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- PDB-8d7k: 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: 8d7k
タイトルBifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap2 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 / neutrophil-mediated killing of fungus / Expression of NOTCH2NL genes / negative regulation of chemotaxis / purinergic nucleotide receptor signaling pathway / acute inflammatory response to antigenic stimulus ...cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / Expression of NOTCH2NL genes / negative regulation of chemotaxis / purinergic nucleotide receptor signaling pathway / acute inflammatory response to antigenic stimulus / caspase binding / positive regulation of leukocyte tethering or rolling / 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 / Activation of Matrix Metalloproteinases / cytokine binding / neutrophil-mediated killing of gram-negative bacterium / monocyte chemotaxis / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / defense response to fungus / Purinergic signaling in leishmaniasis infection / Metabolism of Angiotensinogen to Angiotensins / response to UV / angiotensin maturation / phagocytic vesicle / Degradation of the extracellular matrix / transcription repressor complex / serine-type peptidase activity / positive regulation of MAP kinase activity / protein maturation / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / protein catabolic process / cytokine-mediated signaling pathway / protein processing / positive regulation of immune response / platelet activation / negative regulation of inflammatory response / specific granule lumen / intracellular calcium ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytoplasmic stress granule / transcription corepressor activity / azurophil granule lumen / antibacterial humoral response / peptidase activity / heparin binding / cellular response to lipopolysaccharide / protease binding / : / defense response to Gram-negative bacterium / endopeptidase activity / response to lipopolysaccharide / lysosome / defense response to Gram-positive bacterium / defense response to bacterium / immune response / protein phosphorylation / receptor ligand activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / negative regulation of transcription by RNA polymerase II / cell surface / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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. ...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
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: 3.1 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23日Group: Database references / Structure summary
カテゴリ: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
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
C: Cathepsin G, C-terminal truncated form
B: Extracellular Adherence Protein
A: Neutrophil elastase
F: Cathepsin G, C-terminal truncated form
E: Extracellular Adherence Protein
D: Neutrophil elastase
I: Cathepsin G, C-terminal truncated form
H: Extracellular Adherence Protein
G: Neutrophil elastase
L: Cathepsin G, C-terminal truncated form
K: Extracellular Adherence Protein
J: Neutrophil elastase


分子量 (理論値)分子数
合計 (水以外)238,95812
ポリマ－238,95812
非ポリマー00
水00
1
C: Cathepsin G, C-terminal truncated form
B: Extracellular Adherence Protein
A: Neutrophil elastase


分子量 (理論値)分子数
合計 (水以外)59,7403
ポリマ－59,7403
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-12 kcal/mol
Surface area22980 Å2
手法PISA
2
F: Cathepsin G, C-terminal truncated form
E: Extracellular Adherence Protein
D: Neutrophil elastase


分子量 (理論値)分子数
合計 (水以外)59,7403
ポリマ－59,7403
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-14 kcal/mol
Surface area23270 Å2
手法PISA
3
I: Cathepsin G, C-terminal truncated form
H: Extracellular Adherence Protein
G: Neutrophil elastase


分子量 (理論値)分子数
合計 (水以外)59,7403
ポリマ－59,7403
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-13 kcal/mol
Surface area23480 Å2
手法PISA
4
L: Cathepsin G, C-terminal truncated form
K: Extracellular Adherence Protein
J: Neutrophil elastase


分子量 (理論値)分子数
合計 (水以外)59,7403
ポリマ－59,7403
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-13 kcal/mol
Surface area23300 Å2
手法PISA
単位格子
Length a, b, c (Å)97.594, 107.438, 105.415
Angle α, β, γ (deg.)90.000, 91.520, 90.000
Int Tables number4
Space group name H-MP1211

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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) / Cell: Neutrophil / Plasmid details: Purified from human sputum / 参照: UniProt: P08311
#2: タンパク質
Extracellular Adherence Protein / Protein map


分子量: 11023.418 Da / 分子数: 4 / 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
Neutrophil elastase / Bone marrow serine protease / Elastase-2 / Human leukocyte elastase / HLE / Medullasin / PMN elastase


分子量: 23318.982 Da / 分子数: 4 / Fragment: 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
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: 2.31 Å3/Da / 溶媒含有率: 46.8 %
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: 3.6
詳細: 0.1M Citric acid, 0.15M Lithium Sulfate, 12% PEG-6000

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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: 3.1→50 Å / Num. obs: 39299 / % possible obs: 99.1 % / 冗長度: 4.8 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.071 / Rrim(I) all: 0.16 / Χ2: 1.009 / Net I/σ(I): 7.9 / Num. measured all: 189978
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
3.1-3.2150.70439320.7620.3430.7860.9199.8
3.21-3.344.90.47139320.8660.230.5270.94599.9
3.34-3.494.90.33539260.9240.1640.3751.02999.3
3.49-3.684.80.2438840.9550.1190.2691.08798.9
3.68-3.914.60.17738930.9750.0890.1991.03798.5
3.91-4.214.40.12338480.9830.0640.1390.98697.5
4.21-4.635.10.09739670.9860.0470.1080.9899.8
4.63-5.35.10.08739520.990.0420.0971.02999.8
5.3-6.674.90.08239720.9920.040.0921.05999.7
6.67-504.60.05739930.9920.0290.0641.03798.1

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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
HKL-2000データ削減
HKL-2000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, 1YN3

1hne

1au8

1yn3


解像度: 3.1→43.83 Å / SU ML: 0.39 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 25.75 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2576 1933 5.06 %
Rwork0.1845 36237 -
obs0.1882 38170 95.94 %
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: 118.67 Å2 / Biso mean: 46.5967 Å2 / Biso min: 10.7 Å2
精密化ステップサイクル: final / 解像度: 3.1→43.83 Å
タンパク質核酸リガンド溶媒全体
原子数16684 0 0 0 16684
残基数----2152
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 (%)
3.1-3.170.31081090.23562284239385
3.17-3.260.33541460.23942440258692
3.26-3.360.2951450.22442542268794
3.36-3.460.29731300.20962542267295
3.46-3.590.30621300.19922567269796
3.59-3.730.24781440.18412603274797
3.73-3.90.27421390.18662574271396
3.9-4.110.24291320.17882561269396
4.11-4.360.23781470.16242683283099
4.36-4.70.22431340.1442701283599
4.7-5.170.21841460.152526902836100
5.17-5.920.25081530.17962666281999
5.92-7.450.2761340.19812675280998
7.45-43.830.23381440.18972709285398
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)
11.38791.12440.01730.8317-0.12660.281-0.4402-0.33920.54330.65330.34480.1910.0239-0.4662-0.01340.26520.0543-0.09060.40860.01920.4656-39.205516.428255.05
21.31760.08350.63111.5738-0.83851.82890.105-0.0801-0.1150.00360.1620.46610.1995-0.3657-0.14830.1831-0.0034-0.0080.26190.01230.4336-35.51685.616948.2603
32.1042-0.37940.1322.2024-0.18852.07430.1515-0.2130.13750.0472-0.11290.4942-0.1297-0.2052-0.07210.1801-0.03540.06160.2652-0.02460.2985-30.300612.655552.2413
41.3348-0.5810.22061.7219-0.01390.4646-0.24660.0257-0.0868-0.2816-0.03160.11770.26140.06130.12480.2298-0.0251-0.01470.16810.02520.2844-14.9758-0.878739.3451
52.7812-0.6161-1.48662.331.14413.45010.532-0.3025-0.2799-0.1071-0.2533-0.2818-0.65780.6181-0.270.1748-0.01060.03820.2350.0320.3325-10.9724-5.887545.7276
60.5332-0.2126-0.5221.1837-0.38382.3955-0.0936-0.0438-0.2848-0.1571-0.2260.2433-0.33420.02560.18840.20280.00260.00120.2043-0.01730.3423-17.2741-11.851644.5631
71.493-0.6603-1.12250.21050.42010.6938-0.10090.0754-0.0817-0.6796-0.27750.4632-0.16690.58880.19140.4657-0.0105-0.04890.25540.06810.1946-9.5878-16.628939.3859
81.35860.14280.9361.9006-0.90792.9626-0.42330.7456-0.1595-0.711-0.07940.62610.2732-0.87790.15560.35780.0121-0.00270.1492-0.02730.1943-17.3713-6.287537.0152
91.44820.0444-0.06331.61781.23072.8014-0.4023-0.44160.4158-0.6648-0.1916-0.31720.23661.25940.1490.48970.11540.10760.25010.06870.38029.5364-26.439526.2098
102.48140.0897-0.77641.37930.1431.7861-0.2030.6876-0.0629-0.92730.0911-0.253-0.2824-0.18150.01390.80160.03190.11570.3888-0.03480.3807-3.5881-19.52820.4782
110.45890.00120.20020.23850.05770.0457-0.15970.5255-0.5863-0.8394-0.37560.57630.0101-0.68210.17260.84370.06130.11750.4136-0.09430.5988-14.866-25.36225.1785
121.9893-0.4925-0.38452.23320.00270.9985-0.1283-0.0166-0.3054-0.3602-0.0451-0.38030.26740.1970.11250.46170.01180.14260.3422-0.00180.40340.0122-29.113331.5521
131.7507-0.6706-0.28831.98970.20082.0602-0.5135-1.2965-1.272-0.2202-0.41041.06931.12720.31570.22280.25090.61910.7497-0.2495-0.43240.3328-6.5123-32.127232.1774
142.605-0.12320.26173.3562-0.32991.3552-0.4276-0.42110.06480.5009-0.6369-0.63880.13971.19810.4290.5047-0.0424-0.07740.48790.11410.3481-36.2847-34.871235.1057
152.4083-0.98870.42092.43650.00812.1349-0.27160.1665-0.0865-0.377-0.0666-0.31920.68690.32760.12370.43710.0657-0.04590.3971-0.05810.2952-40.8326-33.463919.9943
162.05810.0686-1.02811.9056-0.9871.66530.0727-0.1414-0.09510.1181-0.11080.1573-0.01260.03740.04570.35750.0022-0.04390.2953-0.02710.2561-49.0565-28.887130.0401
171.93950.1230.17561.3807-0.63531.5796-0.0113-0.1706-0.13350.31260.1539-0.1283-0.03870.2188-0.09120.4320.0249-0.03840.413-0.04830.2663-50.9236-28.548230.7095
181.04550.54910.4621.9266-0.59231.4870.22060.7361-0.27360.0254-0.34720.3156-0.4705-0.0110.0320.35990.0722-0.07890.29880.01080.3196-40.3739-16.284119.3983
192.6702-1.6704-1.12713.65040.79611.1443-0.69580.3236-0.5978-0.3920.3145-0.0431-0.12420.56390.18230.47530.0418-0.03050.6292-0.17020.5329-30.4746-8.6137.3487
203.45590.851-0.84332.985-0.63182.9877-0.16110.8731-0.8133-0.6097-0.41120.23750.10330.1520.220.40840.0158-0.04560.3539-0.18770.2324-44.9036-11.26612.5265
211.8705-2.61520.49083.6965-0.70660.1154-0.50970.9943-0.24450.1548-0.11160.4822-0.13760.60560.02170.7410.114-0.3397-0.1925-1.061-0.9445-54.2676-5.595913.4313
225.17960.14160.64691.9628-0.32031.8491-0.0341-0.7118-0.21840.87070.24930.0405-0.31780.1131-0.17940.4535-0.0168-0.09740.34990.02230.3537-41.4668-3.56420.4914
232.2564-1.2251-0.21331.79160.38021.1077-0.3651-0.2788-0.1189-0.13-0.3084-0.6976-0.60690.71210.03660.61450.018-0.22340.4525-0.2280.325-32.4165-2.337820.5126
240.34970.6061-0.56811.0027-0.71241.2330.0316-0.1878-0.21460.156-0.0796-0.4834-0.4518-0.31550.07820.3675-0.0886-0.07240.4701-0.09680.3117-36.82110.60810.7136
254.2125-0.57720.11371.289-0.12621.35650.1004-0.4203-0.24380.4788-0.1079-0.53410.28530.7623-0.07970.3212-0.1391-0.14650.5181-0.02720.5672-35.2123-9.549818.9501
260.01330.0638-0.1221-0.0391-0.0180.2205-0.2190.65580.342-0.2717-0.4724-0.77460.42020.3790.24740.7082-0.12230.31591.0620.1210.6348-22.89249.4144-8.1664
271.70490.0325-0.22140.02630.28391.75530.3490.7191-0.03090.2691-0.0056-1.02240.09220.3721-0.23030.3602-0.14020.11540.8459-0.16310.6691-19.49515.68887.8747
281.2311-0.0116-0.10071.38480.30970.1138-0.16231.1525-0.03680.05770.0189-1.14350.6636-0.0790.00850.506-0.09380.17121.0754-0.36520.8774-15.3776-0.36912.2723
291.0486-0.80260.0030.97980.37651.25040.3370.1722-0.1505-0.10820.0077-0.8584-0.4090.2642-0.24280.4646-0.18610.03890.6086-0.15170.6298-17.511910.738211.181
301.42330.30550.26561.1745-0.34030.79080.32690.9088-0.0182-0.44970.1436-0.5822-0.5533-0.0385-0.25420.6-0.0790.18710.8705-0.13740.539-29.803912.0025-0.7528
311.13480.32070.36950.8022-0.58120.6112-0.11280.52710.6239-0.20850.23470.2172-0.27910.0385-0.06120.5411-0.10250.10380.60940.08820.4996-36.178217.07362.6421
320.9614-0.3821-0.14460.7339-0.03871.0225-0.05551.21860.9264-1.32770.03190.3040.00430.0083-0.09460.5216-0.17990.20060.88270.15140.2114-34.236211.55561.3665
331.7990.35020.19470.7228-0.03580.41690.09010.26380.41320.72350.0705-0.5037-1.25690.0203-0.04760.5548-0.3550.01820.5975-0.07550.506-22.897619.231512.8693
341.76810.3657-0.20752.3896-0.19960.6524-0.1878-0.49830.04990.07260.05541.1741-0.4861-0.49680.10340.38030.17-0.01390.5938-0.18850.440929.785642.369132.9052
351.8206-0.8693-0.42221.0329-0.02011.734-0.02360.15920.2378-0.6507-0.2050.4678-0.7581-0.25620.14230.39980.0664-0.09870.3859-0.01670.342237.310441.441518.7695
361.9538-0.31660.33791.66660.04691.8229-0.05080.15390.2595-0.7768-0.1226-0.1896-0.05230.21840.07670.2641-0.03210.01710.23150.04180.242949.612436.595119.2343
371.8743-0.48810.60090.4371-0.79991.3577-0.0342-0.54811.2064-0.46850.14780.4441-0.5776-0.371-0.04440.76250.0211-0.03870.15750.16230.395843.53850.049917.1188
383.6063-2.63463.35623.9259-2.86253.2889-0.271-0.38020.7280.4025-0.06660.7299-0.5469-0.30320.1720.73880.04730.00850.3574-0.07420.565238.080153.491328.0391
390.9587-0.35360.17510.5772-0.73191.3466-0.185-0.05421.07520.13150.5032-0.84090.61610.7492-0.20840.6290.1577-0.11850.6303-0.27860.451746.60840.010540.35
401.8412-0.1497-0.58351.74950.03110.5575-0.20950.1564-0.40010.2407-0.19021.15010.4405-0.34080.19270.36110.07540.0350.4774-0.12720.400132.106932.598132.1782
413.0161-0.3561-0.32772.74651.0331.4314-0.2073-0.4034-0.4190.4403-0.5050.15990.47720.57250.37740.4482-0.01180.0250.42510.130.252448.064826.122638.6478
422.12050.0797-0.04961.89240.31851.96770.16840.01340.27720.2716-0.1140.2125-0.17740.03-0.01760.27230.0262-0.09440.2696-0.04230.212145.186936.204231.3141
431.04860.79240.43451.09190.43922.23-0.50480.2109-0.15150.1748-0.174-0.33620.1983-0.63040.14970.1249-0.0522-0.02570.27-0.07350.271638.196623.914219.6941
440.25860.23060.24190.37270.17510.4207-0.5125-0.00510.1514-0.42610.26940.7381-0.5223-0.04550.20240.37840.0221-0.11850.511-0.0340.332429.923421.57686.509
453.41980.97571.11092.53790.13692.5026-0.3480.25530.5374-0.6991-0.43750.49550.41460.50960.13340.3163-0.04730.01170.2792-0.0830.254241.710418.009811.0177
463.0356-0.42830.771.5998-0.46291.3893-0.47250.31110.10740.6473-0.3435-0.29240.4247-0.00020.2670.3206-0.05930.1380.3729-0.17570.155444.390112.441416.8164
470.5628-0.56340.22631.9763-0.50031.2428-0.59540.1040.4115-0.0227-0.67210.77260.2989-0.59370.14220.4631-0.10280.32170.43490.07840.159829.376110.371817.3231
480.18610.25530.54160.24580.61451.47480.46790.0130.02430.6778-0.07020.554-0.2445-0.244-0.04340.1958-0.1789-0.0070.39530.06550.304235.39237.36218.464
494.0061-1.13750.87341.1556-0.76291.9966-0.72410.0169-0.1059-0.1659-0.19340.4256-0.0321-0.35220.23530.4576-0.03990.02670.2058-0.12680.415132.064917.512616.2934
501.71360.21090.40750.820.06620.66830.08880.40940.2167-0.86240.08460.4452-0.36310.07840.06260.4959-0.33960.06180.5898-0.00120.403824.7494-0.7222-12.8774
510.8248-0.06220.46231.04210.18392.0068-0.01190.15160.6366-0.12150.07560.6632-0.1173-0.1566-0.04030.3058-0.0639-0.10240.4117-0.04050.571717.27665.5695-0.3024
520.88560.37780.91480.8181-0.27511.27530.1193-0.20080.40640.0718-0.15650.37360.5514-0.31980.09330.3578-0.0771-0.01710.4449-0.05440.357916.2254-2.34355.2275
531.0511-0.0614-0.20461.1199-0.94630.8373-0.13560.9103-0.66540.28160.3253-0.28050.7392-0.03130.03360.5958-0.0881-0.05280.3307-0.15080.366929.6655-14.0936-1.7563
541.45880.18080.04790.76370.71541.4062-0.04850.08040.3021-0.22510.0285-0.1020.13490.7557-0.02790.3816-0.0906-0.05210.4476-0.0260.227234.0638-1.8192-3.1105
552.22740.20870.15622.78590.46731.8433-0.46210.1008-0.309-0.36370.3985-0.09080.28850.2722-0.01970.318-0.0276-0.03950.4015-0.0510.168429.9453-5.91561.4419
560.02190.36860.12312.74950.09490.11740.4010.1218-1.9138-0.6750.5078-0.35760.68531.776-0.0041-1.80072.63651.8817-1.9022-1.4181-0.43934.5243-2.858636.9846
572.5895-1.64520.38292.02440.19471.11830.2601-0.0639-0.1207-0.6581-0.06650.2390.2678-0.2352-0.04030.24760.00870.00230.1410.0150.391818.5474-0.067943.6541
582.1576-0.6110.04291.961-0.38192.04720.0275-0.0838-0.6942-0.1954-0.21590.37560.0593-0.00730.1090.26870.00010.00190.21750.01250.387518.7238-1.925646.8953
59-0.0194-0.09190.01510.46590.18760.25360.0090.1601-0.97870.1089-0.14520.18520.64190.1163-0.01360.38760.1147-0.03870.23250.07970.615322.7076-13.131745.5556
602.14210.6157-0.1182.06390.67860.93720.1215-0.4417-0.21940.0032-0.121-0.39470.0951-0.1045-0.04590.21070.01320.04880.30020.03520.391535.49043.927445.2465
611.38290.1308-0.1472.3650.19411.65320.3221-0.31020.03630.1922-0.2788-0.6009-0.14230.36670.01440.25-0.01650.04240.34160.07190.307634.33839.450451.6117
621.650.4112-0.65141.5226-0.97462.1102-0.0968-0.4438-0.59730.5310.2362-0.61530.41760.3088-0.00270.39970.043-0.08990.35370.20020.432326.4368-3.160259.0413
630.6772-0.2933-0.51411.1127-0.09260.30590.19290.0698-0.1393-0.1403-0.10540.08310.0017-0.1835-0.0590.31530.0414-0.04630.1609-0.00660.262814.069315.458739.6147
641.7206-0.34721.27881.5857-0.91843.06540.4034-0.3423-0.24940.0735-0.3530.7530.6932-1.689-0.0780.13430.02350.16130.10230.11850.40329.509219.9446.1797
650.94-2.1614-0.89184.85842.0620.83460.6601-0.3807-0.22780.51470.03040.4701-0.3041-0.5942-0.0780.52-0.06990.20470.3026-0.14060.316211.1324.249556.7905
661.47940.0983-0.26041.78770.47751.83610.31040.03780.489-0.3002-0.0728-0.220.08740.9501-0.1850.24560.05070.07590.3027-0.00110.371617.220327.589339.896
671.4431-0.32680.57420.567-0.40310.4401-0.1491-0.00630.3067-0.3299-0.28590.02250.09510.50990.10020.2585-0.00440.04020.213-0.01230.19537.306930.625439.9615
681.31850.07880.40241.27950.48234.3824-0.060.3428-0.6026-0.2221-0.1293-0.5221-0.07340.63330.08810.26980.01890.08060.30260.02680.294416.126521.16337.6095
690.62420.5936-0.94181.5465-1.32432.906-0.32510.10710.185-0.75390.19940.39640.7819-1.3472-0.12420.3163-0.0708-0.10480.42350.17140.3579-12.56238.397726.3366
702.00560.50110.36480.5890.03121.9451-0.17230.47530.2524-0.3957-0.0460.17370.62980.50740.19840.35650.0227-0.03940.34060.03680.26864.735935.380223.0442
710.03770.16470.17851.572-0.31011.4060.16990.7782-0.681-0.9108-0.24580.48751.0398-0.20630.07980.5742-0.0611-0.06980.3954-0.07450.4199-3.203229.926117.3953
721.06770.0276-0.28790.98670.32681.23260.0270.28010.354-0.35870.05080.03340.01130.3722-0.05440.27660.0528-0.03130.41940.12560.27816.538941.443521.0833
731.0807-0.5775-0.36180.364-0.53631.4883-0.06020.02990.4268-0.02460.04230.3478-0.1216-0.09380.05590.23850.0134-0.08120.22940.01260.4192-4.051343.158736.2349
741.63970.02260.04361.82260.35111.27350.05020.07130.443-0.00240.06420.25180.05250.0575-0.08080.18180.0311-0.00380.24160.03290.2820.416243.806334.247
750.10380.0442-0.21992.5956-0.6610.9235-1.13580.15250.2406-0.59420.03290.13630.9349-0.9903-0.0215-0.14670.2491-0.46110.21230.04960.3569-34.470219.107137.4829
761.3867-0.21090.06661.0007-0.62051.20050.27990.02610.2204-0.5889-0.0132-0.2521-0.14310.0215-0.0310.1990.0378-0.07310.2143-0.01630.3016-18.629615.92446.5914
772.2258-0.6020.34722.1728-0.05852.57730.46891.15040.43130.0271-0.2832-0.012-0.713-0.48720.04270.3046-0.129-0.07810.1621-0.07530.4122-20.546121.575634.9395
781.27860.0283-0.42371.557-1.30512.6806-0.0822-0.1685-0.2464-0.0315-0.1986-0.696-0.12880.16250.05780.24680.0297-0.04020.1958-0.02820.3695-17.564613.062354.6287
791.31390.12960.04351.14480.10260.84630.39070.20710.39080.5218-0.11550.2255-0.71420.0641-0.21150.33910.03160.09940.28970.03780.3535-22.218928.175446.801
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'I' and (resid 125 through 141 )I125 - 141
2X-RAY DIFFRACTION2chain 'I' and (resid 142 through 187 )I142 - 187
3X-RAY DIFFRACTION3chain 'I' and (resid 188 through 238 )I188 - 238
4X-RAY DIFFRACTION4chain 'H' and (resid 157 through 186 )H157 - 186
5X-RAY DIFFRACTION5chain 'H' and (resid 187 through 202 )H187 - 202
6X-RAY DIFFRACTION6chain 'H' and (resid 203 through 230 )H203 - 230
7X-RAY DIFFRACTION7chain 'H' and (resid 231 through 242 )H231 - 242
8X-RAY DIFFRACTION8chain 'H' and (resid 243 through 253 )H243 - 253
9X-RAY DIFFRACTION9chain 'G' and (resid 29 through 42 )G29 - 42
10X-RAY DIFFRACTION10chain 'G' and (resid 43 through 95 )G43 - 95
11X-RAY DIFFRACTION11chain 'G' and (resid 96 through 117 )G96 - 117
12X-RAY DIFFRACTION12chain 'G' and (resid 118 through 203 )G118 - 203
13X-RAY DIFFRACTION13chain 'G' and (resid 204 through 246 )G204 - 246
14X-RAY DIFFRACTION14chain 'L' and (resid 16 through 29 )L16 - 29
15X-RAY DIFFRACTION15chain 'L' and (resid 30 through 81 )L30 - 81
16X-RAY DIFFRACTION16chain 'L' and (resid 82 through 187 )L82 - 187
17X-RAY DIFFRACTION17chain 'L' and (resid 188 through 238 )L188 - 238
18X-RAY DIFFRACTION18chain 'K' and (resid 157 through 179 )K157 - 179
19X-RAY DIFFRACTION19chain 'K' and (resid 180 through 188 )K180 - 188
20X-RAY DIFFRACTION20chain 'K' and (resid 189 through 202 )K189 - 202
21X-RAY DIFFRACTION21chain 'K' and (resid 203 through 211 )K203 - 211
22X-RAY DIFFRACTION22chain 'K' and (resid 212 through 221 )K212 - 221
23X-RAY DIFFRACTION23chain 'K' and (resid 222 through 230 )K222 - 230
24X-RAY DIFFRACTION24chain 'K' and (resid 231 through 242 )K231 - 242
25X-RAY DIFFRACTION25chain 'K' and (resid 243 through 253 )K243 - 253
26X-RAY DIFFRACTION26chain 'J' and (resid 29 through 42 )J29 - 42
27X-RAY DIFFRACTION27chain 'J' and (resid 43 through 72 )J43 - 72
28X-RAY DIFFRACTION28chain 'J' and (resid 73 through 95 )J73 - 95
29X-RAY DIFFRACTION29chain 'J' and (resid 96 through 137 )J96 - 137
30X-RAY DIFFRACTION30chain 'J' and (resid 138 through 168 )J138 - 168
31X-RAY DIFFRACTION31chain 'J' and (resid 169 through 188 )J169 - 188
32X-RAY DIFFRACTION32chain 'J' and (resid 189 through 228 )J189 - 228
33X-RAY DIFFRACTION33chain 'J' and (resid 229 through 246 )J229 - 246
34X-RAY DIFFRACTION34chain 'C' and (resid 16 through 29 )C16 - 29
35X-RAY DIFFRACTION35chain 'C' and (resid 30 through 81 )C30 - 81
36X-RAY DIFFRACTION36chain 'C' and (resid 82 through 104 )C82 - 104
37X-RAY DIFFRACTION37chain 'C' and (resid 105 through 114 )C105 - 114
38X-RAY DIFFRACTION38chain 'C' and (resid 115 through 124 )C115 - 124
39X-RAY DIFFRACTION39chain 'C' and (resid 125 through 141 )C125 - 141
40X-RAY DIFFRACTION40chain 'C' and (resid 142 through 163 )C142 - 163
41X-RAY DIFFRACTION41chain 'C' and (resid 164 through 187 )C164 - 187
42X-RAY DIFFRACTION42chain 'C' and (resid 188 through 238 )C188 - 238
43X-RAY DIFFRACTION43chain 'B' and (resid 157 through 174 )B157 - 174
44X-RAY DIFFRACTION44chain 'B' and (resid 175 through 186 )B175 - 186
45X-RAY DIFFRACTION45chain 'B' and (resid 187 through 202 )B187 - 202
46X-RAY DIFFRACTION46chain 'B' and (resid 203 through 221 )B203 - 221
47X-RAY DIFFRACTION47chain 'B' and (resid 222 through 230 )B222 - 230
48X-RAY DIFFRACTION48chain 'B' and (resid 231 through 242 )B231 - 242
49X-RAY DIFFRACTION49chain 'B' and (resid 243 through 253 )B243 - 253
50X-RAY DIFFRACTION50chain 'A' and (resid 29 through 42 )A29 - 42
51X-RAY DIFFRACTION51chain 'A' and (resid 43 through 95 )A43 - 95
52X-RAY DIFFRACTION52chain 'A' and (resid 96 through 137 )A96 - 137
53X-RAY DIFFRACTION53chain 'A' and (resid 138 through 154 )A138 - 154
54X-RAY DIFFRACTION54chain 'A' and (resid 155 through 188 )A155 - 188
55X-RAY DIFFRACTION55chain 'A' and (resid 189 through 246 )A189 - 246
56X-RAY DIFFRACTION56chain 'F' and (resid 16 through 29 )F16 - 29
57X-RAY DIFFRACTION57chain 'F' and (resid 30 through 50 )F30 - 50
58X-RAY DIFFRACTION58chain 'F' and (resid 51 through 104 )F51 - 104
59X-RAY DIFFRACTION59chain 'F' and (resid 105 through 124 )F105 - 124
60X-RAY DIFFRACTION60chain 'F' and (resid 125 through 163 )F125 - 163
61X-RAY DIFFRACTION61chain 'F' and (resid 164 through 220 )F164 - 220
62X-RAY DIFFRACTION62chain 'F' and (resid 221 through 238 )F221 - 238
63X-RAY DIFFRACTION63chain 'E' and (resid 157 through 186 )E157 - 186
64X-RAY DIFFRACTION64chain 'E' and (resid 187 through 202 )E187 - 202
65X-RAY DIFFRACTION65chain 'E' and (resid 203 through 211 )E203 - 211
66X-RAY DIFFRACTION66chain 'E' and (resid 212 through 230 )E212 - 230
67X-RAY DIFFRACTION67chain 'E' and (resid 231 through 242 )E231 - 242
68X-RAY DIFFRACTION68chain 'E' and (resid 243 through 253 )E243 - 253
69X-RAY DIFFRACTION69chain 'D' and (resid 29 through 42 )D29 - 42
70X-RAY DIFFRACTION70chain 'D' and (resid 43 through 75 )D43 - 75
71X-RAY DIFFRACTION71chain 'D' and (resid 76 through 95 )D76 - 95
72X-RAY DIFFRACTION72chain 'D' and (resid 96 through 137 )D96 - 137
73X-RAY DIFFRACTION73chain 'D' and (resid 138 through 188 )D138 - 188
74X-RAY DIFFRACTION74chain 'D' and (resid 189 through 246 )D189 - 246
75X-RAY DIFFRACTION75chain 'I' and (resid 16 through 29 )I16 - 29
76X-RAY DIFFRACTION76chain 'I' and (resid 30 through 63 )I30 - 63
77X-RAY DIFFRACTION77chain 'I' and (resid 64 through 81 )I64 - 81
78X-RAY DIFFRACTION78chain 'I' and (resid 82 through 104 )I82 - 104
79X-RAY DIFFRACTION79chain 'I' and (resid 105 through 124 )I105 - 124

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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