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- PDB-8pnm: Structure of human KCTD15 BTB domain mutant G88D crystal form 2 -

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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: 8pnm

タイトル

Structure of human KCTD15 BTB domain mutant G88D crystal form 2

要素

BTB/POZ domain-containing protein KCTD15

キーワード

GENE REGULATION / Oligomerisation / BTB domain

機能・相同性

機能・相同性情報

Negative regulation of activity of TFAP2 (AP-2) family transcription factors / protein homooligomerization / identical protein binding / nucleus
類似検索 - 分子機能

生物種

Homo sapiens (ヒト)

手法

X線回折 /

シンクロトロン /

分子置換 / 解像度: 1.94 Å

データ登録者

Cruz Walma, D.A. / Cros, J. / Bradshaw, W. / Richardson, W. / Chen, Z. / Chalk, R. / Wilkie, A. / Bullock, A.N.

資金援助

米国, 1件

引用

ジャーナル: J Med Genet / 年: 2024
タイトル: BTB domain mutations perturbing KCTD15 oligomerisation cause a distinctive frontonasal dysplasia syndrome.
著者: Miller, K.A. / Cruz Walma, D.A. / Pinkas, D.M. / Tooze, R.S. / Bufton, J.C. / Richardson, W. / Manning, C.E. / Hunt, A.E. / Cros, J. / Hartill, V. / Parker, M.J. / McGowan, S.J. / Twigg, S.R. ...

履歴

登録	2023年6月30日	登録サイト: PDBE / 処理サイト: PDBE
改定 1.0	2024年3月20日	Provider: repository / タイプ: Initial release
改定 1.1	2024年5月1日	Group: Database references / カテゴリ: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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	8pnm.cif.gz	590.3 KB	表示	PDBx/mmCIF形式
PDB形式	pdb8pnm.ent.gz	400.4 KB	表示	PDB形式
PDBx/mmJSON形式	8pnm.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	8pnm_validation.pdf.gz	517.7 KB	表示	wwPDB検証レポート
文書・詳細版	8pnm_full_validation.pdf.gz	525.7 KB	表示
XML形式データ	8pnm_validation.xml.gz	41 KB	表示
CIF形式データ	8pnm_validation.cif.gz	60.3 KB	表示
アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/pn/8pnm ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pnm	HTTPS FTP

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関連構造データ

関連構造データ	8pnrC C: 同じ文献を引用 (文献)
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	#110 - 2009年2月オーキシンとTIR1ユビキチンリガーゼ (Auxin and TIR1 Ubiquitin Ligase) 類似性 (1) #240 - 2019年12月低酸素誘導因子 (Hypoxia-Inducible Factors) 類似性 (1) #60 - 2004年12月ユビキチン (Ubiquitin) 類似性 (1) #218 - 2018年2月 EPSP合成酵素と除草剤 (EPSP Synthase and Weedkillers) 類似性 (1)

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集合体

登録構造単位

C: BTB/POZ domain-containing protein KCTD15

A: BTB/POZ domain-containing protein KCTD15

G: BTB/POZ domain-containing protein KCTD15

E: BTB/POZ domain-containing protein KCTD15

J: BTB/POZ domain-containing protein KCTD15

D: BTB/POZ domain-containing protein KCTD15

B: BTB/POZ domain-containing protein KCTD15

I: BTB/POZ domain-containing protein KCTD15

H: BTB/POZ domain-containing protein KCTD15

K: BTB/POZ domain-containing protein KCTD15

F: BTB/POZ domain-containing protein KCTD15

L: BTB/POZ domain-containing protein KCTD15

167 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)

C: BTB/POZ domain-containing protein KCTD15

A: BTB/POZ domain-containing protein KCTD15

J: BTB/POZ domain-containing protein KCTD15

D: BTB/POZ domain-containing protein KCTD15

I: BTB/POZ domain-containing protein KCTD15

F: BTB/POZ domain-containing protein KCTD15

登録者が定義した集合体
根拠: mass spectrometry
83.5 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: BTB/POZ domain-containing protein KCTD15

E: BTB/POZ domain-containing protein KCTD15

B: BTB/POZ domain-containing protein KCTD15

H: BTB/POZ domain-containing protein KCTD15

K: BTB/POZ domain-containing protein KCTD15

L: BTB/POZ domain-containing protein KCTD15

登録者が定義した集合体
83.5 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)	71.262, 72.091, 94.413
Angle α, β, γ (deg.)	89.630, 77.080, 60.500
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

非結晶学的対称性 (NCS)

NCSドメイン:

ID	Ens-ID	詳細
d_1	ens_1	(chain "A" and (resid 7 through 16 or (resid 17...
d_2	ens_1	(chain "B" and (resid 7 through 16 or (resid 17...
d_3	ens_1	(chain "C" and (resid 7 through 16 or (resid 17...
d_4	ens_1	(chain "D" and (resid 7 through 16 or (resid 17...
d_5	ens_1	(chain "E" and (resid 7 through 16 or (resid 17...
d_6	ens_1	(chain "F" and (resid 7 through 16 or (resid 17...
d_7	ens_1	(chain "G" and (resid 7 through 16 or (resid 17...
d_8	ens_1	(chain "H" and (resid 7 through 16 or (resid 17...
d_9	ens_1	(chain "I" and (resid 7 through 16 or (resid 17...
d_10	ens_1	(chain "J" and (resid 7 through 16 or (resid 17...
d_11	ens_1	(chain "K" and (resid 7 through 16 or (resid 17...
d_12	ens_1	(chain "L" and (resid 7 through 29 or (resid 30...

NCSドメイン領域:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	ALA	ALA	PHE	PHE	A	B	7 - 37	7 - 37
d_1	2	TYR	TYR	ARG	ARG	A	B	52 - 56	52 - 56
d_1	3	GLY	GLY	PHE	PHE	A	B	58 - 61	58 - 61
d_1	4	TYR	TYR	SER	SER	A	B	63 - 83	63 - 83
d_1	5	LEU	LEU	TYR	TYR	A	B	85 - 86	85 - 86
d_1	6	GLU	GLU	GLU	GLU	A	B	88 - 102	88 - 102
d_2	1	ALA	ALA	PHE	PHE	B	G	7 - 37	7 - 37
d_2	2	TYR	TYR	ARG	ARG	B	G	52 - 56	52 - 56
d_2	3	GLY	GLY	PHE	PHE	B	G	58 - 61	58 - 61
d_2	4	TYR	TYR	SER	SER	B	G	63 - 83	63 - 83
d_2	5	LEU	LEU	TYR	TYR	B	G	85 - 86	85 - 86
d_2	6	GLU	GLU	GLU	GLU	B	G	88 - 102	88 - 102
d_3	1	ALA	ALA	PHE	PHE	C	A	7 - 37	7 - 37
d_3	2	TYR	TYR	ARG	ARG	C	A	52 - 56	52 - 56
d_3	3	GLY	GLY	PHE	PHE	C	A	58 - 61	58 - 61
d_3	4	TYR	TYR	SER	SER	C	A	63 - 83	63 - 83
d_3	5	LEU	LEU	TYR	TYR	C	A	85 - 86	85 - 86
d_3	6	GLU	GLU	GLU	GLU	C	A	88 - 102	88 - 102
d_4	1	ALA	ALA	PHE	PHE	D	F	7 - 37	7 - 37
d_4	2	TYR	TYR	ARG	ARG	D	F	52 - 56	52 - 56
d_4	3	GLY	GLY	PHE	PHE	D	F	58 - 61	58 - 61
d_4	4	TYR	TYR	SER	SER	D	F	63 - 83	63 - 83
d_4	5	LEU	LEU	TYR	TYR	D	F	85 - 86	85 - 86
d_4	6	GLU	GLU	GLU	GLU	D	F	88 - 102	88 - 102
d_5	1	ALA	ALA	PHE	PHE	E	D	7 - 37	7 - 37
d_5	2	TYR	TYR	ARG	ARG	E	D	52 - 56	52 - 56
d_5	3	GLY	GLY	PHE	PHE	E	D	58 - 61	58 - 61
d_5	4	TYR	TYR	SER	SER	E	D	63 - 83	63 - 83
d_5	5	LEU	LEU	TYR	TYR	E	D	85 - 86	85 - 86
d_5	6	GLU	GLU	GLU	GLU	E	D	88 - 102	88 - 102
d_6	1	ALA	ALA	PHE	PHE	F	K	7 - 37	7 - 37
d_6	2	TYR	TYR	ARG	ARG	F	K	52 - 56	52 - 56
d_6	3	GLY	GLY	PHE	PHE	F	K	58 - 61	58 - 61
d_6	4	TYR	TYR	SER	SER	F	K	63 - 83	63 - 83
d_6	5	LEU	LEU	TYR	TYR	F	K	85 - 86	85 - 86
d_6	6	GLU	GLU	GLU	GLU	F	K	88 - 102	88 - 102
d_7	1	ALA	ALA	PHE	PHE	G	C	7 - 37	7 - 37
d_7	2	TYR	TYR	ARG	ARG	G	C	52 - 56	52 - 56
d_7	3	GLY	GLY	PHE	PHE	G	C	58 - 61	58 - 61
d_7	4	TYR	TYR	SER	SER	G	C	63 - 83	63 - 83
d_7	5	LEU	LEU	TYR	TYR	G	C	85 - 86	85 - 86
d_7	6	GLU	GLU	GLU	GLU	G	C	88 - 102	88 - 102
d_8	1	ALA	ALA	PHE	PHE	H	I	7 - 37	7 - 37
d_8	2	TYR	TYR	ARG	ARG	H	I	52 - 56	52 - 56
d_8	3	GLY	GLY	PHE	PHE	H	I	58 - 61	58 - 61
d_8	4	TYR	TYR	SER	SER	H	I	63 - 83	63 - 83
d_8	5	LEU	LEU	TYR	TYR	H	I	85 - 86	85 - 86
d_8	6	GLU	GLU	GLU	GLU	H	I	88 - 102	88 - 102
d_9	1	ALA	ALA	PHE	PHE	I	H	7 - 37	7 - 37
d_9	2	TYR	TYR	ARG	ARG	I	H	52 - 56	52 - 56
d_9	3	GLY	GLY	PHE	PHE	I	H	58 - 61	58 - 61
d_9	4	TYR	TYR	SER	SER	I	H	63 - 83	63 - 83
d_9	5	LEU	LEU	TYR	TYR	I	H	85 - 86	85 - 86
d_9	6	GLU	GLU	GLU	GLU	I	H	88 - 102	88 - 102
d_10	1	ALA	ALA	PHE	PHE	J	E	7 - 37	7 - 37
d_10	2	TYR	TYR	ARG	ARG	J	E	52 - 56	52 - 56
d_10	3	GLY	GLY	PHE	PHE	J	E	58 - 61	58 - 61
d_10	4	TYR	TYR	SER	SER	J	E	63 - 83	63 - 83
d_10	5	LEU	LEU	TYR	TYR	J	E	85 - 86	85 - 86
d_10	6	GLU	GLU	GLU	GLU	J	E	88 - 102	88 - 102
d_11	1	ALA	ALA	PHE	PHE	K	J	7 - 37	7 - 37
d_11	2	TYR	TYR	ARG	ARG	K	J	52 - 56	52 - 56
d_11	3	GLY	GLY	PHE	PHE	K	J	58 - 61	58 - 61
d_11	4	TYR	TYR	SER	SER	K	J	63 - 83	63 - 83
d_11	5	LEU	LEU	TYR	TYR	K	J	85 - 86	85 - 86
d_11	6	GLU	GLU	GLU	GLU	K	J	88 - 102	88 - 102
d_12	1	ALA	ALA	PHE	PHE	L	L	7 - 37	7 - 37
d_12	2	TYR	TYR	ARG	ARG	L	L	52 - 56	52 - 56
d_12	3	GLY	GLY	PHE	PHE	L	L	58 - 61	58 - 61
d_12	4	TYR	TYR	SER	SER	L	L	63 - 83	63 - 83
d_12	5	LEU	LEU	TYR	TYR	L	L	85 - 86	85 - 86
d_12	6	GLU	GLU	GLU	GLU	L	L	88 - 102	88 - 102

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要素

#1: タンパク質	BTB/POZ domain-containing protein KCTD15 / Potassium channel tetramerization domain-containing protein 15 分子量: 13914.711 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KCTD15 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q96SI1
#2: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 246 / 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: 2.45 Å³/Da / 溶媒含有率: 49.71 %
結晶化	温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 12.5% PEG3350, 0.2M Potassium thiocyanate

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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: Diamond / ビームライン: I03 / 波長: 0.976254 Å
検出器	タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年9月25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: 0.976254 Å / 相対比: 1
反射	解像度: 1.94→91.33 Å / Num. obs: 75791 / % possible obs: 92.5 % / 冗長度: 3.6 % / B_iso Wilson estimate: 44.15 Å² / CC_1/2: 0.999 / Net I/σ(I): 14.2
反射シェル	解像度: 1.96→2.12 Å / Num. unique obs: 3791 / CC_1/2: 0.594

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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
autoPROC		データ削減
STARANISO		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 / 解像度: 1.94→61.31 Å / SU ML: 0.2993 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 41.948
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	0.2732	3779	4.99 %
R_work	0.2361	71985	-
obs	0.238	75764	65.14 %

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: 50.34 Å²

精密化ステップ

サイクル: LAST / 解像度: 1.94→61.31 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	9372	0	0	246	9618

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0053	9618
X-RAY DIFFRACTION	f_angle_d	1.0898	13126
X-RAY DIFFRACTION	f_chiral_restr	0.1401	1475
X-RAY DIFFRACTION	f_plane_restr	0.0129	1682
X-RAY DIFFRACTION	f_dihedral_angle_d	6.7429	1332

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	タイプ	Rms dev position (Å)
ens_1	d_2	B	A	X-RAY DIFFRACTION	Torsion NCS	0.471186607408
ens_1	d_3	B	A	X-RAY DIFFRACTION	Torsion NCS	0.641948420155
ens_1	d_4	B	A	X-RAY DIFFRACTION	Torsion NCS	0.573454908337
ens_1	d_5	B	A	X-RAY DIFFRACTION	Torsion NCS	0.493570795265
ens_1	d_6	B	A	X-RAY DIFFRACTION	Torsion NCS	0.713326650839
ens_1	d_7	B	A	X-RAY DIFFRACTION	Torsion NCS	0.53854339964
ens_1	d_8	B	A	X-RAY DIFFRACTION	Torsion NCS	0.564439389567
ens_1	d_9	B	A	X-RAY DIFFRACTION	Torsion NCS	0.505325855411
ens_1	d_10	B	A	X-RAY DIFFRACTION	Torsion NCS	0.657520301405
ens_1	d_11	B	A	X-RAY DIFFRACTION	Torsion NCS	0.770591639411
ens_1	d_12	B	A	X-RAY DIFFRACTION	Torsion NCS	0.640976213641

LS精密化シェル

解像度 (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.94-1.97		0	0.3431	32	X-RAY DIFFRACTION	0.75
1.97-2	0.6511	8	0.3605	122	X-RAY DIFFRACTION	3.04
2-2.02	0.4125	10	0.3002	337	X-RAY DIFFRACTION	8.16
2.02-2.05	0.3467	25	0.3242	628	X-RAY DIFFRACTION	15.3
2.05-2.08	0.4375	53	0.3268	960	X-RAY DIFFRACTION	23.61
2.08-2.11	0.3668	69	0.3315	1277	X-RAY DIFFRACTION	31.1
2.11-2.15	0.3488	83	0.3029	1497	X-RAY DIFFRACTION	36.8
2.15-2.19	0.3206	87	0.2923	1785	X-RAY DIFFRACTION	43.48
2.19-2.23	0.3266	92	0.2798	1981	X-RAY DIFFRACTION	48.11
2.23-2.27	0.3423	132	0.2958	2138	X-RAY DIFFRACTION	52.85
2.27-2.32	0.338	132	0.2858	2343	X-RAY DIFFRACTION	57.49
2.32-2.37	0.3528	124	0.2913	2511	X-RAY DIFFRACTION	61.14
2.37-2.42	0.3296	163	0.2822	2735	X-RAY DIFFRACTION	66.62
2.42-2.48	0.3016	155	0.2768	2914	X-RAY DIFFRACTION	71.76
2.48-2.55	0.3405	171	0.2883	3228	X-RAY DIFFRACTION	78.7
2.55-2.62	0.3733	179	0.2933	3475	X-RAY DIFFRACTION	84.9
2.62-2.71	0.3275	196	0.2936	3734	X-RAY DIFFRACTION	91.33
2.71-2.8	0.34	186	0.2994	3973	X-RAY DIFFRACTION	97.4
2.8-2.92	0.3003	251	0.2905	4020	X-RAY DIFFRACTION	98.32
2.92-3.05	0.3364	180	0.2843	4048	X-RAY DIFFRACTION	98.44
3.05-3.21	0.3125	218	0.2796	4020	X-RAY DIFFRACTION	98.33
3.21-3.41	0.2762	191	0.247	4036	X-RAY DIFFRACTION	98.03
3.41-3.67	0.2735	231	0.2281	3980	X-RAY DIFFRACTION	98.02
3.67-4.04	0.2602	202	0.195	4077	X-RAY DIFFRACTION	98.89
4.04-4.63	0.2107	214	0.1799	4038	X-RAY DIFFRACTION	99.07
4.63-5.83	0.2321	219	0.2026	4062	X-RAY DIFFRACTION	99.21
5.83-61.31	0.2403	208	0.2164	4034	X-RAY DIFFRACTION	98.29

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	0.000339168473141	-0.00154250068678	0.00164322478809	0.00855855274733	0.000818738902725	0.000395383781014	-0.0328669325169	-0.00242661989344	-0.0104474636993	-0.0045334788419	0.0195578535425	-0.0207080196985	-0.0435554130479	-0.0350618906453	-1.86284141818E-5	1.02193384487	-0.0378657942731	-0.0756760183008	0.942840861954	-0.0968659811539	0.375615309693	10.6719920791	21.3910337034	-27.5863378046
2	0.00997549248929	-0.00128083547439	-0.00530415898145	-0.00131404041787	0.00573745459985	0.00380458721546	0.0694476546365	0.0651553322298	0.0391250736146	-0.0644244355245	0.0716415747674	-0.125588122506	-0.125916112553	-0.0445640974419	-6.55420142813E-6	0.384018033135	0.0107730229945	-0.00830151735822	0.299889676926	0.0398192920439	0.334904399548	12.8179292236	22.6071333476	-40.3164428596
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37	-0.00746169868099	-0.0057050814096	-0.00581478357362	-0.00999221154125	0.0223174824214	0.000928589436734	0.111768365939	0.186300128329	-0.0232877340465	-0.231825132714	0.261004648542	-0.0907830657127	-0.0166275187441	-0.00426048279142	-8.44424799594E-7	1.05276265082	0.142176865026	0.592037795718	0.317058708989	-0.347998987129	-0.437303344432	20.6165095221	35.3472796149	-61.9615198867
38	0.0202849582584	0.00948299138976	-0.0229455267016	0.0138703444137	-0.00323347719575	0.0196404396388	-0.151713658525	-0.295306962145	0.374232560854	-0.118830743869	0.173837751047	-0.0418552519423	0.179015596904	0.106771084085	1.11271972646E-6	0.271633496329	0.0955593579883	-0.0828927657624	0.323242714083	-0.0467292207575	0.237626574086	-3.89268622923	60.0264084899	-34.7646909085
39	0.00230689334655	0.0121887188371	-0.00764555437572	0.00294316577002	-0.016572224495	0.00947510061817	-0.153473364251	-0.0704943781676	0.128184660825	0.0553458699959	0.000659563199021	0.0704405505998	0.10349855659	-0.0285077541337	9.75076467398E-7	0.279561348771	0.0962089558803	-0.0158563975999	0.311613079411	-0.0557364962229	0.289646735418	-11.3378035529	62.0919533968	-31.0420381491
40	0.0554182184536	0.0180272262181	-0.0230278052169	0.0790852580428	0.0405519733054	-0.0152602821369	0.144028925868	0.114243433866	0.32577200555	0.00115182323884	-0.126478793849	0.00141096786581	0.11505894053	0.0479935113913	-2.82377229022E-8	0.281994241811	0.0909772442732	-0.0389079345331	0.276606845168	0.0408827241381	0.178798189143	-7.2420021697	57.9214504324	-46.745279308
41	-0.0121309739415	-0.00495345999981	-0.00722446049332	-0.00860937510117	-0.00862086010696	-0.00127133307921	-0.183907738547	0.0759155231142	0.367349039244	-0.133715028666	-0.0582368419628	-0.0842418521728	-0.0499355341282	-0.04229476871	-2.06922195596E-6	0.387159597285	0.139043310583	-0.136300668139	-0.0336501580548	1.0064433077	-1.34158612084	-7.33477308382	64.3610117359	-57.3076484596
42	0.0016168585855	-0.0313601026116	-0.0173628668379	0.0087458144615	0.0188641987258	0.025014602222	-0.260551193323	0.179395042957	0.0788755630063	-0.175747678102	0.0433864258534	0.0308850099998	0.236948981826	0.149037570167	-1.23264506862E-6	0.372189138125	0.0299959481158	-0.0212950284382	0.205736939589	0.0491191753963	0.382555490826	-28.460997588	32.0676669478	-7.76489251187
43	0.00652788079911	-0.0112658382299	0.000525239425746	0.0110567251598	-0.00461682716945	-0.00446041851734	-0.142555117587	-0.0900334470342	0.0735384491488	-0.046456395434	-0.114424374539	-0.0221552625116	-0.0735024861545	-0.210338291717	-5.27798019728E-9	0.0995948540174	0.365876809549	-0.162986763844	-0.169170161475	0.191097744378	1.65323440089	-33.4882903496	43.1563342432	-5.26042309995
44	0.0420401947854	0.0431848399046	0.0194968793808	0.0515296773603	0.0218484310604	0.012131530936	-0.334775816358	-0.00945041620056	0.555667804444	0.0489306182957	-0.224497495398	0.404346487881	0.131456128913	-0.0151038667581	2.4636395374E-8	0.28672672065	-0.0002189200062	0.108142583617	0.336703252722	-0.127013124902	0.441265689976	-25.0897232779	34.7570917265	0.23175360724
45	-0.0353939116923	-0.0494655925884	-7.08679302671E-5	-0.0942891461744	-0.0411737906744	-0.0209803911173	-0.114406947376	-0.0167866969213	0.269372224447	0.403194199298	-0.852924323048	0.362249923601	0.0388479634227	-0.00703133075539	1.32824946409E-7	-1.89193939708	1.80925713521	2.13735422841	-1.12253628718	-1.77511649085	-0.878152312815	-26.3956866695	41.1760410151	13.4325719
46	0.00160801335473	0.00710511797122	0.00581376081179	0.00218074689224	-0.000994268989448	0.00329799496474	0.223294168436	0.0423668032422	-0.0614985975335	-0.0844756566805	0.0894788375759	-0.0874273078792	-0.0614177471012	-0.012206759007	8.11216332964E-6	0.386011135472	0.0115464581396	0.0965494012078	0.336640415148	0.00533242802698	0.292695204994	4.26887037361	24.2312691112	-9.32087683115
47	0.00414270240064	0.0144176544176	0.0125687738062	0.00829282998839	-0.0337421600921	0.029186257451	0.090631543064	0.13326959564	0.0967420528456	-0.435554074213	-0.0252093277009	-0.35824265558	-0.0239906548964	-0.0891677033003	-6.68007425487E-8	0.320233625688	0.0278558150704	0.0455629555317	0.387098223548	0.0192834581045	0.430718726961	11.2225385191	24.4659825756	-6.13243447561
48	0.00871821223953	0.0108534805434	0.0258091355466	0.0217871553433	0.0331521857577	0.00548139703553	-0.0276562136731	0.156485406589	-0.17716963889	0.319662980574	-0.0355511063241	-0.0638209334314	-0.287142127995	-0.182930655421	-1.53036513489E-7	0.395545750276	0.0559404740716	-0.0593508183452	0.312731285843	-0.00745067575104	0.251019020776	2.90429772799	22.3610095	4.42621971178
49	0.00775187810377	0.0671427259763	-0.0223298902845	0.0151218827755	0.0122621029922	-0.0121245225982	-0.164931583763	-0.0465913914527	-0.127125573816	0.325050577098	-0.0420089232639	-0.416364634934	0.13455369227	-0.0345507133725	-5.03174005314E-7	0.361528686126	-0.019424265363	-0.124899701231	0.344792250789	-0.0222411279494	0.245302010879	8.13528032334	19.7311507985	13.1898951484
50	-0.000346386682824	0.00924246274836	-0.0174034304647	0.0245501908635	-0.0300821989246	0.0139340531501	-0.0486223336692	-0.236990057988	0.0305707471412	0.115351980935	0.219743631604	-0.0277960809183	0.0141008249034	-0.0566929957354	-1.11380767081E-6	0.276657923745	-0.000789885527764	-0.138817526835	0.328292703482	-0.1035386698	0.288235771022	17.0397318329	50.4828953591	-33.9597098415
51	0.0162254827868	-0.00212670688449	0.00860884487452	0.00338409086873	0.0211505466137	0.00613147659414	0.0510451004099	-0.228294141696	-0.0452338922884	0.0428469745054	0.167503009632	-0.149295889235	-0.0892257488319	0.0180486332722	-3.68847874401E-6	0.366991305424	-0.184845896221	-0.0974742470869	0.101152058493	-0.151004061989	1.11250872047	20.8538141525	61.7752754106	-37.7609887471
52	0.0486931318824	-0.0243586483786	-0.00802929690241	0.0404492513937	-0.03730861701	-0.00143874965491	-0.25369162633	-0.194195540106	0.0817553025866	0.0262009953629	0.0249381491984	-0.132879146647	0.0662084251607	-0.159370772318	-8.66800838669E-8	0.314387675524	-0.00304160811702	-0.0167229937259	0.350248685223	-0.0632640205094	0.337569158059	13.1992523897	54.600093701	-39.7728114904
53	0.0409649014273	-0.0119629592997	-0.0011458134363	0.0266948381556	-0.0437335373445	0.0207311897259	0.316948399809	-0.0873860343036	0.124537782053	-0.0836378767724	-0.293260349009	-0.200891020901	0.100652702924	-0.300071227521	1.03073569565E-7	0.36716031898	0.0256344565477	0.0991342420889	0.25681043395	0.00581010497494	0.426887971542	13.9585511833	57.6510241554	-53.1360913542
54	0.00685214726981	-0.000723091157374	-0.0105025662089	0.00233968551427	0.00808789017652	0.0020876836135	-0.080017942989	0.0295757563128	0.131473962459	-0.019941073101	-0.0842230430807	-0.0357224710295	0.0796901613575	0.00848906783898	4.52748186043E-6	0.337656982154	0.0443112483637	0.0057081321234	0.333100605529	0.00806157432929	0.336640654975	-32.1837298683	12.7889649112	-10.3271491513
55	0.00288857601595	0.0107517017962	0.0142823746502	0.00149878846591	-0.0105550122607	0.00961327898891	0.00852970079684	0.0736275077809	0.00347617914943	-0.141736141801	-0.268512987986	0.0921156821047	-0.00210991521884	-0.0606077981458	5.88618570317E-7	0.262938912169	0.0160814974794	0.0184666727583	0.365240094722	-0.0635210168695	0.365967573985	-36.8319932101	11.922026055	-4.32973293459
56	0.00496600344723	0.00248693960572	-0.000311871331947	-0.000218104820705	-0.000391289887768	0.00460886123352	0.00720427676154	0.075036884919	-0.0149145279816	-0.0937094595738	0.132658096139	0.0566851952502	-0.0133235587829	-0.076199164735	4.47173247079E-8	-0.281072064998	0.275835704536	0.154498256438	0.219461661688	-0.0524535544155	1.13755127775	-43.3227526861	16.9991689553	-6.63891121477
57	-0.000643122800296	0.000190244275147	-0.00368960122111	-0.0011690380765	-0.00179453999065	0.00615566960554	0.0517287112053	-0.00789148913632	-0.0169097827168	-0.0157666542181	0.00380995572983	0.0224963962925	-0.0134546876894	0.0272748610423	1.58276956563E-5	0.700287767301	0.0321529683969	-0.11521129133	0.750150699694	0.113608815921	0.683459037589	-36.266964155	18.8343060485	-16.3235433823
58	0.0149645221967	-0.0129444851571	-0.0101115488641	0.0035164059752	-0.00612211767937	0.00271542539427	0.18354967458	-0.250594448671	0.259398245719	0.0645487153896	-0.0372000501224	0.0743047408201	0.174149970513	0.257393673915	1.30151519385E-7	0.281398593482	-0.000803260438402	0.125949822969	0.267119235799	-0.0160098060996	0.346786881323	-32.8199916333	16.4777822678	-0.218637666049
59	-0.00679095938115	-0.000777088256884	-0.00196601487953	-0.0525110538047	-0.030724038431	-0.00178719780603	0.162542068249	-0.0963373245038	0.242948365109	0.70855969409	0.15761722604	0.122176379316	0.0174804908599	0.147375314158	-1.76521782923E-8	-1.91302634135	0.517493088157	2.64024444266	0.34743954211	-0.651750410189	-2.1191153559	-35.6721292396	15.6230759922	11.7655064238
60	0.00810822267645	0.0133594116561	0.00696287082919	0.00385084531494	-0.00275065364706	0.0175684901893	0.027087026652	-0.0332470296917	-0.137401473256	0.171147669878	-0.142220015798	0.0379180802968	-0.0772491530247	0.203586472408	1.32440803853E-6	0.293109014333	-0.0380771465332	-0.0159742216954	0.288604718513	0.0245691216995	0.267454561283	-16.3792261929	44.2809183101	-34.3008196667
61	0.00652189175283	0.00819163560305	-0.00677788530961	-0.00451355913848	0.01203235385	0.00272205741886	0.124511309505	0.0878773755461	-0.194024611615	0.131347534234	0.0730203841144	0.225258360944	-0.147401468281	-0.236459296358	-8.35013009794E-8	0.249859502899	-0.0528092174057	-0.0180560723492	0.33276125819	0.0103283228119	0.5206305368	-27.7764673731	44.3729222756	-39.2743695563
62	-0.00092703528612	-0.000640335892158	0.00122850963995	-0.00499614495886	0.000823078212562	0.000231005452871	-0.0138934987025	-0.0100106612099	-0.000645595094974	0.0345560180883	-0.0900588808348	-0.0366740745357	-0.0559651817481	-0.030505032677	-1.39896303096E-6	0.706011702958	-0.12631454455	0.15450316121	0.93778312702	0.00473269780303	0.750209322949	-24.8145404943	39.7809590041	-28.0584337738
63	0.0351015968998	0.0182009446376	0.0328138034668	0.0109177999294	0.00677224373903	-0.00218222753761	0.0246890757328	0.125249184923	-0.281166066604	-0.137305195142	-0.0947354369869	0.231728310757	-0.183282948845	0.251553121972	-5.55437957927E-9	0.322803563253	-0.0014451349961	-0.0880619693377	0.32359647185	-0.016214195057	0.308480071587	-18.1346851383	41.2336400067	-43.0706494506
64	-0.00381934321518	0.0125719219155	0.0195176452147	0.0167339376939	-0.00508978564258	0.0282740708753	0.105890740644	0.273458800108	-0.23319517517	-0.328266316934	-0.0382480978525	-0.0200983816988	-0.024550233814	-0.00461152384967	-9.81407082852E-8	0.401036392761	0.011010905486	-0.0916944938304	0.461975690534	-0.0689218099565	0.358638371165	-19.9941833523	40.8465924543	-52.6870791156
65	-0.00378176330651	-0.00306348451188	0.00705944103443	-0.0200127040797	0.00236028662072	-0.000133843709464	-0.211022008403	0.0517226747182	0.0477935305977	-0.0600942884104	-0.0450271387592	0.013920076521	0.0301537621707	-0.00990232035025	3.65657265223E-7	-0.155769297988	-0.119671089141	-1.39719922679	0.360117761447	-0.211144149369	-1.18077976464	-23.756812487	44.7149544196	-58.5396546825
66	-0.000564583121057	-0.000635529843646	-0.00105755736748	0.00022977128333	-0.000786018749149	-0.00143358744718	0.045278851114	0.00310805729538	0.0201765807315	0.00182882848532	0.010932305097	0.00910310432162	0.0266915235188	-0.0051791598693	5.78325757369E-7	0.599065566011	-0.0347215786301	0.302861126707	0.449006430716	0.142814527941	0.795075620787	-2.5031074142	10.5947003776	-29.6171426673
67	0.00718447558685	-0.019982162137	0.000846637569775	0.00863900195889	0.000719516711383	0.00193686330106	-0.0447508549644	-0.163461124851	-0.0233784495541	0.024995247569	0.191502168993	0.078417864437	-0.14471713979	-0.267386138505	3.05542196531E-7	0.333924584472	0.0356800049011	0.0287897574035	0.299348625455	0.0986883572753	0.371228109602	5.81634805791	16.0056005534	-37.3602436589
68	0.000102532195191	0.00405011102186	-0.00795302456392	0.00741648761462	0.00436943794507	0.000960662169379	0.031912061375	-0.0959921268652	-0.0622608782797	0.0725912077141	0.0266311158903	-0.0455269459838	-0.00232243633575	-0.0917298065853	4.16796683774E-6	0.319185101345	0.0535519631797	-0.00523231941618	0.321671423137	0.0746166924619	0.482069276266	13.150530122	11.1948050334	-34.4588988028

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 'K' and (resid 40 through 51 )	K	J	40 - 51	38 - 44
2	2	chain 'K' and (resid 52 through 59 )	K	J	52 - 59	45 - 52
3	3	chain 'K' and (resid 60 through 70 )	K	J	60 - 70	53 - 63
4	4	chain 'K' and (resid 71 through 81 )	K	J	71 - 81	64 - 74
5	5	chain 'K' and (resid 82 through 91 )	K	J	82 - 91	75 - 84
6	6	chain 'K' and (resid 92 through 102 )	K	J	92 - 102	85 - 95
7	7	chain 'F' and (resid 3 through 7 )	F	K	3 - 7	1 - 5
8	8	chain 'F' and (resid 8 through 15 )	F	K	8 - 15	6 - 13
9	9	chain 'F' and (resid 16 through 31 )	F	K	16 - 31	14 - 29
10	10	chain 'F' and (resid 32 through 39 )	F	K	32 - 39	30 - 37
11	11	chain 'F' and (resid 40 through 54 )	F	K	40 - 54	38 - 44
12	12	chain 'F' and (resid 55 through 70 )	F	K	55 - 70	45 - 60
13	13	chain 'F' and (resid 71 through 81 )	F	K	71 - 81	61 - 71
14	14	chain 'F' and (resid 82 through 94 )	F	K	82 - 94	72 - 84
15	15	chain 'F' and (resid 95 through 105 )	F	K	95 - 105	85 - 95
16	16	chain 'L' and (resid 3 through 13 )	L	L	3 - 13	1 - 11
17	17	chain 'L' and (resid 14 through 31 )	L	L	14 - 31	12 - 29
18	18	chain 'L' and (resid 32 through 51 )	L	L	32 - 51	30 - 42
19	19	chain 'L' and (resid 52 through 69 )	L	L	52 - 69	43 - 60
20	20	chain 'L' and (resid 70 through 81 )	L	L	70 - 81	61 - 72
21	21	chain 'L' and (resid 82 through 94 )	L	L	82 - 94	73 - 85
22	22	chain 'L' and (resid 95 through 116 )	L	L	95 - 116	86 - 107
23	23	chain 'C' and (resid 4 through 37 )	C	A	4 - 37	1 - 34
24	24	chain 'C' and (resid 38 through 70 )	C	A	38 - 70	35 - 55
25	25	chain 'C' and (resid 71 through 110 )	C	A	71 - 110	56 - 95
26	26	chain 'A' and (resid 5 through 39 )	A	B	5 - 39	1 - 35
27	27	chain 'A' and (resid 40 through 50 )	A	B	40 - 50	36 - 46
28	28	chain 'A' and (resid 51 through 81 )	A	B	51 - 81	47 - 77
29	29	chain 'A' and (resid 82 through 108 )	A	B	82 - 108	78 - 104
30	30	chain 'G' and (resid 5 through 15 )	G	C	5 - 15	1 - 11
31	31	chain 'G' and (resid 16 through 25 )	G	C	16 - 25	12 - 21
32	32	chain 'G' and (resid 26 through 39 )	G	C	26 - 39	22 - 35
33	33	chain 'G' and (resid 40 through 51 )	G	C	40 - 51	36 - 43
34	34	chain 'G' and (resid 52 through 70 )	G	C	52 - 70	44 - 62
35	35	chain 'G' and (resid 71 through 81 )	G	C	71 - 81	63 - 73
36	36	chain 'G' and (resid 82 through 94 )	G	C	82 - 94	74 - 86
37	37	chain 'G' and (resid 95 through 113 )	G	C	95 - 113	87 - 105
38	38	chain 'E' and (resid 4 through 31 )	E	D	4 - 31	1 - 28
39	39	chain 'E' and (resid 32 through 51 )	E	D	32 - 51	29 - 41
40	40	chain 'E' and (resid 52 through 94 )	E	D	52 - 94	42 - 84
41	41	chain 'E' and (resid 95 through 110 )	E	D	95 - 110	85 - 100
42	42	chain 'J' and (resid 4 through 25 )	J	E	4 - 25	1 - 22
43	43	chain 'J' and (resid 26 through 39 )	J	E	26 - 39	23 - 36
44	44	chain 'J' and (resid 40 through 81 )	J	E	40 - 81	37 - 73
45	45	chain 'J' and (resid 82 through 116 )	J	E	82 - 116	74 - 108
46	46	chain 'D' and (resid 6 through 15 )	D	F	6 - 15	1 - 10
47	47	chain 'D' and (resid 16 through 51 )	D	F	16 - 51	11 - 41
48	48	chain 'D' and (resid 52 through 81 )	D	F	52 - 81	42 - 71
49	49	chain 'D' and (resid 82 through 113 )	D	F	82 - 113	72 - 103
50	50	chain 'B' and (resid 2 through 25 )	B	G	2 - 25	1 - 24
51	51	chain 'B' and (resid 26 through 38 )	B	G	26 - 38	25 - 37
52	52	chain 'B' and (resid 39 through 70 )	B	G	39 - 70	38 - 60
53	53	chain 'B' and (resid 71 through 108 )	B	G	71 - 108	61 - 98
54	54	chain 'I' and (resid 4 through 15 )	I	H	4 - 15	1 - 12
55	55	chain 'I' and (resid 16 through 31 )	I	H	16 - 31	13 - 28
56	56	chain 'I' and (resid 32 through 39 )	I	H	32 - 39	29 - 36
57	57	chain 'I' and (resid 40 through 51 )	I	H	40 - 51	37 - 43
58	58	chain 'I' and (resid 52 through 70 )	I	H	52 - 70	44 - 62
59	59	chain 'I' and (resid 71 through 110 )	I	H	71 - 110	63 - 102
60	60	chain 'H' and (resid 3 through 20 )	H	I	3 - 20	1 - 18
61	61	chain 'H' and (resid 21 through 37 )	H	I	21 - 37	19 - 35
62	62	chain 'H' and (resid 38 through 50 )	H	I	38 - 50	36 - 44
63	63	chain 'H' and (resid 51 through 70 )	H	I	51 - 70	45 - 64
64	64	chain 'H' and (resid 71 through 94 )	H	I	71 - 94	65 - 88
65	65	chain 'H' and (resid 95 through 108 )	H	I	95 - 108	89 - 102
66	66	chain 'K' and (resid 3 through 7 )	K	J	3 - 7	1 - 5
67	67	chain 'K' and (resid 8 through 31 )	K	J	8 - 31	6 - 29
68	68	chain 'K' and (resid 32 through 39 )	K	J	32 - 39	30 - 37

+
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

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データを開く

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基本情報

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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

-
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)