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- PDB-8enh: Cross-reactive 3180 TCR recognition of HLA-B*35:01-NP7 epitope fr... -

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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: 8enh

タイトル

Cross-reactive 3180 TCR recognition of HLA-B*35:01-NP7 epitope from 2002 H3N2 influenza strain

要素

(3180 TCR alpha ...) x 2
Beta-2-microglobulin
MHC class I antigen
Nucleoprotein NP7 epitope

キーワード

IMMUNE SYSTEM / HLA B*3501 / NP418 EPITOPE / T CELL IMMUNITY / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE

機能・相同性

機能・相同性情報

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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion ...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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能

生物種

Homo sapiens (ヒト)

Influenza A virus (A型インフルエンザウイルス)

手法

X線回折 /

シンクロトロン /

分子置換 / 解像度: 2.50003195312 Å

データ登録者

Littler, D.R. / Rossjohn, J.

資金援助

オーストラリア, 1件

引用

ジャーナル: To Be Published
タイトル: Molecular determinants of cross-strain influenza A virus recognition by T-cell receptors
著者: Quinones-Parra, S.M. / Littler, D.R. / Rossjohn, J. / Kedzierska, K.

履歴

登録	2022年9月30日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2024年3月27日	Provider: repository / タイプ: Initial release

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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	8enh.cif.gz	1.5 MB	表示	PDBx/mmCIF形式
PDB形式	pdb8enh.ent.gz	1.1 MB	表示	PDB形式
PDBx/mmJSON形式	8enh.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	8enh_validation.pdf.gz	559.8 KB	表示	wwPDB検証レポート
文書・詳細版	8enh_full_validation.pdf.gz	588.8 KB	表示
XML形式データ	8enh_validation.xml.gz	120.3 KB	表示
CIF形式データ	8enh_validation.cif.gz	171.3 KB	表示
アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/en/8enh ftp://data.pdbj.org/pub/pdb/validation_reports/en/8enh	HTTPS FTP

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関連構造データ

関連構造データ	8emfC 8emgC 8emiC 8emjC 8emkC 8en8C 8eo8C 3lksS C: 同じ文献を引用 (文献) S: 精密化の開始モデル
類似構造データ	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: MHC class I antigen

B: Beta-2-microglobulin

C: Nucleoprotein NP7 epitope

D: 3180 TCR alpha chain

E: 3180 TCR alpha chain

F: MHC class I antigen

G: Beta-2-microglobulin

H: Nucleoprotein NP7 epitope

I: 3180 TCR alpha chain

J: 3180 TCR alpha chain

K: MHC class I antigen

L: Beta-2-microglobulin

M: Nucleoprotein NP7 epitope

N: 3180 TCR alpha chain

O: 3180 TCR alpha chain

P: MHC class I antigen

Q: Beta-2-microglobulin

R: Nucleoprotein NP7 epitope

S: 3180 TCR alpha chain

T: 3180 TCR alpha chain

381 kDa, 20 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: MHC class I antigen

B: Beta-2-microglobulin

C: Nucleoprotein NP7 epitope

D: 3180 TCR alpha chain

E: 3180 TCR alpha chain

登録者が定義した集合体
根拠: gel filtration
95.2 kDa, 5 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: MHC class I antigen

G: Beta-2-microglobulin

H: Nucleoprotein NP7 epitope

I: 3180 TCR alpha chain

J: 3180 TCR alpha chain

登録者が定義した集合体
95.2 kDa, 5 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: MHC class I antigen

L: Beta-2-microglobulin

M: Nucleoprotein NP7 epitope

N: 3180 TCR alpha chain

O: 3180 TCR alpha chain

登録者が定義した集合体
95.2 kDa, 5 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: MHC class I antigen

Q: Beta-2-microglobulin

R: Nucleoprotein NP7 epitope

S: 3180 TCR alpha chain

T: 3180 TCR alpha chain

登録者が定義した集合体
95.2 kDa, 5 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)	168.150, 79.550, 172.190
Angle α, β, γ (deg.)	90.000, 95.560, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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要素

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タンパク質 , 2種, 8分子 AFKPBGLQ

#1: タンパク質	MHC class I antigen 分子量: 31940.246 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-B / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: F4NBT2
#2: タンパク質	Beta-2-microglobulin 分子量: 11879.356 Da / 分子数: 4 / Fragment: UNP residues 21-119 / 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 / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61769

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3180 TCR alpha ... , 2種, 8分子 DINSEJOT

#4: タンパク質	3180 TCR alpha chain 分子量: 22731.090 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRAV13 / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#5: タンパク質	3180 TCR alpha chain 分子量: 27591.828 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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タンパク質・ペプチド / 非ポリマー , 2種, 1233分子 CHMR

#3: タンパク質・ペプチド	Nucleoprotein NP7 epitope 分子量: 1066.291 Da / 分子数: 4 / 由来タイプ: 合成由来: (合成) Influenza A virus (strain A/2002/H3N2) (A型インフルエンザウイルス)
#6: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 1229 / 由来タイプ: 天然 / 式: H₂O

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実験情報

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実験

実験	手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶	マシュー密度: 3.01 Å³/Da / 溶媒含有率: 59.14 %
結晶化	温度: 297 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG, 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: MX2 / 波長: 0.95365 Å
検出器	タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2018年1月18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: 0.95365 Å / 相対比: 1
反射	解像度: 2.5→49.5 Å / Num. obs: 156773 / % possible obs: 100 % / 冗長度: 2 % / B_iso Wilson estimate: 41.3228614943 Å² / CC_1/2: 0.998 / R_rim(I) all: 0.053 / Net I/σ(I): 13.5
反射シェル	解像度: 2.5→2.59 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 15158 / CC_1/2: 0.811 / R_rim(I) all: 0.406

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解析

ソフトウェア

名称	バージョン	分類
BUSTER		精密化
PHENIX	1.10.1_2155	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: 3LKS

3lks

解像度: 2.50003195312→49.4650206136 Å / SU ML: 0.299282280684 / 交差検証法: FREE R-VALUE / σ(F): 1.97142969778 / 位相誤差: 24.1366813186
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	0.230295871081	7846	5.00788266006 %
R_work	0.190807497889	148827	-
obs	0.192799955749	156673	99.6375037363 %

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: 47.3384083318 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.50003195312→49.4650206136 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	26442	0	0	1229	27671

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0134044163094	27150
X-RAY DIFFRACTION	f_angle_d	1.58641520851	36897
X-RAY DIFFRACTION	f_chiral_restr	0.101040226762	3922
X-RAY DIFFRACTION	f_plane_restr	0.00690489064974	4837
X-RAY DIFFRACTION	f_dihedral_angle_d	20.2252304119	10033

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 (%)
2.5001-2.5284	0.26312138438	204	0.264036036112	4541	X-RAY DIFFRACTION	91.443438042
2.5284-2.5582	0.305189734529	264	0.25399040086	4956	X-RAY DIFFRACTION	100
2.5582-2.5894	0.299098907436	256	0.247922062826	4937	X-RAY DIFFRACTION	100
2.5894-2.6222	0.303196787415	232	0.245105659765	4961	X-RAY DIFFRACTION	99.9807470158
2.6222-2.6567	0.266317320738	241	0.231560060471	5030	X-RAY DIFFRACTION	99.9810318665
2.6567-2.693	0.263982873902	269	0.233728080649	4897	X-RAY DIFFRACTION	99.9806464099
2.693-2.7315	0.298979060878	267	0.224054252385	4973	X-RAY DIFFRACTION	99.9809196718
2.7315-2.7723	0.272918873334	256	0.22717485404	4892	X-RAY DIFFRACTION	99.9611650485
2.7723-2.8156	0.246987565041	271	0.223520843516	4977	X-RAY DIFFRACTION	100
2.8156-2.8618	0.263719616105	253	0.218481597556	4973	X-RAY DIFFRACTION	100
2.8618-2.9111	0.245498815879	246	0.215589822007	4927	X-RAY DIFFRACTION	100
2.9111-2.964	0.286195772069	270	0.209988907314	4994	X-RAY DIFFRACTION	100
2.964-3.021	0.251370840815	249	0.210550426987	4917	X-RAY DIFFRACTION	99.9806464099
3.021-3.0827	0.287337002758	305	0.214289454675	4912	X-RAY DIFFRACTION	100
3.0827-3.1497	0.275657918573	259	0.207497283097	4966	X-RAY DIFFRACTION	99.9808649062
3.1497-3.223	0.269777334221	284	0.198864786443	4948	X-RAY DIFFRACTION	99.9808905026
3.223-3.3035	0.232999020552	237	0.190310578457	5016	X-RAY DIFFRACTION	100
3.3035-3.3928	0.240833228265	307	0.191686078801	4872	X-RAY DIFFRACTION	99.9613974136
3.3928-3.4927	0.232598519054	296	0.186789094104	4933	X-RAY DIFFRACTION	99.9617663927
3.4927-3.6054	0.230727718795	266	0.182835841234	5007	X-RAY DIFFRACTION	99.9431387415
3.6054-3.7342	0.229803476852	281	0.185171364524	4939	X-RAY DIFFRACTION	99.9234303216
3.7342-3.8836	0.216523689425	254	0.175962718753	4983	X-RAY DIFFRACTION	99.9809087438
3.8836-4.0603	0.207770924725	242	0.172248706031	4995	X-RAY DIFFRACTION	99.9427480916
4.0603-4.2743	0.190672362808	264	0.162087552774	4987	X-RAY DIFFRACTION	99.9429006471
4.2743-4.5419	0.193629019572	261	0.15662132405	5003	X-RAY DIFFRACTION	99.9810066477
4.5419-4.8923	0.174448166892	270	0.157850637541	5016	X-RAY DIFFRACTION	99.9621785174
4.8923-5.3841	0.187643419226	246	0.167203012413	5028	X-RAY DIFFRACTION	99.9431495168
5.3841-6.1619	0.241424165306	275	0.190235158672	5034	X-RAY DIFFRACTION	99.9435240964
6.1619-7.7585	0.238986799593	247	0.199681942862	5088	X-RAY DIFFRACTION	99.9625257635
7.7585-49.4	0.196579005709	274	0.184232522058	5125	X-RAY DIFFRACTION	98.3962092218

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	1.83465823627	0.127961751	0.363161678473	3.30668583524	0.0819174201067	0.371713376765	-0.0565158761191	0.0829328590156	-0.0276637498171	-0.150726483653	0.0161569958496	0.426421916129	-0.0904193224795	-0.0219803554671	-0.0286537666312	0.276258513237	-0.00773472572161	-0.00804331846969	0.233901770734	0.0424318777606	0.396757076128	466.523387212	10.2638697748	216.048281685
2	2.0731533472	0.147607198135	-0.0560315970667	2.82050945149	1.40782207679	2.69747783931	-0.125167539609	0.203388054607	0.33012521483	-0.595386739306	0.32848743579	0.327063796835	-0.668509470209	-0.0728061489325	-0.294990037938	0.538418065516	-0.0266215090027	-0.0302904717277	0.314952663737	0.0757126811048	0.51360393356	470.078869618	21.4127579919	213.336407246
3	0.881225012442	-0.150359053317	-0.113661587651	3.58956973855	0.255309439975	1.47515393086	-0.0393891711516	0.200980832178	-0.059722007061	0.0474144948215	0.184401473437	-0.140796304469	-0.095930244255	0.171511657731	-0.0963731035399	0.258439505026	-0.00440311596805	0.00786857905765	0.257152366279	0.0119668539477	0.23068477628	475.700306122	6.19035678451	211.286505065
4	1.76367820981	0.765800155014	1.38763046593	3.61025963259	0.374529469813	3.60687802896	-0.0668328013042	-0.184917748974	-0.08480193174	0.285626661692	-0.0445772303912	0.00217760758216	-0.397535503556	-0.205283982767	0.00408565075366	0.283376405235	0.0207833809104	0.0699678116628	0.258260507454	0.0791751953901	0.411716448721	469.314642208	1.96848000935	223.107073513
5	1.95792200958	-0.296491790668	-0.304737595484	1.66286468751	0.679204280454	1.53196175078	-0.0976876630921	-0.265524151851	-0.0637724630319	0.179571417313	0.0965010825072	0.00993332799539	-0.0753840403589	0.129722587002	0.0166095323149	0.301164451643	-0.00174350259546	0.00702742732001	0.275473837524	0.0365666591081	0.249271639585	476.50611606	2.25485876213	226.249385273
6	4.32008993081	0.324273954771	0.452743967974	1.38056307387	0.276849884643	0.782347199432	-0.081537207303	-1.75124546599	0.189409640178	0.22133979649	-0.0110574389984	0.550690537353	0.0116738435781	-0.355989906243	0.033711211294	0.563696652137	0.0789050190103	0.127801325371	0.687292496269	0.0872990638153	0.750111675848	444.942699757	17.914593662	235.685025108
7	0.647122573865	-0.38566320546	-0.223788863215	2.28517013353	-0.500528884234	4.54197558397	-0.199831487248	-0.613127660286	-0.652883434646	0.489526339004	-0.0310020607512	-0.053026594645	0.23262825635	0.176944587071	0.192136110152	0.46419824256	0.0386586029828	0.135313419413	0.618558218458	0.17014141189	0.807694945733	445.681049311	11.2251882538	234.835300937
8	0.841292276742	-0.0553270373418	-0.486153905774	0.0472125377437	-0.0621079171613	0.276185118514	0.0364793876136	-0.890086534141	-0.429592728134	0.832114960517	-0.0501479431101	0.407760719532	-0.241919094586	-0.309504297343	-0.0351913276283	0.757865037831	0.108801858342	0.298037519187	1.12894132458	0.0880253226097	0.825342224834	440.998830861	16.5065040284	241.590290238
9	1.32367942472	-2.36281709029	-0.914092001527	7.58683366638	2.1946294692	2.1179474972	-0.0975625351766	0.110788542095	-0.0371641733045	0.38058749414	-0.0307441421804	0.334769775873	0.199662670886	-0.0868417794857	0.118911041452	0.342901092402	-0.0421705888935	0.021548581681	0.346076193009	0.0293042318924	0.691944224455	447.793256715	6.03998047856	219.578957551
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84	1.44138213036	-0.77109975312	-0.235602423282	1.01646588833	-0.0354358702494	4.42461081267	0.0451462484619	0.527229783221	0.101910109399	-0.451004687479	-0.176259852896	-0.218238726402	0.32595417631	0.645300230519	0.150157233833	0.548892180966	0.113071778969	0.0929555110063	0.806975293423	-0.0473157501021	0.577820748617	507.897644106	-46.2706494132	174.423364142
85	2.18194885955	-0.354338835327	0.335519295203	2.06870560111	-0.152408945572	1.44324638081	-0.227245235714	-0.0976058410215	0.157865356598	-0.100541814068	-0.0295048745617	-0.68937632103	-0.293753282784	0.414100415517	0.216822458817	0.516367794842	-0.0685594597452	0.0770064952685	0.760562517058	-0.0516462290038	0.593206095571	509.214374701	-38.8577358195	174.707778428
86	0.267133158419	0.00625563893385	-0.537138909689	0.745403508274	0.547839507418	1.5176793648	0.0734849234657	0.319428608768	0.364749725027	-0.260754191103	-0.167601341316	-0.825782677857	0.155933108859	1.17816545088	0.144340527198	0.549615478337	0.18598913092	0.169269320855	1.12748974852	0.0763539221043	0.739760038456	514.855399267	-45.2982977832	171.253971344
87	1.91233860622	0.634125514121	0.364140502046	5.061000529	1.793293826	2.27577521246	0.279414744713	0.0694532586545	0.370608636016	-0.421311239269	-0.312464333302	-0.00239493855879	-0.622510127484	-0.440362865407	-0.0458217952423	0.49749300919	0.0150356973859	0.0365403281674	0.619925663802	-0.032609784541	0.413843113382	493.955708076	-31.3922210795	176.230861224
88	1.93004259432	1.18027629298	1.5639923776	1.92743566482	-0.358233569856	2.76432133423	0.235621797635	-0.142359688197	-0.724467761758	-0.361035932901	-0.187151010308	-0.3879357012	0.111581132014	0.776277070831	-0.00248203156826	0.62933851958	-0.000819083003504	-0.00234950042589	0.615396171827	-0.0539764773498	0.446934877755	494.506991824	-53.6601511606	167.618514677
89	0.52857454742	-0.281329712211	-0.184132876067	0.377429049731	0.304336645941	1.0305015004	0.123154047673	0.0476272407688	-0.103809358143	-0.100740040499	-0.206406802693	0.159308786869	0.415339012466	-0.321457665077	0.0767533387369	0.509289986474	0.0423027455919	0.0063061570233	0.562001398725	-0.0476081629853	0.344149801363	491.256910187	-41.2682994922	175.084624452
90	0.211613467846	0.335041946762	0.373487982254	3.73754145582	5.16510712198	7.02656061416	-0.1511838046	0.331419787792	0.00853672836685	-0.396769048716	-0.685795797718	0.782628104498	-0.546306690486	-0.461400435925	0.589642035465	0.532331308967	0.0713569480181	-0.0176243527424	0.632851266414	-0.0788187583023	0.424375810361	482.896615872	-35.2237782281	171.925834523
91	4.15966808304	-0.483906567485	0.0556274404465	4.77747227582	-0.719699701285	4.43011694019	0.111259023674	-0.166047733401	0.16148715301	-0.0454201281715	0.126014361643	0.190362547736	0.678451386174	-0.545255901724	-0.217335432303	0.542377728515	0.0473824570238	0.0971113100944	0.688944798373	-0.019966942268	0.688215988576	480.261160374	-44.5190035153	175.474177676
92	0.27615511604	-0.115355581228	0.695149623606	2.17305421384	1.71766532083	3.05253429464	0.0730806226538	0.487534243268	-0.313750806751	0.0700052841404	0.247076326983	-0.258857206681	0.35955743771	0.0727285927263	-0.235780385261	0.391083815256	0.0140495172833	0.0281953452285	0.48746332431	-0.0738727415736	0.367670150815	490.412402755	-38.1988926451	181.934808374
93	0.175986936961	-0.422846060045	-0.34941177556	3.68534637298	2.40772259367	2.32188320167	0.212409006134	0.340744310657	-0.0215809753194	-0.682146741894	-0.169008161884	0.0873259684417	-0.622826552544	-0.434565436234	-0.0614557359707	0.623125313733	0.101150130708	0.031397810809	0.709041516331	-0.01647452577	0.401071414592	487.205623368	-35.3044268429	166.237067922
94	3.60681513815	-2.37842165946	-0.391564687273	6.73260731771	-0.181884974053	1.50106347624	-0.292180712608	0.656143696581	-0.126046083826	-0.0302372318629	0.00643795831066	-0.598693256129	0.192241222129	-0.333335021586	0.194749024394	0.52916126061	0.108973227512	0.0220375050401	0.787433992237	-0.125808693524	0.350191687516	494.753352102	-39.408240707	164.611760212
95	1.24931424728	-0.927316443474	-0.105928200217	1.18734241064	0.855470390232	1.14641036729	-0.0316577771642	0.166233477954	0.044543625663	0.163249490759	-0.154344596147	-0.29583532963	0.134400158328	0.103731810451	0.152679171056	0.229900876719	-0.00238359513225	0.027741127026	0.269465899772	-0.00606948002673	0.242915888323	487.131905847	-33.5006390917	206.564069138
96	0.881300421001	-0.259333562366	0.0112697774012	1.05865864306	0.571480176795	3.95073750083	-0.152525970129	-0.338879036314	-0.108021486805	0.32754253209	0.0355823340737	-0.0111541255513	0.658194731885	0.343060795934	0.132537213943	0.568264579924	0.070038803236	-0.0419021949538	0.424946974105	0.0547319523767	0.375821707914	488.638775066	-42.8577911522	231.962466152
97	1.75502589311	-0.103862760217	-0.0512674334089	1.57638049953	-0.774440530663	0.899477601222	-0.130387308709	-0.0901813634483	0.265987791038	0.349840051699	0.15504613711	-0.0264785808993	-0.109297787477	0.0970732903153	-0.0305866913785	0.375020483033	0.0100371512768	-0.0222243102746	0.30585122059	0.0296572516658	0.252555731787	486.485598029	-31.1900675114	228.868906459
98	0.8675658347	-0.486640276522	-1.62942751396	3.53509897895	4.76151438303	7.59012405806	0.04330490316	-0.374702984308	-0.495227733601	0.311099886298	-0.101431079796	-0.940525506378	-0.437706970523	1.14043134383	0.19562991982	0.417569323976	-0.104789517727	-0.0992802649564	0.53528456338	0.0841587014621	0.365239078491	499.789012837	-33.3260217629	227.394168584
99	1.95844874119	0.726776071026	0.507511511977	3.29311504371	1.33335599896	3.29658660272	0.182165136154	-0.270943689863	-0.461091704883	0.600544660501	0.306905052732	-0.550461398588	0.709293934628	0.635333940162	-0.328428399022	0.459600852323	0.0964145625004	-0.0356099886524	0.460190601471	0.0404414558046	0.3963503072	495.843408829	-41.9341313222	228.115116328
100	1.63180690618	0.0443237994355	-0.04263108814	1.16546796222	0.382279584349	3.24310744766	-0.190744565254	-0.208765351104	0.0442109548127	0.365165069475	0.0904948524458	-0.0656634817315	0.252654348185	0.150910298004	0.130386819022	0.429345555206	0.0604071773066	-0.0113429256485	0.307250063301	0.0344588666112	0.294375287323	485.462925486	-36.0704767343	230.013194086
101	0.0283862587156	-0.126462304787	-0.153545933472	0.853241465517	1.81676109319	4.02527821769	-0.320024474419	-0.0673465733841	0.28531563636	0.356996393833	0.117499572119	-0.411071500674	-0.0753357212881	0.184293398032	0.269294194924	0.88232390711	0.145640175985	-0.0682117024161	0.548389864485	-0.0808637849695	0.421597848658	490.546824697	-30.7424652389	253.463036365
102	1.57594962321	1.5830086323	0.88966357901	3.91469665636	-0.609379033652	1.50336580851	0.429315440624	-0.590152041125	0.367541690916	0.485098666089	-0.0660360458226	1.07424815991	-0.0875612332204	-0.584691617527	0.298025545681	1.59944384821	0.191346081945	-0.0184855731864	0.482286933858	-0.143275567385	0.125827843026	473.453485019	-17.3167830496	265.635474094
103	4.63935567685	0.526276090832	-0.173750776991	1.37451547673	0.31902464191	1.19180208602	0.246030232628	-0.500861914105	-0.71195849728	0.521007564138	0.0296113381197	0.258354330143	0.427173549747	-0.25331372796	-0.280369705913	1.46996362858	-0.0550272820035	-0.0298297713978	0.631314364686	0.0570407085135	0.669882302171	477.500233098	-32.8930076568	260.981701742
104	3.91940838446	0.491623294416	-0.923681418676	2.46934999809	-0.409814172136	1.9054691687	-0.640526350709	0.369563124476	-0.0161703080897	0.198247471471	0.42122718073	-0.330018995722	0.288854799313	0.000827094223611	0.185649662287	1.06528350999	0.0736593297227	-0.0818422101327	0.50801188067	-0.0180330276505	0.338379508918	482.247663561	-23.0316111975	256.155991287
105	0.0449297528128	-0.0759919881034	-0.133527813088	2.06501189887	1.05946827797	1.01920500419	0.174687842755	-0.399201875255	-0.125084526507	0.250150430482	-0.656660328781	0.475963415121	0.091817362389	-0.685286860082	0.470592194658	1.27772898253	-0.00769646047158	-0.0170341709589	0.861005609202	-0.0853304638081	0.585896186423	469.728463539	-32.2213607873	267.150284354
106	1.81492878404	-0.593612373074	-0.511247861481	1.55324380271	0.531394658624	2.30514218671	-0.121239454659	-0.0762789749743	-0.14472708616	0.189296538768	0.0271559301662	0.289086609169	0.169487267857	-0.238767837066	0.0596624469991	0.281827090966	-0.0157722054003	0.0514110831499	0.228834960666	0.0320730694373	0.325718696855	468.158317429	-28.4948589947	224.630770652
107	2.07934546522	-0.120944326124	0.976400367817	1.53565587392	-0.455795506501	2.50809865178	-0.238339483834	-0.089311680812	0.231147598215	0.30665100769	0.0359612126476	0.102149067937	-0.382473726602	-0.150400761502	0.191181812428	0.847961865502	0.0524058467951	-0.00112280951204	0.341340499347	-0.0259393944363	0.370489069791	471.402346188	-14.544322403	251.925021017

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 2 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 56 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 84 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 85 through 118 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 119 through 174 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 175 through 219 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 220 through 240 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 241 through 276 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 11 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 12 through 19 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 20 through 41 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 42 through 46 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 47 through 61 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 62 through 71 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 72 through 77 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 78 through 90 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 91 through 99 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1 through 9 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 0 through 120 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 121 through 134 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 135 through 153 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 154 through 218 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 3 through 136 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 137 through 257 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 2 through 162 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 163 through 276 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 1 through 11 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 12 through 19 )
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 20 through 30 )
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 31 through 41 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 42 through 46 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 47 through 51 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 52 through 61 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 62 through 71 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 72 through 77 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 78 through 90 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 91 through 99 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 1 through 9 )
39	X-RAY DIFFRACTION	39	chain 'I' and (resid 0 through 37 )
40	X-RAY DIFFRACTION	40	chain 'I' and (resid 38 through 57 )
41	X-RAY DIFFRACTION	41	chain 'I' and (resid 58 through 91 )
42	X-RAY DIFFRACTION	42	chain 'I' and (resid 92 through 120 )
43	X-RAY DIFFRACTION	43	chain 'I' and (resid 121 through 134 )
44	X-RAY DIFFRACTION	44	chain 'I' and (resid 135 through 153 )
45	X-RAY DIFFRACTION	45	chain 'I' and (resid 154 through 193 )
46	X-RAY DIFFRACTION	46	chain 'I' and (resid 194 through 218 )
47	X-RAY DIFFRACTION	47	chain 'J' and (resid 2 through 136 )
48	X-RAY DIFFRACTION	48	chain 'J' and (resid 137 through 257 )
49	X-RAY DIFFRACTION	49	chain 'K' and (resid 1 through 56 )
50	X-RAY DIFFRACTION	50	chain 'K' and (resid 57 through 84 )
51	X-RAY DIFFRACTION	51	chain 'K' and (resid 85 through 103 )
52	X-RAY DIFFRACTION	52	chain 'K' and (resid 104 through 118 )
53	X-RAY DIFFRACTION	53	chain 'K' and (resid 119 through 162 )
54	X-RAY DIFFRACTION	54	chain 'K' and (resid 163 through 185 )
55	X-RAY DIFFRACTION	55	chain 'K' and (resid 186 through 206 )
56	X-RAY DIFFRACTION	56	chain 'K' and (resid 207 through 229 )
57	X-RAY DIFFRACTION	57	chain 'K' and (resid 230 through 262 )
58	X-RAY DIFFRACTION	58	chain 'K' and (resid 263 through 274 )
59	X-RAY DIFFRACTION	59	chain 'L' and (resid 0 through 11 )
60	X-RAY DIFFRACTION	60	chain 'L' and (resid 12 through 19 )
61	X-RAY DIFFRACTION	61	chain 'L' and (resid 20 through 41 )
62	X-RAY DIFFRACTION	62	chain 'L' and (resid 42 through 51 )
63	X-RAY DIFFRACTION	63	chain 'L' and (resid 52 through 71 )
64	X-RAY DIFFRACTION	64	chain 'L' and (resid 72 through 90 )
65	X-RAY DIFFRACTION	65	chain 'L' and (resid 91 through 99 )
66	X-RAY DIFFRACTION	66	chain 'M' and (resid 1 through 9 )
67	X-RAY DIFFRACTION	67	chain 'N' and (resid -1 through 18 )
68	X-RAY DIFFRACTION	68	chain 'N' and (resid 19 through 57 )
69	X-RAY DIFFRACTION	69	chain 'N' and (resid 58 through 75 )
70	X-RAY DIFFRACTION	70	chain 'N' and (resid 76 through 91 )
71	X-RAY DIFFRACTION	71	chain 'N' and (resid 92 through 120 )
72	X-RAY DIFFRACTION	72	chain 'N' and (resid 121 through 134 )
73	X-RAY DIFFRACTION	73	chain 'N' and (resid 135 through 153 )
74	X-RAY DIFFRACTION	74	chain 'N' and (resid 154 through 168 )
75	X-RAY DIFFRACTION	75	chain 'N' and (resid 169 through 193 )
76	X-RAY DIFFRACTION	76	chain 'N' and (resid 194 through 210 )
77	X-RAY DIFFRACTION	77	chain 'O' and (resid 2 through 136 )
78	X-RAY DIFFRACTION	78	chain 'O' and (resid 137 through 257 )
79	X-RAY DIFFRACTION	79	chain 'P' and (resid 2 through 56 )
80	X-RAY DIFFRACTION	80	chain 'P' and (resid 57 through 84 )
81	X-RAY DIFFRACTION	81	chain 'P' and (resid 85 through 118 )
82	X-RAY DIFFRACTION	82	chain 'P' and (resid 119 through 162 )
83	X-RAY DIFFRACTION	83	chain 'P' and (resid 163 through 174 )
84	X-RAY DIFFRACTION	84	chain 'P' and (resid 175 through 218 )
85	X-RAY DIFFRACTION	85	chain 'P' and (resid 219 through 240 )
86	X-RAY DIFFRACTION	86	chain 'P' and (resid 241 through 276 )
87	X-RAY DIFFRACTION	87	chain 'Q' and (resid 1 through 11 )
88	X-RAY DIFFRACTION	88	chain 'Q' and (resid 12 through 19 )
89	X-RAY DIFFRACTION	89	chain 'Q' and (resid 20 through 30 )
90	X-RAY DIFFRACTION	90	chain 'Q' and (resid 31 through 46 )
91	X-RAY DIFFRACTION	91	chain 'Q' and (resid 47 through 51 )
92	X-RAY DIFFRACTION	92	chain 'Q' and (resid 52 through 71 )
93	X-RAY DIFFRACTION	93	chain 'Q' and (resid 72 through 90 )
94	X-RAY DIFFRACTION	94	chain 'Q' and (resid 91 through 99 )
95	X-RAY DIFFRACTION	95	chain 'R' and (resid 1 through 9 )
96	X-RAY DIFFRACTION	96	chain 'S' and (resid -1 through 37 )
97	X-RAY DIFFRACTION	97	chain 'S' and (resid 38 through 57 )
98	X-RAY DIFFRACTION	98	chain 'S' and (resid 58 through 75 )
99	X-RAY DIFFRACTION	99	chain 'S' and (resid 76 through 91 )
100	X-RAY DIFFRACTION	100	chain 'S' and (resid 92 through 120 )
101	X-RAY DIFFRACTION	101	chain 'S' and (resid 121 through 134 )
102	X-RAY DIFFRACTION	102	chain 'S' and (resid 135 through 153 )
103	X-RAY DIFFRACTION	103	chain 'S' and (resid 154 through 168 )
104	X-RAY DIFFRACTION	104	chain 'S' and (resid 169 through 193 )
105	X-RAY DIFFRACTION	105	chain 'S' and (resid 194 through 211 )
106	X-RAY DIFFRACTION	106	chain 'T' and (resid 2 through 136 )
107	X-RAY DIFFRACTION	107	chain 'T' and (resid 137 through 255 )

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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

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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

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ムービー

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構造ビューア

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ビューアのログ

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このページ

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このウェブサイト

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オプション

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データを開く

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基本情報

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構造の表示

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ダウンロードとリンク

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ダウンロード

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検証レポート

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関連構造データ

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リンク

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集合体

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要素

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タンパク質 , 2種, 8分子 AFKPBGLQ

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3180 TCR alpha ... , 2種, 8分子 DINSEJOT

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タンパク質・ペプチド / 非ポリマー , 2種, 1233分子 CHMR

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実験情報

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実験

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試料調製

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データ収集

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解析

+
万見について

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お知らせ

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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

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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 , 2種, 8分子 AFKPBGLQ

-3180 TCR alpha ... , 2種, 8分子 DINSEJOT

-タンパク質・ペプチド / 非ポリマー , 2種, 1233分子 CHMR

-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 , 2種, 8分子 AFKPBGLQ

-
3180 TCR alpha ... , 2種, 8分子 DINSEJOT

-
タンパク質・ペプチド / 非ポリマー , 2種, 1233分子 CHMR

-
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)