[日本語] English
万見
- PDB-7oay: Nanobody F2 bound to RBD -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7oay
タイトルNanobody F2 bound to RBD
要素
  • F2 nanobody
  • Spike protein S1
キーワードANTIVIRAL PROTEIN / Spike / nanobody / high affinity
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Lama glama (ラマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.34 Å
データ登録者Naismith, J.H. / Mikolajek, H.
資金援助 英国, 2件
組織認可番号国
Wellcome Trust100209/Z/12/Z) 英国
Engineering and Physical Sciences Research CouncilEP/S025243/1 英国
引用
ジャーナル: Nat Commun / 年: 2021
タイトル: A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19.
著者: Jiandong Huo / Halina Mikolajek / Audrey Le Bas / Jordan J Clark / Parul Sharma / Anja Kipar / Joshua Dormon / Chelsea Norman / Miriam Weckener / Daniel K Clare / Peter J Harrison / Julia A ...著者: Jiandong Huo / Halina Mikolajek / Audrey Le Bas / Jordan J Clark / Parul Sharma / Anja Kipar / Joshua Dormon / Chelsea Norman / Miriam Weckener / Daniel K Clare / Peter J Harrison / Julia A Tree / Karen R Buttigieg / Francisco J Salguero / Robert Watson / Daniel Knott / Oliver Carnell / Didier Ngabo / Michael J Elmore / Susan Fotheringham / Adam Harding / Lucile Moynié / Philip N Ward / Maud Dumoux / Tessa Prince / Yper Hall / Julian A Hiscox / Andrew Owen / William James / Miles W Carroll / James P Stewart / James H Naismith / Raymond J Owens /
要旨: SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain ...SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain antibodies (nanobodies) have significant potential. Their small size and stability mean that nanobodies are compatible with respiratory administration. We report four nanobodies (C5, H3, C1, F2) engineered as homotrimers with pmolar affinity for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Crystal structures show C5 and H3 overlap the ACE2 epitope, whilst C1 and F2 bind to a different epitope. Cryo Electron Microscopy shows C5 binding results in an all down arrangement of the Spike protein. C1, H3 and C5 all neutralize the Victoria strain, and the highly transmissible Alpha (B.1.1.7 first identified in Kent, UK) strain and C1 also neutralizes the Beta (B.1.35, first identified in South Africa). Administration of C5-trimer via the respiratory route showed potent therapeutic efficacy in the Syrian hamster model of COVID-19 and separately, effective prophylaxis. The molecule was similarly potent by intraperitoneal injection.
#1: ジャーナル: Res Sq / 年: 2021
タイトル: A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19
著者: Huo, J. / Mikolajek, H. / Le Bas, A. / Clark, J. / Sharma, P. / Kipar, A. / Dormon, J. / Norman, C. / Weckener, M. / Clare, D. / Harrison, P. / Tree, J. / Buttigieg, K. / Salguero, F. / ...著者: Huo, J. / Mikolajek, H. / Le Bas, A. / Clark, J. / Sharma, P. / Kipar, A. / Dormon, J. / Norman, C. / Weckener, M. / Clare, D. / Harrison, P. / Tree, J. / Buttigieg, K. / Salguero, F. / Watson, R. / Knott, D. / Carnell, O. / Ngabo, D. / Elmore, M. / Fotheringham, S. / Harding, A. / Ward, P. / Moynie, L. / Dumoux, M. / Hall, Y. / Hiscox, J. / Owen, A. / James, W. / Carroll, M. / Stewart, J. / Naismith, J. / Owens, R.
履歴
登録2021年4月20日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年8月11日Provider: repository / タイプ: Initial release
改定 2.02021年10月6日Group: Atomic model / Data collection / Database references
カテゴリ: atom_site / citation ...atom_site / citation / citation_author / diffrn_source / pdbx_database_proc
Item: _atom_site.pdbx_tls_group_id / _diffrn_source.pdbx_synchrotron_site
改定 2.12024年1月31日Group: Data collection / Derived calculations / Refinement description
カテゴリ: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site / _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

-
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

-
集合体

登録構造単位
AAA: Spike protein S1
BBB: F2 nanobody
CCC: Spike protein S1
DDD: F2 nanobody
EEE: Spike protein S1
FFF: F2 nanobody
GGG: Spike protein S1
HHH: F2 nanobody
III: Spike protein S1
JJJ: F2 nanobody
KKK: Spike protein S1
LLL: F2 nanobody
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)233,40218
ポリマ－232,07512
非ポリマー1,3276
水5,819323
1
AAA: Spike protein S1
BBB: F2 nanobody
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,9003
ポリマ－38,6792
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
CCC: Spike protein S1
DDD: F2 nanobody
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,9003
ポリマ－38,6792
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
EEE: Spike protein S1
FFF: F2 nanobody
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,9003
ポリマ－38,6792
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
GGG: Spike protein S1
HHH: F2 nanobody
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,9003
ポリマ－38,6792
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
5
III: Spike protein S1
JJJ: F2 nanobody
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,9003
ポリマ－38,6792
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
6
KKK: Spike protein S1
LLL: F2 nanobody
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,9003
ポリマ－38,6792
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)108.420, 108.420, 165.538
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11AAA
21CCC
32AAA
42EEE
53AAA
63GGG
74AAA
84III
95AAA
105KKK
116BBB
126DDD
137BBB
147FFF
158BBB
168HHH
179BBB
189JJJ
1910BBB
2010LLL
2111CCC
2211EEE
2312CCC
2412GGG
2513CCC
2613III
2714CCC
2814KKK
2915DDD
3015FFF
3116DDD
3216HHH
3317DDD
3417JJJ
3518DDD
3618LLL
3719EEE
3819GGG
3920EEE
4020III
4121EEE
4221KKK
4322FFF
4422HHH
4523FFF
4623JJJ
4724FFF
4824LLL
4925GGG
5025III
5126GGG
5226KKK
5327HHH
5427JJJ
5528HHH
5628LLL
5729III
5829KKK
5930JJJ
6030LLL

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLYSLYSAAAA331 - 5282 - 199
211ASNASNLYSLYSCCCC331 - 5282 - 199
322ILEILEPROPROAAAA332 - 5273 - 198
422ILEILEPROPROEEEE332 - 5273 - 198
533THRTHRPROPROAAAA333 - 5274 - 198
633THRTHRPROPROGGGG333 - 5274 - 198
744ASNASNLYSLYSAAAA331 - 5282 - 199
844ASNASNLYSLYSIIII331 - 5282 - 199
955ILEILEPROPROAAAA332 - 5273 - 198
1055ILEILEPROPROKKKK332 - 5273 - 198
1166GLNGLNSERSERBBBB1 - 1251 - 125
1266GLNGLNSERSERDDDD1 - 1251 - 125
1377GLNGLNVALVALBBBB1 - 1231 - 123
1477GLNGLNVALVALFFFF1 - 1231 - 123
1588GLNGLNSERSERBBBB1 - 1251 - 125
1688GLNGLNSERSERHHHH1 - 1251 - 125
1799GLNGLNSERSERBBBB1 - 1251 - 125
1899GLNGLNSERSERJJJJ1 - 1251 - 125
191010GLNGLNSERSERBBBB1 - 1251 - 125
201010GLNGLNSERSERLLLL1 - 1251 - 125
211111ILEILEPROPROCCCC332 - 5273 - 198
221111ILEILEPROPROEEEE332 - 5273 - 198
231212THRTHRPROPROCCCC333 - 5274 - 198
241212THRTHRPROPROGGGG333 - 5274 - 198
251313ASNASNLYSLYSCCCC331 - 5282 - 199
261313ASNASNLYSLYSIIII331 - 5282 - 199
271414ILEILEPROPROCCCC332 - 5273 - 198
281414ILEILEPROPROKKKK332 - 5273 - 198
291515GLNGLNVALVALDDDD1 - 1231 - 123
301515GLNGLNVALVALFFFF1 - 1231 - 123
311616GLNGLNSERSERDDDD1 - 1251 - 125
321616GLNGLNSERSERHHHH1 - 1251 - 125
331717GLNGLNSERSERDDDD1 - 1251 - 125
341717GLNGLNSERSERJJJJ1 - 1251 - 125
351818GLNGLNSERSERDDDD1 - 1251 - 125
361818GLNGLNSERSERLLLL1 - 1251 - 125
371919THRTHRPROPROEEEE333 - 5274 - 198
381919THRTHRPROPROGGGG333 - 5274 - 198
392020ILEILEPROPROEEEE332 - 5273 - 198
402020ILEILEPROPROIIII332 - 5273 - 198
412121ILEILELYSLYSEEEE332 - 5283 - 199
422121ILEILELYSLYSKKKK332 - 5283 - 199
432222GLNGLNVALVALFFFF1 - 1231 - 123
442222GLNGLNVALVALHHHH1 - 1231 - 123
452323GLNGLNVALVALFFFF1 - 1231 - 123
462323GLNGLNVALVALJJJJ1 - 1231 - 123
472424GLNGLNVALVALFFFF1 - 1231 - 123
482424GLNGLNVALVALLLLL1 - 1231 - 123
492525THRTHRPROPROGGGG333 - 5274 - 198
502525THRTHRPROPROIIII333 - 5274 - 198
512626THRTHRPROPROGGGG333 - 5274 - 198
522626THRTHRPROPROKKKK333 - 5274 - 198
532727GLNGLNSERSERHHHH1 - 1251 - 125
542727GLNGLNSERSERJJJJ1 - 1251 - 125
552828GLNGLNSERSERHHHH1 - 1251 - 125
562828GLNGLNSERSERLLLL1 - 1251 - 125
572929ILEILEPROPROIIII332 - 5273 - 198
582929ILEILEPROPROKKKK332 - 5273 - 198
593030GLNGLNSERSERJJJJ1 - 1251 - 125
603030GLNGLNSERSERLLLL1 - 1251 - 125

NCSアンサンブル:
ID詳細
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60

-
要素

#1: タンパク質
Spike protein S1


分子量: 23716.580 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#2: 抗体
F2 nanobody


分子量: 14962.622 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Escherichia coli (大腸菌)
#3: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 323 / 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

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.42 Å3/Da / 溶媒含有率: 49.18 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1M SPG, pH 8, 25 % Peg 1500,

-
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: 0.9762 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2020年7月22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: 0.9762 Å / 相対比: 1
反射解像度: 2.34→94 Å / Num. obs: 91842 / % possible obs: 100 % / 冗長度: 10.1 % / CC1/2: 1 / Rpim(I) all: 0.051 / Net I/σ(I): 9.9
反射 シェル解像度: 2.34→2.4 Å / 冗長度: 7 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4643 / CC1/2: 0.5 / Rpim(I) all: 0.7 / % possible all: 99.6

-
解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0267精密化
xia2データ削減
xia2データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6ZBP

6zbp


解像度: 2.34→93.895 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 20.742 / SU ML: 0.216 / 交差検証法: FREE R-VALUE / ESU R: 0.367 / ESU R Free: 0.23 / 詳細: Hydrogens have been added in their riding positions
Rfactor反射数%反射
Rfree0.2275 4643 5.057 %
Rwork0.1919 87174 -
all0.194 --
obs-91817 99.977 %
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータBiso mean: 53.178 Å2
Baniso -1Baniso -2Baniso -3
1-0.024 Å20.012 Å2-0 Å2
2--0.024 Å2-0 Å2
3----0.077 Å2
精密化ステップサイクル: LAST / 解像度: 2.34→93.895 Å
タンパク質核酸リガンド溶媒全体
原子数15292 0 84 323 15699
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01215826
X-RAY DIFFRACTIONr_bond_other_d0.0010.01814182
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.6621530
X-RAY DIFFRACTIONr_angle_other_deg1.2871.58332532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72951921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37821.604879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.259152358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.13715108
X-RAY DIFFRACTIONr_chiral_restr0.0690.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024154
X-RAY DIFFRACTIONr_nbd_refined0.1940.22459
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.212959
X-RAY DIFFRACTIONr_nbtor_refined0.1740.27669
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.27675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2446
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.229
X-RAY DIFFRACTIONr_nbd_other0.2570.2149
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2750.210
X-RAY DIFFRACTIONr_mcbond_it1.8833.477720
X-RAY DIFFRACTIONr_mcbond_other1.8823.4697719
X-RAY DIFFRACTIONr_mcangle_it3.0865.1949629
X-RAY DIFFRACTIONr_mcangle_other3.0865.1959630
X-RAY DIFFRACTIONr_scbond_it2.1033.6788106
X-RAY DIFFRACTIONr_scbond_other2.1033.6788106
X-RAY DIFFRACTIONr_scangle_it3.3855.43511901
X-RAY DIFFRACTIONr_scangle_other3.3855.43611902
X-RAY DIFFRACTIONr_lrange_it5.50538.72916771
X-RAY DIFFRACTIONr_lrange_other5.50138.69816753
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.056107
X-RAY DIFFRACTIONr_ncsr_local_group_20.070.056159
X-RAY DIFFRACTIONr_ncsr_local_group_30.0850.056033
X-RAY DIFFRACTIONr_ncsr_local_group_40.0770.056174
X-RAY DIFFRACTIONr_ncsr_local_group_50.0870.056029
X-RAY DIFFRACTIONr_ncsr_local_group_60.0490.053977
X-RAY DIFFRACTIONr_ncsr_local_group_70.0350.053967
X-RAY DIFFRACTIONr_ncsr_local_group_80.060.053934
X-RAY DIFFRACTIONr_ncsr_local_group_90.0510.053946
X-RAY DIFFRACTIONr_ncsr_local_group_100.0450.053992
X-RAY DIFFRACTIONr_ncsr_local_group_110.0880.056002
X-RAY DIFFRACTIONr_ncsr_local_group_120.0720.056097
X-RAY DIFFRACTIONr_ncsr_local_group_130.0910.056067
X-RAY DIFFRACTIONr_ncsr_local_group_140.0760.056134
X-RAY DIFFRACTIONr_ncsr_local_group_150.0530.053940
X-RAY DIFFRACTIONr_ncsr_local_group_160.0630.053933
X-RAY DIFFRACTIONr_ncsr_local_group_170.0670.053929
X-RAY DIFFRACTIONr_ncsr_local_group_180.0440.053987
X-RAY DIFFRACTIONr_ncsr_local_group_190.0890.055970
X-RAY DIFFRACTIONr_ncsr_local_group_200.0760.056070
X-RAY DIFFRACTIONr_ncsr_local_group_210.0910.056002
X-RAY DIFFRACTIONr_ncsr_local_group_220.0640.053898
X-RAY DIFFRACTIONr_ncsr_local_group_230.0560.053909
X-RAY DIFFRACTIONr_ncsr_local_group_240.0420.053953
X-RAY DIFFRACTIONr_ncsr_local_group_250.0790.056026
X-RAY DIFFRACTIONr_ncsr_local_group_260.0590.056147
X-RAY DIFFRACTIONr_ncsr_local_group_270.060.053919
X-RAY DIFFRACTIONr_ncsr_local_group_280.0640.053952
X-RAY DIFFRACTIONr_ncsr_local_group_290.0770.056052
X-RAY DIFFRACTIONr_ncsr_local_group_300.060.053943
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.087310.05009
12CCCX-RAY DIFFRACTIONLocal ncs0.087310.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.070320.05009
24EEEX-RAY DIFFRACTIONLocal ncs0.070320.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.084770.05009
36GGGX-RAY DIFFRACTIONLocal ncs0.084770.05009
47AAAX-RAY DIFFRACTIONLocal ncs0.076560.05009
48IIIX-RAY DIFFRACTIONLocal ncs0.076560.05009
59AAAX-RAY DIFFRACTIONLocal ncs0.086740.05009
510KKKX-RAY DIFFRACTIONLocal ncs0.086740.05009
611BBBX-RAY DIFFRACTIONLocal ncs0.049150.0501
612DDDX-RAY DIFFRACTIONLocal ncs0.049150.0501
713BBBX-RAY DIFFRACTIONLocal ncs0.035050.05011
714FFFX-RAY DIFFRACTIONLocal ncs0.035050.05011
815BBBX-RAY DIFFRACTIONLocal ncs0.059660.0501
816HHHX-RAY DIFFRACTIONLocal ncs0.059660.0501
917BBBX-RAY DIFFRACTIONLocal ncs0.051340.0501
918JJJX-RAY DIFFRACTIONLocal ncs0.051340.0501
1019BBBX-RAY DIFFRACTIONLocal ncs0.04470.05011
1020LLLX-RAY DIFFRACTIONLocal ncs0.04470.05011
1121CCCX-RAY DIFFRACTIONLocal ncs0.087940.05008
1122EEEX-RAY DIFFRACTIONLocal ncs0.087940.05008
1223CCCX-RAY DIFFRACTIONLocal ncs0.072460.05009
1224GGGX-RAY DIFFRACTIONLocal ncs0.072460.05009
1325CCCX-RAY DIFFRACTIONLocal ncs0.090840.05009
1326IIIX-RAY DIFFRACTIONLocal ncs0.090840.05009
1427CCCX-RAY DIFFRACTIONLocal ncs0.075960.05009
1428KKKX-RAY DIFFRACTIONLocal ncs0.075960.05009
1529DDDX-RAY DIFFRACTIONLocal ncs0.053440.0501
1530FFFX-RAY DIFFRACTIONLocal ncs0.053440.0501
1631DDDX-RAY DIFFRACTIONLocal ncs0.062830.0501
1632HHHX-RAY DIFFRACTIONLocal ncs0.062830.0501
1733DDDX-RAY DIFFRACTIONLocal ncs0.067020.0501
1734JJJX-RAY DIFFRACTIONLocal ncs0.067020.0501
1835DDDX-RAY DIFFRACTIONLocal ncs0.043990.0501
1836LLLX-RAY DIFFRACTIONLocal ncs0.043990.0501
1937EEEX-RAY DIFFRACTIONLocal ncs0.089040.05009
1938GGGX-RAY DIFFRACTIONLocal ncs0.089040.05009
2039EEEX-RAY DIFFRACTIONLocal ncs0.076340.05009
2040IIIX-RAY DIFFRACTIONLocal ncs0.076340.05009
2141EEEX-RAY DIFFRACTIONLocal ncs0.090720.05009
2142KKKX-RAY DIFFRACTIONLocal ncs0.090720.05009
2243FFFX-RAY DIFFRACTIONLocal ncs0.064340.0501
2244HHHX-RAY DIFFRACTIONLocal ncs0.064340.0501
2345FFFX-RAY DIFFRACTIONLocal ncs0.055530.0501
2346JJJX-RAY DIFFRACTIONLocal ncs0.055530.0501
2447FFFX-RAY DIFFRACTIONLocal ncs0.042490.0501
2448LLLX-RAY DIFFRACTIONLocal ncs0.042490.0501
2549GGGX-RAY DIFFRACTIONLocal ncs0.079440.05009
2550IIIX-RAY DIFFRACTIONLocal ncs0.079440.05009
2651GGGX-RAY DIFFRACTIONLocal ncs0.058920.05009
2652KKKX-RAY DIFFRACTIONLocal ncs0.058920.05009
2753HHHX-RAY DIFFRACTIONLocal ncs0.060430.0501
2754JJJX-RAY DIFFRACTIONLocal ncs0.060430.0501
2855HHHX-RAY DIFFRACTIONLocal ncs0.063660.0501
2856LLLX-RAY DIFFRACTIONLocal ncs0.063660.0501
2957IIIX-RAY DIFFRACTIONLocal ncs0.0770.05009
2958KKKX-RAY DIFFRACTIONLocal ncs0.0770.05009
3059JJJX-RAY DIFFRACTIONLocal ncs0.059530.0501
3060LLLX-RAY DIFFRACTIONLocal ncs0.059530.0501
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.34-2.4010.2993040.33564730.33367770.520.5251000.336
2.401-2.4660.3473420.31163200.31266620.6720.6921000.308
2.466-2.5380.3413340.361000.30264390.7440.76899.92230.295
2.538-2.6160.3074020.28957730.2961800.8120.81599.91910.278
2.616-2.7020.3093250.2758020.27261300.8410.84599.95110.253
2.702-2.7960.2992830.25455380.25658230.8610.86999.96570.23
2.796-2.9020.2763100.24253850.24456960.8710.88399.98240.216
2.902-3.020.2522680.22751270.22953970.9020.91399.96290.202
3.02-3.1540.2542700.21349250.21551950.9120.9261000.189
3.154-3.3080.2482780.21347150.21549930.920.9311000.193
3.308-3.4870.2222310.20645560.20747880.930.94299.97910.192
3.487-3.6980.2491940.19542650.19744590.9190.941000.179
3.698-3.9530.1921930.17540230.17642160.9480.9561000.162
3.953-4.2690.1991880.14737440.14939320.9570.9671000.135
4.269-4.6760.1451660.11634480.11736150.9770.97999.97230.111
4.676-5.2260.1891280.13231490.13432770.9660.9761000.124
5.226-6.0310.2231370.15627500.15928870.9550.9661000.146
6.031-7.3790.1671460.14522840.14624300.9650.9681000.138
7.379-10.4040.1621040.13917720.1418770.9660.97299.94670.14
10.404-93.8950.171400.19310050.19210450.9810.9551000.203
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)
15.7589-0.1554-2.69760.9922-1.28623.40050.03440.1764-0.2863-0.2131-0.01280.03130.1945-0.0766-0.02160.1651-0.08180.03240.11170.01060.113121.803-15.195-9.298
23.64860.3751-0.94048.8785-0.99227.32820.1420.13630.0495-0.1399-0.0386-0.0549-0.41190.3818-0.10350.0776-0.06930.00050.1006-0.00850.064730.668-6.494-0.875
32.0616-0.27890.04182.1222-0.3472.6050.0781-0.1731-0.08860.0410.11320.30480.1194-0.4398-0.19140.098-0.0806-0.01190.1240.04620.06315.747-16.1662.242
43.34671.0603-0.23123.7894-0.08384.46570.0057-0.13080.24970.17070.028-0.2634-0.22590.6423-0.03370.0412-0.0298-0.01080.202-0.07890.113342.912-12.88416.632
58.08223.3806-1.54388.88553.1722.26560.269-0.00480.187-0.629-0.086-0.3943-0.4102-0.1029-0.18290.146-0.06650.04780.3918-0.04630.353152.984-7.25311.366
61.80620.00760.33130.7345-0.46133.914-0.0693-0.17890.22950.01590.0729-0.2771-0.19150.9282-0.00360.0991-0.04520.01080.3143-0.10950.166545.664-12.87615.885
71.89291.28640.50041.5187-0.11385.80350.1229-0.12120.25080.21880.0933-0.1692-0.35320.3552-0.21620.0818-0.0264-0.02540.1315-0.15880.263838.264-7.80116.176
87.060.4973-9.04413.8962.49914.70080.06740.6669-0.0765-0.4098-0.45850.2791-0.0948-1.21390.39110.32850.0678-0.10270.22160.01420.156820.482-68.023-11.661
95.2979-1.4989-4.17841.39730.35554.59750.18820.1895-0.0829-0.3571-0.2920.0240.0922-0.08470.10370.18980.0055-0.06260.17620.01940.100919.225-73.497-6.766
105.1606-1.3728-2.12725.50371.61979.51540.43070.37890.1189-0.3738-0.0351-0.4884-0.57180.6382-0.39560.1376-0.0548-0.02920.1859-0.02380.178129.501-65.9961.237
112.18650.4212-0.27632.3963-0.03861.39690.1973-0.1646-0.06840.3073-0.19950.3060.0357-0.16930.00220.1631-0.073-0.03330.0747-0.01260.101413.926-73.9445.236
121.75293.4462-1.16237.1595-0.90155.78880.0769-0.0267-0.08160.1510.2235-0.23910.03091.0226-0.30040.12650.0319-0.13240.3665-0.06440.181246.748-75.87924.015
134.1130.71460.06613.50980.09115.24310.06480.02910.2691-0.10490.111-0.2249-0.2460.8109-0.17580.0729-0.0307-0.04780.2943-0.08160.143844.216-73.5815.276
149.0629-1.8768-0.79698.6961-3.82674.65290.21010.0042-0.1083-0.2801-0.1529-0.00870.06130.2466-0.05710.0523-0.021-0.03990.1571-0.03810.066433.594-72.36.043
150.0990.1582-0.55451.9029-0.05365.12050.0808-0.08970.10740.01760.1070.0616-0.25290.5417-0.18780.1469-0.10040.0730.1696-0.1280.338138.741-69.21819.44
167.83891.6539-4.40282.6033-0.60916.87360.1589-1.28460.04540.693-0.39190.1180.10950.48260.23290.3447-0.1048-0.0020.2643-0.05520.15233.919-38.58713.19
174.14490.5582-0.58131.3720.38731.81160.0551-0.2834-0.10460.3548-0.07090.083-0.2117-0.05290.01580.17260.00850.00710.0536-0.0350.108933.353-43.0998.213
184.2480.22970.04343.0188-0.61772.70120.03370.252-0.3493-0.189-0.0765-0.33120.05410.42670.04280.11610.0091-0.01310.1131-0.05190.115740.279-46.372-3.948
191.9561-0.55910.82372.98910.70180.86660.0145-0.01670.0992-0.17580.0374-0.1808-0.03730.1384-0.05190.113-0.0071-0.02110.1811-0.08080.061937.87-42.985-0.172
204.1014-4.3987-2.22067.37061.3893.46690.11170.06630.1168-0.11370.07410.2134-0.1464-0.2954-0.18580.09120.0179-0.09680.1738-0.03940.19898.341-44.416-23.002
211.3442-1.35571.34842.28272.101914.714-0.22350.4215-0.10590.3404-0.3440.23690.39580.81370.56760.2107-0.05560.09570.24280.01430.29419.985-56.234-14.324
223.0871-0.39920.26312.3818-0.50652.7746-0.0013-0.07210.37160.12610.07480.3055-0.319-0.4779-0.07350.08280.0760.01080.1064-0.02360.166110.09-40.669-13.821
231.30830.30621.06260.82250.61185.4284-0.1703-0.01410.04180.05790.19150.2396-0.2902-0.2739-0.02120.0930.0543-0.01630.08510.05380.145117.13-38.074-15.464
249.8026-2.20537.34976.1018-3.292312.2269-0.2703-0.942-0.03720.50310.16360.1873-0.3191-0.55780.10670.1353-0.0680.07550.26110.03550.147714.471-14.95263.37
253.6258-1.46862.86442.6417-3.28664.47910.0399-0.4145-0.2123-0.14640.08940.05040.192-0.2742-0.12920.1403-0.05320.05630.20350.01690.087818.445-12.79258.434
261.76280.13290.06163.3436-0.78051.902-0.02830.09990.332-0.28670.06430.18530.0338-0.1396-0.03590.049-0.02990.00320.1084-0.00680.091116.919-4.31945.752
272.4370.96080.97622.0012-0.30343.3534-0.0905-0.09660.1131-0.10050.14330.2015-0.0712-0.0631-0.05280.0669-0.00860.04990.0856-0.00030.08217.33-11.48751.444
281.27673.0396-0.606710.0909-4.16933.18640.00730.1368-0.3049-0.35050.067-0.37660.44670.1137-0.07440.31730.08450.06380.2669-0.08540.194238.417-30.09828.999
292.92610.6736-0.51395.39041.17334.4277-0.0983-0.0173-0.40540.2067-0.01680.00360.83290.23590.11510.27990.0969-0.0310.1126-0.04190.1134.818-29.89937.552
309.77367.0247-2.562610.9467-2.60674.472-0.0008-0.05320.118-0.04980.18780.3560.51850.2728-0.1870.17570.01550.00980.0501-0.03030.068827.262-22.06846.526
312.71792.183-0.30711.9542-1.15254.1290.05720.1678-0.1224-0.04840.1363-0.05570.4524-0.0253-0.19350.2069-0.0092-0.01750.0602-0.05920.101428.193-28.05733.162
328.5286-5.1943.06598.7831-2.9941.5919-0.2503-0.8050.20620.53160.2844-0.0721-0.3626-0.2222-0.03420.2206-0.05740.14690.5070.09130.305720.129-76.37566.615
333.3057-2.51370.47473.7581-1.1432.88310.0038-0.3837-0.13290.13730.06680.12060.2796-0.5921-0.07070.2593-0.04390.08940.3920.07160.19623.962-74.0561.604
343.1008-1.5478-0.04783.15990.52532.71050.18170.04930.03-0.2496-0.11020.3306-0.2563-0.5993-0.07150.08240.02840.01360.31280.02150.144622.213-66.3649.573
350.9079-0.1242-0.7322.35540.67560.93310.06070.0065-0.0642-0.1245-0.14470.5353-0.0824-0.40360.0840.14550.0080.04690.67240.11570.267520.897-69.83953.109
362.59550.74270.90870.2738-0.26724.87390.00370.225-0.3035-0.03760.0691-0.09220.34910.1007-0.07270.11920.0317-0.11160.1993-0.04670.17738.459-87.74931.162
372.74250.3047-1.02264.06171.07413.61780.1026-0.0466-0.45540.294-0.00430.10640.9177-0.171-0.09830.3212-0.0204-0.14880.1577-0.00220.201434.172-94.20837.484
383.4271-2.6595-1.70037.30590.22125.435-0.020.0449-0.1281-0.0815-0.16030.11080.6554-0.13170.18040.1614-0.1071-0.0840.23430.03830.222929.456-84.45748.042
392.57552.4950.90252.73180.30353.24240.12580.0088-0.06380.0005-0.06290.18040.2285-0.1511-0.0630.1555-0.0523-0.13430.192-0.05770.296928.108-89.27734.162
4012.9191-0.5378-9.76596.0185.262211.3570.02330.6429-0.0534-0.7897-0.22620.1738-0.5267-0.59960.20290.55260.0983-0.03570.34950.04480.1266-31.203-37.842-9.036
414.4366-2.2453-2.35222.58661.28023.6250.24890.599-0.0204-0.6035-0.2504-0.1931-0.22050.03540.00150.2485-0.06970.00340.22770.02660.1535-33.379-43.456-4.687
423.338-1.6878-3.81170.91842.321710.57950.48460.1310.2573-0.3513-0.0481-0.1618-0.55180.3897-0.43650.3972-0.04680.10350.2126-0.02940.2672-22.527-37.9033.82
433.10650.86310.30812.1208-0.21821.69010.0238-0.0419-0.04320.0186-0.04190.20860.0611-0.19590.01810.1304-0.0679-0.03290.09-0.00680.0687-38.954-43.8617.317
443.47143.7501-2.13515.0836-0.78053.5793-0.1291-0.0469-0.1883-0.03420.1732-0.31230.21840.3938-0.04410.12820.0287-0.03310.16530.02950.1218-8.4-50.01127.506
453.92551.09331.13033.5025-0.14674.4373-0.13320.28710.0638-0.14290.0728-0.22-0.06530.49880.06030.04480.00160.0390.1351-0.02790.085-9.961-47.58618.608
467.61691.56222.63939.8921-1.04021.18850.30450.40740.074-0.418-0.3104-0.03130.21740.22540.00590.15990.0311-0.01990.1344-0.0810.0871-19.534-45.1048.508
471.66611.3216-0.66732.7522-1.00363.34480.0402-0.11660.1528-0.02670.024-0.07350.03060.1058-0.06410.0342-0.00450.01290.0241-0.03040.0422-14.942-42.33822.244
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA347 - 368
2X-RAY DIFFRACTION2ALLAAA369 - 378
3X-RAY DIFFRACTION3ALLAAA379 - 527
4X-RAY DIFFRACTION4ALLBBB1 - 63
5X-RAY DIFFRACTION5ALLBBB64 - 69
6X-RAY DIFFRACTION6ALLBBB70 - 104
7X-RAY DIFFRACTION7ALLBBB105 - 124
8X-RAY DIFFRACTION8ALLCCC333 - 346
9X-RAY DIFFRACTION9ALLCCC347 - 368
10X-RAY DIFFRACTION10ALLCCC369 - 378
11X-RAY DIFFRACTION11ALLCCC379 - 527
12X-RAY DIFFRACTION12ALLDDD1 - 23
13X-RAY DIFFRACTION13ALLDDD24 - 99
14X-RAY DIFFRACTION14ALLDDD100 - 106
15X-RAY DIFFRACTION15ALLDDD107 - 124
16X-RAY DIFFRACTION16ALLEEE333 - 346
17X-RAY DIFFRACTION17ALLEEE347 - 371
18X-RAY DIFFRACTION18ALLEEE372 - 488
19X-RAY DIFFRACTION19ALLEEE489 - 527
20X-RAY DIFFRACTION20ALLFFF1 - 24
21X-RAY DIFFRACTION21ALLFFF25 - 32
22X-RAY DIFFRACTION22ALLFFF33 - 103
23X-RAY DIFFRACTION23ALLFFF104 - 124
24X-RAY DIFFRACTION24ALLGGG333 - 346
25X-RAY DIFFRACTION25ALLGGG347 - 373
26X-RAY DIFFRACTION26ALLGGG374 - 492
27X-RAY DIFFRACTION27ALLGGG493 - 527
28X-RAY DIFFRACTION28ALLHHH1 - 24
29X-RAY DIFFRACTION29ALLHHH25 - 99
30X-RAY DIFFRACTION30ALLHHH100 - 106
31X-RAY DIFFRACTION31ALLHHH107 - 124
32X-RAY DIFFRACTION32ALLIII333 - 346
33X-RAY DIFFRACTION33ALLIII347 - 371
34X-RAY DIFFRACTION34ALLIII372 - 487
35X-RAY DIFFRACTION35ALLIII488 - 527
36X-RAY DIFFRACTION36ALLJJJ1 - 32
37X-RAY DIFFRACTION37ALLJJJ33 - 99
38X-RAY DIFFRACTION38ALLJJJ100 - 106
39X-RAY DIFFRACTION39ALLJJJ107 - 124
40X-RAY DIFFRACTION40ALLKKK333 - 346
41X-RAY DIFFRACTION41ALLKKK347 - 368
42X-RAY DIFFRACTION42ALLKKK369 - 378
43X-RAY DIFFRACTION43ALLKKK379 - 527
44X-RAY DIFFRACTION44ALLLLL1 - 23
45X-RAY DIFFRACTION45ALLLLL24 - 99
46X-RAY DIFFRACTION46ALLLLL100 - 106
47X-RAY DIFFRACTION47ALLLLL107 - 124

+
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://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

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

+
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

+
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。

-
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