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- PDB-7ke5: Heavy chain ferritin with N-terminal EBNA1 epitope -

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基本情報

登録情報
データベース: PDB / ID: 7ke5
タイトルHeavy chain ferritin with N-terminal EBNA1 epitope
要素Epstein-Barr nuclear antigen 1,Ferritin heavy chain
キーワードOXIDOREDUCTASE / Protein nanocage / vaccine / virus like particle
機能・相同性
機能・相同性情報


host cell PML body / viral latency / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドデオキシリボヌクレアーゼ / iron ion sequestering activity / symbiont-mediated disruption of host cell PML body / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase ...host cell PML body / viral latency / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドデオキシリボヌクレアーゼ / iron ion sequestering activity / symbiont-mediated disruption of host cell PML body / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / regulation of DNA replication / ferroxidase activity / enzyme-substrate adaptor activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / endonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / Neutrophil degranulation / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / cytosol / cytoplasm
類似検索 - 分子機能
Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. ...Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
類似検索 - ドメイン・相同性
: / Ferritin heavy chain / Epstein-Barr nuclear antigen 1
類似検索 - 構成要素
生物種Epstein-Barr virus (ヘルペスウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Pederick, J.P. / Bruning, J.B.
引用ジャーナル: Vaccine / 年: 2021
タイトル: Immunogenicity study of engineered ferritins with C- and N-terminus insertion of Epstein-Barr nuclear antigen 1 epitope.
著者: Qu, Y. / Zhang, B. / Wang, Y. / Yin, S. / Pederick, J.L. / Bruning, J.B. / Sun, Y. / Middelberg, A. / Bi, J.
履歴
登録2020年10月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年9月1日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

ダウンロードとリンク

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集合体

登録構造単位
A: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
B: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
C: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
D: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
E: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
F: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
G: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
H: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
I: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
J: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
K: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
L: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)283,75734
ポリマ－282,13112
非ポリマー1,62622
水63135
1
A: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
B: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
C: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
D: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
E: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
F: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
G: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
H: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
I: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
J: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
K: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
L: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
ヘテロ分子

A: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
B: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
C: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
D: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
E: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
F: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
G: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
H: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
I: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
J: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
K: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
L: Epstein-Barr nuclear antigen 1,Ferritin heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)567,51468
ポリマ－564,26124
非ポリマー3,25344
水39622
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+21
Buried area94740 Å2
ΔGint-382 kcal/mol
Surface area139480 Å2
手法PISA
単位格子
Length a, b, c (Å)219.323, 219.323, 148.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 5 through 13 or resid 15...
21(chain B and (resid 5 through 13 or resid 15...
31(chain C and (resid 5 through 13 or resid 15...
41(chain D and (resid 5 through 13 or resid 15...
51(chain E and (resid 5 through 13 or resid 15...
61(chain F and (resid 5 through 13 or resid 15...
71(chain G and (resid 5 through 13 or resid 15...
81(chain H and (resid 5 through 13 or resid 15...
91(chain I and (resid 5 through 13 or resid 15...
101(chain J and (resid 5 through 13 or resid 15...
111(chain K and (resid 5 through 13 or resid 15...
121(chain L and (resid 5 through 13 or resid 15...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRHISHIS(chain A and (resid 5 through 13 or resid 15...AA5 - 1332 - 40
12ASPASPALAALA(chain A and (resid 5 through 13 or resid 15...AA15 - 5242 - 79
13THRTHRGLYGLY(chain A and (resid 5 through 13 or resid 15...AA5 - 17632 - 203
14GLNGLNGLNGLN(chain A and (resid 5 through 13 or resid 15...AA5885
15THRTHRGLYGLY(chain A and (resid 5 through 13 or resid 15...AA5 - 17632 - 203
16THRTHRGLYGLY(chain A and (resid 5 through 13 or resid 15...AA5 - 17632 - 203
17THRTHRGLYGLY(chain A and (resid 5 through 13 or resid 15...AA5 - 17632 - 203
18THRTHRGLYGLY(chain A and (resid 5 through 13 or resid 15...AA5 - 17632 - 203
19THRTHRGLYGLY(chain A and (resid 5 through 13 or resid 15...AA5 - 17632 - 203
21THRTHRHISHIS(chain B and (resid 5 through 13 or resid 15...BB5 - 1332 - 40
22ASPASPASNASN(chain B and (resid 5 through 13 or resid 15...BB15 - 2142 - 48
23ARGARGARGARG(chain B and (resid 5 through 13 or resid 15...BB2249
24THRTHRGLYGLY(chain B and (resid 5 through 13 or resid 15...BB5 - 17632 - 203
25THRTHRGLYGLY(chain B and (resid 5 through 13 or resid 15...BB5 - 17632 - 203
26THRTHRGLYGLY(chain B and (resid 5 through 13 or resid 15...BB5 - 17632 - 203
27THRTHRGLYGLY(chain B and (resid 5 through 13 or resid 15...BB5 - 17632 - 203
31THRTHRHISHIS(chain C and (resid 5 through 13 or resid 15...CC5 - 1332 - 40
32ASPASPASNASN(chain C and (resid 5 through 13 or resid 15...CC15 - 2142 - 48
33THRTHRGLYGLY(chain C and (resid 5 through 13 or resid 15...CC5 - 17632 - 203
34THRTHRGLYGLY(chain C and (resid 5 through 13 or resid 15...CC5 - 17632 - 203
35THRTHRGLYGLY(chain C and (resid 5 through 13 or resid 15...CC5 - 17632 - 203
36THRTHRGLYGLY(chain C and (resid 5 through 13 or resid 15...CC5 - 17632 - 203
37THRTHRGLYGLY(chain C and (resid 5 through 13 or resid 15...CC5 - 17632 - 203
38THRTHRGLYGLY(chain C and (resid 5 through 13 or resid 15...CC5 - 17632 - 203
41THRTHRHISHIS(chain D and (resid 5 through 13 or resid 15...DD5 - 1332 - 40
42ASPASPASNASN(chain D and (resid 5 through 13 or resid 15...DD15 - 2142 - 48
43ARGARGARGARG(chain D and (resid 5 through 13 or resid 15...DD2249
44THRTHRGLYGLY(chain D and (resid 5 through 13 or resid 15...DD5 - 17632 - 203
45THRTHRGLYGLY(chain D and (resid 5 through 13 or resid 15...DD5 - 17632 - 203
46THRTHRGLYGLY(chain D and (resid 5 through 13 or resid 15...DD5 - 17632 - 203
47THRTHRGLYGLY(chain D and (resid 5 through 13 or resid 15...DD5 - 17632 - 203
51THRTHRHISHIS(chain E and (resid 5 through 13 or resid 15...EE5 - 1332 - 40
52ASPASPASNASN(chain E and (resid 5 through 13 or resid 15...EE15 - 2142 - 48
53ARGARGARGARG(chain E and (resid 5 through 13 or resid 15...EE2249
54THRTHRGLYGLY(chain E and (resid 5 through 13 or resid 15...EE5 - 17632 - 203
55THRTHRGLYGLY(chain E and (resid 5 through 13 or resid 15...EE5 - 17632 - 203
56THRTHRGLYGLY(chain E and (resid 5 through 13 or resid 15...EE5 - 17632 - 203
57THRTHRGLYGLY(chain E and (resid 5 through 13 or resid 15...EE5 - 17632 - 203
61THRTHRHISHIS(chain F and (resid 5 through 13 or resid 15...FF5 - 1332 - 40
62ASPASPASNASN(chain F and (resid 5 through 13 or resid 15...FF15 - 2142 - 48
63ARGARGARGARG(chain F and (resid 5 through 13 or resid 15...FF2249
64THRTHRGLYGLY(chain F and (resid 5 through 13 or resid 15...FF5 - 17632 - 203
65THRTHRGLYGLY(chain F and (resid 5 through 13 or resid 15...FF5 - 17632 - 203
66THRTHRGLYGLY(chain F and (resid 5 through 13 or resid 15...FF5 - 17632 - 203
67THRTHRGLYGLY(chain F and (resid 5 through 13 or resid 15...FF5 - 17632 - 203
71THRTHRHISHIS(chain G and (resid 5 through 13 or resid 15...GG5 - 1332 - 40
72ASPASPASNASN(chain G and (resid 5 through 13 or resid 15...GG15 - 2142 - 48
73ARGARGARGARG(chain G and (resid 5 through 13 or resid 15...GG2249
74THRTHRGLYGLY(chain G and (resid 5 through 13 or resid 15...GG5 - 17632 - 203
75THRTHRGLYGLY(chain G and (resid 5 through 13 or resid 15...GG5 - 17632 - 203
76THRTHRGLYGLY(chain G and (resid 5 through 13 or resid 15...GG5 - 17632 - 203
77THRTHRGLYGLY(chain G and (resid 5 through 13 or resid 15...GG5 - 17632 - 203
81THRTHRHISHIS(chain H and (resid 5 through 13 or resid 15...HH5 - 1332 - 40
82ASPASPASNASN(chain H and (resid 5 through 13 or resid 15...HH15 - 2142 - 48
83THRTHRGLYGLY(chain H and (resid 5 through 13 or resid 15...HH5 - 17632 - 203
84THRTHRGLYGLY(chain H and (resid 5 through 13 or resid 15...HH5 - 17632 - 203
85THRTHRGLYGLY(chain H and (resid 5 through 13 or resid 15...HH5 - 17632 - 203
86THRTHRGLYGLY(chain H and (resid 5 through 13 or resid 15...HH5 - 17632 - 203
87THRTHRGLYGLY(chain H and (resid 5 through 13 or resid 15...HH5 - 17632 - 203
88THRTHRGLYGLY(chain H and (resid 5 through 13 or resid 15...HH5 - 17632 - 203
91THRTHRHISHIS(chain I and (resid 5 through 13 or resid 15...II5 - 1332 - 40
92ASPASPASNASN(chain I and (resid 5 through 13 or resid 15...II15 - 2142 - 48
93THRTHRGLYGLY(chain I and (resid 5 through 13 or resid 15...II5 - 17632 - 203
94THRTHRGLYGLY(chain I and (resid 5 through 13 or resid 15...II5 - 17632 - 203
95THRTHRGLYGLY(chain I and (resid 5 through 13 or resid 15...II5 - 17632 - 203
96THRTHRGLYGLY(chain I and (resid 5 through 13 or resid 15...II5 - 17632 - 203
97THRTHRGLYGLY(chain I and (resid 5 through 13 or resid 15...II5 - 17632 - 203
98THRTHRGLYGLY(chain I and (resid 5 through 13 or resid 15...II5 - 17632 - 203
101THRTHRHISHIS(chain J and (resid 5 through 13 or resid 15...JJ5 - 1332 - 40
102ASPASPASNASN(chain J and (resid 5 through 13 or resid 15...JJ15 - 2142 - 48
103ARGARGARGARG(chain J and (resid 5 through 13 or resid 15...JJ2249
104THRTHRGLYGLY(chain J and (resid 5 through 13 or resid 15...JJ5 - 17632 - 203
105THRTHRGLYGLY(chain J and (resid 5 through 13 or resid 15...JJ5 - 17632 - 203
106THRTHRGLYGLY(chain J and (resid 5 through 13 or resid 15...JJ5 - 17632 - 203
107THRTHRGLYGLY(chain J and (resid 5 through 13 or resid 15...JJ5 - 17632 - 203
111THRTHRHISHIS(chain K and (resid 5 through 13 or resid 15...KK5 - 1332 - 40
112ASPASPASNASN(chain K and (resid 5 through 13 or resid 15...KK15 - 2142 - 48
113ARGARGARGARG(chain K and (resid 5 through 13 or resid 15...KK2249
114THRTHRGLYGLY(chain K and (resid 5 through 13 or resid 15...KK5 - 17632 - 203
115THRTHRGLYGLY(chain K and (resid 5 through 13 or resid 15...KK5 - 17632 - 203
116THRTHRGLYGLY(chain K and (resid 5 through 13 or resid 15...KK5 - 17632 - 203
117THRTHRGLYGLY(chain K and (resid 5 through 13 or resid 15...KK5 - 17632 - 203
121THRTHRHISHIS(chain L and (resid 5 through 13 or resid 15...LL5 - 1332 - 40
122ASPASPASNASN(chain L and (resid 5 through 13 or resid 15...LL15 - 2142 - 48
123ARGARGARGARG(chain L and (resid 5 through 13 or resid 15...LL2249
124THRTHRGLYGLY(chain L and (resid 5 through 13 or resid 15...LL5 - 17632 - 203
125THRTHRGLYGLY(chain L and (resid 5 through 13 or resid 15...LL5 - 17632 - 203
126THRTHRGLYGLY(chain L and (resid 5 through 13 or resid 15...LL5 - 17632 - 203
127THRTHRGLYGLY(chain L and (resid 5 through 13 or resid 15...LL5 - 17632 - 203

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要素

#1: タンパク質
Epstein-Barr nuclear antigen 1,Ferritin heavy chain / EBV nuclear antigen 1 / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


分子量: 23510.877 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Epstein-Barr virus (strain B95-8) (ヘルペスウイルス), (組換発現) Homo sapiens (ヒト)
株: B95-8
遺伝子: EBNA1, BKRF1, FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P03211, UniProt: P02794, ferroxidase
#2: 化合物
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#3: 化合物
ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 16 / 由来タイプ: 合成 / 式: Fe
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 35 / 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N

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.17 Å3/Da / 溶媒含有率: 61.15 %
結晶化温度: 289.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: 0.1M ammonium citrate tribasic pH 7.0, 12% PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX1 / 波長: 0.9537 Å
検出器タイプ: DECTRIS EIGER2 X 9M / 検出器: PIXEL / 日付: 2019年9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: 0.9537 Å / 相対比: 1
反射解像度: 2.8→48.82 Å / Num. obs: 85483 / % possible obs: 95.9 % / 冗長度: 20.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.056 / Rrim(I) all: 0.259 / Net I/σ(I): 7.9 / Num. measured all: 1766865 / Scaling rejects: 44
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.8515.60.8986650842600.9750.2280.9282.691.6
14.82-48.8224.10.078165276860.9970.0170.0820.396.8

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation8.36 Å48.82 Å
Translation8.36 Å48.82 Å

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
Aimless0.7.4データスケーリング
PHASER2.8.3位相決定
PHENIX1.18.2-3874精密化
PDB_EXTRACT3.25データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 6J4A

6j4a


解像度: 2.8→48.82 Å / SU ML: 0.32 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 43.45 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3165 4124 5.08 %
Rwork0.2743 77051 -
obs0.2765 81175 91.03 %
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Biso max: 98.93 Å2 / Biso mean: 26.6994 Å2 / Biso min: 7.74 Å2
精密化ステップサイクル: final / 解像度: 2.8→48.82 Å
タンパク質核酸リガンド溶媒全体
原子数16575 0 64 35 16674
Biso mean--27.3 20.62 -
残基数----2046
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A8953X-RAY DIFFRACTION9.472TORSIONAL
12B8953X-RAY DIFFRACTION9.472TORSIONAL
13C8953X-RAY DIFFRACTION9.472TORSIONAL
14D8953X-RAY DIFFRACTION9.472TORSIONAL
15E8953X-RAY DIFFRACTION9.472TORSIONAL
16F8953X-RAY DIFFRACTION9.472TORSIONAL
17G8953X-RAY DIFFRACTION9.472TORSIONAL
18H8953X-RAY DIFFRACTION9.472TORSIONAL
19I8953X-RAY DIFFRACTION9.472TORSIONAL
110J8953X-RAY DIFFRACTION9.472TORSIONAL
111K8953X-RAY DIFFRACTION9.472TORSIONAL
112L8953X-RAY DIFFRACTION9.472TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.830.39361440.33432568271290
2.83-2.870.41390.31742560269989
2.87-2.90.34261220.30622591271390
2.9-2.940.35491330.3072600273390
2.94-2.980.37951450.29322588273389
2.98-3.020.37551540.33562529268389
3.02-3.070.35521400.32132569270989
3.07-3.120.30781370.30272531266888
3.12-3.170.38061230.29342540266388
3.17-3.220.34431300.29472545267587
3.22-3.280.35291440.29122516266088
3.28-3.350.43381300.30862583271389
3.35-3.410.33681380.29662571270988
3.41-3.490.36471140.29672557267187
3.49-3.570.33491480.27972463261186
3.57-3.660.3451340.28422587272189
3.66-3.760.27411550.25712626278192
3.76-3.870.30831300.28032673280391
3.87-3.990.35671660.26832655282191
3.99-4.140.271430.26822659280291
4.14-4.30.29691450.25532644278991
4.3-4.50.26331360.25112762289894
4.5-4.730.29471550.23852766292195
4.73-5.030.28671520.24532826297896
5.03-5.420.28861430.24672863300697
5.42-5.960.27891520.25122936308898
5.96-6.820.2851740.2622906308098
6.82-8.590.24251470.24682963311098
8.59-48.820.2871510.25152874302590
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.5350.7009-0.70182.6409-1.07441.3386-0.057-0.13520.0619-0.46080.03650.0640.28360.09820.02010.1421-0.01180.00260.198-0.00210.166308.7073141.0699113.2713
20.6566-0.3286-0.07311.6455-0.98880.82940.03220.0720.2008-0.11630.1314-0.13760.0504-0.0601-0.09520.21770.01910.03350.2175-0.04030.1819305.161144.0435115.1919
30.42770.0440.29590.3538-0.34991.76870.0962-0.0736-0.0839-0.0966-0.10720.20740.02760.08630.01510.17910.06470.02680.244-0.01490.1685316.7642144.6311116.9289
41.13021.3636-0.96531.7146-1.63932.8367-0.0058-0.1114-0.1007-0.0928-0.0544-0.04140.06840.0358-0.03440.15850.04320.00030.1982-0.12550.3286314.6501135.3047134.9622
50.2370.1714-0.1781.8447-0.92551.4140.0450.007-0.0787-0.43140.08080.2680.31360.06360.03350.20950.0290.01950.1841-0.03850.1318295.7727127.2938112.6639
60.38970.0925-0.13992.0082-1.99431.86990.03260.1744-0.13190.25090.18070.0421-0.0666-0.4069-0.15540.2216-0.03050.0190.1447-0.00550.2375292.9476140.6092112.7385
72.90391.83-2.61544.672-3.08993.2188-0.27360.04960.172-0.68330.1291-0.43620.4668-0.5091-0.06020.31250.0045-0.0010.1991-0.05640.1054301.1741127.5843110.4889
80.6183-0.41140.73273.6736-1.56631.7848-0.0361-0.17560.1323-0.0993-0.0665-0.08990.08390.1080.07250.18480.02280.02580.2502-0.05980.1484286.585128.3303107.997
90.5721-0.35420.4654.9462-0.90310.8903-0.04020.11940.05930.2712-0.0359-0.2047-0.18450.24230.01320.1705-0.02060.0640.2256-0.07110.1753280.5526146.9499102.7397
100.7666-0.5749-0.05820.3809-0.11391.05540.0286-0.06990.02420.0901-0.10980.0683-0.2387-0.271-0.15320.0928-0.13650.04520.22060.00320.1327224.3325160.5593159.4798
110.65540.7294-0.77442.7158-1.81871.6750.0870.03420.01590.1490.05980.35110.03740.0704-0.00330.10440.0193-0.03520.1542-0.01790.2458232.3221168.6558152.1792
122.7789-0.52581.75283.9637-3.03934.6906-0.08280.08520.2283-0.30170.46870.30790.0294-0.377-0.34870.0990.03280.06590.2378-0.08160.3425220.0087158.2754155.9038
132.20980.2669-0.7021.56251.26271.4062-0.4992-0.05910.04350.1197-0.46840.2453-0.3130.11290.4750.5165-0.0263-0.18480.36910.11810.4288222.1408180.7106146.8021
140.18620.8786-0.80524.4448-3.60333.2511-0.11120.17220.07690.23920.37730.6666-0.1318-0.5846-0.14410.21390.04370.01190.36930.02690.0587224.1662172.0351164.8774
150.41460.6523-0.33341.7652-1.18180.8415-0.0238-0.18370.18020.205-0.1220.1772-0.12290.310.1180.2129-0.05730.1420.27720.02740.1311230.5729158.8889172.6146
160.4490.4526-0.25483.7459-2.62242.11630.19840.032-0.07410.1979-0.4577-0.437-0.28130.47220.11880.29040.0627-0.06510.2872-0.01470.1267233.3781181.5587161.9774
170.3206-0.1689-0.00720.13650.02550.00980.19380.65880.2675-0.37060.0942-0.0441-0.48770.2489-0.01910.2863-0.0029-0.06320.4588-0.00660.1905228.4422194.2869150.3208
181.51912.082-1.5253.1113-1.32773.72270.03590.05920.1395-0.09130.0386-0.0721-0.0526-0.11410.12920.1748-0.0148-0.03610.3555-0.03870.1525238.3486188.2542148.829
190.95190.40810.47170.20560.13540.401-0.06890.03390.3079-0.0988-0.1025-0.1294-0.03350.0618-0.5971-0.06320.1293-0.17120.25110.03650.5216224.8062178.9263126.1877
200.9857-0.73010.6221.9369-2.01743.0970.22240.0386-0.0076-0.21910.0040.27190.52820.1024-0.0760.21970.0256-0.01130.1802-0.01130.1831225.194155.1051144.9074
210.0863-0.12860.08793.11-2.4962.5316-0.16680.07340.0754-0.2219-0.1477-0.58180.29730.37920.13810.2043-0.0151-0.0660.2531-0.00750.1877232.8434159.4685141.5647
224.27052.3723-3.14985.3105-4.56536.42650.0745-0.21050.39440.65630.68420.5899-0.2128-0.4784-0.63050.29320.0998-0.02630.17550.01370.191219.8579169.6668140.8533
232.6067-4.71-0.28838.56060.57550.0812-0.266-0.066-0.1854-0.4960.43541.2236-0.27390.0097-0.2010.31470.04540.05360.26920.16980.4766220.2513146.8305149.248
240.4234-0.65321.00254.3675-3.29893.31830.1512-0.2166-0.1999-0.3450.30030.62030.2156-0.3529-0.23510.1690.0293-0.05720.1935-0.01970.2617224.139152.2342132.1499
250.2582-0.1150.30521.4054-0.8940.78010.10510.23180.2271-0.1827-0.0320.21610.08510.11950.31460.26020.1101-0.10520.16110.12290.2859230.5786165.3515124.6047
262.3266-0.33590.75473.2075-1.80241.26150.08-0.08660.2724-0.0717-0.2814-0.14610.30170.1626-0.09560.28690.03180.0530.25750.00960.1085233.3673142.6402135.294
271.1269-0.2560.63261.7598-0.64071.64740.41750.03610.1745-0.08140.04090.0452-0.09920.24620.03590.30680.086-0.00470.3218-0.09170.0581236.2478134.7007148.0812
281.0325-0.06361.15410.79370.26411.3134-0.15240.1912-0.2105-0.04950.20290.0829-0.26110.269-0.15470.2328-0.02350.02030.1634-0.02430.1797274.9372109.7037137.64
293.79330.42772.72950.60710.5152.4023-0.09930.2438-0.06070.01840.01560.06950.120.2020.11110.1466-0.0101-0.02250.1665-0.00240.2343282.4617117.8007144.655
308.1131-0.95867.0652.7279-2.60837.36540.47060.1332-0.87330.0288-0.2175-0.09250.6902-0.1436-0.1960.17360.01250.01170.2321-0.1280.2041269.073105.1984140.8916
318.48975.2872-1.33683.2932-0.84540.2415-0.02950.4291-1.0567-0.158-0.0408-0.8150.04630.08520.13870.34990.20940.03930.3641-0.06560.3044292.4148106.0315148.5013
324.26130.88063.17250.19050.75322.71740.0915-0.08030.07050.0018-0.0636-0.03450.0885-0.0841-0.06510.2688-0.0254-0.01950.1653-0.02240.1152281.6451111.9883129.4592
332.72090.9061.98930.99481.06414.2519-0.01110.2064-0.05080.10.04570.0317-0.40040.2575-0.02830.27240.00450.05830.14340.02860.1846299.5841120.1419140.8821
341.5661.7386-0.11062.2848-0.80341.32920.11330.1676-0.2927-0.3173-0.2-0.48930.27810.1857-0.01910.20320.2649-0.0580.09370.01340.302293.3598110.4544171.0134
352.4259-0.96622.19360.6908-0.59162.17260.0656-0.21340.0755-0.0056-0.04170.0606-0.0343-0.13040.08350.2139-0.00090.01140.15540.04280.2474271.099114.2675153.5855
363.54962.11694.25773.45982.56876.06350.3416-0.0785-0.2242-0.1012-0.09250.08580.63970.135-0.29270.20570.02310.02210.1385-0.02450.2925279.5029105.3772155.6363
373.799-0.70962.0960.5398-0.67191.68570.1164-0.02-0.2161-0.0132-0.0061-0.11850.3985-0.0633-0.20250.2870.05780.03010.2096-0.00480.226270.0253111.522165.6279
381.7463-1.64651.37841.6223-1.35553.7716-0.04460.1052-0.0495-0.0577-0.0036-0.3013-0.2561-0.2578-0.00670.26220.02740.04310.17020.01180.1953253.4674120.0478156.3862
390.08470.50110.04312.00880.68420.8779-0.07540.05240.0905-0.2404-0.0010.2065-0.1322-0.02690.09160.13920.0314-0.02740.21-0.00680.1746244.3846183.2143113.4506
400.373-0.0969-0.48892.20641.62221.6783-0.16680.0803-0.00120.1690.21570.14710.21940.127-0.08170.17670.0438-0.04310.159-0.0020.4062247.8689180.2632115.7886
410.8505-0.1573-0.13460.07440.23421.3350.12630.09380.19760.0379-0.163-0.08120.1138-0.2666-0.01290.21370.0351-0.03240.26590.02470.1808236.1638179.3046116.9998
421.67111.52631.82563.22732.54743.0676-0.19710.07740.4572-0.27490.17440.0297-0.03930.1460.02420.1847-0.00560.01650.16940.08990.2895238.4863189.1169135.1895
430.68250.10850.14921.7310.63050.4155-0.18810.17560.2311-0.06120.13490.24630.07770.01150.06560.2202-0.0572-0.01690.24440.053-0.0504257.1581192.5539110.8923
440.5001-0.093-0.31893.26572.53272.63040.03140.11330.15270.22180.10510.242-0.01640.2287-0.03940.1477-0.0538-0.05350.20250.00510.1393258.4429190.6654115.4604
450.96140.2001-0.12610.11180.15020.26840.05910.0088-0.43990.09430.0097-0.14870.1084-0.24480.0430.2803-0.0056-0.03080.20880.06090.0698264.397192.7844103.3379
460.5795-0.9046-0.42333.38261.09850.3733-0.02630.0189-0.1067-0.03810.01490.31040.0152-0.1304-0.03030.22940.0033-0.0330.20090.04590.1987271.4759184.7047107.102
470.2283-0.3816-0.06781.5050.67040.9786-0.01230.02780.03290.29360.1453-0.27670.13270.11590.0410.16160.00270.03750.16190.00710.182257.3894127.3842184.5844
480.01170.00460.01193.69062.05711.0753-0.0657-0.10770.1733-0.54810.1249-0.1765-0.08960.0084-0.110.18070.0309-0.0080.2304-0.0440.219260.1111140.7449184.413
491.1637-1.1495-1.48132.8731.75193.7663-0.16060.21320.05370.46280.07730.02030.3880.1674-0.6020.35820.1780.07650.35360.0151-0.1642251.7815127.3106186.564
500.49951.01210.86643.91991.70031.7370.22030.0262-0.0729-0.14250.0628-0.2074-0.4371-0.2805-0.00890.15770.03260.04060.23970.02370.159266.5707128.4685189.1695
511.11620.09960.58285.83930.45070.32340.12210.07760.12080.0851-0.00930.0859-0.0409-0.3236-0.0370.1512-0.01720.06360.19350.02360.2119272.6956147.1042194.4671
520.7714-0.0564-0.33440.80380.26080.7615-0.0986-0.0035-0.33350.3239-0.09170.21890.21130.0307-0.00620.3260.06940.05630.22770.0658-0.1637244.4071141.1502183.9384
530.29230.25990.42193.20923.0934.4267-0.1687-0.0843-0.07970.01680.1837-0.06520.0580.60.11770.1770.0063-0.00490.21220.02470.1894248.5487143.1154177.054
540.7232-2.0296-0.50276.33930.56121.63160.0055-0.3460.23860.5811-0.20830.42790.26250.29640.05080.1598-0.02030.03860.2424-0.00770.1971246.5811146.2567194.3109
551.40920.40860.88650.59420.07930.6186-0.0922-0.11920.0609-0.3514-0.00610.19040.0963-0.24720.28240.5047-0.1907-0.07140.2458-0.16090.2662241.4565127.4019179.0337
561.0259-0.12960.25182.15871.49821.33440.0705-0.12510.02380.1201-0.0727-0.2996-0.04-0.090.07790.1859-0.0001-0.0010.23870.01950.132235.5095147.9095180.4823
572.2721-0.1162-0.6812.1862.59273.45370.0535-0.1944-0.39980.46990.0069-0.37870.0224-0.02010.12280.3140.00280.01770.19270.09840.115238.3651135.1039162.195
582.2084-0.3615-1.24280.53090.09051.01020.10460.15590.04640.1597-0.052-0.2329-0.0926-0.15970.06150.16420.0209-0.01580.2114-0.04760.2793241.7678142.7723112.691
593.8910.5051-1.9390.3571-0.32621.07750.3017-0.1680.3499-0.1283-0.09950.1586-0.24860.0111-0.12360.31490.01740.03850.14430.03610.1136254.9117145.5379112.7219
603.7524-0.6812-2.70761.22061.64423.6012-0.09970.8063-0.1855-0.1995-0.25570.2036-0.2046-0.2516-0.0340.2199-0.0792-0.09640.4162-0.15730.0973241.7793137.1991110.5669
612.54060.12-1.5091.336-0.79191.5449-0.0015-0.0749-0.10510.07090.00950.14060.13260.12610.09890.260.0162-0.06370.0926-0.03040.1359242.5445151.998108.2064
624.62910.4026-0.19040.9462-0.29530.2845-0.1134-0.062-0.4045-0.05270.012-0.01350.23790.08240.10090.18380.0259-0.01090.1801-0.08070.2763261.4015157.9107102.7501
631.3925-0.0072-0.62320.28150.24690.85430.06840.31460.03230.01640.09390.11010.1726-0.2168-0.08660.24350.0120.01550.2027-0.01690.1336258.8534128.8921110.4214
641.70490.2232-1.48590.4891-0.00331.5340.1083-0.1630.03310.0395-0.0940.28620.13290.114-0.08680.1742-0.0055-0.14480.26250.036-0.2624253.636134.1854121.663
653.2629-0.5873-1.24150.4802-0.46941.80920.17450.5172-0.0021-0.40510.0075-0.16450.0193-0.32770.16260.39230.07280.1060.1064-0.05170.1365260.6414131.9221102.8221
660.08970.11810.1160.9769-0.72831.05580.01520.01530.3870.06370.16120.16540.22370.0386-0.13680.30520.0198-0.05220.1843-0.0190.2454253.4399120.9365118.6223
672.1097-0.9188-2.11960.70420.96732.114-0.1296-0.19310.0735-0.07220.14880.01970.02230.1008-0.0410.19880.0156-0.07710.2305-0.00010.1745255.9166123.9252129.0395
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'K' and (resid 5 through 48 )K5 - 48
2X-RAY DIFFRACTION2chain 'K' and (resid 49 through 85 )K49 - 85
3X-RAY DIFFRACTION3chain 'K' and (resid 86 through 137 )K86 - 137
4X-RAY DIFFRACTION4chain 'K' and (resid 138 through 176 )K138 - 176
5X-RAY DIFFRACTION5chain 'L' and (resid 5 through 41 )L5 - 41
6X-RAY DIFFRACTION6chain 'L' and (resid 42 through 75 )L42 - 75
7X-RAY DIFFRACTION7chain 'L' and (resid 76 through 90 )L76 - 90
8X-RAY DIFFRACTION8chain 'L' and (resid 91 through 137 )L91 - 137
9X-RAY DIFFRACTION9chain 'L' and (resid 138 through 176 )L138 - 176
10X-RAY DIFFRACTION10chain 'A' and (resid 5 through 41 )A5 - 41
11X-RAY DIFFRACTION11chain 'A' and (resid 42 through 75 )A42 - 75
12X-RAY DIFFRACTION12chain 'A' and (resid 76 through 90 )A76 - 90
13X-RAY DIFFRACTION13chain 'A' and (resid 91 through 95 )A91 - 95
14X-RAY DIFFRACTION14chain 'A' and (resid 96 through 123 )A96 - 123
15X-RAY DIFFRACTION15chain 'A' and (resid 124 through 137 )A124 - 137
16X-RAY DIFFRACTION16chain 'A' and (resid 138 through 158 )A138 - 158
17X-RAY DIFFRACTION17chain 'A' and (resid 159 through 163 )A159 - 163
18X-RAY DIFFRACTION18chain 'A' and (resid 164 through 176 )A164 - 176
19X-RAY DIFFRACTION19chain 'B' and (resid 5 through 13 )B5 - 13
20X-RAY DIFFRACTION20chain 'B' and (resid 14 through 48 )B14 - 48
21X-RAY DIFFRACTION21chain 'B' and (resid 49 through 76 )B49 - 76
22X-RAY DIFFRACTION22chain 'B' and (resid 77 through 86 )B77 - 86
23X-RAY DIFFRACTION23chain 'B' and (resid 87 through 95 )B87 - 95
24X-RAY DIFFRACTION24chain 'B' and (resid 96 through 123 )B96 - 123
25X-RAY DIFFRACTION25chain 'B' and (resid 124 through 137 )B124 - 137
26X-RAY DIFFRACTION26chain 'B' and (resid 138 through 158 )B138 - 158
27X-RAY DIFFRACTION27chain 'B' and (resid 159 through 176 )B159 - 176
28X-RAY DIFFRACTION28chain 'C' and (resid 5 through 41 )C5 - 41
29X-RAY DIFFRACTION29chain 'C' and (resid 42 through 76 )C42 - 76
30X-RAY DIFFRACTION30chain 'C' and (resid 77 through 86 )C77 - 86
31X-RAY DIFFRACTION31chain 'C' and (resid 87 through 95 )C87 - 95
32X-RAY DIFFRACTION32chain 'C' and (resid 96 through 137 )C96 - 137
33X-RAY DIFFRACTION33chain 'C' and (resid 138 through 176 )C138 - 176
34X-RAY DIFFRACTION34chain 'D' and (resid 5 through 13 )D5 - 13
35X-RAY DIFFRACTION35chain 'D' and (resid 14 through 75 )D14 - 75
36X-RAY DIFFRACTION36chain 'D' and (resid 76 through 90 )D76 - 90
37X-RAY DIFFRACTION37chain 'D' and (resid 91 through 137 )D91 - 137
38X-RAY DIFFRACTION38chain 'D' and (resid 138 through 176 )D138 - 176
39X-RAY DIFFRACTION39chain 'E' and (resid 5 through 48 )E5 - 48
40X-RAY DIFFRACTION40chain 'E' and (resid 49 through 85 )E49 - 85
41X-RAY DIFFRACTION41chain 'E' and (resid 86 through 137 )E86 - 137
42X-RAY DIFFRACTION42chain 'E' and (resid 138 through 176 )E138 - 176
43X-RAY DIFFRACTION43chain 'F' and (resid 5 through 48 )F5 - 48
44X-RAY DIFFRACTION44chain 'F' and (resid 49 through 85 )F49 - 85
45X-RAY DIFFRACTION45chain 'F' and (resid 86 through 123 )F86 - 123
46X-RAY DIFFRACTION46chain 'F' and (resid 124 through 176 )F124 - 176
47X-RAY DIFFRACTION47chain 'G' and (resid 5 through 41 )G5 - 41
48X-RAY DIFFRACTION48chain 'G' and (resid 42 through 75 )G42 - 75
49X-RAY DIFFRACTION49chain 'G' and (resid 76 through 90 )G76 - 90
50X-RAY DIFFRACTION50chain 'G' and (resid 91 through 137 )G91 - 137
51X-RAY DIFFRACTION51chain 'G' and (resid 138 through 176 )G138 - 176
52X-RAY DIFFRACTION52chain 'H' and (resid 5 through 48 )H5 - 48
53X-RAY DIFFRACTION53chain 'H' and (resid 49 through 75 )H49 - 75
54X-RAY DIFFRACTION54chain 'H' and (resid 76 through 85 )H76 - 85
55X-RAY DIFFRACTION55chain 'H' and (resid 86 through 95 )H86 - 95
56X-RAY DIFFRACTION56chain 'H' and (resid 96 through 137 )H96 - 137
57X-RAY DIFFRACTION57chain 'H' and (resid 138 through 176 )H138 - 176
58X-RAY DIFFRACTION58chain 'I' and (resid 5 through 41 )I5 - 41
59X-RAY DIFFRACTION59chain 'I' and (resid 42 through 75 )I42 - 75
60X-RAY DIFFRACTION60chain 'I' and (resid 76 through 90 )I76 - 90
61X-RAY DIFFRACTION61chain 'I' and (resid 91 through 137 )I91 - 137
62X-RAY DIFFRACTION62chain 'I' and (resid 138 through 176 )I138 - 176
63X-RAY DIFFRACTION63chain 'J' and (resid 5 through 41 )J5 - 41
64X-RAY DIFFRACTION64chain 'J' and (resid 42 through 75 )J42 - 75
65X-RAY DIFFRACTION65chain 'J' and (resid 76 through 85 )J76 - 85
66X-RAY DIFFRACTION66chain 'J' and (resid 86 through 123 )J86 - 123
67X-RAY DIFFRACTION67chain 'J' and (resid 124 through 176 )J124 - 176

+
万見について

-
お知らせ

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

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

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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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