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- PDB-6niu: Crystal structure of a human anti-ZIKV-DENV neutralizing antibody... -

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基本情報

登録情報
データベース: PDB / ID: 6niu
タイトルCrystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ4 in complex with ZIKV E glycoprotein
要素
  • Envelope protein E
  • Human MZ4 Fab heavy chain
  • Human MZ4 Fab light chain
キーワードViral protein/IMMUNE SYSTEM / ZIKV-DENV / Antibody / human / Vaccination / ANTIVIRAL PROTEIN / IMMUNE SYSTEM / Viral protein-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / molecular adaptor activity / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / centrosome / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
類似検索 - 分子機能
Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Genome polyprotein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Zika virus (ジカ熱ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4.303 Å
データ登録者Sankhala, R.S. / Dussupt, V. / Donofrio, G. / Choe, M. / Modjarrad, K. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
資金援助 米国, 1件
組織認可番号国
Other governmentW81XWH-07-2-0067 米国
引用ジャーナル: Nat. Med. / 年: 2020
タイトル: Potent Zika and dengue cross-neutralizing antibodies induced by Zika vaccination in a dengue-experienced donor.
著者: Dussupt, V. / Sankhala, R.S. / Gromowski, G.D. / Donofrio, G. / De La Barrera, R.A. / Larocca, R.A. / Zaky, W. / Mendez-Rivera, L. / Choe, M. / Davidson, E. / McCracken, M.K. / Brien, J.D. / ...著者: Dussupt, V. / Sankhala, R.S. / Gromowski, G.D. / Donofrio, G. / De La Barrera, R.A. / Larocca, R.A. / Zaky, W. / Mendez-Rivera, L. / Choe, M. / Davidson, E. / McCracken, M.K. / Brien, J.D. / Abbink, P. / Bai, H. / Bryan, A.L. / Bias, C.H. / Berry, I.M. / Botero, N. / Cook, T. / Doria-Rose, N.A. / Escuer, A.G.I. / Frimpong, J.A. / Geretz, A. / Hernandez, M. / Hollidge, B.S. / Jian, N. / Kabra, K. / Leggat, D.J. / Liu, J. / Pinto, A.K. / Rutvisuttinunt, W. / Setliff, I. / Tran, U. / Townsley, S. / Doranz, B.J. / Rolland, M. / McDermott, A.B. / Georgiev, I.S. / Thomas, R. / Robb, M.L. / Eckels, K.H. / Barranco, E. / Koren, M. / Smith, D.R. / Jarman, R.G. / George, S.L. / Stephenson, K.E. / Barouch, D.H. / Modjarrad, K. / Michael, N.L. / Joyce, M.G. / Krebs, S.J.
履歴
登録2018年12月31日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年12月25日Provider: repository / タイプ: Initial release
改定 1.12020年2月19日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22020年2月26日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.32023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.42024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
H: Human MZ4 Fab heavy chain
L: Human MZ4 Fab light chain
B: Envelope protein E
A: Envelope protein E
Z: Envelope protein E
E: Envelope protein E
F: Human MZ4 Fab heavy chain
G: Human MZ4 Fab light chain
I: Human MZ4 Fab heavy chain
J: Human MZ4 Fab light chain
M: Human MZ4 Fab heavy chain
N: Human MZ4 Fab light chain


分子量 (理論値)分子数
合計 (水以外)293,39612
ポリマ－293,39612
非ポリマー00
水00
1
H: Human MZ4 Fab heavy chain
L: Human MZ4 Fab light chain
Z: Envelope protein E
E: Envelope protein E
M: Human MZ4 Fab heavy chain
N: Human MZ4 Fab light chain


分子量 (理論値)分子数
合計 (水以外)146,6986
ポリマ－146,6986
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Envelope protein E
A: Envelope protein E
F: Human MZ4 Fab heavy chain
G: Human MZ4 Fab light chain
I: Human MZ4 Fab heavy chain
J: Human MZ4 Fab light chain


分子量 (理論値)分子数
合計 (水以外)146,6986
ポリマ－146,6986
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)113.530, 137.260, 136.790
Angle α, β, γ (deg.)80.120, 65.740, 65.750
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21chain B
31chain E
41chain Z
12chain F
22chain H
32chain I
42chain M
13chain G
23chain J
33chain L
43chain N

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILESERSERchain AAD1 - 4031 - 403
21ILEILESERSERchain BBC1 - 4031 - 403
31ILEILESERSERchain EEF1 - 4031 - 403
41ILEILESERSERchain ZZE1 - 4031 - 403
12GLNGLNSERSERchain FFG1 - 1131 - 120
22GLNGLNSERSERchain HHA1 - 1131 - 120
32GLNGLNSERSERchain III1 - 1131 - 120
42GLNGLNSERSERchain MMK1 - 1131 - 120
13GLNGLNLEULEUchain GGH1 - 1071 - 111
23GLNGLNLEULEUchain JJJ1 - 1071 - 111
33GLNGLNLEULEUchain LLB1 - 1071 - 111
43GLNGLNLEULEUchain NNL1 - 1071 - 111

NCSアンサンブル:
ID
1
2
3

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要素

#1: 抗体
Human MZ4 Fab heavy chain


分子量: 13219.568 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 詳細 (発現宿主): pVRC8400 / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)
#2: 抗体
Human MZ4 Fab light chain


分子量: 11731.954 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 詳細 (発現宿主): pVRC8400 / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)
#3: タンパク質
Envelope protein E


分子量: 48397.520 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) (ジカ熱ウイルス)
株: isolate ZIKV/Human/French Polynesia/10087PF/2013 / 詳細 (発現宿主): pMT-BiP / 細胞株 (発現宿主): DS2
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
参照: UniProt: A0A024B7W1
Has protein modificationY

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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: 4.85 Å3/Da / 溶媒含有率: 74.65 % / 解説: Plate like crystals
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 9.5
詳細: 1.26 M ammonium sulfate, 0.1 M CHES/NaOH (pH 9.5) and 0.2 M sodium chloride

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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: APS / ビームライン: 19-BM / 波長: 0.97 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2017年12月15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: 0.97 Å / 相対比: 1
反射解像度: 4.2→50 Å / Num. obs: 16201 / % possible obs: 53.2 % / 冗長度: 1.6 %
詳細: The diffraction data was corrected for anisotropy using diffraction anisotropy correction server, which resulted in less reflections for refinement
Rpim(I) all: 0.23 / Rsym value: 0.23 / Net I/σ(I): 2.64
反射 シェル解像度: 4.2→4.35 Å / Num. unique obs: 2954 / Rsym value: 0.515

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
PDB_EXTRACT3.25データ抽出
HKL-2000データ削減
HKL-2000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: 4UTA, 5IRE

4uta

5ire


解像度: 4.303→9.997 Å / SU ML: 0.96 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 45.06
Rfactor反射数%反射
Rfree0.359 629 4.96 %
Rwork0.2641 --
obs0.2689 12689 29.63 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 387.47 Å2 / Biso mean: 142.9901 Å2 / Biso min: 18.39 Å2
精密化ステップサイクル: final / 解像度: 4.303→9.997 Å
タンパク質核酸リガンド溶媒全体
原子数19232 0 0 0 19232
残基数----2520
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A4828X-RAY DIFFRACTION1.298TORSIONAL
12B4828X-RAY DIFFRACTION1.298TORSIONAL
13E4828X-RAY DIFFRACTION1.298TORSIONAL
14Z4828X-RAY DIFFRACTION1.298TORSIONAL
21F1448X-RAY DIFFRACTION1.298TORSIONAL
22H1448X-RAY DIFFRACTION1.298TORSIONAL
23I1448X-RAY DIFFRACTION1.298TORSIONAL
24M1448X-RAY DIFFRACTION1.298TORSIONAL
31G1340X-RAY DIFFRACTION1.298TORSIONAL
32J1340X-RAY DIFFRACTION1.298TORSIONAL
33L1340X-RAY DIFFRACTION1.298TORSIONAL
34N1340X-RAY DIFFRACTION1.298TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.303-4.69490.3676290.21125135425
4.6949-5.28460.3256890.22921805189418
5.2846-6.35930.36552090.26424228443742
6.3593-9.9970.36453020.28115514581654
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)
10.02410.003-0.00840.00460.0007-0.0008-0.15850.0170.09820.12780.05360.04910.19410.0754-0.00030.45930.15270.07920.55920.26291.2312-80.9185.72584.491
20.0092-0.0034-0.00130.00350.00720.00580.1878-0.07640.0664-0.0550.14410.0374-0.0959-0.0194-0.00051.0925-0.49890.19690.91050.22750.9687-72.91764.28288.204
30.1224-0.03470.03040.016-0.007-0.00170.73210.12250.0921-0.17380.1557-0.0025-0.26780.08530.05530.84760.36950.08720.56320.11310.4969-74.43986.80986.324
40.2610.10570.17470.1352-0.11550.5134-0.19360.30830.0647-0.1094-0.14680.0435-0.3570.3393-0.03660.8413-0.0760.10830.7874-0.41231.6685-73.83482.08397.397
50.06740.06340.08070.07680.09690.1019-0.0856-0.17440.1116-0.4041-0.0284-0.0794-0.259-0.00150.01041.4457-0.5475-0.19530.44190.53431.2154-67.6577.51197.398
6-0.00360.00040.01180.0039-0.01380.0241-0.26370.3057-0.11160.05590.05850.1405-0.17970.2733-0.0010.1585-0.25820.19680.586-0.08360.7726-69.39782.61885.988
70.02430.00710.00420.0007-0.00640.0104-0.05190.0006-0.03140.11220.11730.1133-0.04070.04080.00010.8759-0.3276-0.03671.34960.00180.5327-73.8865.76896.353
80.0939-0.00360.0198-0.00110.00320.0078-0.12680.090.1238-0.02060.02020.0405-0.0352-0.02660.05670.99280.2832-0.44350.8832-0.11410.5566-80.3679.59993.469
90.9721-1.1489-0.0421.5142-0.34690.83640.06880.7934-0.7088-0.3015-0.14880.6740.2441-0.4095-0.224-0.2160.3731-0.29020.95870.36280.9519-79.72493.54494.645
106.5071.3653-0.41314.6658-2.45653.4163-0.12970.0159-0.5827-0.03470.05690.89350.27580.3059-0.12070.28740.3938-0.1430.799-0.3111.2579-80.41566.00390.375
110.22170.0098-0.07270.2060.10490.0761-0.12660.04030.00370.0072-0.0933-0.01760.17050.1662-0.15960.4096-0.68140.16120.61320.38830.9489-84.49581.604112.948
120.0092-0.00690.00990.03920.00660.00160.05250.0266-0.03710.08890.0588-0.02750.0106-0.03310.0321.4520.71190.1320.6952-1.20841.0249-105.67386.089109.875
130.0597-0.00110.0162-0.0028-0.00280.00260.0187-0.01750.0103-0.03540.07040.1107-0.0785-0.0624-0.00011.2734-0.4466-0.42091.40930.18071.6342-92.92687.737112.703
140.0799-0.0364-0.03810.0525-0.01920.0374-0.01560.1947-0.026-0.3225-0.47170.1170.22430.4575-0.05540.17640.4412-0.33390.9584-0.09981.161-82.79690.137108.219
150.0706-0.0268-0.11280.11650.06810.18-0.0186-0.2087-0.0189-0.02330.03740.0039-0.31160.01120.11520.5334-0.2243-0.51561.04990.18270.7577-91.33783.99296.338
160.14220.00140.07760.02960.0390.08290.0670.11690.0801-0.0721-0.0119-0.0539-0.01580.00560.09910.862-0.5631.15750.49770.08230.8549-90.30697.91599.537
170.03580.00680.04060.02530.00690.0558-0.01470.19180.01070.08950.0532-0.0964-0.0581-0.2605-0.00110.18910.2362-0.0390.4247-0.21750.7145-96.45495.022104.03
180.0917-0.01080.02890.037-0.02660.02440.0361-0.02920.021-0.13410.12840.07690.0117-0.0430.04490.972-0.49940.51711.11830.4350.9108-90.62492.347112.5
190.0251-0.0111-0.03120.14490.05360.0526-0.00660.1131-0.0045-0.0949-0.0863-0.1050.10950.1206-0.02790.93650.4552-0.34580.83150.00331.1116-103.96385.304101.535
200.15260.0424-0.11250.0809-0.02190.07820.1715-0.01360.11710.01690.2755-0.1613-0.0862-0.1040.28710.51340.2680.82170.73720.00140.8321-84.87185.43105.281
210.4169-0.7274-0.08511.28650.12280.1196-0.17890.1868-0.0925-0.598-0.02710.55160.49470.0455-0.56381.3405-0.0582-0.5692-0.38290.08620.5345-77.47284.687107.212
220.22620.0141-1.05065.812-0.35874.88880.02240.23120.03360.4344-0.22280.9447-0.1898-1.34190.16780.7921-0.10780.4780.972-0.25140.547-103.60579.041107.781
231.7126-0.7271-0.05941.5128-0.37630.1510.1431-0.067-0.32640.70720.36770.61690.2310.45120.01091.11070.4379-0.09181.1545-0.37550.8348-115.47868.31383.213
241.2080.3467-0.16631.8474-0.48593.14990.2616-0.13060.19680.47510.4891-0.15080.36480.75960.20540.96510.11640.47330.7412-0.72640.6759-61.29269.05868.979
250.4222-0.99110.51792.5159-1.31321.02040.12780.0672-0.1680.63910.7322-0.28470.01330.7167-0.12571.27760.2405-0.55960.4632-0.10171.1973-47.20762.50267.882
260.39010.319-0.11250.31930.02270.72330.48760.3749-0.34480.74240.25840.2709-0.7540.32490.23630.6367-0.4509-0.15281.4720.31611.0946-81.15672.28273.236
271.1860.4357-1.04840.4915-0.73981.42880.03620.50190.2741-0.6203-0.4565-0.2035-1.1454-0.2830.62151.2155-0.2126-0.14480.9642-0.24271.3389-114.87881.03774.697
281.6697-0.0602-1.07870.11650.65512.03520.9317-0.70170.09790.15240.3626-0.00271.02330.9585-0.2830.6332-0.070.05270.66380.39721.1532-79.30265.35572.959
290.5219-0.35370.02790.6131-0.19320.1665-0.0826-0.7133-0.00040.38540.5060.02050.22420.32770.36520.6022-0.69450.19290.54490.920.1208-120.0772.1376.609
300.2430.0538-0.09760.0165-0.03540.2426-0.382-0.1420.35350.1170.0656-0.0862-0.2073-0.05570.10.53680.2760.02860.51930.15791.4039-137.71267.16175.314
310.8088-0.2841-0.44281.4323-0.04420.3734-0.1948-0.30270.2909-0.3144-0.4105-0.2380.19310.2427-0.13610.70370.5652-0.03730.61740.48781.0529-135.42865.06471.964
323.4744-1.40490.92321.18580.51290.6955-0.2427-0.02160.43920.30260.1944-0.38630.1423-0.1308-0.00420.817-0.06140.11690.3876-0.04511.196-69.19546.79451.133
330.73120.6596-0.25910.99450.70932.4747-0.19010.3154-0.0150.1376-0.1481-0.33320.0028-0.37070.33360.7726-0.00870.10080.73380.08460.9749-24.78545.86852.155
340.7121-0.88310.07391.2940.32140.26250.87150.46170.2962-0.04381.02520.4192-0.6347-0.52440.12850.5896-0.0445-0.2310.89020.31470.5753-59.161115.02299.551
350.5014-0.6411-0.33741.0031-0.0741.502-0.62230.31870.43580.31740.00780.1129-0.02710.1399-0.7082-0.17890.2268-0.39291.90140.18460.9988-4.563114.401114.009
360.29440.37970.37470.1184-0.01931.11060.7514-0.0767-0.41320.04380.19740.01660.01870.97170.75880.7490.3425-0.47210.00580.68630.4039-26.088114.171109.933
370.8606-0.25880.00880.5296-0.04071.0516-0.1731-0.09590.27460.052-0.1355-0.36680.65390.08980.46260.43370.0112-0.44030.52530.36330.8051-69.213111.52107.128
380.420.4481-0.09220.84620.61260.9987-0.40840.62350.8972-0.1382-0.2450.49710.608-0.2430.13610.41290.23650.09740.94130.49610.7141-80.31119.578107.089
393.2119-1.46280.71150.685-0.48181.33320.56311.00990.4447-0.8276-0.6605-0.5309-0.46540.4893-0.34392.13090.35140.04870.7466-0.19270.813616.317147.591128.816
402.819-1.3740.05421.5804-1.11451.2240.2717-0.3038-0.46950.2592-0.0170.06190.75990.5075-0.27010.5513-0.37010.06391.1992-0.64921.362-28.763131.207133.296
410.83360.35830.03071.09020.61480.59070.22170.1940.2252-0.3626-1.0560.6491-1.0681-1.172-0.30480.0441-0.69361.10570.22620.30210.3146-36.182133.419128.914
423.4705-2.1783-2.0062.43941.71686.8852-0.06090.1036-0.43960.12030.02170.2910.5891-0.28380.07170.4758-0.44670.4481.39770.06020.922720.515133.165139.997
431.30380.35620.97320.5484-0.16570.90440.2230.18190.2666-0.36530.35440.3101-0.5694-0.60840.88770.5370.6175-0.35390.46970.1335-0.5582-0.647144.547135.154
443.29610.34490.03452.78240.9732.0099-0.1873-0.14590.4142-0.30060.1338-0.67220.28070.0672-0.32340.8073-0.20310.34480.8082-0.45481.2091-35.012130.723125.989
450.81610.17330.11670.8428-0.32180.71410.69230.5140.2018-0.6776-0.4305-0.07870.06160.2160.41621.05320.0362-0.59990.92820.37350.80652.57140.247131.891
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471.93960.40690.30341.42750.23020.89940.20060.03060.3828-0.77440.32940.2368-0.2105-0.0846-0.01630.34780.05610.17471.2514-0.36082.633136.791136.296125.207
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5010.82660.13220.67720.10070.0142-0.0484-0.01390.0624-0.02180.0360.0090.0453-0.03350.05240.3114-0.2099-0.55730.01130.11880.2788-131.394105.37695.485
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530.30440.3505-0.29580.4117-0.35280.2724-0.2952-0.0919-0.1272-0.1421-0.4215-0.1663-0.14970.3415-0.05710.6437-0.2161-0.20681.8659-0.0340.7632-135.382106.73981.306
540.005-0.0063-0.00180.0323-0.02670.011-0.39630.08770.0088-0.0954-0.24590.2297-0.2937-0.11670.00041.5735-0.710.0681.83890.18762.3288-122.34896.04385.714
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560.08910.0931-0.01440.2746-0.07140.0224-0.0073-0.2521-0.19570.1028-0.08360.02020.21730.00640.01110.5976-0.3164-0.68590.4253-0.8890.3934-126.688101.82395.639
570.0156-0.07270.01830.3077-0.08730.0216-0.2093-0.091-0.08850.29650.14690.10460.13950.26050.06980.94810.07090.12670.8628-0.07530.2294-134.113110.99486.498
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610.4080.00150.38350.272-0.08560.39810.1213-0.08360.07980.1480.0986-0.0812-0.129-0.15030.22640.57650.09520.0260.8523-0.33990.3731-161.80698.7871.388
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630.00330.0027-0.00440.0043-0.00540.00960.05070.0204-0.0474-0.022-0.0654-0.10890.0412-0.01190.010.9887-0.0948-0.05010.60950.09391.0587-145.68496.98179.321
640.00440.00260.00880.01170.00080.0003-0.2098-0.08090.05190.1555-0.0270.03190.0298-0.07260.00040.6050.0324-0.02540.8179-0.27111.0086-147.93699.8286.068
650.03750.11230.04870.31470.05090.1515-0.0912-0.0450.0105-0.1969-0.0804-0.02430.2721-0.0311-0.13570.64230.4205-0.03380.5034-0.86750.3911-149.186.26183.318
660.2179-0.0982-0.00240.0978-0.08570.1068-0.027-0.1103-0.02480.31530.25470.1706-0.3284-0.15210.06740.55120.5925-0.18570.3046-0.21140.4861-148.07790.45671.858
670.2769-0.33990.19690.4691-0.23230.14210.0844-0.1920.10150.4067-0.00170.1577-0.3943-0.1129-0.10560.7167-0.42170.26360.5950.10380.6693-160.65999.1880.029
680.09570.17520.21740.72020.19810.6277-0.07310.12870.1356-0.1735-0.09590.09730.0068-0.0074-0.43810.75910.2869-0.22531.1445-0.96230.9152-136.20798.52374.791
690.5244-0.0051-0.74230.131-0.07911.11230.0042-1.5487-1.0291-0.03880.40070.4610.2859-0.9851-0.94910.4277-0.3338-0.06941.46110.76010.7529-139.711101.78974.556
700.83110.3120.1170.3682-0.06670.06610.0757-0.40760.034-0.2031-0.50730.59720.1761-0.43360.19851.0611-0.5581-0.66981.5917-0.4731.0424-160.386105.26973.954
710.0399-0.0083-0.01030.0129-0.00480.00190.07030.12970.4716-0.08810.09850.1104-0.1004-0.0167-0.00070.93760.48450.05161.43050.20260.1859-21.28324.2111.785
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730.1833-0.2397-0.27940.29720.35420.3509-0.27520.36210.03070.0485-0.5603-0.02270.1020.4703-0.06840.29110.0643-0.39990.77410.06990.7157-20.10835.90516.643
740.3066-0.1925-0.37270.12430.25290.4948-0.3289-0.5816-0.1520.1725-0.04850.06630.343-0.0227-0.28940.52870.0681-0.29541.47010.65420.5811-31.20935.00418.37
750.0922-0.05570.06950.0228-0.03480.02020.2427-0.13410.36440.26340.2270.0909-0.0802-0.5422-0.00030.6812-0.093-0.05791.1798-0.19321.1217-23.82329.09714.365
761.5692-1.42740.86771.4472-0.76260.73710.05040.37140.4221-0.0054-0.0637-0.1092-0.1896-0.10170.2207-0.12590.20750.24130.7780.69710.8267-19.76735.04934.343
770.2785-0.2966-0.00040.5217-0.06570.015-0.10070.554-0.2245-0.3105-0.49250.10590.32180.43950.23250.9267-0.09410.33771.11510.5541.6963-15.74828.1311.559
780.2312-0.0899-0.07380.1299-0.077-0.0113-0.2809-0.2763-0.0609-0.16090.09960.04520.079-0.48020.321-0.2616-1.10870.9837-1.18830.7846-0.3601-9.00248.60823.278
79-0.00560.0023-0.00410.0492-0.01810.0080.07510.1481-0.0088-0.0205-0.12810.041-0.065-0.0046-0.03530.7150.3607-0.00420.3674-0.86840.8897-7.59734.74723.002
800.4209-0.01780.03130.13310.06550.04070.2507-0.1808-0.1603-0.0990.20120.0541-0.0151-0.1050.25130.6207-0.15920.2070.4717-0.11560.6702-4.83537.10334.6
811.5594-0.75750.26010.8379-0.04540.5213-0.16350.2956-0.1467-0.0376-0.21710.076-0.25770.53110.61420.5847-0.0636-0.39780.25150.0680.8891-8.10544.9223.165
820.17770.05580.0203-0.00010.01390.2417-0.1128-0.3941-0.39110.20650.2670.11630.05280.00780.22850.63520.28620.4652-0.4283-0.56410.607134.087159.475168.855
830.27020.1104-0.09570.233-0.06290.13590.02730.03550.0227-0.0515-0.05870.01310.0318-0.0209-0.0820.3715-0.2629-0.54151.4189-0.02150.911732.152158.176150.741
840.3734-0.0925-0.2910.3089-0.08450.33930.15620.23810.2228-0.07830.11170.0455-0.2723-0.23780.32150.87360.01710.10540.4731-0.45281.138634.139150.077163.019
850.56250.0430.18760.00040.01070.5689-0.1059-0.1367-0.0734-0.0406-0.1404-0.08950.18630.399-0.08960.5081-0.87570.08410.45350.25591.124536.317145.3168.05
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870.0956-0.015-0.04870.00130.0310.20010.00830.29870.18910.04690.07530.16710.0067-0.28040.2752-0.2216-0.26450.62040.98040.49830.367225.517148.225167.701
880.188-0.01510.0570.06180.05120.0347-0.10830.04280.1467-0.30290.07690.1991-0.2083-0.08320.02791.0101-0.63840.01110.33880.38861.097728.711155.542169.17
890.00460.0032-0.01420.009-0.01680.02620.04830.06990.0394-0.0401-0.03240.1458-0.02390.06430.01540.4648-0.44090.15970.6035-0.11260.603238.101152.047165.637
902.6145-1.23790.44523.6738-1.02621.5159-0.4809-0.72080.37441.50510.1734-0.8905-0.62290.13670.16170.58940.1909-0.14790.19590.26130.433437.797149.311152.349
912.987-0.42032.15855.2389-1.34819.8216-0.0783-0.0403-0.062-0.20820.0875-0.01910.05150.35670.02280.68240.10770.10141.15550.39271.70737.935155.365179.249
920.00290.0043-0.00350.0168-0.00860.0062-0.1154-0.0396-0.05540.0735-0.0437-0.03120.01670.0187-0.00011.1022-0.36760.13571.03720.0661.610843.073130.04166.328
930.0048-0.0042-0.00840.0290.02480.0085-0.0056-0.0532-0.02120.00320.02480.04750.0291-0.0524-0.00620.32570.2629-0.13160.61470.10830.862358.511134.201160.263
940.0178-0.00770.00530.020.01520.0267-0.0057-0.0027-0.0112-0.00490.0872-0.1319-0.05240.20220.01620.4357-0.2074-0.21451.71150.41631.021135.467132.281153.649
950.14380.0364-0.01740.0356-0.0086-0.00060.01060.1596-0.04260.1188-0.0929-0.0122-0.0378-0.076-0.03780.2572-0.1307-0.3354-0.2009-0.59590.426246.928143.2158.482
960.02880.0337-0.0130.0306-0.01330.00550.019-0.25810.0296-0.01370.0324-0.1551-0.04210.0474-0.06280.5307-0.1781-0.6433-0.0467-0.25860.976948.712149.44161.664
970.0122-0.01620.0380.0142-0.06080.27530.0215-0.09890.14560.00320.0550.0746-0.1690.01310.23730.4730.04680.35620.49-0.03670.769850.331146.769147.824
98-0.00150.00150.00230.0661-0.15480.34870.21680.09020.0652-0.11390.2744-0.0773-0.011-0.1890.06070.77310.1390.3109-0.2808-0.01710.521149.397135.184152.109
990.03040.0236-0.02210.06950.02570.0404-0.14940.0569-0.03120.1974-0.02880.00440.0048-0.0203-0.14290.46920.07490.579-0.0972-0.58840.557561.676144.288160.498
1000.06560.0050.0122-0.0049-0.010.04570.03030.08160.0495-0.05-0.0924-0.2022-0.0390.0518-0.03490.8118-0.3318-0.84641.23050.41880.459642.89140.075160.297
1010.9866-0.3511-0.40711.17890.47841.0059-0.0604-0.2290.0693-0.06460.74950.01970.39740.50780.25461.37420.33350.00790.3859-0.67860.374442.782138.254162.955
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:8 )H1 - 8
2X-RAY DIFFRACTION2( CHAIN H AND RESID 9:17 )H9 - 17
3X-RAY DIFFRACTION3( CHAIN H AND RESID 18:32 )H18 - 32
4X-RAY DIFFRACTION4( CHAIN H AND RESID 33:59 )H33 - 59
5X-RAY DIFFRACTION5( CHAIN H AND RESID 60:72 )H60 - 72
6X-RAY DIFFRACTION6( CHAIN H AND RESID 73:82 )H73 - 82
7X-RAY DIFFRACTION7( CHAIN H AND RESID 83:87 )H83 - 87
8X-RAY DIFFRACTION8( CHAIN H AND RESID 88:95 )H88 - 95
9X-RAY DIFFRACTION9( CHAIN H AND RESID 96:106 )H96 - 106
10X-RAY DIFFRACTION10( CHAIN H AND RESID 107:113 )H107 - 113
11X-RAY DIFFRACTION11( CHAIN L AND RESID 1:8 )L1 - 8
12X-RAY DIFFRACTION12( CHAIN L AND RESID 9:18 )L9 - 18
13X-RAY DIFFRACTION13( CHAIN L AND RESID 19:24 )L19 - 24
14X-RAY DIFFRACTION14( CHAIN L AND RESID 25:38 )L25 - 38
15X-RAY DIFFRACTION15( CHAIN L AND RESID 39:48 )L39 - 48
16X-RAY DIFFRACTION16( CHAIN L AND RESID 49:58 )L49 - 58
17X-RAY DIFFRACTION17( CHAIN L AND RESID 59:66 )L59 - 66
18X-RAY DIFFRACTION18( CHAIN L AND RESID 67:75 )L67 - 75
19X-RAY DIFFRACTION19( CHAIN L AND RESID 76:84 )L76 - 84
20X-RAY DIFFRACTION20( CHAIN L AND RESID 85:92 )L85 - 92
21X-RAY DIFFRACTION21( CHAIN L AND RESID 93:102 )L93 - 102
22X-RAY DIFFRACTION22( CHAIN L AND RESID 103:107 )L103 - 107
23X-RAY DIFFRACTION23( CHAIN B AND RESID 1:50 )B1 - 50
24X-RAY DIFFRACTION24( CHAIN B AND RESID 51:82 )B51 - 82
25X-RAY DIFFRACTION25( CHAIN B AND RESID 83:108 )B83 - 108
26X-RAY DIFFRACTION26( CHAIN B AND RESID 109:143 )B109 - 143
27X-RAY DIFFRACTION27( CHAIN B AND RESID 144:184 )B144 - 184
28X-RAY DIFFRACTION28( CHAIN B AND RESID 185:275 )B185 - 275
29X-RAY DIFFRACTION29( CHAIN B AND RESID 276:325 )B276 - 325
30X-RAY DIFFRACTION30( CHAIN B AND RESID 326:361 )B326 - 361
31X-RAY DIFFRACTION31( CHAIN B AND RESID 362:403 )B362 - 403
32X-RAY DIFFRACTION32( CHAIN A AND RESID 1:275 )A1 - 275
33X-RAY DIFFRACTION33( CHAIN A AND RESID 276:403 )A276 - 403
34X-RAY DIFFRACTION34( CHAIN Z AND RESID 1:50 )Z1 - 50
35X-RAY DIFFRACTION35( CHAIN Z AND RESID 51:82 )Z51 - 82
36X-RAY DIFFRACTION36( CHAIN Z AND RESID 83:278 )Z83 - 278
37X-RAY DIFFRACTION37( CHAIN Z AND RESID 279:342 )Z279 - 342
38X-RAY DIFFRACTION38( CHAIN Z AND RESID 343:403 )Z343 - 403
39X-RAY DIFFRACTION39( CHAIN E AND RESID 1:50 )E1 - 50
40X-RAY DIFFRACTION40( CHAIN E AND RESID 51:72 )E51 - 72
41X-RAY DIFFRACTION41( CHAIN E AND RESID 73:143 )E73 - 143
42X-RAY DIFFRACTION42( CHAIN E AND RESID 144:164 )E144 - 164
43X-RAY DIFFRACTION43( CHAIN E AND RESID 165:218 )E165 - 218
44X-RAY DIFFRACTION44( CHAIN E AND RESID 219:257 )E219 - 257
45X-RAY DIFFRACTION45( CHAIN E AND RESID 258:304 )E258 - 304
46X-RAY DIFFRACTION46( CHAIN E AND RESID 305:361 )E305 - 361
47X-RAY DIFFRACTION47( CHAIN E AND RESID 362:403 )E362 - 403
48X-RAY DIFFRACTION48( CHAIN F AND RESID 1:8 )F1 - 8
49X-RAY DIFFRACTION49( CHAIN F AND RESID 9:17 )F9 - 17
50X-RAY DIFFRACTION50( CHAIN F AND RESID 18:24 )F18 - 24
51X-RAY DIFFRACTION51( CHAIN F AND RESID 25:32 )F25 - 32
52X-RAY DIFFRACTION52( CHAIN F AND RESID 33:39 )F33 - 39
53X-RAY DIFFRACTION53( CHAIN F AND RESID 40:51 )F40 - 51
54X-RAY DIFFRACTION54( CHAIN F AND RESID 52:59 )F52 - 59
55X-RAY DIFFRACTION55( CHAIN F AND RESID 60:72 )F60 - 72
56X-RAY DIFFRACTION56( CHAIN F AND RESID 73:82 )F73 - 82
57X-RAY DIFFRACTION57( CHAIN F AND RESID 83:95 )F83 - 95
58X-RAY DIFFRACTION58( CHAIN F AND RESID 96:106 )F96 - 106
59X-RAY DIFFRACTION59( CHAIN F AND RESID 107:113 )F107 - 113
60X-RAY DIFFRACTION60( CHAIN G AND RESID 1:8 )G1 - 8
61X-RAY DIFFRACTION61( CHAIN G AND RESID 9:18 )G9 - 18
62X-RAY DIFFRACTION62( CHAIN G AND RESID 19:32 )G19 - 32
63X-RAY DIFFRACTION63( CHAIN G AND RESID 33:38 )G33 - 38
64X-RAY DIFFRACTION64( CHAIN G AND RESID 39:48 )G39 - 48
65X-RAY DIFFRACTION65( CHAIN G AND RESID 49:61 )G49 - 61
66X-RAY DIFFRACTION66( CHAIN G AND RESID 62:75 )G62 - 75
67X-RAY DIFFRACTION67( CHAIN G AND RESID 76:84 )G76 - 84
68X-RAY DIFFRACTION68( CHAIN G AND RESID 85:95 )G85 - 95
69X-RAY DIFFRACTION69( CHAIN G AND RESID 96:102 )G96 - 102
70X-RAY DIFFRACTION70( CHAIN G AND RESID 103:107 )G103 - 107
71X-RAY DIFFRACTION71( CHAIN I AND RESID 1:17 )I1 - 17
72X-RAY DIFFRACTION72( CHAIN I AND RESID 18:32 )I18 - 32
73X-RAY DIFFRACTION73( CHAIN I AND RESID 33:51 )I33 - 51
74X-RAY DIFFRACTION74( CHAIN I AND RESID 52:72 )I52 - 72
75X-RAY DIFFRACTION75( CHAIN I AND RESID 73:95 )I73 - 95
76X-RAY DIFFRACTION76( CHAIN I AND RESID 96:101 )I96 - 101
77X-RAY DIFFRACTION77( CHAIN I AND RESID 102:113 )I102 - 113
78X-RAY DIFFRACTION78( CHAIN J AND RESID 1:38 )J1 - 38
79X-RAY DIFFRACTION79( CHAIN J AND RESID 39:49 )J39 - 49
80X-RAY DIFFRACTION80( CHAIN J AND RESID 50:61 )J50 - 61
81X-RAY DIFFRACTION81( CHAIN J AND RESID 62:107 )J62 - 107
82X-RAY DIFFRACTION82( CHAIN M AND RESID 1:25 )M1 - 25
83X-RAY DIFFRACTION83( CHAIN M AND RESID 26:32 )M26 - 32
84X-RAY DIFFRACTION84( CHAIN M AND RESID 33:39 )M33 - 39
85X-RAY DIFFRACTION85( CHAIN M AND RESID 40:51 )M40 - 51
86X-RAY DIFFRACTION86( CHAIN M AND RESID 52:59 )M52 - 59
87X-RAY DIFFRACTION87( CHAIN M AND RESID 60:72 )M60 - 72
88X-RAY DIFFRACTION88( CHAIN M AND RESID 73:87 )M73 - 87
89X-RAY DIFFRACTION89( CHAIN M AND RESID 88:95 )M88 - 95
90X-RAY DIFFRACTION90( CHAIN M AND RESID 96:106 )M96 - 106
91X-RAY DIFFRACTION91( CHAIN M AND RESID 107:113 )M107 - 113
92X-RAY DIFFRACTION92( CHAIN N AND RESID 1:8 )N1 - 8
93X-RAY DIFFRACTION93( CHAIN N AND RESID 9:24 )N9 - 24
94X-RAY DIFFRACTION94( CHAIN N AND RESID 25:32 )N25 - 32
95X-RAY DIFFRACTION95( CHAIN N AND RESID 33:38 )N33 - 38
96X-RAY DIFFRACTION96( CHAIN N AND RESID 39:48 )N39 - 48
97X-RAY DIFFRACTION97( CHAIN N AND RESID 49:61 )N49 - 61
98X-RAY DIFFRACTION98( CHAIN N AND RESID 62:75 )N62 - 75
99X-RAY DIFFRACTION99( CHAIN N AND RESID 76:84 )N76 - 84
100X-RAY DIFFRACTION100( CHAIN N AND RESID 85:92 )N85 - 92
101X-RAY DIFFRACTION101( CHAIN N AND RESID 93:107 )N93 - 107

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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://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