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- PDB-6w9v: Structure of human MAIT A-F7 TCR in complex with patient MR1-R9H ... -

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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: 6w9v

タイトル

Structure of human MAIT A-F7 TCR in complex with patient MR1-R9H without ligand

要素

Beta-2-microglobulinΒ2-ミクログロブリン
Major histocompatibility complex class I-related gene protein
TCR-alpha chain
TCR-beta chain

キーワード

IMMUNE SYSTEM (免疫系) / MAIT / MR1 /

metabolite (代謝物質)

機能・相同性

機能・相同性情報

positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I /

beta-2-microglobulin binding /

T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I /

beta-2-microglobulin binding /

T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin /

regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium /

免疫応答 / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane /

小胞体 /

ゴルジ体 /

focal adhesion /

自然免疫系 / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity /

ゴルジ体 /

小胞体 / protein homodimerization activity /

extracellular space / extracellular exosome / extracellular region /

生体膜 / identical protein binding /

細胞膜 /

細胞質基質
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: 1.95 Å

データ登録者

Awad, W. / Rossjohn, J.

資金援助

オーストラリア, 1件

引用

ジャーナル: Sci Immunol / 年: 2020
タイトル: Absence of mucosal-associated invariant T cells in a person with a homozygous point mutation in MR1 .
著者: Howson, L.J. / Awad, W. / von Borstel, A. / Lim, H.J. / McWilliam, H.E.G. / Sandoval-Romero, M.L. / Majumdar, S. / Hamzeh, A.R. / Andrews, T.D. / McDermott, D.H. / Murphy, P.M. / Le Nours, J. ...

履歴

登録	2020年3月23日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2020年8月5日	Provider: repository / タイプ: Initial release
改定 1.1	2020年9月30日	Group: Database references / カテゴリ: citation / Item: _citation.title
改定 1.2	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	6w9v.cif.gz	841.5 KB	表示	PDBx/mmCIF形式
PDB形式	pdb6w9v.ent.gz	579 KB	表示	PDB形式
PDBx/mmJSON形式	6w9v.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/w9/6w9v ftp://data.pdbj.org/pub/pdb/validation_reports/w9/6w9v	HTTPS FTP

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関連構造データ

関連構造データ	6w9uC 6pucS 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	6pum-1 6pvd-1 5u72-1 4pjh-2 6pue-1 6pui-1 4pj5-2 6pue-2 4pje-2 6rpb-3 6w9u-1 6pul-1 4pjf-2 3vxu-1 5d7j-1 4pjg-1 6puh-2 6pug-1 4pjh-1 6pud-1 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	#62 - 2005年2月主要組織適合性複合体 (Major Histocompatibility Complex) 類似性 (1) #63 - 2005年3月 T細胞受容体 (T-Cell Receptor) 類似性 (1)

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集合体

登録構造単位

A: Major histocompatibility complex class I-related gene protein

B: Beta-2-microglobulin

C: Major histocompatibility complex class I-related gene protein

D: TCR-alpha chain

E: TCR-beta chain

F: Beta-2-microglobulin

G: TCR-alpha chain

H: TCR-beta chain

ヘテロ分子

189 kDa, 8 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: Major histocompatibility complex class I-related gene protein

B: Beta-2-microglobulin

G: TCR-alpha chain

H: TCR-beta chain

ヘテロ分子

登録者が定義した集合体
根拠: surface plasmon resonance
94.3 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)

C: Major histocompatibility complex class I-related gene protein

D: TCR-alpha chain

E: TCR-beta chain

F: Beta-2-microglobulin

ヘテロ分子

登録者が定義した集合体
94.2 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)	216.990, 70.405, 142.901
Angle α, β, γ (deg.)	90.000, 104.152, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

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要素

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タンパク質 , 4種, 8分子 ACBFDGEH

#1: タンパク質	Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein 分子量: 31692.623 Da / 分子数: 2 / 変異: R9H / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MR1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q95460
#2: タンパク質	Beta-2-microglobulin / Β2-ミクログロブリン分子量: 11879.356 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769
#3: タンパク質	TCR-alpha chain 分子量: 22781.268 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)
#4: タンパク質	TCR-beta chain 分子量: 27677.760 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)

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非ポリマー , 3種, 1392分子

#5: 化合物	ChemComp-ACT / ACETATE ION / 酢酸イオン / 酢酸塩分子量: 59.044 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C₂H₃O₂
#6: 化合物	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル / グリセリン分子量: 92.094 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C₃H₈O₃
#7: 水	ChemComp-HOH / water / 水分子量: 18.015 Da / 分子数: 1386 / 由来タイプ: 天然 / 式: H₂O

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詳細

研究の焦点であるリガンドがあるか	N

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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: 2.84 Å³/Da / 溶媒含有率: 56.73 %
結晶化	温度: 298 K / 手法: 蒸気拡散法 / pH: 6.3 / 詳細: PEG3350, BTP, Cacl2

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9536 Å
検出器	タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年7月6日
放射	プロトコル: LAUE / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長	波長: 0.9536 Å / 相対比: 1
反射	解像度: 1.95→46.19 Å / Num. obs: 152021 / % possible obs: 99.56 % / 冗長度: 3.5 % / B_iso Wilson estimate: 35.28 Å² / CC_1/2: 0.997 / Net I/σ(I): 10.3
反射シェル	解像度: 1.95→2.02 Å / Num. unique obs: 15086 / CC_1/2: 0.592

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.17.1_3660	精密化
XDS		データ削減
XDS		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: 6PUC

6puc

解像度: 1.95→46.19 Å / SU ML: 0.2144 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 22.0256

	R_factor	反射数	%反射
R_free	0.2001	7600	5 %
R_work	0.1604	-	-
obs	0.1625	151938	99.58 %

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

B_iso mean: 45.28 Å²

精密化ステップ

サイクル: LAST / 解像度: 1.95→46.19 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	12650	0	32	1390	14072

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0126	13601
X-RAY DIFFRACTION	f_angle_d	1.1704	18649
X-RAY DIFFRACTION	f_chiral_restr	0.0775	2006
X-RAY DIFFRACTION	f_plane_restr	0.0077	2425
X-RAY DIFFRACTION	f_dihedral_angle_d	19.637	1939

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 (%)
1.95-1.97	0.3029	252	0.2844	4800	X-RAY DIFFRACTION	99.53
1.97-2	0.3055	252	0.2621	4748	X-RAY DIFFRACTION	99.56
2-2.02	0.3173	259	0.2509	4774	X-RAY DIFFRACTION	99.55
2.02-2.05	0.2693	221	0.2339	4830	X-RAY DIFFRACTION	99.76
2.05-2.07	0.249	260	0.2253	4842	X-RAY DIFFRACTION	99.69
2.07-2.1	0.2255	251	0.2143	4725	X-RAY DIFFRACTION	99.84
2.1-2.13	0.2503	240	0.2155	4849	X-RAY DIFFRACTION	99.67
2.13-2.16	0.2469	244	0.2101	4768	X-RAY DIFFRACTION	99.9
2.16-2.2	0.2631	253	0.2042	4846	X-RAY DIFFRACTION	99.86
2.2-2.23	0.2379	252	0.1934	4749	X-RAY DIFFRACTION	99.84
2.23-2.27	0.25	246	0.1949	4840	X-RAY DIFFRACTION	99.94
2.27-2.31	0.2539	241	0.195	4774	X-RAY DIFFRACTION	99.82
2.31-2.36	0.2439	270	0.1922	4825	X-RAY DIFFRACTION	99.9
2.36-2.4	0.2432	255	0.1813	4775	X-RAY DIFFRACTION	99.84
2.4-2.46	0.2449	245	0.1778	4820	X-RAY DIFFRACTION	99.9
2.46-2.51	0.2419	259	0.1824	4819	X-RAY DIFFRACTION	99.76
2.51-2.58	0.2378	265	0.1733	4774	X-RAY DIFFRACTION	99.88
2.58-2.65	0.2235	260	0.1777	4810	X-RAY DIFFRACTION	99.76
2.65-2.72	0.2372	253	0.1783	4825	X-RAY DIFFRACTION	99.74
2.72-2.81	0.2242	240	0.1778	4827	X-RAY DIFFRACTION	99.63
2.81-2.91	0.2186	252	0.1721	4828	X-RAY DIFFRACTION	99.67
2.91-3.03	0.2342	251	0.1704	4770	X-RAY DIFFRACTION	99.01
3.03-3.17	0.2161	257	0.1616	4804	X-RAY DIFFRACTION	99.41
3.17-3.33	0.1839	255	0.1568	4810	X-RAY DIFFRACTION	99.29
3.33-3.54	0.1918	238	0.1393	4835	X-RAY DIFFRACTION	99.45
3.54-3.82	0.1782	258	0.1302	4818	X-RAY DIFFRACTION	99.49
3.82-4.2	0.1513	256	0.1304	4856	X-RAY DIFFRACTION	99.34
4.2-4.81	0.1358	257	0.1074	4825	X-RAY DIFFRACTION	99.3
4.81-6.05	0.1561	276	0.1329	4847	X-RAY DIFFRACTION	98.86
6.06-46.19	0.2006	282	0.1722	4925	X-RAY DIFFRACTION	98.25

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	0.895785219377	-0.233283988475	-0.0641934025322	0.881400469688	0.756876389879	1.38227643175	0.0375370276616	0.130241761413	0.148874493811	-0.131881784231	0.0762585950236	-0.0920375317101	0.052528886413	0.121759568912	-1.87249979662E-5	0.217826344009	-0.0299344390847	-0.0179311746619	0.320777861268	-0.00801015216991	0.326993432206	50.9356507347	77.6195976665	223.904407188
2	0.631739703857	0.084500682459	-0.207037005125	0.34963885702	0.28250095758	0.285241941626	0.0259427291912	-0.124748921277	0.211483658978	0.233255609243	0.0105587898107	0.0487785414735	-0.0694566328106	-0.0012725491257	5.10471392865E-5	0.277175692077	0.00264178451493	-0.00735980102628	0.277820125359	0.00149295834602	0.387540922637	42.2321540418	82.2341404244	236.017025808
3	0.463417564477	0.689868138405	0.326792315845	1.00235496453	0.575125414008	0.660890254638	0.157788860022	0.020300008836	-0.193025860477	-0.0342360479364	0.0183934475439	0.209366601219	0.117607020783	0.0312955879299	-1.23972163539E-5	0.252340953762	0.00564184261096	-0.00887856083445	0.28417172936	-0.00167804465346	0.287207951041	43.7722192053	71.4713538253	234.217714053
4	1.00616140904	0.0550488606686	-0.330433104048	0.838494677102	-0.577667534005	0.494294986304	-0.0636140035523	-0.120704983209	0.339222081999	0.214670816701	0.0376301382574	-0.123525822528	-0.169377482528	-0.0526317084628	-0.00102145471803	0.333387661467	0.0937373483511	-0.109230360244	0.500336337389	-0.183909449484	0.457413333039	69.7806125193	79.9557058507	255.944262694
5	0.00438745849654	-0.00940021770158	-0.0158150119987	0.0698730618587	-0.00523956987412	0.00883391305006	-0.0793547970705	-0.0568354942539	0.524372033559	0.525241151271	0.209075171319	-0.323034935548	-0.295746406629	-0.284899956479	-8.37951468071E-5	0.406251436305	0.00358686302644	0.0151700543521	0.439425908748	-0.0410604505979	0.708205029134	54.258378058	96.8411649239	235.585185502
6	0.156109127527	0.248750204497	-0.20350712936	0.435073721689	-0.237290274479	0.446698589113	-0.211880652547	-0.0207718188666	0.276022884611	0.134993158888	0.195035771554	-0.309723688074	-0.105289939109	0.525053721637	0.403556442237	0.254566518083	-0.00779981781133	-0.087101256405	0.599671716461	-0.0805967876478	0.648482430589	74.4867207041	84.4961071795	238.410439074
7	0.0144131946341	-0.00210962077823	-0.086573878259	0.0425152182904	-0.0746782210687	0.318164607183	0.291227503805	0.412940645961	0.527006727297	-0.338851151571	-0.061217429692	-0.244622774854	-0.905472474157	0.049026554925	0.152746196782	0.359632803855	-0.170502339623	0.0299793608389	0.488221391833	0.0275843414092	0.697019733124	66.0548776807	92.8690289013	229.397308281
8	0.236173559221	0.201760763776	-0.179303854193	0.143463798351	-0.117946801467	0.12368335076	0.232739437282	0.325797417497	0.448619478227	-0.349475008519	-0.42416123559	-0.584219324087	0.0858022572658	0.437869889679	-0.0370728053544	0.388864045567	-0.166741663552	0.0632686323426	0.847455783051	0.0711450428552	0.905199748427	77.4265013681	89.9191012581	226.874956749
9	0.0218985768463	0.0133749087521	-0.0240223121017	0.0115228552676	0.021124660335	0.0173367859595	-0.0980072669172	0.195643951152	0.034761075072	-0.0233712443096	0.25219191348	-0.0196071001669	-0.316798062657	0.108278129278	0.00022217286871	0.333138805615	-0.0195668536127	0.0243480270308	0.386707790063	-0.0353275678863	0.470755683262	59.9888243392	82.2747904106	229.403415665
10	0.142346096188	0.125146450327	0.118181024188	0.253146081831	-0.127594471554	0.17022756943	-0.235019804118	-0.222691724131	0.289301653153	-0.12073246853	0.182846637437	-0.242325379048	0.057771912094	0.353576597429	3.02310631988E-5	0.229990892468	-0.0208837920025	0.00853137332946	0.467514572969	-0.0220649852606	0.485302304111	65.5822070578	84.5119173796	233.712069438
11	0.000333588082043	0.00230842992291	0.0014383631182	0.00646924091167	-0.00425888902138	-0.0120183962493	0.177986383384	0.0143783980134	0.249834100932	0.167488643641	0.349444761034	-0.197976818287	-0.217594938002	0.179555431941	0.141067493011	0.184071457479	-0.0957057749701	-0.215089307633	1.47741253107	-0.153436278277	1.24193950979	87.9976405084	90.3818108577	237.972220911
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47	1.49144704455	0.615414843183	0.064199176822	1.14785499732	-0.690942708081	1.50139884142	-0.0247883101629	-0.11194103163	-0.0947863600244	-0.172333861809	-0.0718315224943	0.121839790535	0.0980878120591	0.0784460598458	4.41427444654E-5	0.335027781013	-0.0123681529469	0.0157040829015	0.249220501682	0.0328789908586	0.305288190019	2.77937964202	46.00750004	200.029412598
48	0.263586491835	-0.0396033803135	-0.0961727170975	0.0654918781627	-0.000710639454919	0.0223785038301	-0.265501911239	-0.14886527601	-0.724267840916	-0.480112408284	0.0147029785373	-0.0433052315507	0.819412451619	0.290372145767	-0.0191779804542	0.551656207907	-0.038937262943	0.114560457114	0.266832216569	0.0163917907513	0.511986763397	2.34838967045	34.942501823	195.419658361
49	0.237876176619	-0.070351370287	-0.0691530407487	0.303817704399	0.0362838841285	0.0844845204345	0.255829706071	0.03739314067	-0.557693990137	-0.688986951707	0.18247617709	-0.0355428423471	0.202591121733	-0.244361608541	0.00448028662252	0.445772700177	-0.0877105575207	-0.0394798309905	0.314433784509	0.0646756113486	0.425448009698	-7.85341593686	36.5855866529	201.180976618
50	1.63629310332	0.273201396483	0.572521792815	0.990082055149	0.907691183193	1.41427488548	-0.15913542265	0.339843677212	0.100793667493	-0.0364131243749	0.0769941154714	0.0170199412325	-0.0944968728049	0.164345851372	0.000281917366085	0.280762444	-0.105580569846	-0.0110561423586	0.349734958405	0.0591943228064	0.249696978112	34.8698090689	67.0086066256	202.614178967
51	0.223828916376	-0.0496524038602	-0.238546731073	0.259450439088	-0.0729054772226	0.17354152687	-0.0235266165003	0.218510974694	0.005407980989	0.206375051612	0.130685425409	0.111242621651	0.192674269416	0.559406448107	9.2952159531E-5	0.340096744354	-0.0623520131024	-0.0608436383424	0.35394701339	0.0266653662222	0.336325675247	30.7621962704	71.720399408	216.344628082
52	-0.05773264287	0.0332596548758	0.0234170230543	0.0280988812508	0.136751839631	0.0874891955176	-0.0344542632158	-0.155331768455	-0.0774980025079	0.0427923394453	-0.0397110659743	0.0810143201182	0.148334160621	0.403460987647	-0.000167936294926	0.319679576924	-0.0320374674166	0.0108818927449	0.491305604093	0.0332719472282	0.313738434441	26.9402963601	53.8840253734	188.178397201
53	1.06192710633	0.0548812155891	-0.354789350176	0.778106466867	-0.658144606695	1.45566575449	0.0772580882965	-0.210467827456	-0.119813223492	0.00944703852164	-0.0880470988859	0.0503879240399	-0.121705981801	0.158245982074	-0.000188030104862	0.306104528658	-0.0444639073618	-0.00365504344133	0.227235787615	0.00987676449062	0.245484056085	5.4747935739	53.5197998044	195.309504852
54	0.00525390884674	0.00497304319491	-0.0543526105185	-0.0521704106675	0.122059472807	0.327605857832	0.28436502635	0.246053130794	0.20171724926	-0.197919013032	0.0566105121925	0.0512045402359	-0.216600712755	0.105910895861	0.0511242886651	0.397357379217	-0.0366781570309	0.00908876157613	0.279484663792	0.073949097153	0.386745741832	-1.15316985425	62.0266976756	189.870264374
55	0.283922821243	-0.101983129768	0.18466246611	0.68282601007	0.0166701836627	1.02429019057	0.206904054352	-0.0557559843585	0.115109157394	-0.0225940409866	-0.0467730363178	-0.0520971511369	-0.0678540713907	0.148219552294	0.000148688825185	0.349167104005	-0.0519126581477	-0.0201431315976	0.315360886784	0.0411519682418	0.271515215521	16.1230599529	58.9906555061	182.116865325

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 0 through 84 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 85 through 133 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 134 through 182 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183 through 270 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 0 through 5 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 6 through 30 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 31 through 41 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 42 through 51 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 52 through 56 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 57 through 71 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 72 through 77 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 78 through 90 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 91 through 97 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 0 through 84 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 85 through 171 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 172 through 270 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 17 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 18 through 37 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 38 through 52 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 53 through 75 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 76 through 91 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 92 through 102 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 103 through 116 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 117 through 150 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 151 through 175 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 176 through 198 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 3 through 37 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 38 through 94 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 95 through 109 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 110 through 124 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 125 through 140 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 141 through 203 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 204 through 225 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 226 through 243 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 0 through 19 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 20 through 30 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 31 through 41 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 42 through 51 )
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 52 through 61 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 62 through 71 )
41	X-RAY DIFFRACTION	41	chain 'F' and (resid 72 through 90 )
42	X-RAY DIFFRACTION	42	chain 'F' and (resid 91 through 99 )
43	X-RAY DIFFRACTION	43	chain 'G' and (resid 2 through 52 )
44	X-RAY DIFFRACTION	44	chain 'G' and (resid 53 through 75 )
45	X-RAY DIFFRACTION	45	chain 'G' and (resid 76 through 91 )
46	X-RAY DIFFRACTION	46	chain 'G' and (resid 92 through 120 )
47	X-RAY DIFFRACTION	47	chain 'G' and (resid 121 through 175 )
48	X-RAY DIFFRACTION	48	chain 'G' and (resid 176 through 190 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 191 through 202 )
50	X-RAY DIFFRACTION	50	chain 'H' and (resid 1 through 94 )
51	X-RAY DIFFRACTION	51	chain 'H' and (resid 95 through 109 )
52	X-RAY DIFFRACTION	52	chain 'H' and (resid 110 through 124 )
53	X-RAY DIFFRACTION	53	chain 'H' and (resid 125 through 202 )
54	X-RAY DIFFRACTION	54	chain 'H' and (resid 203 through 215 )
55	X-RAY DIFFRACTION	55	chain 'H' and (resid 216 through 244 )

+
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

-
タンパク質 , 4種, 8分子 ACBFDGEH

-
非ポリマー , 3種, 1392分子

-
詳細

-
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

-タンパク質 , 4種, 8分子 ACBFDGEH

-非ポリマー , 3種, 1392分子

-詳細

-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

-
タンパク質 , 4種, 8分子 ACBFDGEH

-
非ポリマー , 3種, 1392分子

-
詳細

-
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)