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- PDB-9atk: 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: 9atk
タイトルBIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap4 of S. aureus
要素
  • Cathepsin-G
  • Extracellular Adherence Protein
  • Neutrophil elastase
キーワードPROTEIN BINDING / PROTEASE INHIBITOR / IMMUNE EVASION
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 / defense response to fungus / phagocytosis / 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 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 / antibacterial humoral response / azurophil granule lumen / 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 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: 2.11 Å
データ登録者Mishra, N.B. / 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)R35GM140852 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2024年2月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年6月12日Provider: repository / タイプ: Initial release
改定 1.12024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
改定 1.22024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
D: Neutrophil elastase
C: Extracellular Adherence Protein
E: Cathepsin-G
F: Extracellular Adherence Protein
G: Neutrophil elastase
H: Cathepsin-G
I: Extracellular Adherence Protein
B: Cathepsin-G
J: Neutrophil elastase
K: Cathepsin-G
L: Extracellular Adherence Protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)250,34024
ポリマ－244,21012
非ポリマー6,13012
水13,818767
1
A: Neutrophil elastase
C: Extracellular Adherence Protein
B: Cathepsin-G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)62,5936
ポリマ－61,0533
非ポリマー1,5403
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint10 kcal/mol
Surface area24310 Å2
手法PISA
2
D: Neutrophil elastase
E: Cathepsin-G
F: Extracellular Adherence Protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)62,7396
ポリマ－61,0533
非ポリマー1,6873
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint14 kcal/mol
Surface area24630 Å2
手法PISA
3
G: Neutrophil elastase
H: Cathepsin-G
I: Extracellular Adherence Protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)62,5936
ポリマ－61,0533
非ポリマー1,5403
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint6 kcal/mol
Surface area24750 Å2
手法PISA
4
J: Neutrophil elastase
K: Cathepsin-G
L: Extracellular Adherence Protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)62,4156
ポリマ－61,0533
非ポリマー1,3623
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint13 kcal/mol
Surface area24050 Å2
手法PISA
単位格子
Length a, b, c (Å)82.207, 85.527, 89.536
Angle α, β, γ (deg.)82.77, 85.23, 83.60
Int Tables number1
Space group name H-MP1

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要素

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タンパク質 , 3種, 12分子 ADGJCFILEHBK

#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: 4 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / Cell: Neutrophil / 参照: UniProt: P08246, leukocyte elastase
#2: タンパク質
Extracellular Adherence Protein / Protein map


分子量: 12336.466 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)
遺伝子: map, SAV1938 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q99QS1
#3: タンパク質
Cathepsin-G


分子量: 25397.131 Da / 分子数: 4 / Fragment: C-terminal truncation (UNP residues 21-243) / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / Cell: Neutrophil / 参照: UniProt: P08311

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糖 , 4種, 12分子

#4: 多糖
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 732.682 Da / 分子数: 4 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 570.542 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: 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: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 1種, 767分子

#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 767 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.54 Å3/Da / 溶媒含有率: 51.48 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M sodium citrate (pH 5.5) 12% (w/v) PEG-6K

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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: 2023年3月2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: 2.1→50 Å / Num. obs: 124283 / % possible obs: 90.4 % / 冗長度: 2.8 % / CC1/2: 0.966 / CC star: 0.991 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.111 / Rrim(I) all: 0.202 / Χ2: 1.005 / Net I/σ(I): 7.1 / Num. measured all: 347150
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.182.10.528120400.3860.7470.4320.6850.90787
2.18-2.262.20.455123880.6150.8730.3550.5790.97790.2
2.26-2.372.30.386124130.610.8710.2910.4861.01590.5
2.37-2.492.50.312121140.8040.9440.230.3890.96888
2.49-2.652.60.275116950.8730.9660.1950.3390.98885.2
2.65-2.852.80.479129970.0180.1860.3260.580.98294.5
2.85-3.1430.234128920.9080.9760.1550.2811.04393.7
3.14-3.593.30.189124080.9450.9860.1220.2250.97490.3
3.59-4.523.50.121125540.9740.9940.0760.1431.0991.3
4.52-503.50.11127820.9210.9790.070.131.01392.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20.1_4487: ???)精密化
HKL-2000データスケーリング
HKL-2000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.11→47.89 Å / SU ML: 0.24 / 交差検証法: FREE R-VALUE / σ(F): 0.18 / 位相誤差: 24.58 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2325 1860 1.59 %
Rwork0.1786 --
obs0.1795 117167 84.83 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.11→47.89 Å
タンパク質核酸リガンド溶媒全体
原子数16816 0 406 767 17989
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00817526
X-RAY DIFFRACTIONf_angle_d0.90523694
X-RAY DIFFRACTIONf_dihedral_angle_d14.6826674
X-RAY DIFFRACTIONf_chiral_restr0.0592748
X-RAY DIFFRACTIONf_plane_restr0.0093048
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.170.28741120.24327098X-RAY DIFFRACTION68
2.17-2.230.28691250.22818092X-RAY DIFFRACTION77
2.23-2.30.26991520.21188381X-RAY DIFFRACTION81
2.3-2.380.23771440.20118628X-RAY DIFFRACTION82
2.38-2.480.26671380.20288540X-RAY DIFFRACTION82
2.48-2.590.30291270.20827985X-RAY DIFFRACTION76
2.59-2.730.27361650.20789286X-RAY DIFFRACTION89
2.73-2.90.2721550.21019579X-RAY DIFFRACTION92
2.9-3.120.28031660.19639640X-RAY DIFFRACTION92
3.12-3.440.26211470.18379490X-RAY DIFFRACTION91
3.44-3.940.20941380.1568924X-RAY DIFFRACTION85
3.94-4.960.17061550.138510057X-RAY DIFFRACTION96
4.96-47.890.1931360.16669607X-RAY DIFFRACTION92
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)
13.54430.4323-0.02331.81620.00121.91360.01290.0485-0.040.0936-0.06490.28240.1843-0.37930.04480.2485-0.04240.03040.2088-0.04750.239-24.4569-9.666622.9347
23.6026-0.94760.38571.5364-0.07143.6766-0.01250.22660.2272-0.2766-0.0295-0.13030.1153-0.15950.13430.2633-0.02850.05110.1865-0.03590.2277-13.4131-10.521714.3058
32.7376-0.1421-1.13991.25490.11561.615-0.10020.0012-0.10390.0052-0.095-0.18910.16810.13630.13630.3111-0.01550.03060.15430.00370.1655-9.2923-12.446618.5734
42.0005-0.4040.60022.8468-0.52323.8286-0.1921-0.16110.3830.0995-0.08510.5445-0.601-0.58590.20220.33560.0553-0.06670.24-0.11130.3186-10.551728.807479.7974
55.3095-1.52952.31614.8501-2.33823.044-0.3298-0.7092-0.80340.80570.1710.4250.208-1.1846-0.00370.60840.18760.03610.598-0.23480.5707-19.344330.215689.4087
62.3099-0.7008-0.66432.97691.14853.4991-0.17730.32150.6362-0.039-0.23460.2737-0.5748-0.23870.09810.42850.0509-0.15520.1567-0.03060.3759-7.323333.381572.8202
74.30711.2723-0.41512.0262-1.53212.6812-0.2441-0.21210.47830.3822-0.14410.0944-0.76060.23510.29910.4713-0.136-0.11630.23010.0220.36248.621232.088883.2208
83.2332-1.50760.04381.03991.26374.3316-0.0693-0.3997-0.21740.1187-0.1350.096-0.33540.04250.05780.31-0.0136-0.03410.19140.01280.20161.564921.227785.5911
92.9521-0.40330.45773.1121-0.05111.4157-0.0192-0.3675-0.05480.3722-0.2446-0.1966-0.31180.13870.1220.3157-0.0815-0.07390.251-0.02570.14163.122121.442384.253
103.0973-0.30950.35952.3146-1.65723.17670.16850.2350.6689-0.1576-0.5928-0.0831-0.61780.4750.27760.4889-0.0515-0.10310.20610.02380.29652.660134.612671.8268
116.95530.59932.67246.18911.81754.81180.1815-0.4963-0.1128-0.0136-0.25690.28070.1527-0.3458-0.01770.2153-0.00340.05210.13330.03360.176-9.040820.457534.5888
120.27241.03230.30067.57322.38760.7354-0.1060.00590.5405-1.1946-0.31950.1307-0.4262-0.07720.43510.38140.0697-0.02120.2988-0.06610.3806-18.57513.734623.7651
135.870.6167-0.8362.29610.13810.8797-0.06250.26680.0418-0.21150.1203-0.1009-0.0086-0.0521-0.07660.3007-0.00540.01040.1843-0.02730.1952-1.312314.663525.7502
148.77290.8738-3.58073.0739-0.26621.7928-0.0588-1.4854-0.35910.6336-0.2870.08570.11120.42520.18510.3919-0.03310.03670.3007-0.07830.2186-10.20186.658335.1521
152.39351.04190.85615.79521.99392.70390.0319-0.2259-0.11840.1617-0.20070.2331-0.0415-0.1680.19290.2393-0.01660.03980.17480.01040.1548-9.85587.410429.5143
164.20590.43160.49972.63340.60662.951-0.1156-0.0649-0.15850.0252-0.29540.55830.0784-0.57230.23460.2327-0.04760.04320.274-0.10630.3752-25.4115-15.495862.964
176.7927-0.22120.35382.44951.24262.6855-0.0861-0.8285-0.03850.2818-0.13080.36530.2065-0.39460.26420.3059-0.04620.09050.2736-0.02380.3347-24.2083-16.104667.6515
182.39570.81831.45820.32780.69841.72080.057-0.3589-0.60880.95690.02140.53980.117-1.150.17040.4494-0.11460.25150.57370.09330.6626-30.4297-23.22871.5223
191.1969-0.0834-0.21161.1704-0.25240.5225-0.29760.3941-1.1943-0.1722-0.25740.6190.6507-0.32610.00420.3278-0.27260.130.4098-0.42710.7428-23.2186-26.495453.9042
206.9713-0.65390.07222.41821.06363.4971-0.19450.7568-0.1589-0.2883-0.0357-0.0655-0.1148-0.04070.15290.3127-0.09070.00140.2938-0.04340.2192-13.515-13.487751.6433
213.70950.9306-0.1335.0617-1.76774.5849-0.23620.1612-0.774-0.10270.12840.09020.4462-0.42460.06260.2934-0.00760.06630.179-0.07730.3645-15.6175-22.94459.1216
227.25430.93870.46134.4688-2.36872.00340.23650.05710.33380.0252-0.23040.6714-0.2002-0.6231-0.31330.2076-0.0048-0.0320.2458-0.10930.2517-15.51970.607669.0361
231.26221.63971.20427.36422.56531.53590.086-0.11860.0240.0929-0.35630.35860.2177-0.22760.26530.20370.00520.00860.2963-0.0360.193-15.00751.291971.1087
244.3705-0.74760.55253.3163-1.31370.6019-0.1113-0.3445-0.13420.40550.1408-0.15010.0757-0.0476-0.04880.2082-0.0216-0.02660.2169-0.04770.1236-3.4317-1.985974.0059
252.84320.05110.80985.0780.35131.24590.05240.25370.1201-0.3629-0.14970.2682-0.2071-0.06450.09430.2576-0.0097-0.01110.2108-0.00130.1313-7.51659.125368.4907
262.9974-1.4527-0.54493.5695-0.64161.9135-0.0472-0.1387-0.6208-0.1835-0.4071-0.43170.55960.83380.14490.43380.2080.12360.5020.22710.600127.2544-21.150681.0614
275.2929-0.9109-0.94622.99480.26773.9196-0.1072-0.6084-0.81120.252-0.04250.07740.15510.07330.11830.25260.05140.06180.32470.18850.361616.6682-15.141788.1778
283.751-0.57180.08461.7416-0.34673.5978-0.0126-0.2755-0.61860.0261-0.17170.09260.3621-0.02130.12750.27270.00650.07330.26350.08890.36712.5465-15.365183.2544
293.0752.9941.22114.22970.3141.3858-0.16371.1096-0.2359-0.41270.2861-0.56060.16270.859-0.04810.3114-0.01660.06880.59490.02950.3247.566319.604348.7209
306.29150.9887-1.47994.0308-0.73414.6318-0.027-0.5269-0.04440.1483-0.1555-0.31460.20130.20990.03740.18080.003-0.01190.28860.03890.275640.414823.763765.3237
317.6827-0.24320.39943.2493-0.53183.1620.0487-0.75540.33890.32530.0294-0.0931-0.08650.0344-0.14280.2846-0.0242-0.0050.27390.03960.220541.034124.11164.8006
321.9543-1.2251-0.62241.4195-0.61342.8840.0228-0.25460.7090.16640.0653-0.5022-0.15020.5178-0.09240.2779-0.1258-0.0170.38950.02460.602849.243231.885861.1299
330.40840.89530.04685.75480.60610.8458-0.16630.37380.6684-0.50480.52960.4945-0.5466-0.3434-0.23060.39920.05040.05270.61810.28610.564633.66331.196745.3708
343.5469-4.50040.84138.75222.36384.17220.1137-0.2334-0.43210.5559-0.58580.48540.909-0.46620.52660.4181-0.02230.04660.3977-0.03950.368242.11459.141954.5967
354.68840.58452.06553.66690.41862.57440.23120.74720.2464-0.3365-0.26440.5327-0.2974-0.2323-0.05820.2912-0.0128-0.02130.44850.14630.331825.253223.890347.4986
362.33810.46941.05491.21650.08941.9244-0.13750.4234-0.12940.04550.1850.05820.10780.0482-0.01750.3158-0.04240.01840.49330.06160.30631.334217.114548.1568
373.95820.1088-1.36554.50823.02636.04370.15030.47950.7828-0.1226-0.16210.21890.12480.3585-0.01990.22650.0437-0.00580.32370.16550.273331.893324.68651.305
387.6028-0.87530.51032.7773-1.87982.02230.0655-0.36271.31760.42710.3050.021-0.44870.03810.31360.4103-0.0730.22040.2505-0.01540.931334.919439.475962.8672
391.89540.5782-0.04877.4014-3.2456.85560.18-0.30310.04590.3459-0.468-0.97840.10610.34670.23970.27780.0006-0.02570.37130.14330.356432.51777.908868.7459
401.21571.7703-2.41536.9128-3.23384.79260.0708-0.0981-0.31150.0075-0.0370.0539-0.1172-0.05850.06310.2743-0.0007-0.03070.38130.10280.405530.892112.101465.0769
412.14492.4191-0.5683.19680.18311.6740.078-0.39640.20470.8693-0.8502-0.9432-0.90681.01950.17580.3561-0.1768-0.15690.54530.33840.607733.8374-1.508380.9132
422.9838-2.43481.60386.21870.01371.9066-0.0459-0.34440.2410.9143-0.1462-0.1304-0.21870.08690.22070.2566-0.06730.02220.34820.08220.252324.71599.126674.2945
433.6673-3.4397-1.05866.29950.27441.6809-0.04480.2722-0.3153-0.0458-0.15240.18410.08290.18240.16210.2136-0.04650.03220.29630.03410.203720.54024.059667.9949
440.93691.5075-0.7162.65-0.99480.6449-0.03130.0783-0.041-0.1545-0.243-0.49080.23740.40140.21630.25240.02980.06730.41080.11380.302124.3213-0.086971.4828
452.8615-1.37910.60134.2443-2.58884.3593-0.0224-0.6092-0.08230.4467-0.12791.2339-0.2114-0.30750.05770.2481-0.03160.10550.3318-0.05510.2872-15.751138.408450.55
464.08510.8185-0.14286.06751.02262.631-0.02510.02860.0739-0.2318-0.02670.535-0.0863-0.09950.0260.163-0.001-0.01930.16210.01190.1392-10.961236.51632.9313
473.2409-1.946-3.12584.39171.94565.73510.07490.5156-0.07040.0137-0.21.02750.0491-1.1575-0.06660.2064-0.0013-0.00090.3808-0.01820.4666-22.847538.415438.2204
483.064-0.38840.3422.784-0.63522.47990.02070.00910.5396-0.1713-0.0702-0.1444-0.2150.120.03550.2-0.03640.00030.1604-0.02430.2447-5.39441.818437.2533
493.27121.68470.38963.2629-3.51855.9125-0.2874-0.6045-0.8711-0.33130.0521.06480.9492-0.5818-0.26720.3243-0.0390.11520.29120.03520.4941-17.379926.033646.7552
500.1440.5696-0.22152.5607-0.55151.85750.0799-1.03910.30790.52120.0384-0.45410.11860.5292-0.12120.355-0.0037-0.08220.47-0.08530.24481.836531.883852.7256
513.132-0.92850.40712.76640.76132.8438-0.0482-0.7772-0.44060.35250.0736-0.28450.46920.2686-0.07750.31430.034-0.0240.32350.07210.29182.019428.670647.2455
523.3323-0.45750.41693.37580.02234.0882-0.0506-0.29780.35770.1073-0.0191-0.411-0.150.0897-0.04870.1394-0.020.0130.193-0.02570.19850.021838.462141.554
534.94071.0487-0.91042.4517-0.47233.64-0.04140.1639-0.0373-0.3385-0.1981-0.80650.06470.87750.13980.2974-0.02710.11420.42750.08930.477434.455512.981412.1416
541.40430.43331.13061.52470.12022.35610.3455-1.24710.35080.3061-0.3506-0.3022-0.25990.68550.12730.3902-0.1853-0.00090.5519-0.00310.349529.790316.595626.013
553.17180.90020.12462.21540.05761.66270.33670.35190.8454-0.3798-0.2702-0.2183-0.78390.54050.04220.4568-0.22360.150.39070.07720.611929.12624.471513.3735
566.5824-2.29760.59273.66842.17317.60650.19180.1796-1.3485-0.2532-0.00860.40390.2671-0.4256-0.15890.3966-0.01180.06190.3406-0.0520.467825.26114.11646.4589
576.2557-0.0618-0.52463.3987-1.03433.65930.31820.54720.8589-0.329-0.1553-0.0935-0.6475-0.3561-0.16380.375-0.0045-0.03590.21490.02470.291413.583518.647812.807
585.40140.2466-1.0292.5492-0.3113.29360.225-0.08990.6784-0.4556-0.1488-0.0245-0.58960.29630.09440.3592-0.04210.0260.19330.00830.259520.217217.977115.3272
594.4609-1.0558-0.73053.3746-0.45650.3332-0.2831-0.4549-0.40631.05470.0969-1.38950.31480.48510.04360.28640.0031-0.12040.33040.09430.504432.9104-31.114546.2322
602.9205-1.02370.10162.5367-0.66433.1445-0.07630.146-0.1953-0.5901-0.0814-0.28990.21330.06860.26860.24030.00380.03510.2290.02840.389522.8026-30.399730.7997
614.06070.27711.02361.1835-0.01122.16150.118-0.0732-0.4266-0.3957-0.3764-0.98040.13610.60570.30140.28590.06580.14970.42170.08240.630635.4972-33.154832.4673
622.7665-0.2476-1.33823.62070.38093.2840.01780.3081-0.4178-0.2288-0.08740.0290.2082-0.04140.0230.2127-0.05060.03720.20320.01230.406419.4704-35.288632.3148
635.1825-0.03780.28264.15830.64843.7212-0.0227-0.3210.15510.5584-0.0067-0.2524-0.31140.1035-0.09330.27530.0473-0.02540.21970.04390.29123.5168-26.080648.1754
643.26440.64620.50997.7566-0.03737.9545-0.1036-0.7173-0.29991.1698-0.00490.9870.4636-0.93810.21120.37510.07570.13790.41660.04380.48936.7231-20.460548.1907
653.40140.08330.57024.51190.68422.935-0.2105-0.11060.1660.43380.1059-0.1434-0.3530.15370.080.34290.0299-0.02570.32030.05460.310821.1679-19.871248.493
662.60570.0150.39384.26650.85442.0705-0.1201-0.2059-0.34630.12040.11780.284-0.04180.01290.01860.17050.01090.06590.21940.09080.371915.0753-30.663442.5235
678.6735-0.1831-4.70643.1258-1.82585.7359-0.25360.0111-0.8741-0.0906-0.04830.05890.2641-0.04890.42180.30960.0041-0.01650.26140.03820.321524.4159-12.629327.6908
683.87764.2523-3.22215.5442-5.29896.3638-0.18910.1084-0.53530.1589-0.1025-0.4168-0.3943-0.25540.34050.21770.0117-0.00850.30710.01340.285421.2229-15.52131.5037
691.9053-1.9655-1.40556.72096.97317.5717-0.6604-0.8911-1.134-0.80650.1641-0.14031.26450.1850.23240.57090.0580.16290.28480.11530.542229.3964-4.952115.3495
706.67462.4984-2.50518.3187-2.9675.3299-0.08060.4632-0.3576-0.69080.06470.23110.26380.08620.00630.24450.01840.01340.2255-0.01190.265516.8036-9.314622.9912
715.69674.6274-1.31845.69461.82456.3893-0.35940.13360.6709-0.22320.1289-0.550.08910.7980.16190.22530.0609-0.01170.22830.0220.32795.013-8.411125.9504
726.14975.8026-1.07935.8336-1.79883.2070.3752-0.62580.61370.3793-0.3885-0.2794-0.44690.32870.02210.3180.0053-0.04040.25710.02680.26218.0684-2.273931.5702
734.6909-1.30332.83083.6169-1.24346.27580.4251-0.74660.50280.3801-0.5245-0.4401-0.49370.4079-0.00250.3301-0.1006-0.05880.23540.04370.302225.93771.413630.7003
740.6535-1.57810.04614.8075-1.11342.32390.20890.1006-0.1099-0.2505-0.1461-0.00080.01060.1165-0.12310.3037-0.0086-0.01430.2639-0.00120.256518.97893.298721.1305
752.86093.31310.4876.5148-2.81224.5504-0.0669-1.2363-0.10370.0004-0.3558-0.84120.32050.89510.39090.33590.0411-0.06210.3260.04760.423224.0312-6.197230.2051
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 168 )
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 246 )
4X-RAY DIFFRACTION4chain 'D' and (resid 29 through 83 )
5X-RAY DIFFRACTION5chain 'D' and (resid 84 through 95 )
6X-RAY DIFFRACTION6chain 'D' and (resid 96 through 137 )
7X-RAY DIFFRACTION7chain 'D' and (resid 138 through 154 )
8X-RAY DIFFRACTION8chain 'D' and (resid 155 through 188 )
9X-RAY DIFFRACTION9chain 'D' and (resid 189 through 228 )
10X-RAY DIFFRACTION10chain 'D' and (resid 229 through 246 )
11X-RAY DIFFRACTION11chain 'C' and (resid 371 through 389 )
12X-RAY DIFFRACTION12chain 'C' and (resid 390 through 400 )
13X-RAY DIFFRACTION13chain 'C' and (resid 401 through 427 )
14X-RAY DIFFRACTION14chain 'C' and (resid 428 through 444 )
15X-RAY DIFFRACTION15chain 'C' and (resid 445 through 468 )
16X-RAY DIFFRACTION16chain 'E' and (resid 16 through 63 )
17X-RAY DIFFRACTION17chain 'E' and (resid 64 through 104 )
18X-RAY DIFFRACTION18chain 'E' and (resid 105 through 114 )
19X-RAY DIFFRACTION19chain 'E' and (resid 115 through 141 )
20X-RAY DIFFRACTION20chain 'E' and (resid 142 through 197 )
21X-RAY DIFFRACTION21chain 'E' and (resid 198 through 238 )
22X-RAY DIFFRACTION22chain 'F' and (resid 371 through 380 )
23X-RAY DIFFRACTION23chain 'F' and (resid 381 through 400 )
24X-RAY DIFFRACTION24chain 'F' and (resid 401 through 427 )
25X-RAY DIFFRACTION25chain 'F' and (resid 428 through 468 )
26X-RAY DIFFRACTION26chain 'G' and (resid 29 through 137 )
27X-RAY DIFFRACTION27chain 'G' and (resid 138 through 168 )
28X-RAY DIFFRACTION28chain 'G' and (resid 169 through 246 )
29X-RAY DIFFRACTION29chain 'H' and (resid 16 through 29 )
30X-RAY DIFFRACTION30chain 'H' and (resid 30 through 63 )
31X-RAY DIFFRACTION31chain 'H' and (resid 64 through 104 )
32X-RAY DIFFRACTION32chain 'H' and (resid 105 through 124 )
33X-RAY DIFFRACTION33chain 'H' and (resid 125 through 141 )
34X-RAY DIFFRACTION34chain 'H' and (resid 142 through 154 )
35X-RAY DIFFRACTION35chain 'H' and (resid 155 through 178 )
36X-RAY DIFFRACTION36chain 'H' and (resid 179 through 197 )
37X-RAY DIFFRACTION37chain 'H' and (resid 198 through 228 )
38X-RAY DIFFRACTION38chain 'H' and (resid 229 through 238 )
39X-RAY DIFFRACTION39chain 'I' and (resid 371 through 380 )
40X-RAY DIFFRACTION40chain 'I' and (resid 381 through 393 )
41X-RAY DIFFRACTION41chain 'I' and (resid 394 through 400 )
42X-RAY DIFFRACTION42chain 'I' and (resid 401 through 416 )
43X-RAY DIFFRACTION43chain 'I' and (resid 417 through 444 )
44X-RAY DIFFRACTION44chain 'I' and (resid 445 through 468 )
45X-RAY DIFFRACTION45chain 'B' and (resid 16 through 29 )
46X-RAY DIFFRACTION46chain 'B' and (resid 30 through 63 )
47X-RAY DIFFRACTION47chain 'B' and (resid 64 through 81 )
48X-RAY DIFFRACTION48chain 'B' and (resid 82 through 141 )
49X-RAY DIFFRACTION49chain 'B' and (resid 142 through 154 )
50X-RAY DIFFRACTION50chain 'B' and (resid 155 through 168 )
51X-RAY DIFFRACTION51chain 'B' and (resid 169 through 197 )
52X-RAY DIFFRACTION52chain 'B' and (resid 198 through 238 )
53X-RAY DIFFRACTION53chain 'J' and (resid 29 through 95 )
54X-RAY DIFFRACTION54chain 'J' and (resid 96 through 117 )
55X-RAY DIFFRACTION55chain 'J' and (resid 118 through 154 )
56X-RAY DIFFRACTION56chain 'J' and (resid 155 through 168 )
57X-RAY DIFFRACTION57chain 'J' and (resid 169 through 188 )
58X-RAY DIFFRACTION58chain 'J' and (resid 189 through 246 )
59X-RAY DIFFRACTION59chain 'K' and (resid 16 through 29 )
60X-RAY DIFFRACTION60chain 'K' and (resid 30 through 63 )
61X-RAY DIFFRACTION61chain 'K' and (resid 64 through 81 )
62X-RAY DIFFRACTION62chain 'K' and (resid 82 through 124 )
63X-RAY DIFFRACTION63chain 'K' and (resid 125 through 163 )
64X-RAY DIFFRACTION64chain 'K' and (resid 164 through 178 )
65X-RAY DIFFRACTION65chain 'K' and (resid 179 through 197 )
66X-RAY DIFFRACTION66chain 'K' and (resid 198 through 238 )
67X-RAY DIFFRACTION67chain 'L' and (resid 371 through 380 )
68X-RAY DIFFRACTION68chain 'L' and (resid 381 through 393 )
69X-RAY DIFFRACTION69chain 'L' and (resid 394 through 400 )
70X-RAY DIFFRACTION70chain 'L' and (resid 401 through 416 )
71X-RAY DIFFRACTION71chain 'L' and (resid 417 through 425 )
72X-RAY DIFFRACTION72chain 'L' and (resid 426 through 435 )
73X-RAY DIFFRACTION73chain 'L' and (resid 436 through 444 )
74X-RAY DIFFRACTION74chain 'L' and (resid 445 through 456 )
75X-RAY DIFFRACTION75chain 'L' and (resid 457 through 468 )

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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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

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