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- PDB-6puc: Structure of human MAIT A-F7 TCR in complex with human MR1-5-OP-RU -

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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: 6puc

タイトル

Structure of human MAIT A-F7 TCR in complex with human MR1-5-OP-RU

要素

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

キーワード

IMMUNE SYSTEM (免疫系) / MAIT / MR1 / Metablite presentation

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: 1.85 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: Nat.Immunol. / 年: 2020
タイトル: The molecular basis underpinning the potency and specificity of MAIT cell antigens.
著者: Awad, W. / Ler, G.J.M. / Xu, W. / Keller, A.N. / Mak, J.Y.W. / Lim, X.Y. / Liu, L. / Eckle, S.B.G. / Le Nours, J. / McCluskey, J. / Corbett, A.J. / Fairlie, D.P. / Rossjohn, J.

履歴

登録	2019年7月18日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2020年2月19日	Provider: repository / タイプ: Initial release
改定 1.1	2020年3月11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_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
改定 1.2	2020年3月18日	Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.3	2020年4月1日	Group: Database references / カテゴリ: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.4	2023年10月11日	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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	6puc.cif.gz	844.2 KB	表示	PDBx/mmCIF形式
PDB形式	pdb6puc.ent.gz	578.9 KB	表示	PDB形式
PDBx/mmJSON形式	6puc.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/pu/6puc ftp://data.pdbj.org/pub/pdb/validation_reports/pu/6puc	HTTPS FTP

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関連構造データ

関連構造データ	6pudC 6pueC 6pufC 6pugC 6puhC 6puiC 6pujC 6pukC 6pulC 6pumC 4l4tS 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	6pul-2 5d7j-2 6pug-2 4pj7-1 4l4t-1 5u1r-2 5u2v-2 4pjc-1 4pjh-1 6w9v-2 4mnq-d 4pj5-1 6pud-2 5u17-1 6puk-2 4pja-1 6pug-1 6pui-2 6puk-1 6puj-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: Human TCR alpha chain

E: Human TCR beta chain

F: Beta-2-microglobulin

G: Human TCR alpha chain

H: Human 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: Human TCR alpha chain

H: Human TCR beta chain

ヘテロ分子

登録者が定義した集合体
根拠: surface plasmon resonance
94.5 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: Human TCR alpha chain

E: Human TCR beta chain

F: Beta-2-microglobulin

ヘテロ分子

登録者が定義した集合体
94.6 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)	217.967, 70.248, 143.634
Angle α, β, γ (deg.)	90.000, 104.808, 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 分子量: 31711.670 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: 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	Human 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	Human 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 , 5種, 1691分子

#5: 化合物	ChemComp-Q87 / 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-オキソプロピリデンアミノ)-6-[[(2S,3S,4R)-2,3,4,5-テトラヒドロキシペンチル]アミノ](以下略) 分子量: 330.294 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C₁₂H₁₈N₄O₇ / タイプ: SUBJECT OF INVESTIGATION
#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: 3 / 由来タイプ: 合成 / 式: C₃H₈O₃
#7: 化合物	ChemComp-CL / CHLORIDE ION / クロリド / 塩化物分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#8: 化合物	ChemComp-NA / SODIUM ION / ナトリウムカチオン分子量: 22.990 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Na
#9: 水	ChemComp-HOH / water / 水分子量: 18.015 Da / 分子数: 1682 / 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	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: 2.83 Å³/Da / 溶媒含有率: 56.47 %
結晶化	温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法詳細: 100 mM BTP (pH 6.0 - 6.5), 8-20% PEG3350 and 200 mM sodium acetate

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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: MX1 / 波長: 0.9537 Å
検出器	タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2017年6月23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: 0.9537 Å / 相対比: 1
反射	解像度: 1.85→48.34 Å / Num. obs: 179134 / % possible obs: 99.9 % / 冗長度: 5 % / B_iso Wilson estimate: 28.73 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.067 / Net I/σ(I): 10.6
反射シェル	解像度: 1.85→1.88 Å / 冗長度: 5 % / R_merge(I) obs: 0.791 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8788 / % possible all: 99.8

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.16_3549	精密化
XDS		データ削減
Aimless		データスケーリング
PHASER		位相決定

精密化

構造決定の手法:

分子置換
開始モデル: 4L4T

4l4t

解像度: 1.85→48.34 Å / SU ML: 0.1743 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 19.2521
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	0.1783	9024	5.04 %
R_work	0.1594	169945	-
obs	0.1604	178969	99.83 %

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: 40.44 Å²

精密化ステップ

サイクル: LAST / 解像度: 1.85→48.34 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	12593	0	66	1686	14345

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0072	13432
X-RAY DIFFRACTION	f_angle_d	0.8849	18393
X-RAY DIFFRACTION	f_chiral_restr	0.0587	1989
X-RAY DIFFRACTION	f_plane_restr	0.006	2403
X-RAY DIFFRACTION	f_dihedral_angle_d	15.7788	8132

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 (%)
1.85-1.87	0.297	325	0.2757	5558	X-RAY DIFFRACTION	99.76
1.87-1.89	0.2659	275	0.258	5689	X-RAY DIFFRACTION	99.82
1.89-1.92	0.2895	316	0.2552	5561	X-RAY DIFFRACTION	99.73
1.92-1.94	0.2709	318	0.2463	5629	X-RAY DIFFRACTION	99.8
1.94-1.97	0.2561	303	0.2284	5611	X-RAY DIFFRACTION	99.86
1.97-1.99	0.2378	300	0.2149	5652	X-RAY DIFFRACTION	99.88
1.99-2.02	0.2229	313	0.2046	5632	X-RAY DIFFRACTION	99.92
2.02-2.05	0.2302	338	0.1962	5630	X-RAY DIFFRACTION	99.98
2.05-2.08	0.2325	294	0.1922	5638	X-RAY DIFFRACTION	99.85
2.08-2.12	0.2165	303	0.1829	5645	X-RAY DIFFRACTION	99.88
2.12-2.15	0.197	312	0.1795	5598	X-RAY DIFFRACTION	99.97
2.15-2.19	0.1932	283	0.1732	5723	X-RAY DIFFRACTION	99.98
2.19-2.24	0.1904	295	0.1709	5588	X-RAY DIFFRACTION	99.93
2.24-2.28	0.224	288	0.1771	5668	X-RAY DIFFRACTION	99.78
2.28-2.33	0.2108	302	0.1761	5654	X-RAY DIFFRACTION	99.93
2.33-2.38	0.2132	298	0.1735	5673	X-RAY DIFFRACTION	99.98
2.38-2.44	0.1974	317	0.1662	5642	X-RAY DIFFRACTION	99.95
2.44-2.51	0.2097	312	0.1701	5658	X-RAY DIFFRACTION	99.9
2.51-2.58	0.1917	276	0.1674	5681	X-RAY DIFFRACTION	99.92
2.58-2.67	0.189	272	0.1681	5671	X-RAY DIFFRACTION	99.87
2.67-2.76	0.1725	314	0.1664	5666	X-RAY DIFFRACTION	99.92
2.76-2.87	0.1992	290	0.1686	5689	X-RAY DIFFRACTION	99.93
2.87-3	0.1712	298	0.1565	5675	X-RAY DIFFRACTION	99.95
3-3.16	0.1842	284	0.1551	5672	X-RAY DIFFRACTION	99.87
3.16-3.36	0.1642	307	0.1533	5733	X-RAY DIFFRACTION	99.87
3.36-3.62	0.1415	309	0.1382	5656	X-RAY DIFFRACTION	99.85
3.62-3.98	0.1557	296	0.1352	5727	X-RAY DIFFRACTION	99.77
3.98-4.56	0.1238	318	0.118	5693	X-RAY DIFFRACTION	99.82
4.56-5.75	0.1432	290	0.1251	5798	X-RAY DIFFRACTION	99.87
5.75-48.35	0.1811	278	0.1702	5835	X-RAY DIFFRACTION	98.58

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	1.57164219181	-0.121128560509	-0.0692662511979	1.23121824527	0.801415656517	1.64069961012	0.00853804828263	0.109825175141	0.238724233758	-0.0580587041269	0.0859690392427	-0.124131289273	-0.000824206558391	0.189184669525	-0.0828971105279	0.123390616778	-0.0400070344136	-0.0165092053341	0.182171559947	-0.0158391977975	0.226554767997	48.3413001284	77.3862555794	224.361296711
2	1.15377883922	0.0770567568043	-0.280737021374	1.2865434521	0.236232366692	0.683772187306	0.00820114019599	-0.0959351324457	0.293326235431	0.119294311878	0.0262055749887	0.248264639925	-0.0561788729198	-0.0248228926731	-0.0328700563957	0.182070554199	-0.0071748356356	-0.00809814841753	0.155782866994	-0.0286071993769	0.296304758349	36.0504202977	80.7616604943	234.885136602
3	1.62707475905	0.4095923101	0.855179513935	0.568325345818	-0.231453508864	0.821585240851	-0.0887103909528	-0.25268204692	0.277388132893	0.238191689669	0.116129734505	-0.119877193561	-0.0602685571078	0.212950211483	0.000490133377385	0.305501869035	0.103275678937	-0.0762465560436	0.46037101507	-0.166233796311	0.362560145542	62.7832513453	75.0481191545	247.742829657
4	0.656393761469	1.19793200345	1.07060681252	6.18175361277	3.36354774735	2.79182075336	-0.0261919092003	-0.226923657113	0.328595506537	0.554763941573	0.0126324080554	-0.153033608334	-0.20204713429	-0.0366717598282	-0.0166372418081	0.426269625672	0.103437235919	-0.095027837762	0.6320278589	-0.226993098944	0.429561082623	68.6153661206	78.0136643839	262.536664529
5	1.33971826743	-0.342314572184	-0.0571383331967	1.00255785531	-0.132423058821	1.08189330199	0.0187189075632	-0.0653194342529	0.375395967688	0.133279770108	0.0629106363544	0.118080991888	-0.244006280505	0.214294311713	-0.108362909727	0.371278528357	-0.0753172572444	-0.0667974551839	0.451468042013	-0.166993046498	0.675653670954	59.9164131582	92.3301787338	238.353779276
6	0.320128106272	-0.22313504086	0.129144703144	0.178517681925	-0.229372926716	0.970402852936	-0.202444510447	-0.258931437422	0.0508693821231	-0.0281746306335	-0.0462896709843	-0.644415851737	0.0260637759082	0.644735720629	0.127844318867	0.348167819447	0.0256446568356	-0.163142359147	0.797332570987	-0.128458454398	0.798796481968	80.7144250511	80.0164835078	240.84404542
7	1.31202500976	-0.547408836558	0.256825800217	0.332098073043	-0.201837957423	0.191256432814	-0.0837839674289	0.168146248825	-0.0904676963897	-0.130096216043	0.246127453144	-0.414446953311	-0.0491991618717	0.498729226949	-0.107626496148	0.264562210364	-0.062910033763	-0.0668383798495	0.570735631134	-0.126382055689	0.661553568959	68.9610683333	84.9677421827	236.030427709
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44	1.09606374272	0.442756888965	0.0290321948889	1.22439535275	0.323903892408	0.78171574956	-0.0356170564466	0.0901270847016	0.0337819721407	0.00584627151585	0.0733832518862	0.00475703138176	0.11655766115	-0.0214918409153	-0.0288462376178	0.247408594679	-0.0382557495328	-0.00507281783235	0.160670205177	0.0294163418397	0.249969649255	23.9940993214	59.950953809	222.451980436
45	3.62975767877	0.0214391412518	1.25434051383	0.873989806257	0.360958382765	1.75187774557	-0.0387002509273	-0.325333722551	-0.0338998337343	0.022187584003	0.0197950474417	-0.00251816049076	0.141439678919	-0.197439305867	-0.00617540980926	0.270312592173	-0.0435612816842	0.00901846010079	0.162970459347	0.0199859857002	0.272402322655	19.5349245358	58.8727085711	230.057549472
46	2.64791936403	0.579552136847	0.453240595084	0.712874248806	0.0822515312779	0.760934990069	-0.00582754294208	0.00811656716187	0.105028519734	0.0166731375475	0.0459861020711	0.152872534467	-0.00906267312106	-0.107722920384	-0.00635370703878	0.292675395193	-0.0433230937923	0.00468836212675	0.166817812951	0.0256208671229	0.275704851383	14.604086756	58.1486499399	219.356503302
47	1.28215816346	0.51750767752	0.365940824713	0.807298251342	0.326589690849	0.655202567922	-0.188755037773	0.179877179261	-0.049928802768	-0.124814818939	0.15619315388	-0.0143793613096	0.0101163000413	0.0849499668157	0.00124253044886	0.202406656429	-0.0354630918933	-0.000823541969638	0.165721522561	0.0166683423098	0.184490452304	26.230086132	57.0566642099	218.30266715
48	2.49774296783	0.552652462828	0.861824445057	1.44595185458	-0.558546870777	0.656363910836	0.0449103206958	-0.324083474485	-0.0112520209866	-0.120699622845	-0.193541978542	0.127551511599	0.0815956981925	-0.28752475168	0.161475042371	0.276705504879	-0.0385710582981	0.0184137675049	0.194536386516	0.0250662476375	0.262839972953	-7.17437765326	45.4187938166	208.23349102
49	0.438877097276	0.152476950806	-0.636264668157	0.449257444965	-0.452915528612	3.40234568072	-0.0824050900327	0.159247935068	-0.17761599687	-0.206030014836	0.0103421699615	0.10260972888	0.204070767441	-0.256715364687	0.0891536158732	0.384966182978	-0.0377927460737	0.0225297469873	0.187353153151	-0.0241391807775	0.277739081748	-2.51571315442	45.5427056423	190.329228066
50	2.00546635377	0.481337797888	-0.446937088928	0.838519128776	0.155882626488	3.64283531528	0.0555731347351	-0.314613684848	-0.0166976494384	-0.0738475783829	-0.0556616195152	-0.08874738672	0.0959222807158	0.211601568488	0.0151733501423	0.293171818008	-0.0318891338592	0.0298476406483	0.175269780856	0.0363649404756	0.28109902052	1.18827419558	46.6219151029	204.208071867
51	1.28617707032	1.09368867317	-1.87320973755	0.912351597598	-1.6000543775	2.72539990141	-0.0964926620977	0.286490544264	-0.482494133629	-0.469687022976	0.0704963940294	-0.155230528477	0.560520038102	-0.178450088872	0.0251852049542	0.637012237332	-0.0703825364207	0.138529786226	0.242290503074	-0.0850592379363	0.529232656407	-0.497014407344	34.8583646073	191.486556882
52	4.27513258172	-0.844223055619	0.608168047398	1.83167426793	-0.0876907356046	2.20503176041	0.227504949421	-0.140386387866	-0.69364825087	-0.423774872885	-0.20522362927	-0.0119794152291	0.602929564347	-0.0708158741542	0.0153595430332	0.425948770932	-0.0316636665672	0.0284309916556	0.224356091204	0.0620574720757	0.460444529219	-5.69167849678	35.7329211068	203.426094348
53	1.30212041616	0.350731354214	0.185878076301	1.18637077853	0.737898667476	1.45243651135	-0.0741702662303	0.192794547108	0.126029478875	-0.0587240826643	0.00613630788196	0.0332097888727	-0.133510779783	0.135928146973	0.0709502165397	0.24979363518	-0.0591378140654	-0.0162203319042	0.237879212752	0.049611167514	0.245130185964	31.9229919393	67.4298242038	204.647782954
54	1.49128481101	0.521443492636	0.988127824278	0.492692656118	0.156204886408	0.781814267472	0.0597001182146	-0.0493985769396	-0.1318812435	-0.00819062048707	-0.0165032233754	-0.0225725337698	0.125440631446	0.235023412627	0.0390381767318	0.208870778053	-0.00373321352121	0.00691734439605	0.215334363259	0.0166740711586	0.216564751133	24.2738693344	54.0219838254	188.626610964
55	2.12263094372	0.487157044521	-0.640869617291	0.824637609191	-0.38065224236	1.31144450682	0.0570724220374	-0.139619265583	-0.00500109346255	-0.0234712213783	-0.0461484833718	0.0344469486638	-0.0645239542182	0.0980780540737	-0.0193241472086	0.305266274852	-0.0300275858176	0.0121822935822	0.161171837998	0.00568841850322	0.249231868117	2.73309715589	53.5959724038	195.755423493
56	2.29445451404	-0.549401361293	0.334125575056	0.167173020683	-0.0527384438887	0.110282359255	0.0541559269378	0.17533899259	0.276435161783	-0.0647351360505	0.102850544315	0.193038212911	-0.20753628402	-0.0249904769257	-0.15962471099	0.378543477658	-0.0241899651481	0.0250373834738	0.238889424992	0.061940995594	0.371938804195	-3.49765294523	61.7612564487	190.331874212
57	1.42420079132	-0.0113740203247	-0.425598469462	1.35398033352	-0.0999367024616	1.47057838747	0.0401993777368	0.128091008619	0.0983498885103	-0.107300290658	-0.0194332926789	-0.0509685650881	-0.0323683999291	0.0708256695627	-0.00195895828981	0.255217636327	-0.0554240592387	-0.0282515073824	0.236743004554	0.0356227424903	0.1791646825	14.3510663468	58.8120677868	182.396519576

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 158 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 159 through 245 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 246 through 270 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 0 through 11 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 12 through 19 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 20 through 30 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 31 through 41 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 42 through 51 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 52 through 61 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 62 through 71 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 72 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 55 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 56 through 158 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 159 through 171 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 172 through 195 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 196 through 237 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 238 through 270 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 2 through 17 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 18 through 37 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 38 through 52 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 53 through 75 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 76 through 91 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 92 through 102 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 103 through 116 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 117 through 150 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 151 through 175 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 176 through 188 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 189 through 198 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 3 through 73 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 74 through 124 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 125 through 203 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 204 through 243 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 0 through 11 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 12 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 56 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 57 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 98 )
43	X-RAY DIFFRACTION	43	chain 'G' and (resid 2 through 17 )
44	X-RAY DIFFRACTION	44	chain 'G' and (resid 18 through 52 )
45	X-RAY DIFFRACTION	45	chain 'G' and (resid 53 through 75 )
46	X-RAY DIFFRACTION	46	chain 'G' and (resid 76 through 91 )
47	X-RAY DIFFRACTION	47	chain 'G' and (resid 92 through 108 )
48	X-RAY DIFFRACTION	48	chain 'G' and (resid 109 through 120 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 121 through 135 )
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 136 through 175 )
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 176 through 185 )
52	X-RAY DIFFRACTION	52	chain 'G' and (resid 186 through 200 )
53	X-RAY DIFFRACTION	53	chain 'H' and (resid 1 through 109 )
54	X-RAY DIFFRACTION	54	chain 'H' and (resid 110 through 124 )
55	X-RAY DIFFRACTION	55	chain 'H' and (resid 125 through 202 )
56	X-RAY DIFFRACTION	56	chain 'H' and (resid 203 through 215 )
57	X-RAY DIFFRACTION	57	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 , 5種, 1691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 , 5種, 1691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 , 5種, 1691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)