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- PDB-7ke3: Heavy chain ferritin with C-terminal EBNA1 epitope -

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基本情報

登録情報
データベース: PDB / ID: 7ke3
タイトルHeavy chain ferritin with C-terminal EBNA1 epitope
要素Ferritin heavy chain,Epstein-Barr nuclear antigen 1
キーワードOXIDOREDUCTASE / Protein nanoparticle / vaccine / virus like particle
機能・相同性
機能・相同性情報


host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / 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 / enzyme-substrate adaptor activity / : / symbiont-mediated disruption of host cell PML body / autolysosome / Scavenging by Class A Receptors ...host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / 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 / enzyme-substrate adaptor activity / : / symbiont-mediated disruption of host cell PML body / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / regulation of DNA replication / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / endonuclease activity / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / DNA-binding transcription factor activity / negative regulation of cell population proliferation / virus-mediated perturbation of host defense response / Neutrophil degranulation / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol
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Homo sapiens (ヒト)
Epstein-Barr virus (ヘルペスウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å
データ登録者Pederick, J.L. / 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 / pdbx_initial_refinement_model

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


分子量 (理論値)分子数
合計 (水以外)283,98038
ポリマ－282,13012
非ポリマー1,85026
水12,809711
1
A: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
B: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
C: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
D: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
E: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
F: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
G: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
H: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
I: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
J: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
K: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
L: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
ヘテロ分子

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


分子量 (理論値)分子数
合計 (水以外)567,96076
ポリマ－564,26124
非ポリマー3,70052
水43224
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 area97230 Å2
ΔGint-469 kcal/mol
Surface area130760 Å2
手法PISA
単位格子
Length a, b, c (Å)217.882, 217.882, 147.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDモデル要素
11C-304-

FE

21E-301-

FE

31C-450-

HOH

41E-455-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 23 through 48 or resid 50...
21(chain B and (resid 23 through 48 or resid 50...
31(chain C and (resid 23 through 48 or resid 50...
41(chain D and (resid 23 through 48 or resid 50...
51(chain E and (resid 23 through 48 or resid 50...
61(chain F and (resid 23 through 48 or resid 50...
71(chain G and (resid 23 through 48 or resid 50...
81(chain H and (resid 23 through 48 or resid 50...
91(chain I and (resid 23 through 48 or resid 50...
101(chain J and (resid 23 through 48 or resid 50...
111(chain K and (resid 23 through 48 or resid 50...
121(chain L and (resid 23 through 48 or resid 50...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 23 through 48 or resid 50...A23 - 48
121(chain A and (resid 23 through 48 or resid 50...A50 - 52
131(chain A and (resid 23 through 48 or resid 50...A53
141(chain A and (resid 23 through 48 or resid 50...A6 - 176
151(chain A and (resid 23 through 48 or resid 50...A6 - 176
161(chain A and (resid 23 through 48 or resid 50...A6 - 176
211(chain B and (resid 23 through 48 or resid 50...B23 - 48
221(chain B and (resid 23 through 48 or resid 50...B50 - 52
231(chain B and (resid 23 through 48 or resid 50...B53
241(chain B and (resid 23 through 48 or resid 50...B6 - 176
251(chain B and (resid 23 through 48 or resid 50...B6 - 176
261(chain B and (resid 23 through 48 or resid 50...B6 - 176
311(chain C and (resid 23 through 48 or resid 50...C23 - 48
321(chain C and (resid 23 through 48 or resid 50...C50 - 52
331(chain C and (resid 23 through 48 or resid 50...C53
341(chain C and (resid 23 through 48 or resid 50...C5 - 176
351(chain C and (resid 23 through 48 or resid 50...C5 - 176
361(chain C and (resid 23 through 48 or resid 50...C5 - 176
371(chain C and (resid 23 through 48 or resid 50...C5 - 176
381(chain C and (resid 23 through 48 or resid 50...C5 - 176
391(chain C and (resid 23 through 48 or resid 50...C5 - 176
411(chain D and (resid 23 through 48 or resid 50...D23 - 48
421(chain D and (resid 23 through 48 or resid 50...D50 - 52
431(chain D and (resid 23 through 48 or resid 50...D53
441(chain D and (resid 23 through 48 or resid 50...D6 - 176
451(chain D and (resid 23 through 48 or resid 50...D6 - 176
461(chain D and (resid 23 through 48 or resid 50...D6 - 176
511(chain E and (resid 23 through 48 or resid 50...E23 - 48
521(chain E and (resid 23 through 48 or resid 50...E50 - 52
531(chain E and (resid 23 through 48 or resid 50...E53
541(chain E and (resid 23 through 48 or resid 50...E5 - 176
551(chain E and (resid 23 through 48 or resid 50...E5 - 176
561(chain E and (resid 23 through 48 or resid 50...E5 - 176
571(chain E and (resid 23 through 48 or resid 50...E5 - 176
581(chain E and (resid 23 through 48 or resid 50...E5 - 176
611(chain F and (resid 23 through 48 or resid 50...F23 - 48
621(chain F and (resid 23 through 48 or resid 50...F50 - 60
631(chain F and (resid 23 through 48 or resid 50...F62
641(chain F and (resid 23 through 48 or resid 50...F65 - 67
651(chain F and (resid 23 through 48 or resid 50...F88 - 101
661(chain F and (resid 23 through 48 or resid 50...F5 - 176
671(chain F and (resid 23 through 48 or resid 50...F5 - 176
681(chain F and (resid 23 through 48 or resid 50...F5 - 176
691(chain F and (resid 23 through 48 or resid 50...F5 - 176
6101(chain F and (resid 23 through 48 or resid 50...F5 - 176
6111(chain F and (resid 23 through 48 or resid 50...F5 - 176
711(chain G and (resid 23 through 48 or resid 50...G23 - 48
721(chain G and (resid 23 through 48 or resid 50...G50 - 52
731(chain G and (resid 23 through 48 or resid 50...G53
741(chain G and (resid 23 through 48 or resid 50...G5 - 176
751(chain G and (resid 23 through 48 or resid 50...G5 - 176
761(chain G and (resid 23 through 48 or resid 50...G5 - 176
771(chain G and (resid 23 through 48 or resid 50...G5 - 176
781(chain G and (resid 23 through 48 or resid 50...G5 - 176
811(chain H and (resid 23 through 48 or resid 50...H23 - 48
821(chain H and (resid 23 through 48 or resid 50...H50 - 52
831(chain H and (resid 23 through 48 or resid 50...H53
841(chain H and (resid 23 through 48 or resid 50...H5 - 176
851(chain H and (resid 23 through 48 or resid 50...H5 - 176
861(chain H and (resid 23 through 48 or resid 50...H5 - 176
871(chain H and (resid 23 through 48 or resid 50...H5 - 176
881(chain H and (resid 23 through 48 or resid 50...H5 - 176
911(chain I and (resid 23 through 48 or resid 50...I23 - 48
921(chain I and (resid 23 through 48 or resid 50...I50 - 60
931(chain I and (resid 23 through 48 or resid 50...I62
941(chain I and (resid 23 through 48 or resid 50...I0
951(chain I and (resid 23 through 48 or resid 50...I5 - 176
961(chain I and (resid 23 through 48 or resid 50...I5 - 176
971(chain I and (resid 23 through 48 or resid 50...I5 - 176
981(chain I and (resid 23 through 48 or resid 50...I5 - 176
991(chain I and (resid 23 through 48 or resid 50...I5 - 176
9101(chain I and (resid 23 through 48 or resid 50...I5 - 176
9111(chain I and (resid 23 through 48 or resid 50...I5 - 176
1011(chain J and (resid 23 through 48 or resid 50...J23 - 48
1021(chain J and (resid 23 through 48 or resid 50...J50 - 52
1031(chain J and (resid 23 through 48 or resid 50...J53
1041(chain J and (resid 23 through 48 or resid 50...J5 - 176
1051(chain J and (resid 23 through 48 or resid 50...J5 - 176
1061(chain J and (resid 23 through 48 or resid 50...J5 - 176
1111(chain K and (resid 23 through 48 or resid 50...K23 - 48
1121(chain K and (resid 23 through 48 or resid 50...K50 - 52
1131(chain K and (resid 23 through 48 or resid 50...K53
1141(chain K and (resid 23 through 48 or resid 50...K5 - 176
1151(chain K and (resid 23 through 48 or resid 50...K5 - 176
1161(chain K and (resid 23 through 48 or resid 50...K5 - 176
1171(chain K and (resid 23 through 48 or resid 50...K5 - 176
1181(chain K and (resid 23 through 48 or resid 50...K5 - 176
1211(chain L and (resid 23 through 48 or resid 50...L23 - 48
1221(chain L and (resid 23 through 48 or resid 50...L50 - 52
1231(chain L and (resid 23 through 48 or resid 50...L53
1241(chain L and (resid 23 through 48 or resid 50...L5 - 176
1251(chain L and (resid 23 through 48 or resid 50...L5 - 176
1261(chain L and (resid 23 through 48 or resid 50...L5 - 176
1271(chain L and (resid 23 through 48 or resid 50...L5 - 176
1281(chain L and (resid 23 through 48 or resid 50...L5 - 176
1291(chain L and (resid 23 through 48 or resid 50...L5 - 176

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要素

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


分子量: 23510.867 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Homo sapiens (ヒト), (組換発現) Epstein-Barr virus (strain B95-8) (ヘルペスウイルス)
遺伝子: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15, EBNA1, BKRF1
株: B95-8 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P02794, UniProt: P03211, 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: 20 / 由来タイプ: 合成 / 式: Fe
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 711 / 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: 3.1 Å3/Da / 溶媒含有率: 60.27 %
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 / 詳細: 0.1M HEPES pH 7.0, 30% Jeffamine M-600 pH 7.0

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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10月9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: 2.2→48.72 Å / Num. obs: 177978 / % possible obs: 99.9 % / 冗長度: 27.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.336 / Rpim(I) all: 0.065 / Rrim(I) all: 0.342 / Net I/σ(I): 8.9 / Num. measured all: 4871537
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
2.2-2.2427.62.54924013187030.9070.4932.5971.699.8
12.05-48.7225.20.05631305124110.0120.05729.898.6

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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
Rotation8.38 Å48.72 Å
Translation8.38 Å48.72 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: 2.2→48.72 Å / SU ML: 0.24 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 34.75 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2705 8841 5.01 %
Rwork0.2407 167570 -
obs0.2422 176411 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Biso max: 88.63 Å2 / Biso mean: 26.4795 Å2 / Biso min: 15.41 Å2
精密化ステップサイクル: final / 解像度: 2.2→48.72 Å
タンパク質核酸リガンド溶媒全体
原子数16158 0 68 711 16937
Biso mean--33.46 31.71 -
残基数----2001
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A7885X-RAY DIFFRACTION7.108TORSIONAL
12B7885X-RAY DIFFRACTION7.108TORSIONAL
13C7885X-RAY DIFFRACTION7.108TORSIONAL
14D7885X-RAY DIFFRACTION7.108TORSIONAL
15E7885X-RAY DIFFRACTION7.108TORSIONAL
16F7885X-RAY DIFFRACTION7.108TORSIONAL
17G7885X-RAY DIFFRACTION7.108TORSIONAL
18H7885X-RAY DIFFRACTION7.108TORSIONAL
19I7885X-RAY DIFFRACTION7.108TORSIONAL
110J7885X-RAY DIFFRACTION7.108TORSIONAL
111K7885X-RAY DIFFRACTION7.108TORSIONAL
112L7885X-RAY DIFFRACTION7.108TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.32172940.28595522581699
2.23-2.250.37642760.35795463573998
2.25-2.280.35233030.32195415571898
2.28-2.310.32562670.27095574584199
2.31-2.340.30843100.257455425852100
2.34-2.370.28952830.2515587587099
2.37-2.40.27412780.249655425820100
2.4-2.440.282840.255155765860100
2.44-2.480.29132930.24455735866100
2.48-2.520.26242670.23855935860100
2.52-2.560.27443290.23755485877100
2.56-2.610.25742820.237555835865100
2.61-2.660.26282860.227156015887100
2.66-2.710.24982810.22755589587099
2.71-2.770.23953090.23645556586599
2.77-2.840.25032970.22815551584899
2.84-2.910.25052980.23025585588399
2.91-2.990.26332930.22685589588299
2.99-3.070.27743010.22955580588199
3.07-3.170.26622740.21185605587999
3.17-3.290.22613260.21745593591999
3.29-3.420.24662920.22045619591199
3.42-3.570.22862790.22575592587199
3.57-3.760.27792890.22925586587598
3.76-40.26432900.225607589799
4-4.310.25992980.21765645594399
4.31-4.740.22743270.21935620594799
4.74-5.420.28143170.255612592998
5.42-6.830.35323210.291957646085100
6.83-48.720.27082970.26275758605595
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)
10.75-0.18510.12161.834-1.96321.22830.1330.0354-0.10070.11960.16260.4243-0.2369-0.2054-0.17290.235-0.0190.02080.2062-0.04810.218222.7324159.9763158.033
20.24771.1292-0.67244.2458-2.09522.021-0.08980.0766-0.0806-0.0760.0132-0.45670.08680.06940.08390.17930.0223-0.01080.3024-0.01470.2931230.7068167.4572150.7484
31.62550.20141.16521.9441-0.90841.60650.1853-0.1469-0.2049-0.23250.20230.61050.0243-0.2741-0.32570.2427-0.0120.06510.3459-0.02390.2687219.259158.5068154.3104
40.37291.5349-0.95074.0477-2.03551.77720.1738-0.10760.06880.0893-0.04830.4131-0.1658-0.1185-0.01650.18110.0250.03560.2791-0.04860.2957224.9446166.5658165.9341
50.671.1712-1.83591.4302-2.50064.4541-0.0921-0.12180.1151-0.0101-0.1465-0.2528-0.02910.07560.17790.2269-0.0078-0.02480.242-0.05790.2339232.998183.9013155.0022
66.51234.1769-1.89693.2632-0.80971.3828-0.72360.3983-0.9886-0.7971-0.1923-1.0226-0.0631-0.10410.36170.13880.0453-0.16630.19430.19610.1882223.7734177.2122124.8195
71.137-0.96330.53683.6505-2.57591.59880.17070.1927-0.0895-0.2561-0.05840.40920.25460.0974-0.12580.22040.0064-0.00840.2097-0.02260.2689223.5393154.3831143.3475
80.6078-2.66490.40929.0628-5.42384.2641-0.16790.06090.2115-0.0851-0.2063-0.83260.04340.15010.34330.1973-0.0211-0.02360.1915-0.00540.2331231.2824157.6888141.038
91.5226-0.538-1.36141.8936-0.33491.56080.2245-0.09120.09260.3620.31410.4926-0.2772-0.3216-0.53750.2242-0.1098-0.05730.2868-0.04060.2146219.4358163.5632140.3869
100.9608-1.70331.37878.6886-6.34896.45370.2267-0.1128-0.2949-0.39550.40721.00780.2512-0.126-0.58510.21880.0351-0.01320.2911-0.01410.269222.6414150.8568131.3585
116.858-1.75492.83663.4424-1.24934.04540.20681.1897-0.1807-0.3049-0.0972-0.21310.22041.0748-0.08320.33010.0305-0.04480.3228-0.01480.2461229.0617164.2369123.4954
121.8902-2.03671.35346.7432-3.58173.60410.1745-0.10890.43490.5047-0.6014-0.4843-0.15050.58310.35720.17410.0149-0.02590.31010.00890.2475231.8235142.052134.052
135.26422.15352.39813.5104-0.98157.45020.31-1.1122-0.68720.32390.0030.2743-0.3861-0.7062-0.4220.28170.01550.01150.31160.01430.3105227.0071129.1072145.5309
141.420.1460.05254.2252-2.07354.7681-0.0174-0.1160.0957-0.02970.0788-0.1735-0.0218-0.2732-0.13230.28830.09530.00570.27450.00730.1348236.7752135.1149147.0149
152.7342-2.4477-0.16162.34120.93262.6354-0.13410.11550.0540.31610.17930.29720.04850.27760.04960.3031-0.0578-0.01350.1863-0.00940.1723257.9205109.7357125.1721
162.69040.20282.13171.1611-0.14541.82360.2121-0.0386-0.19250.09310.0058-0.00630.20070.0335-0.16470.26950.01240.06570.2511-0.02770.212281.3708109.8867143.3157
177.53052.40564.11840.38911.17213.3229-0.3063-0.07660.8163-0.02-0.06720.2671-0.2348-0.1340.31350.25880.03220.02040.19040.00350.3232278.0068117.5657141.0631
181.94751.15060.33030.6842-0.98421.1042-0.1307-0.059-0.590.04940.25860.15040.0047-0.2559-0.13640.2121-0.0170.00560.2507-0.08670.3227272.1774105.7761140.3973
195.03990.9892.64790.76681.24022.4978-0.09150.1666-0.2019-0.15720.071-0.05610.07080.1926-0.00640.2687-0.00720.08430.1558-0.02290.2464280.143111.2454128.5683
202.08921.24832.43860.84081.06683.8003-0.05290.05240.17440.0256-0.1188-0.2685-0.06330.02510.12530.28180.00480.05550.2350.01880.2842297.7989119.0869139.4623
211.42650.5066-0.39561.8170.46820.3304-0.08760.07090.0631-0.2242-0.09730.25010.06020.36990.33150.1870.0066-0.06510.35120.08650.334290.9281110.1339169.7949
223.4939-0.48442.85010.3839-0.20482.38240.075-0.116-0.55280.04310.18320.1301-0.0771-0.0861-0.24960.19580.00140.03870.16440.00940.2484268.0461109.9161151.2984
237.6473-2.54253.7725-0.0017-0.87052.1162-0.3096-0.09190.47410.0161-0.0524-0.2445-0.2525-0.07510.39410.23110.01840.01030.20280.00190.2865271.2155117.7156153.7024
241.5221-1.0677-1.55971.59811.31921.6409-0.23810.3193-0.497-0.15390.1860.03320.03050.8305-0.14470.3016-0.09720.0813-0.01210.04930.2992277.1973105.7783154.1975
256.9317-1.49916.03970.6168-1.50495.54330.107-0.4572-0.8093-0.14340.29110.1518-0.2447-0.3939-0.46060.29370.03460.0150.26410.00770.2729264.4187109.0881163.0219
263.5876-0.54050.47211.93390.2442.4953-0.1675-0.22840.16160.4171-0.00820.0431-0.2038-0.04070.13840.34180.03440.04890.29680.06150.2694277.9885115.4197171.1132
271.5774-1.53731.18680.6026-1.44552.3031-0.03740.2825-0.1726-0.1250.0335-0.1727-0.15940.00830.04520.25930.0220.00750.16830.00260.1783251.5511119.1909155.0904
281.6273-1.16520.3611.11610.10151.4891-0.6750.68040.07330.43170.0578-0.14370.75270.2423-0.05590.4086-0.0153-0.27310.376-0.08620.1596241.5611162.550999.087
290.590.53510.65861.64851.26162.173-0.0326-0.00610.0873-0.2365-0.05270.1511-0.1825-0.09250.1370.1730.0074-0.01480.19450.03640.2523243.0324187.3404116.0112
300.14480.5225-0.71994.94515.85516.83220.14390.0334-0.04450.15360.1027-0.26820.23410.0879-0.20890.22830.06620.0160.25720.01760.2465246.8102179.9299118.8409
310.00080.4914-0.60941.6165-0.28141.4193-0.0192-0.023-0.0479-0.7191-0.0359-0.1293-0.2947-0.11250.12560.16940.0371-0.03420.27650.01090.1715243.0517183.231106.9888
321.0770.81441.20073.53633.10742.61340.1145-0.02310.1661-0.0021-0.22390.34520.0384-0.29470.09840.22290.02860.02680.27150.05640.1847233.8391175.4871115.9211
331.53141.93851.72822.99851.94733.1114-0.0157-0.00550.12170.02190.12440.0784-0.05680.0649-0.18370.20680.0164-0.00240.2360.05040.2342236.8731187.8233133.8645
341.41591.6126-1.26111.824-1.05276.19250.27310.420.62880.4170.27310.20130.1177-0.2469-0.3940.29620.0597-0.03450.21660.05090.3676256.3501210.6843122.7467
350.4297-0.21280.08933.17321.12530.3634-0.04640.1056-0.0259-0.37480.0960.2147-0.0791-0.0712-0.07040.2796-0.0276-0.00110.2610.02990.1881255.2118185.6285106.1625
360.8407-1.5315-1.41017.39555.63953.4336-0.096-0.18960.12680.496-0.0058-0.25570.2350.10980.09810.21720.0085-0.07120.27630.02380.1638259.0492185.9491114.2261
372.8775-0.6658-0.20512.3352.78413.17690.2020.01760.13-0.2208-0.73880.2012-0.2781-0.91450.35330.32220.0132-0.03640.24860.11490.2323250.6167194.7447109.8451
38-0.0966-0.3896-0.32464.57572.31132.44590.17470.0540.0196-0.3109-0.0423-0.2616-0.1947-0.1527-0.08720.1593-0.01340.01010.20180.02170.2109265.743196.3497108.0469
390.87690.6878-0.44054.76721.76720.91910.07640.20260.07050.085-0.28280.21870.125-0.22030.18960.2233-0.0226-0.03790.27860.01630.2985270.7121175.742101.4669
401.2883-0.82572.1870.6355-1.10656.9111-0.09040.23070.350.19380.12050.3225-0.3903-0.0787-0.21230.17410.04360.03670.19330.07020.2363256.4542111.4547171.7705
41-0.02650.58590.2353.71982.10811.02030.11070.0083-0.03340.4457-0.1647-0.20270.1605-0.16720.05170.1813-0.0022-0.00510.22830.02390.2221255.4336136.4932188.309
421.18691.31580.58275.41695.50432.9964-0.230.0980.0241-0.90240.4971-0.1219-0.30410.4555-0.20410.339-0.0088-0.02430.260.00970.2145259.3057135.8233179.9226
433.5197-0.485-1.1210.53060.15881.17570.1309-0.0647-0.26530.2173-0.27540.01070.0366-0.81920.30970.24180.0383-0.010.23210.05950.157249.8734128.6084186.0149
440.02740.33970.68064.49762.62361.50440.1137-0.0123-0.0585-0.0173-0.0404-0.249-0.0299-0.1375-0.05240.2711-0.0502-0.01540.25140.04760.2058265.9173125.7699186.3652
450.2094-1.30410.20275.20540.39140.1746-0.00960.03820.06860.06050.04150.0073-0.12870.017-0.06630.1924-0.03960.01940.22630.03710.2464270.9058146.2218192.9861
468.71072.7579-2.78095.037-1.56630.9499-0.445-1.2683-0.39010.4435-0.4742-0.0932-0.1799-0.1310.57080.3324-0.0547-0.0060.2036-0.04290.2558241.9376159.5472195.444
470.4363-0.5348-0.24432.35431.94822.03710.07030.184-0.02780.217-0.2017-0.03690.3476-0.04190.110.20080.01910.00570.25860.00820.2368241.9599137.9909181.6062
483.8869-0.4592-1.19772.4578-2.63723.6334-0.4685-0.3742-0.4251-0.72340.1246-0.21010.34030.12630.09670.40820.00740.02320.2944-0.03470.2655248.1502121.3494165.822
490.2558-0.11040.92924.86755.11346.2006-0.13050.08090.15540.56150.16780.17060.48780.3852-0.09670.2361-0.05640.05770.23390.02430.2149246.9749142.1454175.7793
501.1529-0.01560.3430.4463-0.94881.92510.3767-0.5795-0.1346-0.1505-0.5608-0.16020.1191-0.33050.10260.3306-0.01920.00940.30150.02910.2547243.5476139.6432188.2094
511.5326-0.7686-1.87445.42214.39934.70310.2048-0.0544-0.09050.3342-0.23570.0760.1904-0.39970.1040.19150.0395-0.02210.23250.04420.218232.4534141.1153176.9961
522.4823-0.56070.7654.21441.62342.82770.0562-0.17570.6373-0.12950.1708-0.5971-0.32680.4919-0.15830.19720.00890.01180.3351-0.030.26236.8068156.6462181.9593
530.7979-1.0411-1.11112.66582.76252.28540.0317-0.0336-0.0517-0.11540.0056-0.0071-0.1006-0.04820.00620.23610.0389-0.00430.24280.05040.174236.991134.4034160.7307
541.5346-0.3139-1.42020.2330.12030.8277-0.0360.1184-0.1445-0.0184-0.0705-0.04670.0455-0.03440.09910.2710.0057-0.05350.2419-0.01630.294240.0572141.7841111.6233
553.4817-0.1729-2.97371.2387-0.87771.96990.25540.32320.00360.0596-0.0330.0003-0.2282-0.366-0.15870.237-0.0326-0.04250.2637-0.00760.1734253.433144.2373111.6152
560.96290.2928-1.01982.72911.0370.6554-0.03720.5674-0.3275-0.1681-0.11050.2463-0.0101-0.42280.23020.35220.0562-0.02850.35010.00240.137240.62136.8425109.9232
573.7065-0.1924-1.71951.2641-0.2682.0231-0.075-0.00060.12910.06020.12610.04480.0694-0.1061-0.06270.2666-0.0325-0.05930.21550.02210.1821239.2803151.9712108.1964
585.0928-0.4781-1.23580.7262-0.19990.5497-0.009-0.14850.1193-0.01880.0439-0.07020.1540.0558-0.06260.2299-0.03-0.03680.2258-0.02060.1734259.5189156.9638101.7383
592.3454-0.1036-1.01440.55250.20731.5499-0.24290.2251-0.3271-0.00180.07680.04690.2185-0.17540.11660.24770.00060.00170.2008-0.01160.2172257.0587128.0168109.3193
603.8406-0.5754-4.29810.2728-0.02584.09750.24710.08560.18580.0001-0.0449-0.0781-0.20380.0802-0.19130.2019-0.0185-0.02340.2382-0.04320.198251.8367133.3872120.8089
611.36290.09461.12871.2066-1.03111.6396-0.58390.00370.6777-0.4880.61230.34960.6102-0.0776-0.08650.2713-0.0514-0.00040.2566-0.05080.2078253.0853129.6371106.4027
623.4016-0.4993-3.32631.06980.16973.065-0.17790.18560.0733-0.25560.0943-0.03010.2169-0.18620.06410.29580.0201-0.00830.2315-0.03590.1952260.1723120.1188115.9245
632.7905-1.8429-1.85591.30771.66112.3653-0.0418-0.2453-0.2005-0.022-0.03820.01760.01060.02940.07710.24330.0115-0.04660.2271-0.00090.1639247.8628123.2154133.9654
643.9393-1.4916-1.1961.7730.74932.966-0.21330.38280.043-0.79240.0562-0.1346-0.3649-0.84310.00280.265-0.18610.12740.3092-0.04350.2157307.4806159.335298.9755
650.88040.7298-1.11043.0686-1.62112.3223-0.0405-0.0487-0.2447-0.2022-0.1295-0.2367-0.03010.17110.18270.19490.00840.00690.2187-0.0210.2304307.624138.0797112.5746
660.23980.256-0.50392.8676-3.0212.162-0.0629-0.0187-0.0616-0.0540.015-0.08260.0198-0.1844-0.01520.2645-0.01250.01820.2118-0.02910.2652302.4194138.6874120.057
67-0.48990.25770.55421.53241.24021.1220.10010.1764-0.0775-0.6269-0.05490.08390.50180.23290.1310.18460.05470.03330.3549-0.02420.2751305.883137.455106.2384
680.45130.2828-0.58872.9419-2.54043.54540.0568-0.0996-0.01080.0691-0.1144-0.052-0.1310.20710.13820.1620.02050.00530.2897-0.03310.2355315.4495146.498115.761
691.31051.3422-1.07943.1667-2.80022.8131-0.0136-0.06750.062-0.01850.07490.15780.12170.018-0.14190.2490.01980.02910.2545-0.04840.3267312.518134.2355133.7684
701.0180.3713-0.03121.4687-0.29270.9581-0.06870.1143-0.0812-0.18290.0827-0.07310.1425-0.05040.00760.27260.02140.05620.2579-0.02580.1783293.8049126.404111.5354
710.7757-0.870.3353.5827-3.26541.744-0.034-0.12650.03420.0593-0.092-0.0222-0.1180.110.10520.2918-0.02770.02730.2028-0.04880.1898291.1055140.0501111.3282
722.06940.2805-1.01931.3417-0.8722.2161-0.0280.048-0.0868-0.134-0.328-0.26260.18630.47160.16350.25280.0180.02120.2203-0.08070.1537298.6931127.1895109.8723
73-0.0325-0.0443-0.04433.8223-1.44211.50170.0761-0.0115-0.0129-0.0578-0.1849-0.02570.03470.10460.0920.1888-0.03420.01690.2308-0.03710.2494283.6763125.6035108.1755
740.53340.40930.55454.5087-0.89330.6030.03670.2181-0.19670.3011-0.1393-0.1275-0.18330.18110.07120.2436-0.05470.08040.2668-0.03830.2841278.6341145.9466101.6598
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 41 )A6 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 75 )A42 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 95 )A76 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 137 )A96 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 176 )A138 - 176
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 13 )B6 - 13
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 48 )B14 - 48
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 75 )B49 - 75
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 95 )B76 - 95
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 123 )B96 - 123
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 137 )B124 - 137
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 158 )B138 - 158
13X-RAY DIFFRACTION13chain 'B' and (resid 159 through 163 )B159 - 163
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 176 )B164 - 176
15X-RAY DIFFRACTION15chain 'C' and (resid 5 through 13 )C5 - 13
16X-RAY DIFFRACTION16chain 'C' and (resid 14 through 48 )C14 - 48
17X-RAY DIFFRACTION17chain 'C' and (resid 49 through 75 )C49 - 75
18X-RAY DIFFRACTION18chain 'C' and (resid 76 through 95 )C76 - 95
19X-RAY DIFFRACTION19chain 'C' and (resid 96 through 137 )C96 - 137
20X-RAY DIFFRACTION20chain 'C' and (resid 138 through 176 )C138 - 176
21X-RAY DIFFRACTION21chain 'D' and (resid 6 through 13 )D6 - 13
22X-RAY DIFFRACTION22chain 'D' and (resid 14 through 48 )D14 - 48
23X-RAY DIFFRACTION23chain 'D' and (resid 49 through 75 )D49 - 75
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 95 )D76 - 95
25X-RAY DIFFRACTION25chain 'D' and (resid 96 through 123 )D96 - 123
26X-RAY DIFFRACTION26chain 'D' and (resid 124 through 137 )D124 - 137
27X-RAY DIFFRACTION27chain 'D' and (resid 138 through 176 )D138 - 176
28X-RAY DIFFRACTION28chain 'E' and (resid 5 through 13 )E5 - 13
29X-RAY DIFFRACTION29chain 'E' and (resid 14 through 48 )E14 - 48
30X-RAY DIFFRACTION30chain 'E' and (resid 49 through 75 )E49 - 75
31X-RAY DIFFRACTION31chain 'E' and (resid 76 through 95 )E76 - 95
32X-RAY DIFFRACTION32chain 'E' and (resid 96 through 137 )E96 - 137
33X-RAY DIFFRACTION33chain 'E' and (resid 138 through 176 )E138 - 176
34X-RAY DIFFRACTION34chain 'F' and (resid 5 through 13 )F5 - 13
35X-RAY DIFFRACTION35chain 'F' and (resid 14 through 48 )F14 - 48
36X-RAY DIFFRACTION36chain 'F' and (resid 49 through 75 )F49 - 75
37X-RAY DIFFRACTION37chain 'F' and (resid 76 through 95 )F76 - 95
38X-RAY DIFFRACTION38chain 'F' and (resid 96 through 137 )F96 - 137
39X-RAY DIFFRACTION39chain 'F' and (resid 138 through 176 )F138 - 176
40X-RAY DIFFRACTION40chain 'G' and (resid 5 through 13 )G5 - 13
41X-RAY DIFFRACTION41chain 'G' and (resid 14 through 48 )G14 - 48
42X-RAY DIFFRACTION42chain 'G' and (resid 49 through 76 )G49 - 76
43X-RAY DIFFRACTION43chain 'G' and (resid 77 through 95 )G77 - 95
44X-RAY DIFFRACTION44chain 'G' and (resid 96 through 137 )G96 - 137
45X-RAY DIFFRACTION45chain 'G' and (resid 138 through 176 )G138 - 176
46X-RAY DIFFRACTION46chain 'H' and (resid 5 through 13 )H5 - 13
47X-RAY DIFFRACTION47chain 'H' and (resid 14 through 41 )H14 - 41
48X-RAY DIFFRACTION48chain 'H' and (resid 42 through 48 )H42 - 48
49X-RAY DIFFRACTION49chain 'H' and (resid 49 through 75 )H49 - 75
50X-RAY DIFFRACTION50chain 'H' and (resid 76 through 95 )H76 - 95
51X-RAY DIFFRACTION51chain 'H' and (resid 96 through 123 )H96 - 123
52X-RAY DIFFRACTION52chain 'H' and (resid 124 through 137 )H124 - 137
53X-RAY DIFFRACTION53chain 'H' and (resid 138 through 176 )H138 - 176
54X-RAY DIFFRACTION54chain 'I' and (resid 5 through 41 )I5 - 41
55X-RAY DIFFRACTION55chain 'I' and (resid 42 through 75 )I42 - 75
56X-RAY DIFFRACTION56chain 'I' and (resid 76 through 95 )I76 - 95
57X-RAY DIFFRACTION57chain 'I' and (resid 96 through 137 )I96 - 137
58X-RAY DIFFRACTION58chain 'I' and (resid 138 through 176 )I138 - 176
59X-RAY DIFFRACTION59chain 'J' and (resid 5 through 41 )J5 - 41
60X-RAY DIFFRACTION60chain 'J' and (resid 42 through 75 )J42 - 75
61X-RAY DIFFRACTION61chain 'J' and (resid 76 through 95 )J76 - 95
62X-RAY DIFFRACTION62chain 'J' and (resid 96 through 137 )J96 - 137
63X-RAY DIFFRACTION63chain 'J' and (resid 138 through 176 )J138 - 176
64X-RAY DIFFRACTION64chain 'K' and (resid 5 through 13 )K5 - 13
65X-RAY DIFFRACTION65chain 'K' and (resid 14 through 41 )K14 - 41
66X-RAY DIFFRACTION66chain 'K' and (resid 42 through 76 )K42 - 76
67X-RAY DIFFRACTION67chain 'K' and (resid 77 through 95 )K77 - 95
68X-RAY DIFFRACTION68chain 'K' and (resid 96 through 137 )K96 - 137
69X-RAY DIFFRACTION69chain 'K' and (resid 138 through 176 )K138 - 176
70X-RAY DIFFRACTION70chain 'L' and (resid 5 through 41 )L5 - 41
71X-RAY DIFFRACTION71chain 'L' and (resid 42 through 75 )L42 - 75
72X-RAY DIFFRACTION72chain 'L' and (resid 76 through 95 )L76 - 95
73X-RAY DIFFRACTION73chain 'L' and (resid 96 through 137 )L96 - 137
74X-RAY DIFFRACTION74chain 'L' and (resid 138 through 176 )L138 - 176

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万見について

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お知らせ

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

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

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

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