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- PDB-8d4s: Crystal Structure of Cathepsin G Inhibited by Eap1 from S. aureus -

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基本情報

登録情報
データベース: PDB / ID: 8d4s
タイトルCrystal Structure of Cathepsin G Inhibited by Eap1 from S. aureus
要素
  • Cathepsin G, C-terminal truncated form
  • Extracellular Adherence Protein
キーワードPROTEIN BINDING / Protease Inhibitor / Immune Evasion / Neutrophil / S. aureus
機能・相同性
機能・相同性情報


cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / caspase binding / negative regulation of T cell activation / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation ...cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / caspase binding / negative regulation of T cell activation / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation / Antimicrobial peptides / Activation of Matrix Metalloproteinases / monocyte chemotaxis / extracellular matrix disassembly / defense response to fungus / Purinergic signaling in leishmaniasis infection / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / protein maturation / cytokine-mediated signaling pathway / positive regulation of immune response / protein processing / platelet activation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytoplasmic stress granule / azurophil granule lumen / antibacterial humoral response / peptidase activity / heparin binding / cellular response to lipopolysaccharide / : / defense response to Gram-negative bacterium / lysosome / defense response to Gram-positive bacterium / protein phosphorylation / immune response / receptor ligand activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytosol
類似検索 - 分子機能
MAP domain / MAP domain / MAP repeat profile. / 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 ...MAP domain / MAP domain / MAP repeat profile. / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
類似検索 - ドメイン・相同性
Cathepsin G / Protein map
類似検索 - 構成要素
生物種Staphylococcus aureus subsp. aureus Mu50 (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: 1.95 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)5R35GM140852 米国
引用ジャーナル: J.Biol.Chem. / 年: 2023
タイトル: Characterization of two distinct neutrophil serine protease-binding modes within a Staphylococcus aureus innate immune evasion protein family.
著者: Gido, C.D. / Herdendorf, T.J. / Geisbrecht, B.V.
履歴
登録2022年6月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年12月21日Provider: repository / タイプ: Initial release
改定 1.12023年7月5日Group: Database references / カテゴリ: citation
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
改定 1.22023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 1.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Cathepsin G, C-terminal truncated form
C: Cathepsin G, C-terminal truncated form
E: Cathepsin G, C-terminal truncated form
G: Cathepsin G, C-terminal truncated form
F: Extracellular Adherence Protein
B: Extracellular Adherence Protein
H: Extracellular Adherence Protein
D: Extracellular Adherence Protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)147,21612
ポリマ－146,3318
非ポリマー8854
水9,368520
1
A: Cathepsin G, C-terminal truncated form
B: Extracellular Adherence Protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,8043
ポリマ－36,5832
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-3 kcal/mol
Surface area14890 Å2
手法PISA
2
C: Cathepsin G, C-terminal truncated form
D: Extracellular Adherence Protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,8043
ポリマ－36,5832
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-0 kcal/mol
Surface area14840 Å2
手法PISA
3
E: Cathepsin G, C-terminal truncated form
F: Extracellular Adherence Protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,8043
ポリマ－36,5832
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-4 kcal/mol
Surface area15060 Å2
手法PISA
4
G: Cathepsin G, C-terminal truncated form
H: Extracellular Adherence Protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,8043
ポリマ－36,5832
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-4 kcal/mol
Surface area14890 Å2
手法PISA
単位格子
Length a, b, c (Å)158.189, 165.650, 321.934
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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要素

#1: タンパク質
Cathepsin G, C-terminal truncated form


分子量: 25397.131 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / Plasmid details: Purified from human sputum / 組織: Neutrophil / 参照: UniProt: P08311
#2: タンパク質
Extracellular Adherence Protein / Protein map


分子量: 11185.606 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus subsp. aureus Mu50 (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: 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: 4 / 由来タイプ: 天然 / 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: 520 / 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
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: 3.6 Å3/Da / 溶媒含有率: 65.86 %
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 / pH: 5.5
詳細: 0.1M BisTris (pH 5.5), 0.2M Magnesium Chloride, 25% (w/v) PEG-3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: 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: 2020年11月4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: 1.95→50 Å / Num. obs: 152193 / % possible obs: 99.9 % / 冗長度: 6.9 % / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.093 / Rrim(I) all: 0.251 / Χ2: 1.016 / Net I/σ(I): 9.1 / Num. measured all: 1054098
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.024.91.642150900.4660.8071.8350.93299.9
2.02-2.15.31.488150620.5380.6891.6451.06199.8
2.1-2.27.31.424151600.7710.5641.5331.047100
2.2-2.317.71.074151450.8690.4141.1521.06100
2.31-2.467.60.73151700.9090.2830.7831.007100
2.46-2.657.40.487151810.9360.1920.5241.02100
2.65-2.9170.299151980.9650.1210.3231.003100
2.91-3.337.30.169152630.9760.0660.1820.977100
3.33-4.27.80.145153280.9820.0560.1550.992100
4.2-507.10.231155960.9620.0930.2491.04799.8

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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
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
PHENIX1.9.2精密化
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: 1CGH, 8D4O

1cgh

8d4o


解像度: 1.95→40.52 Å / SU ML: 0.19 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 28.79 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2608 1903 1.31 %
Rwork0.2097 143205 -
obs0.2103 145108 95.29 %
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: 145.87 Å2 / Biso mean: 52.3778 Å2 / Biso min: 23.33 Å2
精密化ステップサイクル: final / 解像度: 1.95→40.52 Å
タンパク質核酸リガンド溶媒全体
原子数10108 0 56 520 10684
Biso mean--85.76 51.56 -
残基数----1268
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 (%)
1.95-20.35481140.28949005911985
2-2.050.29531230.26929376949988
2.05-2.110.28391350.25069503963889
2.11-2.180.32331270.2499591008693
2.18-2.260.24481330.2316100571019094
2.26-2.350.2631390.2149102991043896
2.35-2.460.23311320.21103071043997
2.46-2.590.25871390.2093104631060298
2.59-2.750.24351420.2201105061064898
2.75-2.960.27671380.2214106361077499
2.96-3.260.26591390.2178107131085299
3.26-3.730.24811500.19541071610866100
3.73-4.70.25021430.17751079610939100
4.7-40.520.26261490.2156108691101898
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)
10.9477-0.3117-0.37423.0796-0.86423.65040.27420.0150.2170.46620.00010.4035-0.1178-0.1673-0.25040.3266-0.04520.03040.35090.02370.31315.199133.265829.0191
23.3394-0.224-0.29566.02071.45623.81670.0506-0.2162-0.10980.48930.0342-0.26670.42350.0664-0.00690.3289-0.0481-0.02150.37860.04710.243223.409128.215424.6281
32.9441-0.4518-0.77884.3186-1.24513.3332-0.0108-0.3409-0.27540.55530.0711-0.0280.00910.2103-0.06950.2968-0.0572-0.0620.3540.01110.267424.068229.255231.2436
42.7919-0.89520.80712.01510.37124.1666-0.18940.09210.1838-0.99150.1580.1249-0.43080.55520.07990.3824-0.1220.08490.5069-0.00070.388230.263238.522912.4824
51.5853-0.84690.06351.7794-0.9713.1828-0.144-0.0997-0.4543-0.09880.02740.10990.73070.04390.11270.4649-0.016-0.01710.37110.01630.385820.252620.324626.0763
63.4183-1.90610.22573.373-0.60822.61260.23281.2086-0.414-0.9366-0.49860.11120.6025-0.4870.07510.61630.0567-0.0740.635-0.03740.608310.761831.29179.912
73.2849-1.0490.32542.0377-0.85863.5305-0.3196-0.61390.41010.6790.6382-0.4082-0.5814-0.0285-0.3620.43930.0160.0590.48760.01220.516412.832743.167232.2811
82.98420.0263-0.01632.0106-0.25313.8282-0.04240.83120.3791-0.59240.14330.1291-0.3191-0.5434-0.09940.42360.0143-0.0340.48830.05340.3619.376341.929811.9666
91.3172.5365-0.10275.80932.41857.2191-0.04240.05620.3798-0.36120.31420.373-0.96290.5859-0.15440.6499-0.1187-0.00970.39190.04340.322120.357343.86055.8456
102.1223-0.47010.77580.0518-0.21622.20290.0894-0.09580.541-0.11090.15640.2679-0.6833-0.7173-0.27880.45840.0485-0.02410.46780.11360.452311.58543.948517.5343
111.8148-1.5423-1.05753.6424-0.02993.27650.0793-0.0553-0.0811-0.2538-0.12090.9546-0.0865-0.2869-0.02930.348-0.0279-0.0530.41540.01480.343914.299837.933516.3438
123.4617-1.18570.4162.9032-0.10613.14650.01160.0264-0.3021-0.0420.15810.20630.41870.2909-0.18680.4058-0.06-0.01340.445-0.02360.331423.292428.230611.4544
130.21210.85320.15124.40250.52740.14-0.04790.0355-0.0457-0.6970.3165-0.8892-0.07840.5763-0.26150.396-0.02440.09790.4804-0.03710.428532.138373.94252.9888
143.1224-0.0362-1.28113.48450.41443.41750.01740.22110.4682-0.3940.00930.2815-0.4419-0.2273-0.0040.2993-0.0034-0.06020.38560.07040.314514.891874.7352.8234
153.35860.859-0.66893.62671.40563.15360.09390.2157-0.1504-0.75340.12840.04970.046-0.1243-0.20950.4012-0.0336-0.06960.31140.04520.324317.644670.886250.3198
162.66270.3968-0.50492.23630.78714.1853-0.01670.076-0.1364-0.00310.06020.24090.3612-0.4722-0.00150.2629-0.0498-0.04990.33150.11890.300414.269868.765159.1015
172.44531.88610.54062.82971.04332.22010.1708-0.7734-0.54060.7449-0.1066-0.53770.76220.0734-0.14370.435-0.0161-0.05370.69190.10290.47129.146573.300171.1975
184.7514-0.184-0.2039.65251.12525.7751-0.09080.37560.6182-1.29670.4920.5521-0.9745-0.0157-0.18980.5432-0.0523-0.02080.5590.06160.470126.34385.076348.7377
191.74460.2082-1.04030.6799-0.41074.04020.1124-0.4780.37740.2190.13870.052-0.49240.3744-0.2040.3445-0.03020.04620.4489-0.02240.314425.509384.55971.6001
202.88751.15280.88731.3484-0.18072.6615-0.10230.00160.3005-0.02330.2964-0.2775-0.75470.7178-0.1430.3611-0.07250.00720.4803-0.02740.35527.69885.795163.4958
212.22170.5988-1.18842.92840.48272.83730.08310.12890.1514-0.16340.0509-0.67960.02820.2203-0.15430.23920.0038-0.0190.42910.03230.328125.245579.793264.7934
223.59320.37010.14593.41260.40753.6384-0.1136-0.2424-0.56650.14340.16490.12250.6255-0.2339-0.05650.34790.00830.00160.43910.09040.356716.494669.842269.7816
231.6184-1.04060.66514.26040.52271.362-0.046-0.10350.02080.02230.0568-1.0059-0.44560.6386-0.09730.4372-0.0138-0.06020.4424-0.04110.4561-6.247650.786827.4907
243.66030.9136-0.13914.894-1.79263.21570.1663-0.5034-0.12410.2756-0.14140.4147-0.14960.1317-0.17140.49270.02570.04010.3072-0.02870.3321-23.542350.318627.776
252.69-0.47021.03433.74250.32244.34710.0955-0.16960.03890.22970.02330.1144-0.264-0.15-0.06980.31480.0410.03360.2165-0.01410.236-24.322454.26125.2603
261.89470.39940.9142.55592.04022.065-0.5839-0.12821.0222-0.27510.0843-0.2026-1.18840.75490.54540.5633-0.038-0.01930.3254-0.06770.4495-12.020363.903525.538
272.9845-1.10850.1542.81011.21881.89290.31881.16830.5424-0.5974-0.4492-0.0575-0.98320.5090.05140.52810.1119-0.00130.55410.12780.5297-9.386152.37889.4465
282.99010.675-0.00042.97730.84013.1161-0.0277-0.3599-0.32980.3029-0.0776-0.26640.37540.33260.09950.4220.0891-0.02130.3736-0.0170.4332-9.253141.568624.6193
292.16561.46860.95995.5552-2.39125.93490.01450.3523-0.31140.10890.1305-0.34480.99230.5853-0.15160.59550.1401-0.04480.4566-0.04770.3848-17.51539.21514.5743
302.1941-1.3847-0.45710.972-0.21381.5040.12620.0747-0.2486-0.1997-0.1024-0.29880.51840.2137-0.06010.50140.0952-0.01480.4034-0.06110.4298-10.826939.349416.8167
312.2366-1.24130.9162.0122-0.42552.57290.17810.0413-0.0687-0.0524-0.0614-0.5779-0.04770.0792-0.14030.45710.08540.00860.328-0.00150.3625-13.228845.50515.6713
322.96830.0734-0.33762.77341.70283.0627-0.04170.14830.4632-0.2140.0474-0.2866-0.4821-0.18570.0260.53740.096-0.02220.38530.03260.3073-22.032255.831811.1086
333.5671-0.2220.78893.6492-0.54512.34470.230.17670.0588-0.2684-0.1621-0.1399-0.05160.0627-0.04840.2478-0.00780.03350.24260.00310.2053-20.000310.713753.0631
343.59020.01820.33462.7686-1.13.1276-0.07160.3810.1576-0.47650.24850.3608-0.25080.0271-0.17210.3702-0.01230.04070.27420.04010.4115-19.212814.566646.7678
352.69142.2489-0.01369.49131.12345.29220.1226-0.30630.00470.5524-0.3190.10750.1790.19570.17720.2513-0.0433-0.00090.3714-0.01740.331-10.26634.380867.8674
361.5250.7569-0.06572.175-0.47823.0225-0.2077-0.05750.6936-0.0713-0.00450.1714-0.7198-0.23550.13260.38190.01620.07640.28230.00820.4736-20.664921.901653.7058
372.36060.96910.58682.1776-0.6163.5301-0.1077-1.06510.57740.6573-0.37640.3563-0.3246-0.32040.3970.4382-0.0550.07060.7578-0.15540.5409-29.827811.347570.4938
382.8829-0.18970.02372.0292-1.22774.7061-0.01430.1346-0.2301-0.21760.03840.30610.4377-0.34260.03920.3144-0.0694-0.00820.39650.00570.4478-30.50360.620455.494
393.7515-0.56030.70756.06592.38955.3813-0.1699-0.5053-0.2740.40270.22820.64420.548-0.6188-0.14740.3625-0.07440.06250.44950.02610.3712-21.8328-1.788875.578
403.39240.32070.62060.61980.09622.9532-0.015-0.15050.12510.0740.00750.3204-0.0548-0.2674-0.01090.2602-0.01910.0420.3116-0.01770.2781-24.10036.026465.4025
411.3922-0.30880.53823.6721-2.35353.5698-0.0904-0.1519-0.09280.17570.43070.9375-0.2688-0.5501-0.29830.40280.0430.01720.34430.07140.497-30.942833.524829.2447
426.2913.8493-5.14978.0317-2.29994.3540.90541.39430.50940.31060.46571.16931.5436-1.25420.23660.9747-0.1828-0.52610.8620.12720.9578-37.88728.810214.4243
434.08810.71833.53552.087-0.27939.3279-0.00720.309-0.3666-0.60120.37170.74930.96080.1919-0.34880.5078-0.0166-0.10260.29630.08030.5556-26.680722.151128.5676
441.7996-0.23940.72242.59390.41436.1980.29110.1112-0.74310.07751.07241.32832.0431-1.4861-1.17760.6216-0.15070.05150.5710.19261.0171-34.786621.313131.0779
454.94180.07230.41583.2581-0.84226.5225-0.0864-0.0105-0.629-0.17750.10080.06170.38160.42620.1440.46040.064-0.04370.20590.0210.4086-26.631327.851729.3206
461.0434-0.28980.48953.78340.94012.4577-0.1060.04070.05270.01240.4743-0.8963-0.08160.7234-0.24630.3716-0.12840.00490.4879-0.10520.500531.213150.220530.7109
474.9342-1.8766-0.63294.0793.98974.2659-0.25730.1361-0.48141.0783-0.1233-0.62141.22410.75290.52310.8381-0.43530.44170.8642-0.39151.060539.242154.602617.0221
483.5372-0.8126-2.92041.70881.16678.8097-0.06050.3720.89-1.04190.8936-0.4355-0.87340.7719-0.67130.856-0.2650.02850.5449-0.08420.551228.46961.690727.9035
493.136-0.89090.39782.16691.2547.2676-0.4984-0.09920.3068-0.3633-0.07090.1536-1.24930.18990.67780.5608-0.0942-0.03350.3139-0.02590.500427.764556.792532.977
500.62621.08651.17933.35850.33713.675-0.08740.2869-0.1727-0.44560.3025-0.55430.07510.58-0.17270.2595-0.02030.06760.3341-0.06920.3544-9.2996-7.816550.1638
512.44620.06412.06883.23110.03244.89740.2543-0.086-0.41170.30050.1285-0.67370.78520.2573-0.25420.32960.0397-0.02360.3656-0.05880.4212-8.5351-17.05856.0872
523.06160.48560.72662.55541.30617.5266-0.21310.28-0.3521-0.523-0.0261-0.14530.4059-0.32910.31960.4058-0.06040.07690.2447-0.05810.3941-12.5001-14.595248.0579
532.00950.0457-0.44153.626-1.03332.0608-0.05520.1143-0.1739-0.14580.51720.26850.3743-0.149-0.35330.3718-0.0289-0.01570.39410.10170.345313.14889.120453.9173
541.0461-1.25472.99161.5239-3.64348.77360.12540.48560.7191-1.13510.44090.71590.3998-0.0806-0.40380.6575-0.1687-0.26010.54180.24110.67247.420690.806941.2075
551.4604-0.54790.42631.8926-1.75384.0734-0.0899-0.2071-0.68240.01550.99250.98950.0568-1.2773-0.81190.36610.03960.0350.58940.27040.83123.15793.845451.9794
561.17791.53412.86946.95872.73587.29730.067-1.3440.34020.48460.10191.6741-0.5557-1.7575-0.03270.76510.31580.38840.94940.31550.96191.00896.836865.24
575.5438-1.3764-5.2261.84971.72447.6344-0.6062-0.57040.31130.61530.70220.29940.12130.4863-0.12260.5690.07460.030.4280.15180.494311.3281101.169653.7401
582.97880.0902-2.74431.15420.0025.72020.5153-0.12260.6113-0.21590.10030.3043-1.2526-0.3009-0.58560.57-0.00280.10090.46420.06090.4810.1601104.528750.7752
593.81310.5408-0.33932.8975-1.44718.6574-0.23620.11410.4627-0.0956-0.14990.46110.080.12010.42810.4905-0.0473-0.06520.33470.04970.427710.952898.168748.1979
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 39 )A16 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 56 )A40 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 91 )A57 - 91
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 104 )A92 - 104
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 124 )A105 - 124
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 141 )A125 - 141
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 154 )A142 - 154
8X-RAY DIFFRACTION8chain 'A' and (resid 155 through 168 )A155 - 168
9X-RAY DIFFRACTION9chain 'A' and (resid 169 through 178 )A169 - 178
10X-RAY DIFFRACTION10chain 'A' and (resid 179 through 197 )A179 - 197
11X-RAY DIFFRACTION11chain 'A' and (resid 198 through 220 )A198 - 220
12X-RAY DIFFRACTION12chain 'A' and (resid 221 through 238 )A221 - 238
13X-RAY DIFFRACTION13chain 'C' and (resid 16 through 29 )C16 - 29
14X-RAY DIFFRACTION14chain 'C' and (resid 30 through 50 )C30 - 50
15X-RAY DIFFRACTION15chain 'C' and (resid 51 through 81 )C51 - 81
16X-RAY DIFFRACTION16chain 'C' and (resid 82 through 124 )C82 - 124
17X-RAY DIFFRACTION17chain 'C' and (resid 125 through 141 )C125 - 141
18X-RAY DIFFRACTION18chain 'C' and (resid 142 through 154 )C142 - 154
19X-RAY DIFFRACTION19chain 'C' and (resid 155 through 178 )C155 - 178
20X-RAY DIFFRACTION20chain 'C' and (resid 179 through 197 )C179 - 197
21X-RAY DIFFRACTION21chain 'C' and (resid 198 through 220 )C198 - 220
22X-RAY DIFFRACTION22chain 'C' and (resid 221 through 238 )C221 - 238
23X-RAY DIFFRACTION23chain 'E' and (resid 16 through 29 )E16 - 29
24X-RAY DIFFRACTION24chain 'E' and (resid 30 through 50 )E30 - 50
25X-RAY DIFFRACTION25chain 'E' and (resid 51 through 114 )E51 - 114
26X-RAY DIFFRACTION26chain 'E' and (resid 115 through 124 )E115 - 124
27X-RAY DIFFRACTION27chain 'E' and (resid 125 through 141 )E125 - 141
28X-RAY DIFFRACTION28chain 'E' and (resid 142 through 163 )E142 - 163
29X-RAY DIFFRACTION29chain 'E' and (resid 164 through 178 )E164 - 178
30X-RAY DIFFRACTION30chain 'E' and (resid 179 through 197 )E179 - 197
31X-RAY DIFFRACTION31chain 'E' and (resid 198 through 220 )E198 - 220
32X-RAY DIFFRACTION32chain 'E' and (resid 221 through 238 )E221 - 238
33X-RAY DIFFRACTION33chain 'G' and (resid 16 through 69 )G16 - 69
34X-RAY DIFFRACTION34chain 'G' and (resid 70 through 91 )G70 - 91
35X-RAY DIFFRACTION35chain 'G' and (resid 92 through 104 )G92 - 104
36X-RAY DIFFRACTION36chain 'G' and (resid 105 through 124 )G105 - 124
37X-RAY DIFFRACTION37chain 'G' and (resid 125 through 141 )G125 - 141
38X-RAY DIFFRACTION38chain 'G' and (resid 142 through 163 )G142 - 163
39X-RAY DIFFRACTION39chain 'G' and (resid 164 through 178 )G164 - 178
40X-RAY DIFFRACTION40chain 'G' and (resid 179 through 238 )G179 - 238
41X-RAY DIFFRACTION41chain 'F' and (resid 47 through 93 )F47 - 93
42X-RAY DIFFRACTION42chain 'F' and (resid 94 through 104 )F94 - 104
43X-RAY DIFFRACTION43chain 'F' and (resid 105 through 121 )F105 - 121
44X-RAY DIFFRACTION44chain 'F' and (resid 122 through 133 )F122 - 133
45X-RAY DIFFRACTION45chain 'F' and (resid 134 through 145 )F134 - 145
46X-RAY DIFFRACTION46chain 'B' and (resid 47 through 93 )B47 - 93
47X-RAY DIFFRACTION47chain 'B' and (resid 94 through 102 )B94 - 102
48X-RAY DIFFRACTION48chain 'B' and (resid 103 through 130 )B103 - 130
49X-RAY DIFFRACTION49chain 'B' and (resid 131 through 145 )B131 - 145
50X-RAY DIFFRACTION50chain 'H' and (resid 47 through 93 )H47 - 93
51X-RAY DIFFRACTION51chain 'H' and (resid 94 through 130 )H94 - 130
52X-RAY DIFFRACTION52chain 'H' and (resid 131 through 145 )H131 - 145
53X-RAY DIFFRACTION53chain 'D' and (resid 47 through 65 )D47 - 65
54X-RAY DIFFRACTION54chain 'D' and (resid 66 through 74 )D66 - 74
55X-RAY DIFFRACTION55chain 'D' and (resid 75 through 93 )D75 - 93
56X-RAY DIFFRACTION56chain 'D' and (resid 94 through 104 )D94 - 104
57X-RAY DIFFRACTION57chain 'D' and (resid 105 through 112 )D105 - 112
58X-RAY DIFFRACTION58chain 'D' and (resid 113 through 130 )D113 - 130
59X-RAY DIFFRACTION59chain 'D' and (resid 131 through 145 )D131 - 145

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る