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- PDB-8d7i: Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by... -

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基本情報

登録情報
データベース: PDB / ID: 8d7i
タイトルBifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap1 from S. aureus
要素
  • Cathepsin G, C-terminal truncated form
  • Extracellular Adherence Protein
  • Neutrophil elastase
キーワードHYDROLASE/INHIBITOR / PROTEIN BINDING / Protease Inhibitor / Immune Evasion / Neutrophil / S. aureus / HYDROLASE-INHIBITOR / PROTEIN BINDING complex
機能・相同性
機能・相同性情報


cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling ...cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / purinergic nucleotide receptor signaling pathway / caspase binding / response to yeast / negative regulation of T cell activation / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation / Antimicrobial peptides / pyroptotic inflammatory response / neutrophil-mediated killing of gram-negative bacterium / Activation of Matrix Metalloproteinases / cytokine binding / positive regulation of MAP kinase activity / monocyte chemotaxis / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / defense response to fungus / Purinergic signaling in leishmaniasis infection / response to UV / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / phagocytic vesicle / Degradation of the extracellular matrix / transcription repressor complex / serine-type peptidase activity / positive regulation of smooth muscle cell proliferation / secretory granule / Regulation of Complement cascade / protein maturation / positive regulation of interleukin-8 production / protein catabolic process / positive regulation of immune response / protein processing / platelet activation / negative regulation of inflammatory response / specific granule lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytokine-mediated signaling pathway / intracellular calcium ion homeostasis / cytoplasmic stress granule / azurophil granule lumen / antibacterial humoral response / transcription corepressor activity / peptidase activity / heparin binding / : / cellular response to lipopolysaccharide / protease binding / response to lipopolysaccharide / endopeptidase activity / defense response to Gram-negative bacterium / lysosome / protein phosphorylation / defense response to Gram-positive bacterium / defense response to bacterium / immune response / receptor ligand activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / cell surface / negative regulation of transcription by RNA polymerase II / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
MAP domain / MAP domain / MAP repeat profile. / Ubiquitin-like (UB roll) - #120 / : / Ubiquitin-like (UB roll) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family ...MAP domain / MAP domain / MAP repeat profile. / Ubiquitin-like (UB roll) - #120 / : / Ubiquitin-like (UB roll) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha Beta
類似検索 - ドメイン・相同性
Neutrophil elastase / Cathepsin G / Protein map
類似検索 - 構成要素
生物種Staphylococcus aureus subsp. aureus (黄色ブドウ球菌)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.63 Å
データ登録者Gido, C.D. / Herdendorf, T.J. / Geisbrecht, B.V.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM14852 米国
引用ジャーナル: J.Biol.Chem. / 年: 2024
タイトル: S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases.
著者: Mishra, N. / Gido, C.D. / Herdendorf, T.J. / Hammel, M. / Hura, G.L. / Fu, Z.Q. / Geisbrecht, B.V.
履歴
登録2022年6月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年6月14日Provider: repository / タイプ: Initial release
改定 1.12023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
改定 1.32024年10月23日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: Neutrophil elastase
B: Extracellular Adherence Protein
C: Cathepsin G, C-terminal truncated form
D: Neutrophil elastase
E: Extracellular Adherence Protein
F: Cathepsin G, C-terminal truncated form
G: Neutrophil elastase
H: Extracellular Adherence Protein
I: Cathepsin G, C-terminal truncated form
J: Neutrophil elastase
K: Extracellular Adherence Protein
L: Cathepsin G, C-terminal truncated form
M: Neutrophil elastase
N: Extracellular Adherence Protein
O: Cathepsin G, C-terminal truncated form
P: Neutrophil elastase
Q: Extracellular Adherence Protein
R: Cathepsin G, C-terminal truncated form


分子量 (理論値)分子数
合計 (水以外)359,41018
ポリマ－359,41018
非ポリマー00
水00
1
A: Neutrophil elastase
B: Extracellular Adherence Protein
C: Cathepsin G, C-terminal truncated form


分子量 (理論値)分子数
合計 (水以外)59,9023
ポリマ－59,9023
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-13 kcal/mol
Surface area22980 Å2
手法PISA
2
D: Neutrophil elastase
E: Extracellular Adherence Protein
F: Cathepsin G, C-terminal truncated form


分子量 (理論値)分子数
合計 (水以外)59,9023
ポリマ－59,9023
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-15 kcal/mol
Surface area23280 Å2
手法PISA
3
G: Neutrophil elastase
H: Extracellular Adherence Protein
I: Cathepsin G, C-terminal truncated form


分子量 (理論値)分子数
合計 (水以外)59,9023
ポリマ－59,9023
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-13 kcal/mol
Surface area23270 Å2
手法PISA
4
J: Neutrophil elastase
K: Extracellular Adherence Protein
L: Cathepsin G, C-terminal truncated form


分子量 (理論値)分子数
合計 (水以外)59,9023
ポリマ－59,9023
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-13 kcal/mol
Surface area23520 Å2
手法PISA
5
M: Neutrophil elastase
N: Extracellular Adherence Protein
O: Cathepsin G, C-terminal truncated form


分子量 (理論値)分子数
合計 (水以外)59,9023
ポリマ－59,9023
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-12 kcal/mol
Surface area23270 Å2
手法PISA
6
P: Neutrophil elastase
Q: Extracellular Adherence Protein
R: Cathepsin G, C-terminal truncated form


分子量 (理論値)分子数
合計 (水以外)59,9023
ポリマ－59,9023
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-11 kcal/mol
Surface area23250 Å2
手法PISA
単位格子
Length a, b, c (Å)102.230, 152.270, 296.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質
Neutrophil elastase / Bone marrow serine protease / Elastase-2 / Human leukocyte elastase / HLE / Medullasin / PMN elastase


分子量: 23318.982 Da / 分子数: 6 / 断片: UNP residues 30-247 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / Cell: Neutrophil / Plasmid details: Purified from human sputum / 参照: UniProt: P08246, leukocyte elastase
#2: タンパク質
Extracellular Adherence Protein / Protein map


分子量: 11185.606 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus subsp. aureus (黄色ブドウ球菌)
株: Mu50 / ATCC 700699 / 遺伝子: map, SAV1938 / プラスミド: pT7HMT / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q99QS1
#3: タンパク質
Cathepsin G, C-terminal truncated form


分子量: 25397.131 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / Cell: Neutrophil / Plasmid details: Purified from human sputum / 参照: UniProt: P08311
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: 3.2 Å3/Da / 溶媒含有率: 61.57 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.9
詳細: 0.1M BisTris, 0.2M sodium/potassium tartrate, 14% PEG-8000

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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: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年10月27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: 1 Å / 相対比: 1
反射解像度: 3.63→96.64 Å / Num. obs: 53125 / % possible obs: 99.9 % / 冗長度: 2 % / Biso Wilson estimate: 84.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.04 / Net I/σ(I): 5.1
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
3.63-3.7620.1565.152260.9490.156100
3.76-3.9120.13652740.9690.13100
3.91-4.090.0967.752180.9810.09699.9
4.09-4.320.07310.252200.9870.07399.7
4.3-4.5720.0513.952800.9440.05100
4.57-4.9320.04116.252900.9950.041100
4.93-5.4220.03717.253020.9970.037100
5.42-6.210.03817.653250.9950.038100
6.21-7.8220.02822.353950.9980.02899.9
7.82-84.920.01238.955950.9990.01299.7

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIXv1.9.2精密化
XDSデータ削減
Aimless0.7.3データスケーリング
PHASER位相決定
PDB_EXTRACT3.27データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 1HNE, 1AU8, 8D4O

1hne

1au8

8d4o


解像度: 3.63→96.64 Å / SU ML: 0.35 / 交差検証法: THROUGHOUT / σ(F): 1.51 / 位相誤差: 20.16 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.217 1998 3.9 %
Rwork0.1865 49220 -
obs0.1876 51218 96.33 %
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: 191.27 Å2 / Biso mean: 95.7246 Å2 / Biso min: 47.93 Å2
精密化ステップサイクル: final / 解像度: 3.63→96.64 Å
タンパク質核酸リガンド溶媒全体
原子数25188 0 0 0 25188
残基数----3240
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.63-3.720.27181310.23573243337491
3.72-3.820.25461360.2253330346692
3.82-3.930.23211360.21753336347293
3.93-4.060.24881360.21543377351394
4.06-4.210.24841410.20873436357795
4.21-4.370.19691400.17883475361597
4.37-4.570.19381440.16023539368397
4.57-4.810.18931450.16413566371198
4.81-5.120.18231450.17213575372098
5.12-5.510.21561440.18143554369898
5.51-6.070.24851470.19823620376798
6.07-6.940.24531480.19713636378499
6.94-8.750.21541500.17513686383699
8.75-96.640.19171550.173847400299
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)
11.66150.3573-3.53462.9633-0.50259.38680.1345-0.2599-0.68770.1269-0.8264-0.01060.27211.73420.62140.58050.03570.1541.0167-0.14730.798762.7316-16.6826-34.8427
23.4832-0.25281.14172.19071.37784.3659-0.0993-0.1759-0.13520.54190.4016-0.11890.7765-0.0693-0.31450.81150.07160.06560.61730.02250.657247.398-20.7178-33.4176
31.5976-0.01151.69331.2693-1.43533.23660.0996-0.16760.05670.01410.18150.10980.3355-0.2187-0.27690.7089-0.01550.07230.8794-0.04620.621343.5762-12.2058-30.7717
44.9951-1.5846-1.77364.49220.07253.7941-0.4247-0.13211.10650.43180.897-1.0927-0.51960.9276-0.45530.6771-0.0326-0.07280.903-0.12120.789756.95290.1946-36.9421
54.21620.52192.0192.1475-2.53323.9380.49280.53590.129-0.9086-0.5105-0.6980.75660.64530.03090.7320.15060.19580.7669-0.14260.638856.9629-10.0975-45.2044
65.45390.34920.01062.13120.66473.5510.48090.61430.3122-0.16030.5414-0.6050.07071.4579-0.74860.4660.01770.03760.7883-0.20810.777858.1879-11.525-47.2829
71.27031.2076-0.29032.4239-0.91133.23210.33640.15070.27750.1859-0.12370.0695-0.4643-0.1111-0.25850.63830.05150.04570.7328-0.02880.728850.2632-4.4748-38.8831
84.1319-3.25894.22453.7584-1.97756.37060.1327-0.4316-0.2467-0.45890.30190.03430.4022-0.6086-0.37960.6466-0.06210.05460.75030.02410.812832.2868-25.0489-63.2088
96.44670.63781.23677.1861-1.77628.2906-0.075-0.1672-1.33860.43111.2746-0.66920.7823-0.6037-1.10250.6864-0.0566-0.01120.8386-0.13750.734541.1037-30.771-54.0087
101.64740.58132.65572.9496-1.27769.71040.36930.06940.0722-0.2744-0.1509-0.35670.04912.0008-0.30890.46170.01560.18980.67120.00480.71342.547-21.0297-61.3019
113.34250.9172-1.2651.9283-1.27185.67290.05210.3240.44410.27380.3809-0.0889-0.1128-0.5958-0.32610.54540.07160.01960.60030.01560.71337.0658-13.8041-59.2706
123.37030.66181.17381.15161.28521.5152-0.1024-0.0409-0.1597-0.60310.3389-0.75180.940.6319-0.26170.61960.13790.0820.5030.01880.636445.0467-11.0304-54.3859
134.6021.9789-0.83342.03870.31973.73180.0241-0.49-0.44420.34850.14160.2812-0.2944-1.371-0.08530.67730.08470.08530.6538-0.09760.620236.3471-21.2306-53.9134
140.54761.46980.04354.17171.261.73470.4427-0.2354-0.37380.0086-0.06620.30251.4027-0.8749-0.40811.4344-0.2334-0.26030.99390.21560.943414.0741-40.0591-67.6836
159.85980.87791.68396.15420.33929.0943-0.11140.516-0.9879-0.2841-0.04810.20110.31770.46220.42440.930.0917-0.0160.7587-0.10280.711834.0499-35.8023-66.8305
162.7401-0.75770.29064.1345-1.43473.60680.2657-0.0399-1.09460.30640.1321-0.17451.25780.1447-0.40011.05980.0801-0.24880.6825-0.05030.934728.3901-39.9592-75.9591
172.0319-0.1523-1.22653.64291.84448.63280.61310.41950.6665-0.43-0.03550.65520.1783-2.2911-0.60010.7726-0.0334-0.13691.12750.34771.07611.691-29.7381-82.1407
183.56270.6561.54942.75272.16595.0320.266-0.39820.19380.19360.0650.45960.084-0.9-0.28460.67940.06180.05470.7980.06030.77917.188-24.3637-70.555
194.6589-0.38370.77710.9075-0.74452.8430.4649-0.9833-0.2177-0.0161-0.38750.35490.03720.1265-0.0270.7617-0.0433-0.04350.91550.13360.655415.4492-23.9296-69.2298
202.6698-0.1648-1.02242.47040.48885.4623-0.04980.4196-0.0745-0.2180.05360.46770.404-0.525-0.05290.690.0099-0.12440.70790.0150.820.7955-29.596-80.1186
210.32050.7116-0.8271.9095-3.48118.60430.1388-0.2270.10130.0338-0.29330.1397-0.88211.25030.23370.73410.12560.09790.9638-0.28780.685967.2883-3.2937-89.6819
224.12891.4105-0.07181.16730.1613.53590.0420.66090.3379-0.02420.15170.302-0.0523-0.3445-0.15020.604-0.180.03880.8958-0.04170.6451.80495.2582-90.433
233.6999-0.0920.67886.24560.52565.1913-0.17460.56010.3718-0.6117-0.0389-0.47-0.83480.96450.11561.0451-0.22990.12570.8918-0.04860.648461.637810.115-93.9833
241.96610.2586-0.47332.9346-1.94611.9910.08470.19390.12010.14410.26860.1763-0.5807-0.1641-0.34610.6943-0.04580.05410.8909-0.14790.598748.57921.4758-94.6751
254.352.084-0.9325.2112-2.17161.79950.10630.0380.04630.70090.1249-0.41410.4650.4563-0.20970.70830.05580.05240.8358-0.1230.613659.1315-6.7405-84.1612
260.4011-0.404-1.1644.6449-1.32684.82420.4351-0.3439-0.38860.2098-0.49610.44950.13020.29260.11530.73540.0441-0.0270.7245-0.08090.698354.502-13.3577-80.1601
270.6120.5039-1.09072.0955-0.43964.6002-0.0762-0.20990.0322-0.03830.1329-0.17910.1753-0.1957-0.02830.52270.02940.08450.7566-0.10950.775653.0232-7.8926-84.1925
280.5347-0.50130.98010.8784-0.4392.70470.70320.1921-0.1764-0.47250.2728-0.49-1.1530.7369-1.06991.5254-0.15870.56450.6363-0.0591.120747.150719.1666-66.8829
293.71441.78070.80253.1046-2.29423.4379-0.4268-0.23651.4489-0.1644-0.27641.2489-1.8726-0.9847-0.0211.7571-0.32460.55180.9459-0.24860.876536.71217.6314-58.0078
302.7759-0.04571.23087.96631.23313.2016-0.1386-0.15820.9258-0.59870.9756-1.2565-0.71681.4636-0.93580.9071-0.23290.26970.814-0.13730.861653.882216.9635-72.315
313.4981-0.0071-0.7114.17841.5748.6352-0.2874-0.6833-0.21650.03640.08260.01-0.85410.87390.22760.75950.0190.03810.6881-0.02940.684249.28789.6122-62.1358
325.38933.33223.21452.0099-2.69554.21950.81450.525-0.56151.0841-0.7842-0.09350.35330.0553-0.15630.61950.05520.11780.5291-0.07850.614345.8811.8191-55.1268
333.16011.2771-1.14896.4611-6.46192.07890.3215-0.19650.5016-0.0257-0.01911.2321-0.4710.0496-0.27660.86430.14070.07520.5314-0.06180.583640.09995.6755-66.7591
342.5279-1.172-2.19332.8517-0.12332.8443-0.00270.54340.09170.04570.3948-0.244-0.4696-0.1604-0.34320.6021-0.09080.01130.5295-0.02830.639245.72775.6758-74.4636
353.9637-0.6477-0.75783.3276-0.65534.82720.0340.77520.3378-0.21780.55610.1535-1.1464-0.6826-0.50781.0415-0.02490.02590.8423-0.06090.519542.986313.2513-69.7856
362.73420.19580.14963.23280.72741.77721.08730.70731.1213-1.6951-0.71530.1577-0.0133-0.3672-0.51752.89870.27110.43520.97990.11521.122532.663639.5802-58.8913
371.8170.2711-0.63390.47260.41692.36460.2842-0.43711.32710.86740.135-0.0984-1.00940.3953-0.42241.5339-0.13540.39670.8065-0.25641.113345.870630.8646-52.2374
382.7507-0.525-0.84971.9596-0.32721.42530.2345-0.02980.919-0.25610.538-0.6998-1.49760.5691-0.67191.7043-0.27650.51030.8857-0.24061.055745.348732.9358-50.4629
392.42631.043-0.25933.06660.48433.53230.14940.12840.3793-0.28280.16610.2066-0.9229-0.2907-0.35171.25620.19360.24170.75580.02970.746329.285926.2364-51.4393
401.4307-0.9576-0.11562.1593-1.12881.5968-0.0249-0.0510.1841-0.53510.1116-0.0846-0.5493-0.2269-0.10031.21480.13560.16390.74390.01140.657721.748129.5179-16.6588
414.8302-1.85151.62739.45121.80915.12210.69280.35040.6352-1.048-1.13170.164-1.1965-0.99450.36650.93260.19850.11440.90320.12080.696513.889534.2434-20.3556
423.2238-1.98551.65762.8443-1.42912.91040.45820.6964-0.39350.2960.05310.4931-0.53710.0386-0.42010.95750.10910.2480.63090.01640.624522.504916.395-15.6206
431.45370.03780.2382.5602-1.02132.1769-0.26920.59740.2393-0.17940.2708-0.1048-0.2785-0.1104-0.02981.06160.09070.1740.76770.10870.638823.46527.1804-27.5369
446.6594-1.5760.4277.25621.91035.90311.69330.48280.3613-0.419-0.9351-1.5155-0.84820.7447-0.84240.9481-0.04140.17390.94870.14980.84240.037527.3185-14.3242
453.6905-0.87891.09644.4694-3.15782.1807-0.2718-0.88711.11210.13910.4351-0.9615-0.5368-0.3433-0.28341.10030.08570.04740.7991-0.22240.722529.596132.8135-6.1163
460.882-0.48661.07871.7280.00382.86490.2172-0.05490.14390.1907-0.0888-0.2712-0.36530.1948-0.09781.1487-0.07020.22780.70030.03770.80532.385525.8876-10.0229
472.4680.272-0.77974.0007-0.68243.96310.9840.08880.1106-0.6004-0.69080.2753-0.67990.445-0.39680.95640.15320.02930.90220.07780.60525.459718.25579.7413
486.68710.4691-5.38255.61640.3734.41071.35331.37711.4427-0.88320.34050.2742-1.8753-1.6737-1.82221.32180.22180.25880.87190.29940.91388.763628.8898-3.6635
495.38472.1941-1.78455.9828-3.20368.69720.2849-0.60620.40360.4263-0.51390.1645-1.71650.16970.24170.9210.02270.05460.6435-0.00960.670614.025922.988411.2833
502.2796-0.27251.4581.32421.2064.02230.2910.0696-0.2963-0.3748-0.1696-0.08850.3584-0.2977-0.09780.88670.03130.06020.69890.02080.673817.814515.53397.2895
512.64041.3998-0.41693.0825-0.49022.1973-0.051-0.91690.2839-0.1346-0.12140.0372-1.0624-0.69490.24520.93620.10960.12460.70030.01120.606621.106822.61010.4803
524.0184-0.2997-0.85052.2556-3.11688.06180.1524-0.1684-0.0208-1.7880.3531-0.21061.7115-0.7073-0.36190.92990.0409-0.0130.5658-0.08950.643510.544816.25083.837
532.81540.2001-0.66391.6033-0.21833.76120.33880.32980.3123-0.3217-0.02970.4704-0.4612-1.1951-0.27150.8810.235-0.00441.10520.11850.7094-9.65417.839221.5946
543.9716-1.9288-0.58233.54390.76792.0542-0.4714-0.4032-0.7010.80440.0612-0.47220.3597-1.32570.73160.914-0.1119-0.14490.84070.15030.8043-7.586-0.415429.8541
553.45140.96950.09392.459-0.15882.8366-0.1506-0.0557-0.2097-0.1422-0.1128-0.5080.7603-0.40490.25351.00330.084-0.01140.97740.04590.7491-0.41220.839218.6377
563.1250.14770.25683.65581.44593.24420.24640.1427-0.1444-0.3976-0.17290.23650.1763-0.6429-0.01440.8346-0.0261-0.06670.82880.16260.6871-3.5117.209625.2525
570.82260.99330.69012.60670.17562.86550.17150.10250.3247-0.01250.0616-0.1369-0.71860.4224-0.18980.8599-0.14380.17490.7073-0.0390.735540.61326.905138.0392
584.15132.2672-0.14455.0668-1.47585.76840.209-0.26950.1014-0.03130.0845-1.0872-0.64411.4194-0.26240.6257-0.09150.03450.9497-0.2030.916349.857128.083641.6081
593.17920.26360.32471.51540.75232.7845-0.0148-0.1617-0.2279-0.26440.3741-0.4632-0.19590.1572-0.36220.6411-0.01740.11210.5813-0.04660.641835.94719.960142.5894
600.1015-0.37820.55963.3907-1.49063.54130.94140.29650.563-0.0676-0.34460.8114-1.2707-0.2541-0.5611.12150.12480.25490.7579-0.14590.81222.861732.670436.0662
612.0753-0.5717-1.47842.07413.42638.89711.00221.87111.191-1.01120.1416-0.3697-0.0342-0.2083-1.41561.0569-0.11820.12170.9671-0.0360.849445.055933.672727.0365
621.0402-0.85941.60494.20890.94793.0469-0.20510.32140.78360.1573-0.02081.1248-0.33980.15190.12131.0216-0.04220.13920.70440.04240.784125.308431.353727.7107
635.08560.50040.41836.6626-2.28618.24330.23250.8831-0.3425-1.27730.26430.56490.70040.6572-0.37130.9173-0.10020.20890.5782-0.06790.902934.565133.423725.0257
642.83810.31481.22061.40720.8763.97360.0239-0.12620.3612-0.56310.16660.147-0.5529-0.3392-0.24570.73930.08030.02960.55090.05230.732927.922625.862334.2816
651.3778-0.98810.22385.73480.04547.66760.30030.5463-0.54-0.44650.7519-1.04040.52812.0345-1.07550.59460.11340.06020.7815-0.08310.854251.6199.902415.7278
668.2032-0.8223.29880.5796-1.2553.04790.630.7375-0.3978-0.1924-0.9921-0.17310.90870.73750.14760.78720.1370.23631.5123-0.08530.785449.05166.347610.7373
672.46180.41761.28261.91940.6184.0979-0.00030.44640.151-0.17170.2409-0.2157-0.56250.7786-0.21130.820.07730.03760.8491-0.13310.648446.075617.136314.3328
682.3848-2.20242.71272.8184-0.97935.6440.70350.32180.1954-0.0136-0.24960.2634-0.0480.3786-0.33520.6773-0.01330.13820.69810.05760.723837.518411.320615.0314
690.8536-0.5349-0.72021.54270.69461.1236-0.1082-0.0135-0.1033-0.07180.0543-0.04-0.170.37420.08050.7643-0.10.11240.87920.00710.718641.025514.302319.9318
700.69051.15231.08652.8281.16122.9910.0396-0.0117-0.123-0.03380.3674-0.97490.07061.2241-0.32840.7370.05880.10361.402-0.27681.044262.90220.01431.1125
713.0985-0.8051-0.76494.01490.40172.9277-0.0785-0.33940.00690.31560.25850.12830.58770.1767-0.19080.79840.14690.04211.0446-0.0720.794148.2906-11.69391.7881
722.43710.4158-0.90644.2998-2.09862.5618-0.1079-0.4559-0.1656-0.02030.1631-0.3776-0.1660.353-0.04560.90090.06290.08391.1723-0.15160.78552.55-6.5279-2.3552
731.5705-0.41421.76652.1844-0.43942.96580.32750.43940.3483-0.378-0.2136-0.06270.1151-0.0126-0.11460.72550.10.14220.91290.07440.8591-14.6341-19.9024-66.9201
744.7656-0.93071.4861.84562.07665.91190.35-0.27710.3520.202-0.28830.26190.1158-0.65360.08780.78590.02880.07250.72260.14870.8186-20.6785-15.3517-54.8908
751.44470.55691.22211.8194-0.73253.03410.1084-0.09090.4732-0.0707-0.20870.0495-0.2930.0670.12310.65410.08460.11470.7429-0.03570.9709-15.3377-15.4653-51.4106
761.56981.75821.9732.0650.64727.38980.20080.09790.08240.06740.0202-0.30670.8296-0.0459-0.35280.7130.087-0.00510.5806-0.10590.6984-18.7815-46.0272-51.1368
770.9534-0.51410.68031.6805-1.15974.72990.01240.23080.01010.1485-0.0645-0.20590.22950.40230.10450.66540.04620.03890.6526-0.02910.8924-11.7959-39.7933-46.0132
781.776-0.25570.27324.3706-1.18652.49240.21680.55330.2211-0.2689-0.3359-0.2080.04860.40370.11030.54470.01380.06780.7831-0.02950.8687-14.3114-37.4206-51.8071
792.18172.24372.1033.63761.25762.4650.474-0.75990.3463-0.4629-0.6084-0.5129-0.08640.61630.03890.5015-0.04280.12260.8934-0.09051.0951-8.6796-73.7356-58.1848
801.6827-1.944-0.73753.95811.30613.7649-0.0437-0.1178-0.2807-0.031-0.37021.6395-0.186-0.12640.38330.6091-0.04920.04360.6497-0.04191.0062-22.5366-65.4002-49.4205
816.90620.5973-0.47757.23010.02528.1515-0.37091.13240.9616-1.41110.03761.44660.6912-0.60550.48970.8750.0001-0.23740.7032-0.01830.8797-21.6216-69.2037-61.9575
822.6198-0.69481.49033.0255-1.56163.8460.08820.4195-0.52580.26890.03870.7140.2073-0.6154-0.17690.6305-0.08660.05530.881-0.12441.0035-24.636-66.817-43.7057
837.62560.68932.60184.8411-1.59259.45430.78410.1147-1.3079-0.61270.01270.25261.59431.3612-0.81110.51830.1703-0.07411.0023-0.21330.8628-19.4595-81.9258-53.5374
845.352.4995-1.62265.7894-0.19226.9059-0.3591-0.4003-0.00190.2137-0.057-0.60941.08460.69380.1690.67880.0173-0.09180.4887-0.05510.8152-5.6249-76.3479-40.3274
853.7014-1.3381.33215.54880.47365.6290.2134-0.01760.5117-0.7068-0.3262-1.18560.19430.4675-0.03120.53250.00530.09280.7464-0.04670.8616-4.8585-64.9669-54.5758
861.9683-0.94031.57086.32420.87275.32930.7705-0.82720.51430.6761-0.0524-1.04680.43271.2667-0.78530.8064-0.0602-0.04980.9617-0.21630.8656-1.3791-63.3558-36.6399
871.4030.9176-0.28344.3658-1.11422.5233-0.21840.5162-0.0918-0.00960.31520.1374-0.07060.1093-0.13520.6826-0.01060.03340.7956-0.01780.989-6.7863-65.9828-46.7055
885.3621-1.8267-0.68264.5315-0.48515.6153-0.9034-0.5548-1.1706-0.06310.5157-0.46861.2061-0.34740.4410.9380.06290.030.49420.02460.6542-17.9129-72.5575-36.8597
891.82420.09791.11541.1567-0.15690.90630.1339-2.133-0.35850.71470.04080.4190.0655-0.2966-0.20131.0038-0.16210.1282.0270.22021.0752-25.8432-37.7389-5.7189
903.36952.8598-2.83377.8524-2.86125.5370.1062-1.374-1.28240.7347-0.9819-0.7123-0.14592.25620.92490.88-0.05640.07661.30730.30681.215-14.355-45.5478-20.913
913.5660.7565-2.49390.201-0.26783.38641.0519-2.5845-0.73320.4249-0.9033-0.3896-0.03670.5922-0.15391.2374-0.29050.0441.93670.5531.2611-28.5034-46.9518-2.371
925.28730.4821.98164.72842.57273.94440.0451-1.5177-0.7030.5569-0.49781.07730.2071-0.11190.4680.8649-0.1240.3131.14960.16181.0562-32.1101-38.1576-19.0166
933.1041.72621.18142.0841-0.43513.10550.09630.0525-1.06910.0296-0.5995-0.19440.4408-0.81710.59910.7935-0.11190.07771.0130.00121.131-30.7341-41.9607-27.2156
942.3573-1.81460.79752.9668-0.33782.91860.2932-0.41780.0926-0.0734-0.03540.32050.0643-0.2084-0.13690.805-0.07440.07640.96650.12051.1272-29.7264-37.2148-23.4144
952.0316-0.3727-0.27651.0720.10753.52540.6654-0.9521-0.6177-0.2637-1.2287-1.13061.5304-0.11250.81241.1192-0.0471-0.01391.13670.45191.4846-23.3611-52.3952-16.0922
961.6451-1.05140.68044.02831.25316.06130.4848-0.57470.92090.2354-0.16670.0209-0.80370.3976-0.2850.8325-0.12610.09081.0368-0.13470.9097-6.8031-20.1533-21.9859
970.5046-0.94640.79359.40946.17178.8791-0.3714-0.545-0.1137-0.11570.42460.3098-0.178-0.744-0.02920.6533-0.02340.11530.9266-0.04260.7648-9.4973-23.6108-38.5245
984.57551.76650.65651.3138-0.99961.73570.2022-0.8659-0.08790.2015-0.2983-0.1217-0.31350.39090.13240.9341-0.0420.07180.8279-0.03440.7185-8.517-30.7152-21.9638
993.14191.6253-0.47742.1559-0.3462.06830.3573-0.73271.48040.8313-0.29260.4724-0.59960.2993-0.02671.1264-0.28010.11631.044-0.22641.329611.4589-7.1118-20.254
1001.5494-1.25220.00991.53571.49593.19420.0762-0.46931.15750.4747-0.09320.2529-0.1531-0.22880.05561.1876-0.29270.1521.0521-0.17031.34236.1355-4.9718-23.1365
1012.67531.63911.86393.13093.12295.442-1.1537-0.23570.1662-0.1585-0.04280.1237-0.85830.01151.31531.2603-0.06240.12250.8994-0.11211.472814.43464.073-20.9959
1023.3655-0.76450.60831.78360.86462.44540.1894-0.2501-0.14470.3204-0.5302-0.487-0.57960.54710.1611.1258-0.24590.1061.0852-0.04641.066219.8633-16.1396-23.9251
1034.2021-0.0365-0.39163.1563-0.80154.1942-0.0472-0.50380.316-0.32310.0275-0.65850.11730.5539-0.00370.9364-0.05340.10271.2039-0.13241.061717.9712-19.7684-31.3893
1042.2601-1.05110.61.9995-0.66912.0113-0.08850.0290.8005-0.45790.3435-0.4422-0.28470.2225-0.17780.912-0.29340.14441.0732-0.11621.006714.3206-10.1753-33.1117
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 42 )A29 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 95 )A43 - 95
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 137 )A96 - 137
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 154 )A138 - 154
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 188 )A155 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 203 )A189 - 203
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 246 )A204 - 246
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 65 )B47 - 65
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 74 )B66 - 74
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 93 )B75 - 93
11X-RAY DIFFRACTION11chain 'B' and (resid 94 through 121 )B94 - 121
12X-RAY DIFFRACTION12chain 'B' and (resid 122 through 130 )B122 - 130
13X-RAY DIFFRACTION13chain 'B' and (resid 131 through 145 )B131 - 145
14X-RAY DIFFRACTION14chain 'C' and (resid 16 through 30 )C16 - 30
15X-RAY DIFFRACTION15chain 'C' and (resid 31 through 44 )C31 - 44
16X-RAY DIFFRACTION16chain 'C' and (resid 45 through 124 )C45 - 124
17X-RAY DIFFRACTION17chain 'C' and (resid 125 through 141 )C125 - 141
18X-RAY DIFFRACTION18chain 'C' and (resid 142 through 178 )C142 - 178
19X-RAY DIFFRACTION19chain 'C' and (resid 179 through 197 )C179 - 197
20X-RAY DIFFRACTION20chain 'C' and (resid 198 through 238 )C198 - 238
21X-RAY DIFFRACTION21chain 'D' and (resid 29 through 42 )D29 - 42
22X-RAY DIFFRACTION22chain 'D' and (resid 43 through 75 )D43 - 75
23X-RAY DIFFRACTION23chain 'D' and (resid 76 through 95 )D76 - 95
24X-RAY DIFFRACTION24chain 'D' and (resid 96 through 137 )D96 - 137
25X-RAY DIFFRACTION25chain 'D' and (resid 138 through 168 )D138 - 168
26X-RAY DIFFRACTION26chain 'D' and (resid 169 through 188 )D169 - 188
27X-RAY DIFFRACTION27chain 'D' and (resid 189 through 246 )D189 - 246
28X-RAY DIFFRACTION28chain 'E' and (resid 47 through 56 )E47 - 56
29X-RAY DIFFRACTION29chain 'E' and (resid 57 through 65 )E57 - 65
30X-RAY DIFFRACTION30chain 'E' and (resid 66 through 77 )E66 - 77
31X-RAY DIFFRACTION31chain 'E' and (resid 78 through 93 )E78 - 93
32X-RAY DIFFRACTION32chain 'E' and (resid 94 through 101 )E94 - 101
33X-RAY DIFFRACTION33chain 'E' and (resid 102 through 112 )E102 - 112
34X-RAY DIFFRACTION34chain 'E' and (resid 113 through 133 )E113 - 133
35X-RAY DIFFRACTION35chain 'E' and (resid 134 through 145 )E134 - 145
36X-RAY DIFFRACTION36chain 'F' and (resid 16 through 30 )F16 - 30
37X-RAY DIFFRACTION37chain 'F' and (resid 31 through 56 )F31 - 56
38X-RAY DIFFRACTION38chain 'F' and (resid 57 through 124 )F57 - 124
39X-RAY DIFFRACTION39chain 'F' and (resid 125 through 238 )F125 - 238
40X-RAY DIFFRACTION40chain 'G' and (resid 29 through 75 )G29 - 75
41X-RAY DIFFRACTION41chain 'G' and (resid 76 through 95 )G76 - 95
42X-RAY DIFFRACTION42chain 'G' and (resid 96 through 117 )G96 - 117
43X-RAY DIFFRACTION43chain 'G' and (resid 118 through 137 )G118 - 137
44X-RAY DIFFRACTION44chain 'G' and (resid 138 through 154 )G138 - 154
45X-RAY DIFFRACTION45chain 'G' and (resid 155 through 183 )G155 - 183
46X-RAY DIFFRACTION46chain 'G' and (resid 184 through 246 )G184 - 246
47X-RAY DIFFRACTION47chain 'H' and (resid 47 through 71 )H47 - 71
48X-RAY DIFFRACTION48chain 'H' and (resid 72 through 77 )H72 - 77
49X-RAY DIFFRACTION49chain 'H' and (resid 78 through 93 )H78 - 93
50X-RAY DIFFRACTION50chain 'H' and (resid 94 through 121 )H94 - 121
51X-RAY DIFFRACTION51chain 'H' and (resid 122 through 133 )H122 - 133
52X-RAY DIFFRACTION52chain 'H' and (resid 134 through 145 )H134 - 145
53X-RAY DIFFRACTION53chain 'I' and (resid 16 through 124 )I16 - 124
54X-RAY DIFFRACTION54chain 'I' and (resid 125 through 141 )I125 - 141
55X-RAY DIFFRACTION55chain 'I' and (resid 142 through 187 )I142 - 187
56X-RAY DIFFRACTION56chain 'I' and (resid 188 through 238 )I188 - 238
57X-RAY DIFFRACTION57chain 'J' and (resid 29 through 75 )J29 - 75
58X-RAY DIFFRACTION58chain 'J' and (resid 76 through 95 )J76 - 95
59X-RAY DIFFRACTION59chain 'J' and (resid 96 through 137 )J96 - 137
60X-RAY DIFFRACTION60chain 'J' and (resid 138 through 154 )J138 - 154
61X-RAY DIFFRACTION61chain 'J' and (resid 155 through 168 )J155 - 168
62X-RAY DIFFRACTION62chain 'J' and (resid 169 through 188 )J169 - 188
63X-RAY DIFFRACTION63chain 'J' and (resid 189 through 203 )J189 - 203
64X-RAY DIFFRACTION64chain 'J' and (resid 204 through 246 )J204 - 246
65X-RAY DIFFRACTION65chain 'K' and (resid 47 through 56 )K47 - 56
66X-RAY DIFFRACTION66chain 'K' and (resid 57 through 71 )K57 - 71
67X-RAY DIFFRACTION67chain 'K' and (resid 72 through 93 )K72 - 93
68X-RAY DIFFRACTION68chain 'K' and (resid 94 through 121 )K94 - 121
69X-RAY DIFFRACTION69chain 'K' and (resid 122 through 145 )K122 - 145
70X-RAY DIFFRACTION70chain 'L' and (resid 16 through 124 )L16 - 124
71X-RAY DIFFRACTION71chain 'L' and (resid 125 through 187 )L125 - 187
72X-RAY DIFFRACTION72chain 'L' and (resid 188 through 238 )L188 - 238
73X-RAY DIFFRACTION73chain 'M' and (resid 29 through 137 )M29 - 137
74X-RAY DIFFRACTION74chain 'M' and (resid 138 through 168 )M138 - 168
75X-RAY DIFFRACTION75chain 'M' and (resid 169 through 246 )M169 - 246
76X-RAY DIFFRACTION76chain 'N' and (resid 47 through 93 )N47 - 93
77X-RAY DIFFRACTION77chain 'N' and (resid 94 through 121 )N94 - 121
78X-RAY DIFFRACTION78chain 'N' and (resid 122 through 145 )N122 - 145
79X-RAY DIFFRACTION79chain 'O' and (resid 16 through 29 )O16 - 29
80X-RAY DIFFRACTION80chain 'O' and (resid 30 through 63 )O30 - 63
81X-RAY DIFFRACTION81chain 'O' and (resid 64 through 81 )O64 - 81
82X-RAY DIFFRACTION82chain 'O' and (resid 82 through 114 )O82 - 114
83X-RAY DIFFRACTION83chain 'O' and (resid 115 through 124 )O115 - 124
84X-RAY DIFFRACTION84chain 'O' and (resid 125 through 141 )O125 - 141
85X-RAY DIFFRACTION85chain 'O' and (resid 142 through 163 )O142 - 163
86X-RAY DIFFRACTION86chain 'O' and (resid 164 through 187 )O164 - 187
87X-RAY DIFFRACTION87chain 'O' and (resid 188 through 220 )O188 - 220
88X-RAY DIFFRACTION88chain 'O' and (resid 221 through 238 )O221 - 238
89X-RAY DIFFRACTION89chain 'P' and (resid 29 through 104 )P29 - 104
90X-RAY DIFFRACTION90chain 'P' and (resid 105 through 117 )P105 - 117
91X-RAY DIFFRACTION91chain 'P' and (resid 118 through 137 )P118 - 137
92X-RAY DIFFRACTION92chain 'P' and (resid 138 through 168 )P138 - 168
93X-RAY DIFFRACTION93chain 'P' and (resid 169 through 188 )P169 - 188
94X-RAY DIFFRACTION94chain 'P' and (resid 189 through 228 )P189 - 228
95X-RAY DIFFRACTION95chain 'P' and (resid 229 through 246 )P229 - 246
96X-RAY DIFFRACTION96chain 'Q' and (resid 47 through 93 )Q47 - 93
97X-RAY DIFFRACTION97chain 'Q' and (resid 94 through 102 )Q94 - 102
98X-RAY DIFFRACTION98chain 'Q' and (resid 103 through 145 )Q103 - 145
99X-RAY DIFFRACTION99chain 'R' and (resid 16 through 60 )R16 - 60
100X-RAY DIFFRACTION100chain 'R' and (resid 61 through 104 )R61 - 104
101X-RAY DIFFRACTION101chain 'R' and (resid 105 through 124 )R105 - 124
102X-RAY DIFFRACTION102chain 'R' and (resid 125 through 163 )R125 - 163
103X-RAY DIFFRACTION103chain 'R' and (resid 164 through 205 )R164 - 205
104X-RAY DIFFRACTION104chain 'R' and (resid 206 through 238 )R206 - 238

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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