	-0.18593897242	0.651805623486	0.0337139150566	0.0684201224574	0.631809619723	0.06843211741	0.599153823353	-16.9541853422	0.62361814865	-9.254316126
4	3.33022035091	3.7086293123	-3.33303637747	4.61547807285	0.117962233168	2.20900106992	-0.179927412025	-0.0428768778391	-1.4617500102	0.237266969205	-0.361711722944	-0.65146419286	0.303942470767	0.0671400178454	0.361243070314	0.834144702517	0.0252372413451	-0.0409615182825	0.849990584939	0.102288392266	0.852331191618	-29.0072411857	-15.3999335431	-4.12246493011
5	5.63021663335	-2.61404764523	2.02316795838	7.86078271572	-0.731432711874	4.50862770575	-0.522400923752	-0.758742751873	1.12822222982	0.411978044043	0.996509734621	-1.2937485026	-0.790920805295	-0.275002154943	-0.334304111084	0.985979212652	-0.0117427870747	0.0940607667048	0.613919252707	-0.0893609387609	0.817951469612	4.12546029337	-10.7686442274	6.17971601337
6	6.35969635587	-2.98900198451	0.941763740787	5.42872153615	-3.51396340697	4.93390950295	-0.0192371892865	-0.730660072303	0.47079270069	0.290879871786	0.320669509837	0.00754900451509	-0.231460389048	-0.284432415494	-0.285570484649	0.66322127283	0.047236078026	-0.0449052518149	0.463308601054	-0.0333989616634	0.624519451912	2.28027388169	-26.4280866451	7.30819726844
7	2.07407775437	-5.50158298132	-0.666826529447	3.44963096483	3.28457801316	2.062799438	-0.768562230772	-0.898707545258	1.5271125325	-1.12030715423	1.5276781181	0.255424705378	-1.74974422768	-0.788509844917	-0.678063353624	0.852882135249	0.100143588363	-0.0575672141244	0.666811506915	0.108524542669	0.648608158653	0.65288958081	-17.8329439875	-2.3353549078
8	8.90750118082	0.59449694494	-1.46085835526	5.35558983094	-1.11392662943	5.82003211552	-0.472164008264	0.239414100049	0.0648196433576	-0.114380846713	0.354581815611	-1.0995557878	0.261959147791	0.508432808815	0.116284651675	0.524699902493	0.0232938233264	-0.00205243961327	0.58011194451	-0.00469322898975	0.688361771599	10.2442652572	-25.7782947665	-3.61698033213
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88	5.42604135422	0.546307090515	-0.174207952535	4.45010695337	1.81414371761	9.85537540424	-0.156098244203	0.0411046085829	0.807947383549	0.321308826934	-0.0654637705487	0.494969372771	0.139270413298	0.803339414119	0.350345803512	0.637444431729	-0.0331051289178	-0.0252762924059	0.694175827655	-0.0194956039035	0.888011557867	1.87638373794	-47.1456302908	83.5982482243
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90	1.9792753329	0.101781824486	-1.07114255065	8.64998300256	2.28234525201	7.5219486452	1.43573141053	-0.687368084322	2.87095361044	-0.71614699421	-0.352040693084	1.61543523825	-1.02550299722	-1.68849347253	-0.711591074985	0.869524067536	-0.024998323634	-0.00662470024192	0.889947249651	-0.0539200931175	1.64264593318	-8.77245258676	-33.6481278523	80.2907853046
91	9.67633557545	0.152491697405	-1.16998898188	7.86450682565	0.826550807616	8.80853790106	0.71343026009	0.848577788993	0.310931140842	-0.729714508291	0.106720161083	0.0870198686852	-0.761969045858	0.241806175157	-0.750770060377	1.14056857486	-0.0989393422292	-0.126798121285	0.893440185341	0.0137117837604	0.893119098368	2.24335292222	-43.3947919584	69.8641223371
92	5.04284242359	-0.785623803533	-0.950516815275	4.99803090875	1.60486595041	3.84585841791	0.460946748728	1.49489465202	1.46110782204	-1.76469916042	0.829127640456	0.44267390515	-0.34314682403	-1.28746271655	-0.761183277378	1.45864172946	-0.199725826731	-0.134664341706	0.947803699364	0.409027581657	1.12950000933	1.96404212355	-35.702060535	69.6337759719
93	6.48675491463	2.00130745785	0.0475046155997	7.66921190279	-0.82240380466	0.849355963636	-0.186119111509	0.658812724588	1.72881392822	-1.14367701643	-0.359764402671	1.45907083147	-1.0772154045	-0.078739115631	0.480282193057	1.32329876513	0.0178407045879	-0.222629714947	0.94546283514	0.0510932656122	1.47056482501	-12.0854542526	-36.1490882598	72.7839891523
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97	3.60554992388	-0.809471754932	-0.359416176576	1.72769532863	-1.09902226518	2.04990689991	0.71207976841	0.341037106697	0.712408598628	-1.33246532919	0.403872874564	-2.02887247735	1.15771031887	1.32499093696	-1.28012998571	1.29346664817	-0.0171048590597	0.313047357273	1.71285481913	-0.269600599542	1.05191142639	3.37724829291	-70.8659935909	75.8345473648
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100	2.78925839439	0.937349550503	-0.819362369424	5.30739618105	1.08725002286	5.38449391235	0.237121563103	-0.666835284739	0.767245408029	1.1456192184	0.204277361023	0.00637403056423	-0.567881759319	-0.0349326129816	-0.449550552593	1.65305376394	0.0979629612965	0.290849661194	0.718596874051	-0.0892943419908	1.00753902379	10.065821352	21.6717139626	0.245602078737
101	2.46504917415	-0.510854052	0.724148596046	4.38080360307	1.1300338218	2.52272107876	0.057467697625	-0.487480952929	0.845234572279	0.997418985736	0.370856169718	-0.0604215834106	-0.831704337003	0.822585765712	-0.373553091672	1.44582474096	-0.184797318852	0.011177952486	0.81146476028	-0.16241747418	0.937469965133	21.1469609867	20.6776396356	-0.24862010793
102	3.11143356281	-1.26184520908	1.94859991755	2.55178942593	-1.3012862615	3.04467600658	-0.556131215709	0.558619986481	0.523144969325	0.923324995196	0.10448472909	0.076435097171	-1.6134527119	0.350131318422	0.389118241733	1.19161235441	-0.170428724911	0.109891156174	0.64697052464	-0.0499585636236	1.0305950443	12.7171321265	29.3593041583	-17.1150818134
103	8.68450923849	1.01499918093	-4.02932906956	2.86987611818	-0.409584420041	3.52530523076	0.336114238505	-1.98244422709	-3.04861950404	-0.708301240481	-1.39052629117	-0.106152005938	0.666597457269	1.00105387585	0.386324343335	1.10940727497	0.08429855266	-0.268746423373	1.4430809798	0.068742914862	1.30235945194	-40.0670402598	13.2585213591	-16.2095206468
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105	2.19675872657	0.376491453056	2.59736092884	4.91899448897	0.480927413647	3.55049044499	-0.148963691751	0.478381368292	0.320504396217	0.637695381993	0.103661593575	-1.3651322072	-0.180616622011	1.81318189587	-0.148872318596	0.671899478682	-0.16905682686	-0.103388467818	1.44664750562	-0.1809883004	0.879472854458	-31.570006258	29.0679636399	-19.4354038591
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107	6.81193765166	2.29013151129	0.301094553538	2.04744261098	-1.59516382779	2.08246676137	0.186157913233	0.83087446608	0.399250316383	-0.198323129266	0.0975297149425	0.631807040705	-1.13756827859	1.898831193	-0.324413140899	1.03662798181	-0.257268705006	-0.0251190514551	0.919790138093	-0.028592138595	0.702171316395	-53.4877412785	17.9790859885	-18.219340609
108	2.88655078177	0.772312332583	4.63840105282	0.817316254628	0.94387052348	7.488770113	0.286803889844	2.43970772622	0.342903966682	-0.0332821093345	-0.0952438905008	-0.162767987119	0.455887698545	0.545456529701	0.0220487508933	1.15061725565	-0.115451604157	-0.442189853591	1.66123929	0.330957416014	1.6635280917	-62.3735458322	11.7757834585	-24.2306430602
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111	3.38004920489	-0.817437264221	1.65210498219	0.204578082641	-0.189204316345	5.95275780748	1.05204072639	1.30911336594	-1.37415271234	-0.769213008114	-0.469776312534	0.916854496719	1.60240063089	0.482242980488	-0.342648605871	1.61513346428	-0.0304615548142	-0.131197313898	1.44349208216	-0.137407274123	0.955287275984	2.1975586099	-45.9886143015	42.7184768734
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120	1.87244329771	-0.921770654381	0.0146144854894	2.41399776529	-1.78071636701	2.29749827373	0.563774598688	-0.508665609939	1.05803024307	0.194363552963	-0.650628154094	-0.242721605075	-0.664106468279	-0.109495377882	0.112779769897	1.46790541784	-0.361654284719	0.0993599506485	1.45350444746	0.0128946667298	1.25366116133	-37.4164332923	44.5149749778	60.3793067926
121	3.97547984126	0.884194612381	1.80030273668	3.37529575877	2.24513446591	3.95038619527	-0.604741427367	0.810559994964	0.267059309506	-0.739442665434	0.469632230776	0.873895391035	-0.215438074152	-0.684445144391	0.181694169289	0.716291830962	-0.212738043738	-0.128760403357	1.73431432228	0.00100371114794	0.700234935083	-34.6461839935	38.4194059666	74.9292843993
122	5.30570794103	-2.56509063928	1.40737208567	1.87983725614	-2.41862002995	4.55663934733	1.38063528801	-0.167974875585	0.233186782197	0.143007520179	-0.642383519343	0.293422730322	-0.541682153226	2.64669524065	-1.12839723305	1.1855765981	-0.555470786813	-0.0442294904633	2.26315042855	-0.0745513661373	0.827329595411	-29.3766985726	36.6823983992	64.0633808044
123	2.57145699566	0.262012110342	2.97533097323	6.02643968774	2.67001568631	4.52431266291	0.00834020164098	1.92493476278	0.570962725059	-0.368044616767	0.670216217934	-2.18158757152	-1.40946497768	2.71552247437	-0.742916663345	1.26939409809	-0.928434941666	0.0865634357655	2.60543818343	-0.321341620595	1.12396076966	-19.095688133	43.3257272461	72.3663840084
124	3.47465231073	-1.04698134734	1.2403663307	4.34941164486	0.574400311678	2.64997579327	-0.247948006109	1.42201033993	0.111975928479	-0.413938025882	0.995986789594	-1.49665178794	-0.380788864566	2.69222486339	-0.548505951097	0.759032219558	-0.401471336261	0.00892206936212	2.4926543133	-0.133219019044	0.907110345688	-23.4255365036	34.3205630579	72.2381467264
125	4.14807878496	1.19531136707	3.97912860517	1.82970405113	2.66300778672	5.35103002635	-0.104257866339	1.37809724138	-0.581766539676	0.820006731327	0.525895111301	-0.595638823951	1.39148409338	1.27002046552	-1.07998810555	1.16017217106	-0.0605018395475	-0.102477531287	1.87714513848	-0.29903034257	1.0584659001	-26.4233285304	20.6552189611	72.3291291281
126	2.86807172108	0.852544841989	-0.681236618109	4.41589429562	1.23753177411	3.4195848629	-0.216795065268	1.38926873666	-0.377453393319	-0.648054785924	1.59780329487	-1.24425754672	-0.0940727610132	2.31323180769	-1.43125376602	0.712514557785	-0.216464912888	0.070048652275	2.11355443601	-0.353989475199	1.23585029769	-19.4945137341	31.9371788372	69.2271529466
127	1.01463284399	-0.507312042665	0.093206754511	1.24095741447	-0.430217668813	0.748949449405	0.543444174589	0.327690868151	0.445729900262	-0.318859335007	-0.38179810496	0.246884204051	0.311901050232	0.775164792907	-0.0368043512019	1.39294865833	-0.583277700222	0.256468208192	2.68666342173	-0.576941431087	1.09797747965	-24.26392329	28.0228579669	60.9490510601
128	3.88734603568	0.0367003672855	0.502028197703	4.50407323646	0.355126946102	5.39009105898	-0.736937278558	-0.425399382228	-0.168264854161	-0.0357975687709	0.393140856904	0.518118649784	-0.73268305681	0.950084405839	0.217461305643	1.04656734597	0.0900385542025	-0.0173678908527	1.82531704473	0.149823462141	0.815969651731	-42.9114420218	32.6477081464	59.2731611356
129	1.56228301089	0.746781962202	0.894345402879	1.76665457405	-1.13846378603	2.28898086411	0.608810433064	-1.13104306168	-0.865867093221	0.676751964702	0.193747583724	0.0119772789954	-1.09010462257	0.209776007268	-0.89318344019	1.43437578455	-0.096930051958	-0.0652207098787	1.7531738922	-0.0815664461843	1.15205880031	-54.7131222931	29.705231008	61.1777295984

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 'B' and (resid 115 through 133 )	B	A	115 - 133	1 - 19
2	2	chain 'B' and (resid 134 through 175 )	B	A	134 - 175	20 - 61
3	3	chain 'B' and (resid 176 through 210 )	B	A	176 - 210	62 - 96
4	4	chain 'B' and (resid 211 through 236 )	B	A	211 - 236	97 - 122
5	5	chain 'A' and (resid 115 through 133 )	A	B	115 - 133	1 - 19
6	6	chain 'A' and (resid 134 through 152 )	A	B	134 - 152	20 - 38
7	7	chain 'A' and (resid 153 through 159 )	A	B	153 - 159	39 - 45
8	8	chain 'A' and (resid 160 through 185 )	A	B	160 - 185	46 - 71
9	9	chain 'A' and (resid 186 through 195 )	A	B	186 - 195	72 - 81
10	10	chain 'A' and (resid 196 through 210 )	A	B	196 - 210	82 - 96
11	11	chain 'A' and (resid 211 through 236 )	A	B	211 - 236	97 - 122
12	12	chain 'C' and (resid 115 through 134 )	C	C	115 - 134	1 - 20
13	13	chain 'C' and (resid 135 through 159 )	C	C	135 - 159	21 - 45
14	14	chain 'C' and (resid 160 through 185 )	C	C	160 - 185	46 - 71
15	15	chain 'C' and (resid 186 through 218 )	C	C	186 - 218	72 - 104
16	16	chain 'C' and (resid 219 through 236 )	C	C	219 - 236	105 - 122
17	17	chain 'D' and (resid 115 through 133 )	D	D	115 - 133	1 - 19
18	18	chain 'D' and (resid 134 through 152 )	D	D	134 - 152	20 - 38
19	19	chain 'D' and (resid 153 through 218 )	D	D	153 - 218	39 - 104
20	20	chain 'D' and (resid 219 through 235 )	D	D	219 - 235	105 - 121
21	21	chain 'E' and (resid 115 through 133 )	E	E	115 - 133	1 - 19
22	22	chain 'E' and (resid 134 through 152 )	E	E	134 - 152	20 - 38
23	23	chain 'E' and (resid 153 through 185 )	E	E	153 - 185	39 - 71
24	24	chain 'E' and (resid 186 through 210 )	E	E	186 - 210	72 - 96
25	25	chain 'E' and (resid 211 through 236 )	E	E	211 - 236	97 - 122
26	26	chain 'F' and (resid 115 through 133 )	F	F	115 - 133	1 - 19
27	27	chain 'F' and (resid 134 through 159 )	F	F	134 - 159	20 - 45
28	28	chain 'F' and (resid 160 through 210 )	F	F	160 - 210	46 - 96
29	29	chain 'F' and (resid 211 through 236 )	F	F	211 - 236	97 - 122
30	30	chain 'G' and (resid 115 through 133 )	G	G	115 - 133	1 - 19
31	31	chain 'G' and (resid 134 through 151 )	G	G	134 - 151	20 - 37
32	32	chain 'G' and (resid 152 through 205 )	G	G	152 - 205	38 - 91
33	33	chain 'G' and (resid 206 through 229 )	G	G	206 - 229	92 - 115
34	34	chain 'G' and (resid 230 through 236 )	G	G	230 - 236	116 - 122
35	35	chain 'H' and (resid 115 through 134 )	H	H	115 - 134	1 - 20
36	36	chain 'H' and (resid 135 through 151 )	H	H	135 - 151	21 - 37
37	37	chain 'H' and (resid 152 through 210 )	H	H	152 - 210	38 - 96
38	38	chain 'H' and (resid 211 through 236 )	H	H	211 - 236	97 - 122
39	39	chain 'I' and (resid 115 through 138 )	I	I	115 - 138	1 - 24
40	40	chain 'I' and (resid 139 through 151 )	I	I	139 - 151	25 - 37
41	41	chain 'I' and (resid 152 through 210 )	I	I	152 - 210	38 - 96
42	42	chain 'I' and (resid 211 through 236 )	I	I	211 - 236	97 - 122
43	43	chain 'J' and (resid 116 through 133 )	J	J	116 - 133	1 - 18
44	44	chain 'J' and (resid 134 through 151 )	J	J	134 - 151	19 - 36
45	45	chain 'J' and (resid 152 through 159 )	J	J	152 - 159	37 - 44
46	46	chain 'J' and (resid 160 through 205 )	J	J	160 - 205	45 - 90
47	47	chain 'J' and (resid 206 through 236 )	J	J	206 - 236	91 - 121
48	48	chain 'K' and (resid 115 through 133 )	K	K	115 - 133	1 - 19
49	49	chain 'K' and (resid 134 through 151 )	K	K	134 - 151	20 - 37
50	50	chain 'K' and (resid 152 through 185 )	K	K	152 - 185	38 - 71
51	51	chain 'K' and (resid 186 through 236 )	K	K	186 - 236	72 - 122
52	52	chain 'L' and (resid 115 through 133 )	L	L	115 - 133	1 - 19
53	53	chain 'L' and (resid 134 through 152 )	L	L	134 - 152	20 - 38
54	54	chain 'L' and (resid 153 through 205 )	L	L	153 - 205	39 - 91
55	55	chain 'L' and (resid 206 through 229 )	L	L	206 - 229	92 - 115
56	56	chain 'L' and (resid 230 through 236 )	L	L	230 - 236	116 - 122
57	57	chain 'M' and (resid 115 through 133 )	M	M	115 - 133	1 - 19
58	58	chain 'M' and (resid 134 through 159 )	M	M	134 - 159	20 - 45
59	59	chain 'M' and (resid 160 through 210 )	M	M	160 - 210	46 - 96
60	60	chain 'M' and (resid 211 through 236 )	M	M	211 - 236	97 - 122
61	61	chain 'N' and (resid 115 through 133 )	N	N	115 - 133	1 - 19
62	62	chain 'N' and (resid 134 through 159 )	N	N	134 - 159	20 - 45
63	63	chain 'N' and (resid 160 through 218 )	N	N	160 - 218	46 - 104
64	64	chain 'N' and (resid 219 through 236 )	N	N	219 - 236	105 - 122
65	65	chain 'O' and (resid 116 through 133 )	O	O	116 - 133	1 - 18
66	66	chain 'O' and (resid 134 through 175 )	O	O	134 - 175	19 - 60
67	67	chain 'O' and (resid 176 through 218 )	O	O	176 - 218	61 - 103
68	68	chain 'O' and (resid 219 through 236 )	O	O	219 - 236	104 - 121
69	69	chain 'P' and (resid 115 through 133 )	P	P	115 - 133	1 - 19
70	70	chain 'P' and (resid 134 through 159 )	P	P	134 - 159	20 - 45
71	71	chain 'P' and (resid 160 through 185 )	P	P	160 - 185	46 - 71
72	72	chain 'P' and (resid 186 through 195 )	P	P	186 - 195	72 - 81
73	73	chain 'P' and (resid 196 through 210 )	P	P	196 - 210	82 - 96
74	74	chain 'P' and (resid 211 through 218 )	P	P	211 - 218	97 - 104
75	75	chain 'P' and (resid 219 through 230 )	P	P	219 - 230	105 - 116
76	76	chain 'P' and (resid 231 through 236 )	P	P	231 - 236	117 - 122
77	77	chain 'Q' and (resid 115 through 133 )	Q	Q	115 - 133	1 - 19
78	78	chain 'Q' and (resid 134 through 159 )	Q	Q	134 - 159	20 - 45
79	79	chain 'Q' and (resid 160 through 175 )	Q	Q	160 - 175	46 - 61
80	80	chain 'Q' and (resid 176 through 210 )	Q	Q	176 - 210	62 - 96
81	81	chain 'Q' and (resid 211 through 218 )	Q	Q	211 - 218	97 - 104
82	82	chain 'Q' and (resid 219 through 236 )	Q	Q	219 - 236	105 - 122
83	83	chain 'R' and (resid 115 through 136 )	R	R	115 - 136	1 - 22
84	84	chain 'R' and (resid 137 through 159 )	R	R	137 - 159	23 - 45
85	85	chain 'R' and (resid 160 through 218 )	R	R	160 - 218	46 - 104
86	86	chain 'R' and (resid 219 through 236 )	R	R	219 - 236	105 - 122
87	87	chain 'S' and (resid 115 through 134 )	S	S	115 - 134	1 - 20
88	88	chain 'S' and (resid 135 through 151 )	S	S	135 - 151	21 - 37
89	89	chain 'S' and (resid 152 through 169 )	S	S	152 - 169	38 - 55
90	90	chain 'S' and (resid 170 through 182 )	S	S	170 - 182	56 - 68
91	91	chain 'S' and (resid 183 through 190 )	S	S	183 - 190	69 - 76
92	92	chain 'S' and (resid 191 through 200 )	S	S	191 - 200	77 - 86
93	93	chain 'S' and (resid 201 through 205 )	S	S	201 - 205	87 - 91
94	94	chain 'S' and (resid 206 through 210 )	S	S	206 - 210	92 - 96
95	95	chain 'S' and (resid 211 through 218 )	S	S	211 - 218	97 - 104
96	96	chain 'S' and (resid 219 through 229 )	S	S	219 - 229	105 - 115
97	97	chain 'S' and (resid 230 through 236 )	S	S	230 - 236	116 - 122
98	98	chain 'T' and (resid 115 through 133 )	T	T	115 - 133	1 - 19
99	99	chain 'T' and (resid 134 through 151 )	T	T	134 - 151	20 - 37
100	100	chain 'T' and (resid 152 through 175 )	T	T	152 - 175	38 - 61
101	101	chain 'T' and (resid 176 through 210 )	T	T	176 - 210	62 - 96
102	102	chain 'T' and (resid 211 through 235 )	T	T	211 - 235	97 - 121
103	103	chain 'U' and (resid 116 through 133 )	U	U	116 - 133	1 - 18
104	104	chain 'U' and (resid 134 through 159 )	U	U	134 - 159	19 - 44
105	105	chain 'U' and (resid 160 through 185 )	U	U	160 - 185	45 - 70
106	106	chain 'U' and (resid 186 through 218 )	U	U	186 - 218	71 - 103
107	107	chain 'U' and (resid 219 through 230 )	U	U	219 - 230	104 - 115
108	108	chain 'U' and (resid 231 through 236 )	U	U	231 - 236	116 - 121
109	109	chain 'V' and (resid 117 through 133 )	V	V	117 - 133	1 - 17
110	110	chain 'V' and (resid 134 through 205 )	V	V	134 - 205	18 - 89
111	111	chain 'V' and (resid 206 through 210 )	V	V	206 - 210	90 - 94
112	112	chain 'V' and (resid 211 through 235 )	V	V	211 - 235	95 - 119
113	113	chain 'W' and (resid 115 through 133 )	W	W	115 - 133	1 - 19
114	114	chain 'W' and (resid 134 through 151 )	W	W	134 - 151	20 - 37
115	115	chain 'W' and (resid 152 through 179 )	W	W	152 - 179	38 - 65
116	116	chain 'W' and (resid 180 through 200 )	W	W	180 - 200	66 - 86
117	117	chain 'W' and (resid 201 through 212 )	W	W	201 - 212	87 - 98
118	118	chain 'W' and (resid 213 through 229 )	W	W	213 - 229	99 - 115
119	119	chain 'W' and (resid 230 through 235 )	W	W	230 - 235	116 - 121
120	120	chain 'X' and (resid 115 through 133 )	X	X	115 - 133	1 - 19
121	121	chain 'X' and (resid 134 through 151 )	X	X	134 - 151	20 - 37
122	122	chain 'X' and (resid 152 through 165 )	X	X	152 - 165	38 - 51
123	123	chain 'X' and (resid 166 through 175 )	X	X	166 - 175	52 - 61
124	124	chain 'X' and (resid 176 through 185 )	X	X	176 - 185	62 - 71
125	125	chain 'X' and (resid 186 through 195 )	X	X	186 - 195	72 - 81
126	126	chain 'X' and (resid 196 through 205 )	X	X	196 - 205	82 - 91
127	127	chain 'X' and (resid 206 through 218 )	X	X	206 - 218	92 - 104
128	128	chain 'X' and (resid 219 through 229 )	X	X	219 - 229	105 - 115
129	129	chain 'X' and (resid 230 through 236 )	X	X	230 - 236	116 - 122

+
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)