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万見

- PDB-6zz8: MB_CRS6-15 bound to CrSAS-6_6HR -

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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: 6zz8

タイトル

MB_CRS6-15 bound to CrSAS-6_6HR

要素

Centriole protein
Protein B

キーワード

PROTEIN BINDING / Centriole / Cartwheel / Ring-polymer / Monobody

機能・相同性

機能・相同性情報

cell-substrate junction assembly / proteoglycan binding / extracellular matrix structural constituent / centriole / cell-matrix adhesion / integrin binding / identical protein binding / cytoplasm
類似検索 - 分子機能

生物種

Chlamydomonas reinhardtii (クラミドモナス)

Escherichia coli (大腸菌)

手法

X線回折 /

シンクロトロン /

分子置換 / 解像度: 3.73 Å

データ登録者

Hatzopoulos, G.N. / Kukenshoner, T. / Banterle, N. / Favez, T. / Fluckiger, I. / Hantschel, O. / Gonczy, P.

資金援助

スイス, 2件

引用

ジャーナル: Nat Commun / 年: 2021
タイトル: Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly.
著者: Hatzopoulos, G.N. / Kukenshoner, T. / Banterle, N. / Favez, T. / Fluckiger, I. / Hamel, V. / Andany, S. / Fantner, G.E. / Hantschel, O. / Gonczy, P.

履歴

登録	2020年8月4日	登録サイト: PDBE / 処理サイト: PDBE
改定 1.0	2021年7月7日	Provider: repository / タイプ: Initial release
改定 1.1	2021年7月21日	Group: Derived calculations カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
改定 1.2	2024年1月31日	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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	6zz8.cif.gz	898.5 KB	表示	PDBx/mmCIF形式
PDB形式	pdb6zz8.ent.gz	636.7 KB	表示	PDB形式
PDBx/mmJSON形式	6zz8.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/zz/6zz8 ftp://data.pdbj.org/pub/pdb/validation_reports/zz/6zz8	HTTPS FTP

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関連構造データ

関連構造データ	6zzcC 6zzdC 6zzgC 3q0xS 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	6zz8-3 6zz8-4 6zzc-1 6zz8-2 1za7-d 3a7o-d 3wee-d 5gka-d Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) 類似検索 - 機能・相同性F&H 検索類似検索 - 機能F&H 検索類似検索 - 相同性F&H 検索

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リンク

PDBのページ	PDBj / wwPDB / NCBI
「今月の分子」の関連する項目	#185 - 2015年5月タイチン (Titin) 類似性 (1) #52 - 2004年4月成長ホルモン (Growth Hormone) 類似性 (1) #141 - 2011年9月 O-GlcNAc転移酵素 (O-GlcNAc Transferase) 類似性 (1)

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集合体

登録構造単位

A: Centriole protein

B: Centriole protein

C: Centriole protein

D: Centriole protein

E: Centriole protein

F: Centriole protein

G: Protein B

H: Protein B

I: Protein B

J: Protein B

K: Protein B

L: Protein B

214 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: Centriole protein

B: Centriole protein

G: Protein B

H: Protein B

登録者が定義した集合体
根拠: isothermal titration calorimetry
71.2 kDa, 4 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

D: Centriole protein

J: Protein B

C: Centriole protein

I: Protein B

登録者が定義した集合体
71.2 kDa, 4 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

C: Centriole protein

I: Protein B

D: Centriole protein

J: Protein B

登録者が定義した集合体
71.2 kDa, 4 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

E: Centriole protein

F: Centriole protein

K: Protein B

L: Protein B

登録者が定義した集合体
71.2 kDa, 4 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

単位格子

Length a, b, c (Å)	257.160, 257.160, 125.289
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2
Space group name Hall	P4n2n
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/2 #3: y+1/2,-x+1/2,z+1/2 #4: x+1/2,-y+1/2,-z+1/2 #5: -x+1/2,y+1/2,-z+1/2 #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z

非結晶学的対称性 (NCS)

NCSドメイン:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1
1	2
2	2
3	2
4	2
5	2
6	2

NCSドメイン領域:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	LEU	LEU	(chain 'A' and resid 15 through 217)	A	A	15 - 217	16 - 218
2	2	1	GLY	GLY	LEU	LEU	(chain 'B' and resid 15 through 217)	B	B	15 - 217	16 - 218
3	3	1	GLY	GLY	LEU	LEU	(chain 'C' and resid 15 through 217)	C	C	15 - 217	16 - 218
4	4	1	GLY	GLY	LEU	LEU	(chain 'D' and resid 15 through 217)	D	D	15 - 217	16 - 218
5	5	1	GLY	GLY	LEU	LEU	(chain 'E' and resid 15 through 217)	E	E	15 - 217	16 - 218
6	6	1	GLY	GLY	LEU	LEU	(chain 'F' and resid 15 through 217)	F	F	15 - 217	16 - 218
1	7	2	VAL	VAL	ARG	ARG	(chain 'G' and (resid 1 through 81 or resid 83 through 92))	G	G	1 - 81	3 - 83
1	8	2	ALA	ALA	THR	THR	(chain 'G' and (resid 1 through 81 or resid 83 through 92))	G	G	83 - 92	85 - 94
2	9	2	VAL	VAL	ARG	ARG	(chain 'H' and (resid 1 through 81 or resid 83 through 92))	H	H	1 - 81	3 - 83
2	10	2	ALA	ALA	THR	THR	(chain 'H' and (resid 1 through 81 or resid 83 through 92))	H	H	83 - 92	85 - 94
3	11	2	VAL	VAL	ARG	ARG	(chain 'I' and (resid 1 through 81 or resid 83 through 92))	I	I	1 - 81	3 - 83
3	12	2	ALA	ALA	THR	THR	(chain 'I' and (resid 1 through 81 or resid 83 through 92))	I	I	83 - 92	85 - 94
4	13	2	VAL	VAL	ARG	ARG	(chain 'J' and (resid 1 through 81 or resid 83 through 92))	J	J	1 - 81	3 - 83
4	14	2	ALA	ALA	THR	THR	(chain 'J' and (resid 1 through 81 or resid 83 through 92))	J	J	83 - 92	85 - 94
5	15	2	VAL	VAL	ARG	ARG	(chain 'K' and (resid 1 through 81 or resid 83 through 92))	K	K	1 - 81	3 - 83
5	16	2	ALA	ALA	THR	THR	(chain 'K' and (resid 1 through 81 or resid 83 through 92))	K	K	83 - 92	85 - 94
6	17	2	VAL	VAL	ARG	ARG	(chain 'L' and (resid 1 through 81 or resid 83 through 92))	L	L	1 - 81	3 - 83
6	18	2	ALA	ALA	THR	THR	(chain 'L' and (resid 1 through 81 or resid 83 through 92))	L	L	83 - 92	85 - 94

NCSアンサンブル:

ID
1
2

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要素

#1: タンパク質	Centriole protein 分子量: 25701.127 Da / 分子数: 6 / 由来タイプ: 組換発現由来: (組換発現) Chlamydomonas reinhardtii (クラミドモナス) 遺伝子: CrSAS-6, CHLRE_12g516950v5 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: A9CQL4
#2: タンパク質	Protein B 分子量: 9896.027 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: M1E1G6
#3: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 19 / 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: 5.1 Å³/Da / 溶媒含有率: 75.89 %
結晶化	温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法詳細: 40% MPD, 5% PEG 8000, 0.1M MES pH 6.5, 0.4M DL-Glutamic acid monohydrate

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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: SLS / ビームライン: X06DA / 波長: 1 Å
検出器	タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2019年3月21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 Å / 相対比: 1
反射	解像度: 3.73→49.63 Å / Num. obs: 88072 / % possible obs: 99.02 % / 冗長度: 2 % / B_iso Wilson estimate: 138.8 Å² / R_merge(I) obs: 0.04373 / Net I/σ(I): 10.27
反射シェル	解像度: 3.73→3.78 Å / R_merge(I) obs: 0.637 / Num. unique obs: 8552

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.15_3459	精密化
XDS		データ削減
XDS		データスケーリング
PHASER		位相決定

精密化

構造決定の手法:

分子置換
開始モデル: 3q0x

3q0x

解像度: 3.73→49.63 Å / SU ML: 0.5905 / 交差検証法: FREE R-VALUE / σ(F): 1.32 / 位相誤差: 30.8249
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	0.2671	4139	5.02 %
R_work	0.2251	78339	-
obs	0.2272	82478	99.03 %

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: 227.31 Å²

精密化ステップ

サイクル: LAST / 解像度: 3.73→49.63 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	14307	0	0	19	14326

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.003	14602
X-RAY DIFFRACTION	f_angle_d	0.7133	19833
X-RAY DIFFRACTION	f_chiral_restr	0.0469	2311
X-RAY DIFFRACTION	f_plane_restr	0.0051	2561
X-RAY DIFFRACTION	f_dihedral_angle_d	11.6922	8834

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 (%)
3.73-3.78	0.3938	134	0.3728	2573	X-RAY DIFFRACTION	97.44
3.78-3.82	0.4051	137	0.3604	2619	X-RAY DIFFRACTION	100
3.82-3.87	0.4341	141	0.4091	2622	X-RAY DIFFRACTION	99.89
3.87-3.92	0.4973	134	0.4711	2546	X-RAY DIFFRACTION	95.61
3.92-3.97	0.3897	109	0.4279	2052	X-RAY DIFFRACTION	78.84
3.97-4.02	0.3873	139	0.3471	2658	X-RAY DIFFRACTION	99.96
4.02-4.08	0.3678	140	0.306	2637	X-RAY DIFFRACTION	99.96
4.08-4.14	0.3046	139	0.2982	2633	X-RAY DIFFRACTION	99.96
4.14-4.21	0.3492	134	0.2783	2639	X-RAY DIFFRACTION	99.89
4.21-4.27	0.2704	142	0.2634	2632	X-RAY DIFFRACTION	100
4.27-4.35	0.2704	138	0.2311	2613	X-RAY DIFFRACTION	100
4.35-4.43	0.2863	142	0.2295	2671	X-RAY DIFFRACTION	100
4.43-4.51	0.2769	140	0.2179	2623	X-RAY DIFFRACTION	100
4.51-4.6	0.2573	138	0.2039	2641	X-RAY DIFFRACTION	100
4.6-4.7	0.2137	141	0.2052	2636	X-RAY DIFFRACTION	100
4.7-4.81	0.2907	141	0.2123	2630	X-RAY DIFFRACTION	100
4.81-4.93	0.2401	134	0.2053	2638	X-RAY DIFFRACTION	99.96
4.93-5.07	0.2703	141	0.216	2636	X-RAY DIFFRACTION	100
5.07-5.22	0.3098	136	0.2294	2649	X-RAY DIFFRACTION	99.96
5.22-5.38	0.3174	144	0.229	2616	X-RAY DIFFRACTION	100
5.38-5.58	0.3434	139	0.2458	2641	X-RAY DIFFRACTION	100
5.58-5.8	0.3077	142	0.2452	2627	X-RAY DIFFRACTION	100
5.8-6.06	0.32	141	0.2327	2654	X-RAY DIFFRACTION	100
6.06-6.38	0.304	138	0.2399	2633	X-RAY DIFFRACTION	100
6.38-6.78	0.3243	138	0.2472	2643	X-RAY DIFFRACTION	100
6.78-7.3	0.2427	133	0.2173	2648	X-RAY DIFFRACTION	100
7.3-8.03	0.258	142	0.2012	2636	X-RAY DIFFRACTION	99.96
8.03-9.19	0.2008	133	0.1622	2651	X-RAY DIFFRACTION	100
9.19-11.56	0.1639	143	0.1516	2623	X-RAY DIFFRACTION	99.82
11.56-49.63	0.1972	146	0.1831	2619	X-RAY DIFFRACTION	99.32

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	8.87487142875	-0.0284381964516	1.42691895078	5.78138861028	0.230291490463	8.19407314577	-0.230822915709	-0.0619745229405	1.06541437904	-0.0735433108887	0.0799088100136	-0.381304080617	-0.303037928112	-0.405908068349	0.118345900803	0.740229537411	-0.0214588090528	0.153743996447	0.767901402363	0.295788754927	1.46738841972	18.2792946116	36.2695268287	-20.9303906892
2	5.00286981662	0.43071811974	2.00222153992	0.0464030064456	0.230236306572	1.53760765714	0.814374128189	-3.17776250812	-2.46111567046	3.95325375448	0.625796531019	1.98992411321	2.04740707626	-1.64376157504	-1.31086866866	6.87389245077	0.227117433909	1.15471048104	3.34818677728	0.957289140251	3.78388513088	-2.85455578411	26.1757198857	20.9237937728
3	8.37346610352	3.26351697869	-2.24165732109	6.99544635459	-1.75322128876	6.38294138835	-0.335827639008	0.739413861485	-0.663546375493	-0.388576038398	0.0951210350691	0.288446219623	0.305647315057	-0.287355743289	0.209193538413	0.621981102647	0.182947049534	-0.306917122661	1.07787508818	-0.128217719685	0.949019705658	-14.6498067202	61.1540640221	-5.85160418728
4	3.96271183903	1.09419740401	1.04864573425	7.70524777	-3.59504144886	4.46070871809	-0.110454827196	-2.91646617555	-1.03318266557	5.47865010574	1.10213191726	-1.66511239259	-1.48446811152	-1.01646922785	-1.43138382999	4.24895450648	0.952243811558	-0.675186250372	3.6829698763	0.540971692699	4.18127420977	1.90607877638	29.0846273908	19.1829158391
5	9.14858213728	-1.27219640877	2.03082262012	3.52944012864	1.71866791233	7.29455456892	-0.482758819802	0.394744185299	0.101478904087	-0.179842982329	-0.0285289610619	-0.0316194108802	-0.416926136808	0.43290341732	0.414753202999	0.897348930584	0.0555713733333	0.200310117083	0.878383780179	0.604799239154	1.82645443454	49.9142166048	36.0374732196	-33.1893792135
6	2.63708223208	0.931839874418	0.342540949927	3.11336534628	3.81723488069	2.06672382169	-0.397033467607	2.7933559974	-2.36355088197	2.2619090762	0.431903935331	-0.696770296601	3.40320169247	4.4980223941	1.00398741222	3.55120706196	1.3034962385	1.2473163763	5.81944701953	0.720458529657	5.83655419739	73.0474491754	9.27412840041	-65.2567450599
7	8.56053842252	0.1531699773	-1.23530626977	5.00111434899	-0.962210735435	5.88262040351	0.0204619998499	0.860291649745	0.844163435931	-0.0940194092848	0.409267193428	1.49754252052	-0.00247306034924	-0.215701897342	-0.329855119358	0.636720372643	0.0814593048001	-0.00924949555693	1.11518955447	0.391313648006	1.42989304421	-44.6970451622	74.0565463138	-6.09454095449
8	0.102354380262	0.397312834456	0.0368455413604	2.03713811673	0.622461212123	-0.099881619636	-0.327470264046	-0.574234300627	3.34085246581	0.398828456114	0.772533924576	2.36320866435	-1.19299710235	-0.208847654866	-0.889175583602	4.14172437438	0.385443066198	0.475189786314	2.74268945309	0.00429412796	7.24773123019	-61.1853719824	116.615924775	2.43102077589
9	4.38885943333	1.31848691794	-2.31758822936	8.81564809922	1.88601658022	7.42789302774	0.338905268615	-0.216073849216	0.102504099509	0.837965485643	0.260279121488	-0.434975891192	0.275321917136	0.64669279845	-0.778887847622	1.33876467027	-0.0143761009017	-0.0805114638281	1.38784100409	0.254449922767	0.879960511705	-28.7878342704	117.92221399	12.2046978254
10	0.784048692997	1.90690905497	-1.33410424764	1.89529152712	-1.24124915227	1.76674741507	-1.99776863782	0.167203928282	0.139895842314	-2.54571079431	0.734165452653	3.18529546254	1.6779926862	-1.08962824651	0.991249536802	3.79711453121	0.654682526598	0.667791972978	3.28310022566	0.754159440678	3.86347359989	-34.7873992312	74.8260129731	28.7502291415
11	8.72968815664	-0.458833233057	-3.93992371952	9.25994756852	-0.41890005764	9.49417357312	0.151376187569	-0.0841790798186	0.307208153841	0.0147515677138	-0.0508488388952	0.515689011815	-0.927850005922	-0.650103852634	-0.1789643684	1.43038791848	0.339226054217	-0.322100833885	0.964518454306	-0.256570115105	0.888145541918	-3.14724949723	99.8311382688	45.4494805998
12	3.95842362238	4.43617173912	3.04274836317	4.77116939361	3.4788792357	2.80324839492	-0.0801892963785	3.53324494524	-2.45949226211	-1.81309502471	1.2020850347	0.611246203578	0.65645352364	-1.26434914734	-0.887744383338	3.42082277195	-0.0736092767647	-1.50187278765	4.09526765032	-1.31750135671	4.5092773862	-34.0265584752	75.6542429721	23.8049148049
13	1.99409859249	-8.16710930176	-6.22103526431	6.92006653496	3.7218322825	6.04636964796	-1.52707173119	-2.5650143031	-3.22578129831	0.621066909488	0.391389323478	-0.820246127104	-1.46808924905	2.61249942449	0.680526071485	1.21096046509	-0.392923031925	0.397508457101	1.2682411365	0.326304488696	3.01941667988	6.76448166386	12.1626110704	-6.71046115522
14	3.97365615586	4.16898020214	-5.1712149836	6.00097261685	-3.93178802825	8.2168004855	-0.736717160318	-0.669883135729	-0.532224142525	0.768231970041	-0.283782048192	-1.02945516202	-0.151101601915	0.472434037844	0.908173711021	1.13123622116	-0.167844723188	0.0354697060843	1.20760865804	0.469829164421	2.01645609172	5.87853559321	19.0304279504	-7.87071104421
15	7.94144299884	-7.47647962076	1.05615961409	8.72402791616	-2.01379755749	5.98463479501	1.98003198532	-0.37561005395	0.570969518119	-2.31773212678	-0.872774199082	4.25902541912	1.23126943362	-0.967969716851	-1.1651494323	1.28254364111	-0.411507478982	0.00205907603494	1.75975964442	0.550632932827	2.68968033078	-8.44371968077	18.1286284094	-15.2504321729
16	5.73906517463	4.79255370233	-5.57278846212	7.05445601805	-4.31906240249	5.54731892022	-0.187407234654	-0.3992951013	-0.0521719808356	0.559947999422	0.039722518392	2.570337617	-0.222299208801	-0.224283699969	0.344854776734	1.11125835599	-0.198700401866	0.376207701206	1.2270553647	0.0629573392216	1.91218532383	-1.09602860886	19.6547796773	-9.47576897932
17	4.82420618668	3.10701467621	-4.85631788779	2.47761918224	-3.01440014757	4.7869807557	-0.949094015787	0.934543929595	-0.922529462555	1.2381406841	1.11924930735	0.811097353802	1.64914543409	-1.63073725296	-0.440578869636	1.66311348841	-0.375135326582	0.222665428654	1.3038361847	0.124028663559	1.85775247778	3.77199914509	14.2412164719	-15.1934984187
18	3.02862544714	0.661740892703	-2.3297831687	3.92368396105	4.4245167231	8.30527414489	-1.94806889218	-1.80707583654	1.17537190701	2.26614007162	1.11437407832	0.984848633312	-1.77036239404	-0.537526806437	0.753474390448	1.04004575606	0.0887866583962	-0.0462378541554	1.667411557	-0.338718859769	1.10480035587	-2.21349012819	63.3672164461	19.4452979728
19	8.34203658057	-3.40984393213	2.20952293326	4.87887332767	-3.23276479761	6.32418877133	1.06771821169	1.213166359	-5.15414009928	-0.576646680682	-1.43819963179	0.28377729006	1.71817326902	0.0174078664087	-0.163335203369	1.02115517784	0.207680258392	-0.855311395297	1.06997272884	-0.604615218249	2.54721172149	12.2519408498	51.2264399617	15.7199879855
20	5.77803502386	-4.73292341189	5.24835608463	3.88697196821	-4.37424282892	9.01880563216	-0.350337184371	-2.70242225313	-2.00670214072	-0.0581100252202	1.55479983161	-0.323741866807	0.200955916467	-2.08366340545	-0.702112050805	0.797882366455	0.07992970059	-0.168711561825	1.44416116441	0.0953807775552	1.89904791817	-2.89926563398	59.2336326988	12.9193834978
21	2.72429260104	-1.3221916667	3.67174106187	0.719177863388	-1.50826509956	5.94505425038	-0.190671253158	0.563650710346	0.633925216989	0.393569375862	-0.0768413261506	-0.349664177728	0.502236227109	1.66694374991	0.258700449042	0.0046928478523	0.528417977009	-0.400112179934	0.928519194281	-0.432043241433	3.62255090698	13.2688032342	63.3642158528	9.67754576941
22	3.48504148036	3.5527021408	0.867123353038	3.67173766504	1.47890525323	2.37185477484	1.10194839921	-1.15975205155	0.44639093689	-1.01161359369	-0.876163402813	-0.32369006414	-1.04460775416	1.46060078253	-0.274529160286	1.43359155268	-0.162637181592	-0.232807397842	1.39059457957	-0.0191159165978	2.56174665488	8.70103494829	62.1679938969	5.17306189699
23	2.00132271212	6.21088510759	0.495000235085	6.71998546722	-1.57585311169	8.51513223276	-1.26673079665	0.962168523579	-4.38413073438	0.0843512955972	1.00094821826	1.10990450745	1.65681789826	1.41743143642	0.0513667395314	1.27598972227	0.286550621224	-0.436455178093	0.847298710398	-0.418053937942	2.78626493973	7.63478984639	53.3980147024	9.39288644391
24	0.446432439388	-0.495223545714	1.03134262397	1.20125371422	-2.71323488585	6.66646035292	-0.14048722449	0.089329293343	-0.736804616769	0.34658253475	0.904363107892	-2.41042442988	-1.01052404099	0.776913898433	-0.367700641935	1.03068697161	0.0735116539725	-0.641620664175	1.39297972921	-0.48319709958	2.22698226214	11.9240844768	61.8367860621	12.2426224971
25	3.93374194837	-3.4449950186	2.78639836779	3.94054218147	-4.71075092174	7.25354316964	0.732733527175	0.939863600488	1.22858826903	0.216044263429	-2.45391817422	-0.239018135317	-0.923954344744	0.807537769738	0.97423918241	1.52584131558	0.322364759177	-0.214780343175	0.688570980794	-0.0537831898214	1.74673734182	-2.74339282274	69.5803512744	10.0072650345
26	3.47804538457	0.310058999829	2.26063586964	4.89766356347	-0.405456991113	4.70635779287	0.0329152069921	-0.191588982069	0.416426864973	0.516992682101	0.711198864071	-0.465017311828	0.566437813172	1.69581320915	0.294871271557	0.0510229226643	0.771092468289	-0.888851922729	2.1178215084	-1.25128445836	2.78431240909	15.5818365287	58.7066939179	18.6509606895
27	7.33298773774	6.27741736673	1.94687902351	5.78852928938	0.410464845443	4.86268523715	-0.947059952371	1.28238521815	-2.0748955823	0.0128134781906	1.0968170189	-0.626195625954	2.28909077501	1.62821547677	2.23598046513	1.08662887689	0.251305229829	0.0809287559595	0.768072170001	1.03705406603	1.57229565561	67.7671350785	10.6605936836	-36.6300987646
28	6.60573882715	0.474583201482	-3.07275156119	7.29414450143	4.33840527113	4.43193839067	-0.48689893121	2.59752003086	1.0348929654	-0.653056652184	0.248281301707	-0.128103496253	-0.312059045587	-0.631533036518	0.230014346738	1.14970234275	0.534566614683	0.440287728986	1.71503978393	0.901841140824	1.7644426268	75.2624252636	16.4249018773	-42.7658933695
29	6.22283412112	-1.8333381722	-1.87880444091	3.00546968765	2.50811325662	5.50210740526	1.11958070892	0.0489961657577	-0.527031558678	1.08172098383	0.598603521661	1.06864410911	-0.648642402024	0.839941109653	-0.365929834974	0.958439808816	0.330244760895	0.0125633459498	0.98746616665	0.775833421365	2.45171662512	69.5665171939	21.3640632952	-32.2758467259
30	3.98393472187	-1.93276788247	-4.95136656509	3.55697109823	3.64379570136	6.76005347213	-0.260500992488	2.0072750454	-0.232565594861	-0.177550885044	-0.564398036105	0.695743481271	-0.495720556328	-2.4314941844	0.0208713799382	1.01050377993	0.566824692913	0.498534863709	2.2608413093	0.598237702455	1.02824263262	66.7257013121	19.4278674705	-41.853325227
31	2.60996992898	1.94221322234	-0.605534154376	6.88783405144	5.25367021946	6.20868525489	0.696331637148	-0.643808396883	-1.17592278209	-0.791402634327	-1.07553927746	-2.67973052687	0.157211589183	3.05995510407	0.433943529145	1.25681591533	0.302420284308	0.191134707876	2.24554529504	1.16343534094	2.25716542325	83.4587579522	18.5699720249	-37.2118510305
32	1.85896643378	-1.30517529561	-1.01969407255	3.75738525604	3.83310895897	4.13031638201	0.685317846487	0.0991012017646	1.09441864556	2.21491077401	0.375031597911	-1.14448124868	0.969127230732	-1.01320351518	-0.470020791049	1.49032406353	0.239661080846	0.135800360535	1.15036599142	0.815994531423	1.44294865916	64.6614547184	19.6238418177	-26.3327753851
33	5.1860600389	-4.50650860829	-1.34021986103	6.68244549468	4.84831210774	5.27802839036	0.701469051204	-0.378880785992	2.01039983758	-1.5446360806	0.3123072317	-0.822680736472	2.09628154611	2.37285447466	-0.799557994543	1.26344136427	0.484127585337	0.577756255482	2.0443329716	1.03382059995	2.20116034415	79.8694930028	11.7853115339	-35.2487288461
34	5.42760571529	3.62526125971	0.19831983872	5.27564201117	3.33485329425	4.27958595011	0.237433965043	-0.262359892502	1.86572336445	1.63341394555	-1.42342048076	-0.356055598293	-1.31913149083	1.25029387897	0.889074201744	1.48838050218	-0.365048796364	0.556974963486	2.4856981548	-0.10078578816	1.5566680865	-56.5289530075	87.0766262464	19.0935431598
35	6.88142523901	4.62278689597	-7.17227816636	3.34480800372	-5.24442050548	8.25923033375	1.80732449118	4.16597365721	5.10410578421	-1.85331851774	-0.670457248717	-2.88121929368	-1.19460772331	0.890881775763	-0.516827303445	1.6118216846	0.201587500477	1.29500053363	1.76545198313	-0.156526100633	3.41704128952	-69.3832497688	95.1727096626	12.2878058873
36	3.22447353968	0.640650373375	-5.08232509605	1.92431417468	-2.23056259577	8.75566873043	-0.511104156392	4.60918173823	-1.25473000269	-1.71697218104	-0.397402600085	-3.44854703276	0.526894632827	0.625781653669	0.791158542276	1.69091247146	0.137440265843	0.783034847899	1.49933022947	-0.301456564262	2.46143451115	-62.4703246383	90.1132326192	11.8716765373
37	6.60336235901	-3.31860074541	-1.60930790743	3.97172695245	-2.86637523756	6.31812164001	1.15968635639	-2.45545827792	3.16904810054	-0.530757224354	0.556755940455	-0.349169971202	-1.85533836025	-1.55780654489	-2.03626413908	1.50888144577	0.0742651999103	0.765470517294	1.43333786267	0.0845935533454	2.21759700578	-49.9562573663	80.3706776575	10.0914227126
38	4.49788765009	3.3442157564	-0.538594970541	2.65671013957	0.478856392277	6.87573432066	2.58290256248	0.742756553201	-5.18543759653	0.776805785213	-2.30030206344	-0.237256752547	1.88256392724	-3.15755542821	0.0829443056702	1.18943493577	-0.271804453227	0.753151517942	2.38171343	-0.203093225875	3.63727710471	-71.4585964831	77.5547648774	12.4846494796
39	3.6968097239	3.68414590203	-4.0008911425	6.05231612388	-5.11169246219	5.07171797721	1.65145060211	0.767130530262	0.601168891917	-0.687224365426	0.866217727999	-0.758182246049	-3.14998572484	-0.725807374964	-2.40922614329	1.50612903949	-0.0980507442969	0.865152669584	1.29918680205	0.104079166329	2.48958020901	-58.4182352866	82.4363998574	4.5777699378
40	6.05511173466	-4.09770127063	0.908327962041	3.69647206303	0.0424534289878	2.58365165113	-0.191924096888	-0.652088732318	1.24975427874	-3.60003694793	0.471230328884	-0.332928454473	1.07876022631	0.694744329513	-0.547938371201	1.50358699861	0.155123316532	0.122472885789	1.35062954934	0.44088822789	2.05563647603	-64.693501724	88.5502990285	7.32161620748
41	7.5685005301	3.11306861917	-3.28176026725	9.53996204291	0.692981328052	1.93402412226	-1.22982999349	0.355558685873	-3.50424483704	-1.78543823864	0.693952138961	-1.76917154642	1.14121148569	0.564717995681	0.480139191421	1.69433789988	-0.119681828326	0.939797487057	2.33292776605	-0.460294326655	2.33982287256	-77.5743593651	86.556105865	15.0243419134
42	7.97763458825	-0.188694193509	-2.55527782447	2.83991267283	2.86483143816	3.64609419068	4.30960076377	1.54733779702	0.377206574777	0.751501922193	-3.42282080174	0.972631456289	1.03226160739	-0.879524929516	-0.605673073771	2.21298898801	0.198907438544	0.442208180476	1.24393225961	0.199001920703	2.43771469478	-58.2547805	78.2911845013	13.5617199434
43	4.57039666963	2.50012701522	5.72154924118	1.97550771629	1.7531993964	2.02152804575	0.814048266143	1.06241465621	-1.87430635239	0.86530666254	-0.785593554314	0.976562980181	-1.28511823426	0.57627141056	-0.388055616583	1.50552651538	0.355434723518	0.580279818729	1.27668599879	0.200259156119	2.01975344791	-57.2435658799	75.6241234421	15.0262754572
44	4.14054753759	-2.24783463515	1.09666614716	5.06410661363	4.46156735849	6.93150435111	-0.309832698694	-0.507888655347	-0.0702310890441	0.839742622605	0.686457142311	-0.144788573668	-0.0199004346574	0.117956876941	-0.0749846246451	1.49029262266	1.46302397584	0.348825207705	3.10315079579	-1.36201874544	2.64184771747	-73.1389372724	89.4613276451	18.5861795461
45	3.1482669924	-1.81822774457	-1.94564398344	1.76821131527	1.47753662284	1.3818726724	1.17946014302	-2.38448864581	-2.1965211473	1.28419307747	1.2037477077	2.17993617558	0.997358910459	-0.243932228878	-2.39805881456	2.4140014965	-0.492197385699	0.202515416279	2.95446910003	0.988164914144	2.28854302998	-50.3414185202	99.798269243	28.6034421036
46	9.70024820943	-7.50281576333	-3.86619562118	5.96737127678	3.41786626215	2.68103511138	0.27868457685	-2.72538301867	-1.30854706439	-0.350890298706	1.81035579466	-0.260747900519	1.0475750505	4.06596577398	-1.53180848033	2.59716098303	0.03289057987	0.424808447628	3.78893634466	1.71956266522	2.91165040101	-46.772181945	99.9130421813	28.0811558728
47	5.08526428953	2.22752199638	-3.08460128461	6.48201827346	-2.14731128686	2.02067237942	-0.40543216987	-2.746706422	-0.996978186829	0.604812491492	0.128692808576	1.09565023478	-0.318366446653	1.7997262797	0.263625278297	2.35196079342	-0.0438376075469	0.162282874256	3.02259112488	0.68451962819	1.75615481024	-45.5407640436	107.559255795	31.6060863464
48	5.08659341714	-2.64629306329	-2.6326507253	1.86096190439	-0.255914287744	6.21200448702	2.42946573248	-1.21902486753	1.20997472441	2.01137963187	2.7994973022	3.88719714977	-1.03661630683	-1.13205587352	-5.18367426379	2.37108416834	-0.586978968107	0.20286142436	2.8211824018	0.399807031676	2.89561888841	-51.0254271205	110.81741771	27.2987011115
49	4.49764781787	5.51642193438	4.17275720394	7.12932199777	5.67100975505	4.38082325558	1.25600011872	-0.711253337924	1.07654478645	1.5050802247	-1.46726753441	0.647674940281	1.03765962364	-1.98922158054	0.328028476976	1.58385341536	0.276151433113	-0.417045330117	1.69541723476	-0.611667029503	1.40895420433	-7.21570472939	79.669624139	27.7924334663
50	4.24834373121	-4.38053006607	-5.35415828912	4.66960294966	5.5290536475	6.68058086791	0.843006759083	1.90345556657	0.72664179293	-1.4168454447	-0.0979156472084	-0.458994636521	-2.2831667038	-3.79868983443	-0.561935828228	1.20496062928	0.106297083896	-0.147005592568	1.49615249529	-0.327437685663	1.27966268916	-3.8848660194	86.9794489518	20.8734199406
51	9.4905438266	1.49547450202	6.69562542699	8.14641165459	0.0857786480217	4.81268339806	0.474943710507	1.490149097	-1.00373295506	-2.30359771907	0.885778586143	-0.203399882109	-1.07757920059	0.394037902318	-1.44498138906	1.06918456549	0.296677975706	0.0835643114029	1.33787262146	-0.264970833458	1.13288266251	-7.17848263561	82.8406262789	13.4381435493
52	6.7319753222	4.43864157451	2.95253963614	5.5031681012	-1.71392504394	6.64200742535	0.394525582634	0.857844639197	2.34528803058	0.965919128902	-1.76367278355	-3.73737923602	0.592091532931	3.10886306858	0.982854209319	1.34551831781	0.304586929736	-0.643767778986	1.21446537947	-0.102058074637	2.98253837366	3.43383317826	84.2611563879	34.2865810108
53	4.16696421852	-2.91154382668	-2.70452038865	5.02716679491	-2.44361757199	8.00660338457	1.5139348172	-0.902226774349	1.03758625452	-0.00180327889229	1.81519907664	-0.430259971717	0.557188293867	0.624800273703	-1.62691749651	0.674602728651	0.157736760165	-0.477513470533	1.1823936661	-0.514614880263	2.41033028864	2.5943314393	81.9145644659	26.5606924883
54	6.80344110143	4.05098280003	2.17364282459	2.00012214933	0.0706993364992	0.827602268583	-0.559108511775	3.13340476504	-1.61744008665	-3.79471387251	0.569115012834	-0.999637287671	-0.691277631827	0.0903011648067	0.102319044903	3.78089318461	-0.927012171749	0.306120785106	1.60296541982	-1.2292553886	1.30768398238	-8.81123449204	76.3249744479	11.0470617393

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 7 through 160 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 161 through 221 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 13 through 159 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 160 through 217 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 12 through 160 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 161 through 221 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 15 through 159 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 160 through 221 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 15 through 159 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 160 through 221 )
11	X-RAY DIFFRACTION	11	chain 'F' and (resid 15 through 159 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 160 through 221 )
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 2 through 12 )
14	X-RAY DIFFRACTION	14	chain 'G' and (resid 13 through 33 )
15	X-RAY DIFFRACTION	15	chain 'G' and (resid 34 through 47 )
16	X-RAY DIFFRACTION	16	chain 'G' and (resid 48 through 75 )
17	X-RAY DIFFRACTION	17	chain 'G' and (resid 76 through 92 )
18	X-RAY DIFFRACTION	18	chain 'H' and (resid 2 through 7 )
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 8 through 18 )
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 19 through 32 )
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 33 through 40 )
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 41 through 53 )
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 54 through 62 )
24	X-RAY DIFFRACTION	24	chain 'H' and (resid 63 through 76 )
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 77 through 86 )
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 87 through 92 )
27	X-RAY DIFFRACTION	27	chain 'I' and (resid 3 through 12 )
28	X-RAY DIFFRACTION	28	chain 'I' and (resid 13 through 22 )
29	X-RAY DIFFRACTION	29	chain 'I' and (resid 23 through 53 )
30	X-RAY DIFFRACTION	30	chain 'I' and (resid 54 through 58 )
31	X-RAY DIFFRACTION	31	chain 'I' and (resid 59 through 69 )
32	X-RAY DIFFRACTION	32	chain 'I' and (resid 70 through 86 )
33	X-RAY DIFFRACTION	33	chain 'I' and (resid 87 through 92 )
34	X-RAY DIFFRACTION	34	chain 'J' and (resid 4 through 9 )
35	X-RAY DIFFRACTION	35	chain 'J' and (resid 10 through 15 )
36	X-RAY DIFFRACTION	36	chain 'J' and (resid 16 through 24 )
37	X-RAY DIFFRACTION	37	chain 'J' and (resid 25 through 32 )
38	X-RAY DIFFRACTION	38	chain 'J' and (resid 33 through 47 )
39	X-RAY DIFFRACTION	39	chain 'J' and (resid 48 through 53 )
40	X-RAY DIFFRACTION	40	chain 'J' and (resid 54 through 62 )
41	X-RAY DIFFRACTION	41	chain 'J' and (resid 63 through 68 )
42	X-RAY DIFFRACTION	42	chain 'J' and (resid 69 through 77 )
43	X-RAY DIFFRACTION	43	chain 'J' and (resid 78 through 88 )
44	X-RAY DIFFRACTION	44	chain 'J' and (resid 89 through 92 )
45	X-RAY DIFFRACTION	45	chain 'K' and (resid 3 through 16 )
46	X-RAY DIFFRACTION	46	chain 'K' and (resid 17 through 23 )
47	X-RAY DIFFRACTION	47	chain 'K' and (resid 24 through 69 )
48	X-RAY DIFFRACTION	48	chain 'K' and (resid 70 through 92 )
49	X-RAY DIFFRACTION	49	chain 'L' and (resid 3 through 33 )
50	X-RAY DIFFRACTION	50	chain 'L' and (resid 34 through 57 )
51	X-RAY DIFFRACTION	51	chain 'L' and (resid 58 through 71 )
52	X-RAY DIFFRACTION	52	chain 'L' and (resid 72 through 79 )
53	X-RAY DIFFRACTION	53	chain 'L' and (resid 80 through 89 )
54	X-RAY DIFFRACTION	54	chain 'L' and (resid 90 through 92 )

+
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://pdbjlc1.pdbj.org/emnavi/covid19.php

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

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

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

すべてのお知らせ

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る

-
ムービー

-
構造ビューア

+
ビューアのログ

-
このページ

-
このウェブサイト

-
オプション

+
データを開く

-
基本情報

-
構造の表示

-
ダウンロードとリンク

-
ダウンロード

-
検証レポート

-
関連構造データ

-
リンク

-
集合体

-
要素

-
実験情報

-
実験

-
試料調製

-
データ収集

-
解析

+
万見について

-
お知らせ

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

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)

-ムービー

-構造ビューア

+ビューアのログ

-このページ

-このウェブサイト

-オプション

+データを開く

-基本情報

-構造の表示

-ダウンロードとリンク

-ダウンロード

-検証レポート

-関連構造データ

-リンク

-集合体

-要素

-実験情報

-実験

-試料調製

-データ収集

-解析

+万見について

-お知らせ

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

-2020年8月12日: 新型コロナ情報

+2020年3月5日: 新型コロナウイルスの構造データ

+2019年1月31日: EMDBのIDの桁数の変更

+2017年7月12日: PDB大規模アップデート

-万見 (Yorodumi)

-
ムービー

-
構造ビューア

+
ビューアのログ

-
このページ

-
このウェブサイト

-
オプション

+
データを開く

-
基本情報

-
構造の表示

-
ダウンロードとリンク

-
ダウンロード

-
検証レポート

-
関連構造データ

-
リンク

-
集合体

-
要素

-
実験情報

-
実験

-
試料調製

-
データ収集

-
解析

+
万見について

-
お知らせ

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

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)