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万見

- PDB-8f22: HIV-CA Disulfide linked Hexamer bound to 11l capsid inhibitor. -

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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: 8f22

タイトル

HIV-CA Disulfide linked Hexamer bound to 11l capsid inhibitor.

要素

Capsid protein p24

キーワード

VIRAL PROTEIN / HIV-1 / Human Immunodeficiency Virus / Capsid / HIV-CA / 11l / Capsid Inhibitor / HIV Restriction

機能・相同性

機能・相同性情報

HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...
類似検索 - 分子機能

Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...
類似検索 - ドメイン・相同性

生物種

Human immunodeficiency virus type 1 (ヒト免疫不全ウイルス)

手法

X線回折 /

分子置換 / 解像度: 2.5 Å

データ登録者

Barnett, M.J. / Goldstone, D.C.

資金援助

1件

引用

ジャーナル: Biorxiv / 年: 2023
タイトル: Structure of a benzosulfonamide based inhibitor - bound to a disulfide stabilised HIV-1 capsid hexamer
著者: Barnett, M. / Sun, L. / Xu, S. / Liu, X. / Zhan, P. / Goldstone, D.C.

履歴

登録	2022年11月6日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2023年9月13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	8f22.cif.gz	1020.3 KB	表示	PDBx/mmCIF形式
PDB形式	pdb8f22.ent.gz	694.5 KB	表示	PDB形式
PDBx/mmJSON形式	8f22.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	8f22_validation.pdf.gz	2.6 MB	表示	wwPDB検証レポート
文書・詳細版	8f22_full_validation.pdf.gz	2.6 MB	表示
XML形式データ	8f22_validation.xml.gz	77.3 KB	表示
CIF形式データ	8f22_validation.cif.gz	101.9 KB	表示
アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/f2/8f22 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/8f22	HTTPS FTP

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関連構造データ

関連構造データ	3h47S 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	#163 - 2013年7月 HIVカプシド (HIV Capsid) 類似性 (4)

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集合体

登録構造単位

A: Capsid protein p24

B: Capsid protein p24

C: Capsid protein p24

D: Capsid protein p24

E: Capsid protein p24

F: Capsid protein p24

G: Capsid protein p24

H: Capsid protein p24

I: Capsid protein p24

J: Capsid protein p24

K: Capsid protein p24

L: Capsid protein p24

ヘテロ分子

300 kDa, 12 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

A: Capsid protein p24

B: Capsid protein p24

C: Capsid protein p24

D: Capsid protein p24

E: Capsid protein p24

F: Capsid protein p24

ヘテロ分子

登録者が定義した集合体
根拠: gel filtration
152 kDa, 6 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: Capsid protein p24

H: Capsid protein p24

I: Capsid protein p24

J: Capsid protein p24

K: Capsid protein p24

L: Capsid protein p24

登録者が定義した集合体
根拠: gel filtration
148 kDa, 6 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)	90.951, 91.186, 116.266
Angle α, β, γ (deg.)	87.170, 78.770, 60.370
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	Capsid protein p24 / CA 分子量: 24696.332 Da / 分子数: 12 / 変異: A14C, E45C, W184A, M185A / 由来タイプ: 組換発現由来: (組換発現) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) (ヒト免疫不全ウイルス) 株: isolate NY5 / 遺伝子: gag-pol / プラスミド: pET-22b(+) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): LOBSTR / 参照: UniProt: P12497
#2: 化合物	ChemComp-XBQ / Nalpha-{[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]acetyl}-N-(4-methoxyphenyl)-N-methyl-L-phenylalaninamide 分子量: 579.667 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C₂₉H₃₃N₅O₆S / タイプ: SUBJECT OF INVESTIGATION
#3: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 18 / 由来タイプ: 天然 / 式: H₂O
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: 2.77 Å³/Da / 溶媒含有率: 55.59 % / 解説: Crystal was non-merohedrically twinned.
結晶化	温度: 291.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 詳細: 0.2 M Calcium acetate hydrate, 100 mM sodium cacodylate pH 6.5, 40% w/v PEG300, 0.500 mM 11l, and previous crystal seed solution. Temp details: 18 Degrees Celsius

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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: SEALED TUBE / タイプ: RIGAKU PhotonJet-S / 波長: 1.5418 Å
検出器	タイプ: DECTRIS PILATUS3 R 200K-A / 検出器: PIXEL / 日付: 2020年10月1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: 1.5418 Å / 相対比: 1
反射	解像度: 2.5→15.89 Å / Num. obs: 106374 / % possible obs: 96.6 % / 冗長度: 8.8 % / B_iso Wilson estimate: 20.74 Å² / CC_1/2: 0.97 / CC star: 0.99 / Net I/σ(I): 4.3
反射シェル	解像度: 2.5→2.59 Å / 冗長度: 7.5 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10896 / CC_1/2: 0.18 / CC star: 0.55 / % possible all: 99

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.20.1_4487	精密化
CrysalisPro		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: 3H47

3h47

解像度: 2.5→15.89 Å / SU ML: 0.6326 / 交差検証法: FREE R-VALUE / σ(F): 2.1 / 位相誤差: 41.9185
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	0.3467	5353	5.03 %
R_work	0.3097	101015	-
obs	0.3116	106368	97.01 %

溶媒の処理

減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL

原子変位パラメータ

B_iso mean: 48.25 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.5→15.89 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	17078	0	246	19	17343

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0042	17659
X-RAY DIFFRACTION	f_angle_d	0.8211	23987
X-RAY DIFFRACTION	f_chiral_restr	0.0485	2748
X-RAY DIFFRACTION	f_plane_restr	0.0067	3061
X-RAY DIFFRACTION	f_dihedral_angle_d	23.1959	2529

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 (%)
2.5-2.53	0.3735	208	0.3507	3464	X-RAY DIFFRACTION	98.87
2.53-2.56	0.3867	191	0.3617	3407	X-RAY DIFFRACTION	99.15
2.56-2.59	0.4062	182	0.3664	3445	X-RAY DIFFRACTION	99.07
2.59-2.62	0.4155	181	0.3873	3429	X-RAY DIFFRACTION	99.15
2.62-2.66	0.4271	178	0.3926	3434	X-RAY DIFFRACTION	99.18
2.66-2.69	0.416	163	0.3805	3474	X-RAY DIFFRACTION	99.21
2.69-2.73	0.3491	173	0.3626	3448	X-RAY DIFFRACTION	99.12
2.73-2.77	0.3791	178	0.341	3494	X-RAY DIFFRACTION	99.08
2.77-2.81	0.3805	180	0.341	3371	X-RAY DIFFRACTION	99.05
2.81-2.86	0.3917	174	0.3495	3470	X-RAY DIFFRACTION	99.08
2.86-2.91	0.3863	177	0.3304	3414	X-RAY DIFFRACTION	99.03
2.91-2.96	0.3491	185	0.3257	3477	X-RAY DIFFRACTION	99.32
2.96-3.02	0.3709	166	0.321	3439	X-RAY DIFFRACTION	98.96
3.02-3.08	0.3868	166	0.3318	3423	X-RAY DIFFRACTION	99.09
3.08-3.15	0.3635	144	0.3229	3571	X-RAY DIFFRACTION	99.28
3.15-3.22	0.3429	142	0.3096	3424	X-RAY DIFFRACTION	99.08
3.22-3.3	0.3737	180	0.3212	3434	X-RAY DIFFRACTION	99.1
3.3-3.39	0.3527	165	0.3102	3456	X-RAY DIFFRACTION	98.91
3.39-3.49	0.3469	183	0.2999	3409	X-RAY DIFFRACTION	98.87
3.49-3.6	0.3364	214	0.2893	3426	X-RAY DIFFRACTION	98.7
3.6-3.72	0.3557	222	0.2846	3298	X-RAY DIFFRACTION	97.59
3.72-3.87	0.3719	231	0.2946	3336	X-RAY DIFFRACTION	97.3
3.87-4.04	0.3395	199	0.3018	3353	X-RAY DIFFRACTION	97.02
4.04-4.25	0.2871	199	0.2938	3272	X-RAY DIFFRACTION	95.38
4.25-4.51	0.2852	148	0.2766	3279	X-RAY DIFFRACTION	92.97
4.51-4.85	0.3559	164	0.2747	3150	X-RAY DIFFRACTION	91.32
4.85-5.32	0.2788	187	0.271	3209	X-RAY DIFFRACTION	92.33
5.32-6.06	0.3046	147	0.2767	3272	X-RAY DIFFRACTION	93.19
6.06-7.5	0.3273	133	0.2927	3077	X-RAY DIFFRACTION	88.26
7.5-15.89	0.2837	193	0.2332	2860	X-RAY DIFFRACTION	83.71

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	0.0165602622693	-0.023415949774	-0.0236945774929	0.0279233019566	0.00633441970572	0.0905894901143	0.0784651827708	-0.0390087765882	0.00631735495844	0.0667327261452	-0.0721055704846	-0.0185211089464	0.00662680806169	0.198336261295	0.0388212737388	0.0545779530563	-0.0656639170281	0.0132432213308	0.154293788279	0.0687596562991	0.266206911945	19.9256946901	7.7945573089	4.3399464012
2	0.0453925364541	-0.0325748300619	0.000119787466784	0.0328422431757	0.0337908514969	0.0306494996872	0.0251228019273	0.076978284598	0.0666790654454	-0.100684673486	-0.0187702823247	-0.0149156177603	-0.105365062949	-0.0296263899756	0.0372909232214	0.026615926057	0.0239773875379	0.0668540449564	0.0773494379421	0.0571362465379	-0.200841852526	25.2699188247	13.526021861	8.55145952306
3	0.0730456367342	0.0139946502426	0.0204779629455	0.046835598817	0.00379637044465	0.00919295068727	0.0293784979458	-0.00239404394375	-0.0994681886336	-0.0545438572332	0.0259138321164	-0.0088336942112	-0.0164637727716	-0.0261120559598	0.0562016451328	0.132230996282	-0.0418209594684	0.0521458409058	0.0798420610163	0.0375504342034	0.0933404834167	10.645179506	36.4036618863	-12.7632955487
4	-0.00416350793305	0.00171369289122	0.00439550329668	0.000459808955971	0.0254436417331	0.0675708049756	-0.100050558697	0.0410672416792	-0.032370795153	-0.0186368466424	-0.00224885822743	0.0752752579439	-0.0486859728607	-0.00253469359659	-0.10401697465	0.133531635064	-0.0452804987477	0.0755439899697	0.135727148105	-0.0243529411027	-0.0635761997643	-0.526554143978	15.9144567739	4.78114201304
5	0.077126624088	-0.00051915415482	-0.00972859493213	0.0209409133489	0.00163727964649	0.0114822790438	-0.0459903377028	0.0337426335291	-0.119559839702	0.0114243532813	-0.0362157378196	0.00346878619685	-0.0439727338537	0.0143523724917	-0.0513076494766	0.0926093144545	0.00290539310533	0.0449932340163	0.107199283392	0.0239287471481	0.0532187009601	5.69514340077	30.0134021999	4.27242477242
6	0.0143763750492	-0.01516429058	-0.0136398266119	0.0386853061783	-0.0133902097016	0.0243453995908	0.0379396665219	-0.0264930941497	0.00685595944739	0.0024886699872	-0.0503045049716	-0.00769879265448	0.0111575833787	0.0211741221091	0.00139705507122	0.259764971034	-0.0885452830582	-0.0193371158346	0.0383544438583	0.131565440175	-0.117732998035	7.6345862946	28.4424143443	20.7791200958
7	0.0244394871399	-0.0403201265197	-0.000464634694031	0.0733330375425	-0.0358574707651	0.0262848850318	-0.0524050444866	0.00883225249444	0.00525585364005	-0.030947449933	0.0180117626554	-0.0942456451144	0.033979986695	-0.00252126471629	-0.0255424013355	0.124312100834	-0.0299263655728	0.00770987048123	0.076042672203	0.0173942586713	0.025709634478	-8.41821406218	30.0534474568	-5.31237347398
8	0.0153570106423	-0.00712974507128	-0.00784897633815	0.0117618546667	-0.00138991061362	0.0124303769478	0.0254481617394	-0.010276267193	0.0100043710383	-0.00141080037414	-0.00113621239293	0.00456474673259	-0.013812180413	0.0285089758438	0.0490291949809	0.0381057963882	0.103937876224	-0.0858757250239	0.0493129506083	0.0529696468477	-0.0200675212702	-21.4520545808	29.4508208882	-11.0932430456
9	0.0226735718245	-0.00409631129231	0.0212850255028	-0.000699027419085	-0.00459503890344	0.0201680494135	0.00855881856254	0.0523268704501	0.0193052078759	-0.0232345145482	0.0111057589956	0.0129867748509	-0.000939732974778	-0.0253239138266	0.0129417655753	0.038211549401	0.0769016872468	-0.152817158808	0.0375529120105	0.0805064950963	0.0827813020374	-34.6017109417	27.825376503	-13.0993222247
10	0.013809937137	0.000550377375386	-0.00292306708897	0.00568130970346	0.00124572396839	0.0161510409525	0.00795488337316	-0.0197028046987	0.0229032488294	0.00268504498348	0.00445887510348	-0.0129004507318	0.0030671218387	0.00492654697565	0.00692524379774	0.12796056985	0.0956773797593	0.046350381474	0.135140640818	0.134322603179	0.0990713647138	-10.252714553	9.33462926537	19.4003752232
11	0.0196029556247	-0.0215669657123	0.00234461663155	0.0357723190493	-0.0145487163746	0.0180833060358	0.0773544272557	-0.040880150857	-0.000584411275594	0.00796565892576	0.0398024491863	0.0409948898872	0.0108744934748	-0.0684440344762	0.125146727931	0.0164986374713	0.121421933636	0.00159960724318	-0.0580430085853	0.0432850276467	0.122367148992	-16.3763007103	7.65046903009	-1.2034800421
12	0.0281757130805	0.0443809398757	-0.0131357803795	0.0852795388817	-0.031168095303	0.0132151710028	-0.0993475185923	-0.0432693578802	0.0589142134992	0.0128377559022	-0.0831620680768	-0.0827975896701	-0.0980173762473	-0.0158673669553	-0.126509105575	-0.0387325816877	0.00980750620591	-0.0908817968963	0.102223803555	0.0111843950293	0.169367836338	-23.4778139679	19.9693588558	5.27225771297
13	0.0364297793026	0.00889613512746	0.0196647316519	-0.000238572316706	0.00491162628303	0.00935767352655	-0.0326766723291	-0.00643432969424	-0.00416989698929	0.0342050717714	-0.0143194164773	0.014788373239	0.00994780359513	0.00301704238221	-0.0580613133053	0.0610724100398	0.118375927805	0.0351744111944	0.0236450723032	0.100334265954	-0.00527923973063	-24.255205001	25.4120440865	18.908876091
14	0.159216851288	-0.0492560698431	-0.0163681483073	0.016188221431	0.00443223738156	0.00151188472729	-0.0613961797724	-0.0714438821323	-0.0127116956932	0.00115934778034	-0.00446781401638	0.0270859625147	0.0103369820535	-0.0110772784207	-0.00795844267232	0.258220732098	-0.0463404060895	-0.0380062221289	0.184640089896	-0.0624046643618	0.144984794262	-19.448597183	17.3016665624	23.1117449491
15	0.00963222470219	-0.00756803358398	0.00726817933733	0.0150677550624	-0.013663439542	0.0280982997464	0.00576309047468	-0.0404007353466	0.0538651731321	-0.0318787906408	0.0306734001884	0.00127375424622	0.0216492968607	0.0198704394469	0.0484265656055	0.0266269487918	0.0524412412554	0.00956556530104	0.101246925921	-0.14811842557	0.102244603952	-31.0665245221	8.97788371427	-4.63875693341
16	0.0131766566561	0.000625934201866	0.0118443515485	0.000136714873164	-0.00101452902641	0.0116898960524	0.00764606444199	0.0343381747963	-0.0245411319502	-0.0376598720197	-0.035961815889	0.0225662720749	0.0105236336499	-0.00504450895528	-0.0282790921041	0.11556519961	0.0709446906391	-0.0790136075145	0.143948066586	0.0496619432306	0.320739970145	-33.65142559	-2.39335105019	-11.3675133214
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53	0.0043694423599	0.00444012057268	-0.00575780597883	-0.00145826168373	-0.00312601012118	0.00273008423692	-0.0642025128047	0.0387119761636	-0.00601018834819	0.0675524034335	-0.0550183899115	0.00355286652787	0.0203660787465	-0.0454038302704	-0.000143726258745	0.385883398189	-0.0268723417468	-0.00270837018534	0.33935505832	-0.0565832864608	0.161148659021	-33.667887691	35.0270804408	-61.5715066294
54	0.00363772849392	0.000663737543958	0.00202418616002	0.0624071161952	-0.0449673075355	0.0351901225795	0.037770538811	0.0242621253735	0.0329813626221	-0.0230271976824	-1.67606966403E-5	0.0151565806968	0.012226390161	-0.0311539633861	0.0106327027352	0.375095599864	0.189517426572	0.0921662505961	0.435063049287	-0.106485968691	0.382672759444	-47.888424792	33.6807679958	-69.7820783858
55	-0.000587496179211	-0.000444192429941	-0.000491961493388	-0.000952802286451	-0.000806436881961	0.000144207116842	0.00122259334664	0.00999781638146	-0.00317622250918	-0.00624641349446	-0.00427302423098	0.00327426897282	-0.0115473957271	0.000136930422939	-2.05857686382E-7	0.455841352312	0.0398153967777	-0.0517518685741	0.619731840467	0.0245228710176	0.568683335941	-59.4617535056	30.6294986576	-70.5779184804
56	-0.00275653571313	-0.000690667682935	0.000526583349153	0.00666054253704	-0.0159274587021	0.00896678311833	-0.0310846006707	-0.0832903686744	-0.0107289759252	0.0187237958614	-0.0379803707741	0.0108703764002	-0.0288136457289	-0.0155069569419	-3.05099221558E-6	0.257967102362	0.036829654892	0.0414003865581	0.241918520363	-0.0353825514875	0.30926204866	-42.7218995719	19.463909844	-52.2398110181
57	0.0130451609029	0.0157704828136	-0.0165936241249	0.00185653553543	0.00032780008635	0.00732392396241	0.027239409105	0.0319777222285	0.0909288899044	0.00372640104982	0.0829332050111	-0.00369808077088	-0.0198738016753	-0.0277088127402	1.38968855999E-5	0.281371269001	-0.0704258555801	0.0458885441528	0.476379786969	0.0811071182779	0.164702947604	-55.9602152377	6.64746009008	-65.3351091065
58	-2.98670093958E-5	-0.00070685115017	-0.000376091125248	-0.0010730654888	-0.000489320060128	0.000684292088158	-0.0294701434877	-0.00928304097134	-0.0145823982001	-0.0152508436019	0.029044305191	0.0176006634522	-0.0242579616236	-0.000181650698817	-1.07642200626E-5	0.385773998547	-0.150318087047	0.0680401450337	0.351109238641	-0.00462298625951	0.129360209306	-63.7957417895	-10.8801517691	-70.9933952174
59	0.00173276585867	0.000586333168447	-0.00393643784179	0.000965899165867	-0.00161154992809	0.00996530716399	-0.0126233163544	-0.00191266931514	0.0132502744175	0.0145371389498	-0.0130058629958	0.0197657575877	0.0109293223012	-0.00917524378738	-6.86457133943E-5	0.416430969513	-0.0300028018564	-0.03972982062	0.4163374427	0.0418182388649	0.459026972369	-38.1834217584	3.29371167025	-42.9550387299
60	0.00147712810545	0.000731649566177	0.000356612289747	-9.59998303804E-5	0.000304805113964	9.61089457351E-5	-0.0109667423967	0.0023215614204	-0.0224305065385	-0.0231271022585	0.01408971162	-0.0149802868175	0.0163286430161	0.00870986701879	2.1453448529E-5	0.502790578972	-0.0219612869356	0.0720450497831	0.507212458106	0.0103947649024	0.453344014011	-35.7580290427	0.323494959077	-59.1474900227
61	0.000674398106932	-0.00114936335538	-0.00085185386956	0.000333067205687	0.000475478905263	0.000701579107465	-0.0269482041397	0.000744613077337	-0.0161311741977	0.0218265837113	-0.0372608417595	-0.0299180944689	-0.00442035118128	0.00586879437681	-3.63858521834E-5	0.434688263338	-0.0356395999083	-0.159465817436	0.55134448489	-0.0316788112693	0.385757948217	-37.9384085347	-9.62034536219	-58.7606263825
62	0.000438473737051	-0.00259044337509	0.00306898197406	0.00537931447505	0.00261445023265	0.00251925896704	-0.0205317145932	-0.0322370973964	0.0167593365282	0.0573366966562	0.0127559493286	-0.00893696786531	-0.047016879653	0.0561467035664	1.08095040298E-6	0.274015397023	-0.0264235198781	-0.0804285735684	0.329522783456	-0.0725752389446	0.145731032522	-50.1164564668	-5.24147455693	-53.6578934893
63	-0.000116698544374	-0.000307124072964	-0.000899583110691	-0.00048848961188	-0.000121004830015	0.00185709836454	-0.0180707223094	-0.00287618532991	-0.0061105637256	-0.00694719980762	-0.0110606640214	0.0216481062154	0.00957321397142	-0.0124397295444	-1.4441337098E-6	0.478048749187	0.0124490756881	-0.00627597092484	0.473583579172	0.0673207340193	0.320141561229	-56.5073777092	-5.72763968744	-40.6584243584
64	0.000720549327829	0.000639091353969	0.000124548974685	0.000642736640028	0.000680549137728	0.00108572366737	0.0189053507944	0.0199920222745	0.00270927590752	0.00495171416097	0.0210372463258	-0.0135781868815	-0.01612354616	0.016935020391	-8.72939627918E-6	0.479488298056	-0.0436883059724	-0.0531434582906	0.47447197702	-0.0458251482344	0.386224064311	-48.558821119	-1.62437231852	-37.4568711678
65	-0.00221472780745	0.000624628537707	0.000519524979074	0.000791369196949	-0.00286547189705	0.00174222400695	-0.0273429480458	0.00867902839272	-0.0292838860616	0.00343011324584	0.00705616745919	0.00265552451924	-0.0076168602477	0.00392023864782	-1.06895455632E-5	0.531351658061	0.0458375200123	-0.124329416005	0.295340160716	0.0461508052963	0.380512582174	-47.4242519957	-12.7257289279	-55.1138687969
66	0.000464339917948	-0.00036532589099	0.000788216995727	0.00474712553614	-0.000297869110691	0.000537189269109	0.0088505298945	-0.00306001652449	0.00598090420902	-0.00371272414212	-0.00124030943696	-0.00180825560668	0.00512373272125	-0.00977197162213	-2.61823107002E-6	0.681992081372	-0.0578660918462	-0.0185223414387	0.694222872116	-0.0607519245262	0.662710454463	-44.4450806418	-24.0238004638	-71.9259963372
67	0.00211200794754	0.00360347712015	0.00057660482907	0.00376002368798	-0.000433554555657	0.000475087767444	0.00891197621795	-0.00923566113242	0.0281809699509	0.047192810621	-0.0108461522003	-0.0191787352366	0.0255511520912	-0.00255085841799	-5.80982443272E-5	0.547193819923	0.0432429688018	0.0800607619557	0.416978816702	-0.0612087124298	0.259710338145	-33.5677401641	-25.6445259662	-71.5595245733
68	0.000712502341354	-0.00206962108554	0.000421355285304	0.0027138404736	0.00147953233431	-1.52802672188E-5	-0.0102384108742	-0.00849652834291	-0.00881957904493	-0.0266921988915	-0.0172297719597	-0.0186566692941	0.0196415828268	-0.00638306604663	6.66277777692E-7	0.356947627133	0.0183104948582	-0.0731854584295	0.352330062679	0.0948536299979	0.40058073202	-39.8130751565	-32.9308174802	-67.8059010236
69	0.00152904194953	0.00179510541736	0.00167372266255	0.00119151926486	0.002442188034	-0.000205007935148	-0.00976902802733	0.00578229857557	-0.00581173037496	0.0147380369911	0.00804506396136	0.00483613128762	0.0344160372277	0.0287895746535	-2.10347476221E-6	0.391526756087	-0.0499561998194	0.0774466336244	0.270213956797	-0.135128673089	0.315487365183	-28.7237216605	-37.9482919264	-74.7445845143
70	0.000674654512377	0.000997265243676	0.000146716538944	0.00028473762918	6.34327410746E-5	-1.33513075431E-6	-0.00754788032276	0.00809691464998	0.00764785260918	-0.00705195607969	-0.0059758378956	0.0125468854571	-0.0126970616884	-0.000835165765623	-3.74621418269E-5	0.486426184763	-0.006055346654	-0.0710279799435	0.551400138029	-0.0374502198504	0.586253537707	-28.0229717155	-7.53740852201	-41.7180842125
71	0.000402097620662	0.000143401334763	-0.000358890184794	6.40906914271E-5	8.62206212078E-5	0.000502378743721	0.0357711916971	0.0162924914011	-0.008304288031	0.0137221064013	-0.00483873904145	-0.0125949443064	-0.00528711860144	0.0112085472147	6.34625462948E-5	0.380591867612	-0.0701710431819	-0.0154867432831	0.368848558227	0.0220743509384	0.409512158545	-24.9007730997	-7.37706636514	-59.0619175544
72	0.00135274108787	0.00210375398498	-0.00148243652876	0.000653219161016	0.00571243803116	0.0034061381232	0.00177726077962	-0.0149261207183	0.0161094331167	-0.00704323919699	-0.115879353722	-0.0042557096849	-0.009770913825	0.0130419399152	-1.69255331454E-5	0.453393047296	-0.0179232889773	0.0313374849023	0.306744541254	-0.106448392538	0.323994309691	-23.2945914472	-14.8157238995	-54.9344537193
73	-0.000844935522699	0.00138038871917	-0.00016229082041	0.0087148251938	-0.00959548055301	0.00450373242811	-0.046476455054	-0.00842301581525	-0.0592684911221	0.0800017902005	0.0378147413661	-0.0161823486553	-0.0484665457208	-0.00819556665532	-3.71150964158E-6	0.499340798609	-0.0348651265887	0.0262152972721	0.352740402328	-0.0798146537395	0.443865678578	-27.9676934778	-26.7724613924	-49.1482277173
74	0.000522093841812	0.00207466275183	-6.25956847455E-5	0.000816261216431	0.00031898707781	-0.00011184989881	0.0358056911495	-0.0248758501658	-0.017154171336	0.0151519984267	-0.0001338465097	-0.0340496142222	-0.0143682353437	-0.0188192474156	8.47444835699E-6	0.416338092556	0.0354988774877	-0.114915193119	0.386617713501	0.000737457679913	0.227005437224	-19.1804518716	-23.5055311228	-54.2747220022
75	0.000881344264289	0.00150619122381	-0.000249348405335	0.0011300292935	-0.00107311552299	0.000789730717337	-0.0173826474382	0.010415273194	0.0312809751616	-0.0379573651798	-0.0153507097916	-0.0308892267425	-0.0152044692216	0.00705786275927	2.06621774574E-6	0.326136689915	0.042573344577	0.0599546614719	0.284467433859	0.0806962563465	0.147726542919	-2.94549362073	-20.6670431002	-71.5552391697
76	0.00513542612529	-0.000977729917317	-0.00543218451546	0.000397826718302	1.46853589324E-5	0.00556138789676	-0.00227413742707	0.00314105423714	0.0112945501042	0.0145707828867	-0.0142775470661	0.0164525345733	0.00327806795036	0.00691337949876	3.22643851828E-5	0.293657024585	0.0954887750974	0.0103002653091	0.213288166714	0.00460659436882	0.132212430972	0.426228032854	-28.0169239833	-62.6390263793
77	0.00055197797299	-0.000420231264807	0.000598618450398	0.000532405474201	-3.57389560454E-5	0.0006420687677	-0.00877035756541	0.000833547604205	0.00389647837561	0.0065568034962	0.00562117189015	-0.01137248187	0.000730174900002	-0.00436844561779	4.69295620226E-7	0.648619169908	0.018878045664	-0.00631655057533	0.665475196125	-0.0681187814122	0.610977744114	6.82421355007	-24.3716501487	-74.7101686789
78	-0.000151055174034	-0.00143495657958	0.00106342321549	0.000272739562959	-0.000219043305167	0.000521713664574	-0.0141796996684	0.0225653591919	0.0164353986559	0.0111245677674	0.0210023515299	-0.0101662748496	-0.01744267651	-0.00601615119004	4.4700946222E-5	0.689711147449	0.0589100464412	0.0653824242363	0.612542635572	-0.0885463842705	0.657863992405	14.1834733663	-22.1279960346	-70.1171652295
79	1.69595407773E-5	-0.000187157590148	-0.000634397962887	0.000739025481855	-0.000974775588585	0.00128817908944	-0.0118235445748	-0.00824205946067	-0.000243850172188	-0.00437488787827	0.00544934054279	0.00534470977157	-0.011260894367	0.0143234927824	5.54521080628E-6	0.447628009816	-0.0703717524907	0.0355725374929	0.40440155761	-0.000822264846568	0.437648354736	10.8325438124	-14.1860642222	-68.3217753227
80	0.00203799538165	0.00312232702568	-0.00126110396323	0.00881005547522	0.00266154704872	0.00197410576087	-0.0114803372104	-0.0334063956105	-0.00234777852108	0.0416396464297	-0.0170289716192	0.00307375567017	0.016163806613	-0.0162785412342	-7.26355700889E-5	0.459634148788	-0.0553603086166	-0.104412111292	0.255146345105	0.125923406945	0.125614785697	-13.0915174939	-2.32141408099	-54.0723192631
81	0.00622089497098	-0.00576565563084	-0.00104473744712	0.000401794276379	-0.000717802593886	0.00796622078356	-0.0204687411986	-0.0409248376523	-0.0559081709405	0.0201352194053	-0.09555820985	-0.0469042928444	-0.0106703440728	0.0465200110568	-4.5596991363E-5	0.407476447881	-0.0317574867861	0.169392486633	0.264081271229	-0.0027010471003	0.420388213125	-1.85088527261	-7.41362533	-55.0402619862
82	0.00944918873591	-0.0127908534045	3.09184659578E-5	0.0085117848173	-0.00150686129326	0.000626692322896	-0.0473799423292	0.0313214926916	-0.0207111976182	0.0137004985305	0.00014320228245	0.0856686470739	-0.00654954774582	0.0069195022332	1.56545003621E-5	0.436086055567	0.182787823571	0.0344480570869	0.333518843839	0.0357708828278	0.276455340705	1.23607181394	-8.93385283152	-46.9622290353
83	0.00285827816959	0.000806031106199	0.00184887029339	0.00433458102654	0.00196773709292	0.00115815619504	-0.0346834282528	-0.0193623769493	0.0284684179125	-0.00291926087968	-0.0180542727152	-0.0362522068398	-0.0080620208207	0.0231943172586	-1.10444328759E-5	0.353536776629	-0.150224756824	-0.00646105783118	0.415560602768	0.0498534652248	0.314001140005	9.87516754508	10.2049305826	-71.4927779692
84	0.00328965286744	0.000882567427588	0.00403233703703	-0.000542470348353	-0.00088077253921	0.00334298220281	0.0386884117626	0.00544105408478	-0.0245894732604	-0.030309891817	0.0303366655728	-0.0119596952905	-0.0100684253334	-0.0100725829321	1.58593635091E-5	0.491408076556	-0.0294452558244	-0.124573324501	0.625306593627	-0.0808644892309	0.373218956311	17.8831045289	14.0203572914	-70.3664306669
85	0.00225463680111	0.000305102297901	0.00188633261513	6.55424550213E-5	0.000685815673136	0.00125912402312	0.0237045516879	0.022881869291	-0.0145780122979	-0.00276196507462	0.00535552818625	0.00816708799942	0.0105962328774	0.0122116437936	1.82176677699E-5	0.538613670024	-0.0148299623961	-0.0435541758691	0.629485258073	0.000439467208723	0.464910238553	13.6152999946	24.5933319921	-71.1006536103

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 'A' and (resid 1 through 83 )	A	A	1 - 83	1 - 78
2	2	chain 'A' and (resid 84 through 160 )	A	A	84 - 160	79 - 152
3	3	chain 'A' and (resid 161 through 220 )	A	A	161 - 220	153 - 206
4	4	chain 'B' and (resid 1 through 48 )	B	C	1 - 48	1 - 43
5	5	chain 'B' and (resid 49 through 83 )	B	C	49 - 83	44 - 78
6	6	chain 'B' and (resid 84 through 125 )	B	C	84 - 125	79 - 112
7	7	chain 'B' and (resid 126 through 160 )	B	C	126 - 160	113 - 147
8	8	chain 'B' and (resid 161 through 195 )	B	C	161 - 195	148 - 176
9	9	chain 'B' and (resid 196 through 219 )	B	C	196 - 219	177 - 200
10	10	chain 'C' and (resid 1 through 16 )	C	E	1 - 16	1 - 14
11	11	chain 'C' and (resid 17 through 43 )	C	E	17 - 43	15 - 41
12	12	chain 'C' and (resid 44 through 83 )	C	E	44 - 83	42 - 81
13	13	chain 'C' and (resid 84 through 110 )	C	E	84 - 110	82 - 100
14	14	chain 'C' and (resid 111 through 125 )	C	E	111 - 125	101 - 115
15	15	chain 'C' and (resid 126 through 160 )	C	E	126 - 160	116 - 149
16	16	chain 'C' and (resid 161 through 175 )	C	E	161 - 175	150 - 164
17	17	chain 'C' and (resid 176 through 219 )	C	E	176 - 219	165 - 201
18	18	chain 'D' and (resid 1 through 16 )	D	G	1 - 16	1 - 14
19	19	chain 'D' and (resid 17 through 83 )	D	G	17 - 83	15 - 81
20	20	chain 'D' and (resid 84 through 125 )	D	G	84 - 125	82 - 116
21	21	chain 'D' and (resid 126 through 175 )	D	G	126 - 175	117 - 166
22	22	chain 'D' and (resid 176 through 219 )	D	G	176 - 219	167 - 205
23	23	chain 'E' and (resid 1 through 16 )	E	I	1 - 16	1 - 12
24	24	chain 'E' and (resid 17 through 43 )	E	I	17 - 43	13 - 39
25	25	chain 'E' and (resid 44 through 83 )	E	I	44 - 83	40 - 79
26	26	chain 'E' and (resid 84 through 110 )	E	I	84 - 110	80 - 98
27	27	chain 'E' and (resid 111 through 125 )	E	I	111 - 125	99 - 113
28	28	chain 'E' and (resid 126 through 195 )	E	I	126 - 195	114 - 175
29	29	chain 'E' and (resid 196 through 219 )	E	I	196 - 219	176 - 199
30	30	chain 'F' and (resid 1 through 16 )	F	K	1 - 16	1 - 11
31	31	chain 'F' and (resid 17 through 30 )	F	K	17 - 30	12 - 25
32	32	chain 'F' and (resid 31 through 48 )	F	K	31 - 48	26 - 43
33	33	chain 'F' and (resid 49 through 83 )	F	K	49 - 83	44 - 78
34	34	chain 'F' and (resid 84 through 125 )	F	K	84 - 125	79 - 117
35	35	chain 'F' and (resid 126 through 160 )	F	K	126 - 160	118 - 152
36	36	chain 'F' and (resid 161 through 175 )	F	K	161 - 175	153 - 167
37	37	chain 'F' and (resid 176 through 205 )	F	K	176 - 205	168 - 189
38	38	chain 'F' and (resid 206 through 219 )	F	K	206 - 219	190 - 203
39	39	chain 'G' and (resid 1 through 29 )	G	M	1 - 29	1 - 19
40	40	chain 'G' and (resid 30 through 43 )	G	M	30 - 43	20 - 33
41	41	chain 'G' and (resid 44 through 74 )	G	M	44 - 74	34 - 64
42	42	chain 'G' and (resid 75 through 109 )	G	M	75 - 109	65 - 74
43	43	chain 'G' and (resid 110 through 145 )	G	M	110 - 145	75 - 101
44	44	chain 'G' and (resid 146 through 160 )	G	M	146 - 160	102 - 116
45	45	chain 'G' and (resid 161 through 175 )	G	M	161 - 175	117 - 131
46	46	chain 'G' and (resid 176 through 204 )	G	M	176 - 204	132 - 153
47	47	chain 'G' and (resid 205 through 219 )	G	M	205 - 219	154 - 168
48	48	chain 'H' and (resid 1 through 30 )	H	N	1 - 30	1 - 20
49	49	chain 'H' and (resid 31 through 48 )	H	N	31 - 48	21 - 38
50	50	chain 'H' and (resid 49 through 62 )	H	N	49 - 62	39 - 52
51	51	chain 'H' and (resid 63 through 83 )	H	N	63 - 83	53 - 73
52	52	chain 'H' and (resid 84 through 125 )	H	N	84 - 125	74 - 105
53	53	chain 'H' and (resid 126 through 160 )	H	N	126 - 160	106 - 136
54	54	chain 'H' and (resid 161 through 195 )	H	N	161 - 195	137 - 158
55	55	chain 'H' and (resid 196 through 217 )	H	N	196 - 217	159 - 177
56	56	chain 'I' and (resid 1 through 127 )	I	O	1 - 127	1 - 87
57	57	chain 'I' and (resid 128 through 189 )	I	O	128 - 189	88 - 139
58	58	chain 'I' and (resid 190 through 219 )	I	O	190 - 219	140 - 169
59	59	chain 'J' and (resid 1 through 16 )	J	P	1 - 16	1 - 8
60	60	chain 'J' and (resid 17 through 29 )	J	P	17 - 29	9 - 21
61	61	chain 'J' and (resid 30 through 43 )	J	P	30 - 43	22 - 35
62	62	chain 'J' and (resid 44 through 80 )	J	P	44 - 80	36 - 72
63	63	chain 'J' and (resid 81 through 110 )	J	P	81 - 110	73 - 89
64	64	chain 'J' and (resid 111 through 127 )	J	P	111 - 127	90 - 99
65	65	chain 'J' and (resid 128 through 145 )	J	P	128 - 145	100 - 117
66	66	chain 'J' and (resid 146 through 152 )	J	P	146 - 152	118 - 124
67	67	chain 'J' and (resid 153 through 174 )	J	P	153 - 174	125 - 146
68	68	chain 'J' and (resid 175 through 192 )	J	P	175 - 192	147 - 155
69	69	chain 'J' and (resid 193 through 219 )	J	P	193 - 219	156 - 171
70	70	chain 'K' and (resid 1 through 16 )	K	Q	1 - 16	1 - 9
71	71	chain 'K' and (resid 17 through 29 )	K	Q	17 - 29	10 - 22
72	72	chain 'K' and (resid 30 through 62 )	K	Q	30 - 62	23 - 55
73	73	chain 'K' and (resid 63 through 126 )	K	Q	63 - 126	56 - 84
74	74	chain 'K' and (resid 127 through 145 )	K	Q	127 - 145	85 - 103
75	75	chain 'K' and (resid 146 through 175 )	K	Q	146 - 175	104 - 133
76	76	chain 'K' and (resid 176 through 189 )	K	Q	176 - 189	134 - 142
77	77	chain 'K' and (resid 190 through 197 )	K	Q	190 - 197	143 - 149
78	78	chain 'K' and (resid 198 through 210 )	K	Q	198 - 210	150 - 162
79	79	chain 'K' and (resid 211 through 219 )	K	Q	211 - 219	163 - 171
80	80	chain 'L' and (resid 1 through 29 )	L	R	1 - 29	1 - 19
81	81	chain 'L' and (resid 30 through 78 )	L	R	30 - 78	20 - 68
82	82	chain 'L' and (resid 79 through 145 )	L	R	79 - 145	69 - 105
83	83	chain 'L' and (resid 146 through 176 )	L	R	146 - 176	106 - 136
84	84	chain 'L' and (resid 177 through 195 )	L	R	177 - 195	137 - 147
85	85	chain 'L' and (resid 196 through 219 )	L	R	196 - 219	148 - 164

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

すべてのお知らせ

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る

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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

+
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)