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- PDB-6kc4: Crystal structure of human Fer SH2 domain bound to a phosphopepti... -

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基本情報

登録情報
データベース: PDB / ID: 6kc4
タイトルCrystal structure of human Fer SH2 domain bound to a phosphopeptide (DEpYENVD)
要素
  • Tyrosine-protein kinase Fer
  • phosphopeptide (EDpYENVD)
キーワードTRANSFERASE/SIGNALING PROTEIN / SH2 domain / SIGNALING PROTEIN / TRANSFERASE-SIGNALING PROTEIN complex
機能・相同性
機能・相同性情報


adherens junction disassembly / response to platelet-derived growth factor / diapedesis / extracellular matrix-cell signaling / negative regulation of mast cell activation involved in immune response / regulation of fibroblast migration / regulation of epidermal growth factor receptor signaling pathway / Kit signaling pathway / cellular response to macrophage colony-stimulating factor stimulus / regulation of mast cell degranulation ...adherens junction disassembly / response to platelet-derived growth factor / diapedesis / extracellular matrix-cell signaling / negative regulation of mast cell activation involved in immune response / regulation of fibroblast migration / regulation of epidermal growth factor receptor signaling pathway / Kit signaling pathway / cellular response to macrophage colony-stimulating factor stimulus / regulation of mast cell degranulation / Sertoli cell development / cell-cell adhesion mediated by cadherin / protein phosphatase 1 binding / adherens junction assembly / tyrosine phosphorylation of STAT protein / regulation of lamellipodium assembly / epidermal growth factor receptor binding / positive regulation of actin filament polymerization / interleukin-6-mediated signaling pathway / seminiferous tubule development / germ cell development / Fc-epsilon receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / substrate adhesion-dependent cell spreading / cell projection / adherens junction / non-specific protein-tyrosine kinase / regulation of protein phosphorylation / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / cellular response to reactive oxygen species / microtubule cytoskeleton organization / peptidyl-tyrosine phosphorylation / chemotaxis / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / cell cortex / actin cytoskeleton organization / protein tyrosine kinase activity / response to lipopolysaccharide / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / cell adhesion / intracellular signal transduction / positive regulation of cell migration / protein phosphorylation / lipid binding / positive regulation of cell population proliferation / chromatin / ATP binding / nucleus / cytoplasm / cytosol
類似検索 - 分子機能
Tyrosine-protein kinase Fer, F-BAR domain / Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain ...Tyrosine-protein kinase Fer, F-BAR domain / Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Tyrosine-protein kinase Fer
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.37 Å
データ登録者Matsuura, Y.
資金援助 日本, 1件
組織認可番号国
Japan Society for the Promotion of Science16K07268 日本
引用ジャーナル: Protein Sci. / 年: 2019
タイトル: High-resolution structural analysis shows how different crystallographic environments can induce alternative modes of binding of a phosphotyrosine peptide to the SH2 domain of Fer tyrosine kinase.
著者: Matsuura, Y.
履歴
登録2019年6月27日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02019年9月4日Provider: repository / タイプ: Initial release
改定 1.12019年9月11日Group: Data collection / Database references / カテゴリ: citation / Item: _citation.title
改定 1.22019年10月30日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年11月22日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Tyrosine-protein kinase Fer
B: phosphopeptide (EDpYENVD)
C: Tyrosine-protein kinase Fer
D: phosphopeptide (EDpYENVD)
E: Tyrosine-protein kinase Fer
F: phosphopeptide (EDpYENVD)
G: Tyrosine-protein kinase Fer
H: phosphopeptide (EDpYENVD)
I: Tyrosine-protein kinase Fer
J: phosphopeptide (EDpYENVD)
K: Tyrosine-protein kinase Fer
L: phosphopeptide (EDpYENVD)


分子量 (理論値)分子数
合計 (水以外)76,23712
ポリマ－76,23712
非ポリマー00
水19,3661075
1
A: Tyrosine-protein kinase Fer
B: phosphopeptide (EDpYENVD)


分子量 (理論値)分子数
合計 (水以外)12,7062
ポリマ－12,7062
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-5 kcal/mol
Surface area6020 Å2
手法PISA
2
C: Tyrosine-protein kinase Fer
D: phosphopeptide (EDpYENVD)


分子量 (理論値)分子数
合計 (水以外)12,7062
ポリマ－12,7062
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-6 kcal/mol
Surface area6010 Å2
手法PISA
3
E: Tyrosine-protein kinase Fer
F: phosphopeptide (EDpYENVD)


分子量 (理論値)分子数
合計 (水以外)12,7062
ポリマ－12,7062
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-5 kcal/mol
Surface area5980 Å2
手法PISA
4
G: Tyrosine-protein kinase Fer
H: phosphopeptide (EDpYENVD)


分子量 (理論値)分子数
合計 (水以外)12,7062
ポリマ－12,7062
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-3 kcal/mol
Surface area6000 Å2
手法PISA
5
I: Tyrosine-protein kinase Fer
J: phosphopeptide (EDpYENVD)


分子量 (理論値)分子数
合計 (水以外)12,7062
ポリマ－12,7062
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-4 kcal/mol
Surface area6040 Å2
手法PISA
6
K: Tyrosine-protein kinase Fer
L: phosphopeptide (EDpYENVD)


分子量 (理論値)分子数
合計 (水以外)12,7062
ポリマ－12,7062
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-5 kcal/mol
Surface area6070 Å2
手法PISA
単位格子
Length a, b, c (Å)34.700, 186.661, 50.580
Angle α, β, γ (deg.)90.000, 96.960, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Tyrosine-protein kinase Fer / Feline encephalitis virus-related kinase FER / Fujinami poultry sarcoma/Feline sarcoma-related ...Feline encephalitis virus-related kinase FER / Fujinami poultry sarcoma/Feline sarcoma-related protein Fer / Proto-oncogene c-Fer / Tyrosine kinase 3 / p94-Fer


分子量: 11743.345 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FER, TYK3 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P16591, non-specific protein-tyrosine kinase
#2: タンパク質・ペプチド
phosphopeptide (EDpYENVD)


分子量: 962.805 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1075 / 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Y

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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: 2.15 Å3/Da / 溶媒含有率: 42.77 %
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: 6.8 / 詳細: HEPES, sodium chloride, PEG 3350

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データ収集

回折平均測定温度: 95 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Photon Factory / ビームライン: BL-17A / 波長: 0.98 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年6月23日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.98 Å / 相対比: 1
反射解像度: 1.37→25.87 Å / Num. obs: 130076 / % possible obs: 97.7 % / 冗長度: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.028 / Rrim(I) all: 0.052 / Net I/σ(I): 14.8 / Num. measured all: 409258 / Scaling rejects: 515
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.37-1.392.80.1161628359190.9810.0820.1436.589.8
7.5-25.873.40.04127368130.9860.0270.04926.797

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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
Aimless0.7.1データスケーリング
MOLREP位相決定
PHENIX1.14_3260精密化
PDB_EXTRACT3.25データ抽出
MOSFLMデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 2KK6

2kk6


解像度: 1.37→25.867 Å / SU ML: 0.11 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 18.95
Rfactor反射数%反射
Rfree0.1855 6701 5.15 %
Rwork0.1646 --
obs0.1657 129994 97.64 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 68.74 Å2 / Biso mean: 20.8914 Å2 / Biso min: 5.76 Å2
精密化ステップサイクル: final / 解像度: 1.37→25.867 Å
タンパク質核酸リガンド溶媒全体
原子数5290 0 0 1075 6365
Biso mean---30.33 -
残基数----641
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.38560.21011940.19373757395189
1.3856-1.40190.21231960.19283910410693
1.4019-1.4190.20412060.19183966417295
1.419-1.43690.21662070.19424057426495
1.4369-1.45580.20682360.19043984422096
1.4558-1.47580.21252120.18994060427296
1.4758-1.49690.21962170.18544086430397
1.4969-1.51920.20292230.18244094431797
1.5192-1.54290.20682250.18464059428497
1.5429-1.56820.2061790.17454187436698
1.5682-1.59530.20232340.17434029426397
1.5953-1.62430.19832540.1684059431398
1.6243-1.65550.21212420.17034145438798
1.6555-1.68930.18952590.17063982424196
1.6893-1.7260.20512260.17924121434798
1.726-1.76610.18012210.16354134435599
1.7661-1.81030.19512330.17144203443699
1.8103-1.85920.19012150.17564137435299
1.8592-1.91390.21892300.17734186441699
1.9139-1.97570.18582360.16624158439499
1.9757-2.04630.18012340.16534190442499
2.0463-2.12820.17072170.15824174439199
2.1282-2.2250.19241950.161542164411100
2.225-2.34220.17442350.16694127436298
2.3422-2.48880.18572100.16994223443399
2.4888-2.68080.17062240.17442254449100
2.6808-2.95030.18952270.176241904417100
2.9503-3.37640.18952490.161842084457100
3.3764-4.25080.15192340.136442204454100
4.2508-25.87170.18552310.14674206443799
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)
12.6292.3044-1.42897.7165-1.97953.5429-0.02030.02220.5420.20450.11390.791-0.2985-0.2411-0.05480.07320.0250.03940.15980.04310.2468-9.80287.822623.8081
21.5226-0.36720.44020.2685-0.26810.1723-0.0881-0.0410.02130.01620.0645-0.0633-0.02550.00250.02420.06320.01040.01440.13410.00120.10431.86381.711827.991
33.47781.00250.55854.2611.60192.23930.1938-0.1529-0.11750.4485-0.0006-0.30010.55990.0599-0.1220.14510.0028-0.0230.12140.00620.12940.2799-9.604826.3843
44.46263.61050.66763.4680.00910.5275-0.0143-0.10160.03330.0512-0.0332-0.0292-0.01710.05130.06670.05480.00270.01260.1097-0.00120.06745.0324.917423.5149
51.10080.48780.19636.5115-1.2481.15670.01180.0748-0.1711-0.2768-0.0982-0.35780.18390.20210.05830.08130.0190.03880.1041-0.0070.11954.2891-4.757320.0372
63.324-3.13882.07656.5914-1.73581.31010.05390.21720.1059-0.2623-0.2467-0.19940.06550.14860.14490.08850.00040.03570.13130.00570.09565.69042.230515.9983
79.0196-2.3692.86315.88531.82993.17940.06710.54530.5476-0.69240.00570.0497-0.3799-0.0888-0.14130.2088-0.03640.00010.18260.06620.13761.808614.16489.1171
80.6232-0.76170.43013.64551.41622.23540.0810.27110.0255-0.2631-0.0743-0.12930.04630.24950.00030.1409-0.0083-0.00460.18060.01260.0962-0.79246.30928.7465
90.65640.80110.23553.17070.55190.4169-0.01060.17130.0246-0.26010.06210.29680.086-0.1327-0.04840.1174-0.0148-0.01730.16030.01590.1068-7.74221.394813.1238
101.65050.2167-0.19851.833-0.4591.99110.03070.038-0.0637-0.31120.1439-0.04270.07140.1196-0.17290.1166-0.01590.01530.1216-0.0240.1034-1.9599-5.584415.5582
112.79840.41141.33263.33312.30343.8531-0.0437-0.1824-0.26930.4558-0.07620.46150.2146-0.59160.09760.2024-0.02270.07820.1925-0.00450.1823.3553.097242.2512
120.81341.0814-0.10652.1803-0.47440.2438-0.2069-0.10130.1672-0.29870.1190.2240.00240.08120.06250.20670.01570.00520.1339-0.02130.1596.855616.243638.9556
134.12730.60872.56311.7318-1.34237.4115-0.1056-0.38220.60560.50550.11290.1325-0.38990.0514-0.10150.36360.0275-0.00820.1542-0.03330.17547.735520.681545.2969
141.22160.18210.17761.7779-1.06093.2375-0.1381-0.18190.14240.38130.04160.0643-0.376-0.37510.0670.19020.04330.00620.1136-0.03020.107210.775114.295544.5747
150.5517-0.01110.10641.70490.10323.158-0.0259-0.05020.10750.2755-0.0231-0.1055-0.02510.1207-0.01610.164-0.0014-0.03430.1214-0.0130.095115.251913.765140.1751
161.246-0.4178-0.42463.66383.20574.879-0.0281-0.09530.23420.22490.0241-0.2712-0.38470.18250.02380.2119-0.0308-0.03230.1363-0.00730.123618.236115.119142.5808
176.85690.00720.14625.2904-0.15613.5783-0.07590.1751-0.4976-0.07340.0463-0.13670.3377-0.07740.05110.0944-0.00590.0260.1203-0.01210.140118.7984-1.198930.6565
181.2045-0.050.92791.43740.04732.1582-0.01450.048-0.03930.15540.0127-0.0457-0.01130.0293-0.02060.0942-0.00460.00910.09030.00480.083916.74430.608843.1198
194.76451.1681-0.71744.018-0.26613.7814-0.13010.17040.08250.33680.0103-0.3906-0.18460.26680.06890.1898-0.0356-0.06990.15130.02640.118223.47548.288648.1591
200.36620.6421.06831.16941.95483.2122-0.4305-0.60690.16210.4348-0.14250.2385-0.3447-0.81810.31020.25520.04980.04750.2374-0.07830.1516.611410.489550.2757
213.0121-0.81540.59893.4378-0.4766.04760.1298-0.41690.02910.69010.03320.5026-0.3098-0.0131-0.15730.2004-0.02480.08970.2075-0.03070.211-4.04523.760136.6201
220.67410.1967-0.1540.57910.02972.12750.00350.01380.18760.01550.02570.20220.06620.0151-0.04080.11520.00160.0030.12510.01490.1536-3.659117.95121.8409
237.1422-0.6281-0.83992.4534-3.37765.3898-0.10250.6325-0.3051-0.5646-0.18830.30660.6005-0.09670.12120.04740.2381-0.1636-0.12930.20680.5202-10.315822.444718.1415
241.9382-2.49961.17163.5396-2.42543.44780.1459-0.22780.2505-0.0469-0.00870.5707-0.0335-0.1987-0.06620.08120.0152-0.00110.08940.01770.355-8.75229.430423.1709
255.7971-2.5725-3.16724.49192.84242.3537-0.078-0.01410.00680.2460.04220.02140.16250.15870.0110.0946-0.00170.00980.14160.00330.11933.390918.639323.5608
261.8127-1.30080.73232.0732-0.67181.04050.04340.05770.3073-0.15340.00530.11050.0105-0.0115-0.04660.11180.01080.00030.12090.03470.21250.585726.572421.6894
275.4262-0.52323.90761.7388-0.03025.7411-0.06620.34690.4561-0.0946-0.00110.0105-0.34470.2110.03340.1473-0.00370.02550.11750.04640.19354.601829.18922.9088
282.15110.11070.67522.7764-0.26652.77330.0798-0.06360.3150.1676-0.0557-0.0342-0.23380.07940.00020.1854-0.02930.05520.1014-0.02590.21595.825332.908333.2539
291.3648-1.30840.35151.71971.03144.4039-0.49790.01090.7787-0.1154-0.19440.5038-0.71050.25360.29650.1860.06670.0223-0.0213-0.0520.5735-1.944839.002728.1041
302.20551.4358-0.20942.4921-0.46761.63790.0368-0.01070.2107-0.2067-0.13250.1897-0.1177-0.00680.11270.16040.04920.0260.13230.04230.3593-6.778131.735824.606
316.2003-0.552-1.19094.8277-0.75275.27340.1248-0.6136-0.07260.8173-0.10470.28970.19440.02250.00880.2402-0.03810.05850.18860.01130.17869.457-30.235258.6626
320.79730.23240.25731.3404-0.53842.06350.02690.0362-0.02880.02030.01740.11870.107-0.1239-0.01330.08120.00260.01440.11160.01020.099110.2876-22.745246.8655
332.08781.3185-0.0735.48332.58243.6533-0.17430.32030.139-0.63860.10160.1105-0.3399-0.05470.08710.1650.0009-0.0180.14020.01170.117511.658-11.408845.299
340.7979-0.8588-0.65612.40831.872.07420.01680.0584-0.0338-0.0449-0.00820.03850.0584-0.02050.00550.07790.002-0.00230.10780.00190.075116.0567-23.9245.461
350.7881-0.7921-0.00757.2628-0.14711.28870.08140.09240.172-0.0898-0.065-0.3571-0.09670.1205-0.02310.069-0.00480.01980.11430.00440.130218.8618-16.393746.6983
360.9765-0.420.26673.8321-1.72782.61650.02690.02420.12060.0875-0.1675-0.5359-0.03540.22610.03730.06770.00340.0060.12560.00280.14123.1639-21.36947.6467
373.05820.7655-0.21873.60690.60316.1868-0.0143-0.1784-0.28250.5497-0.0846-0.16090.08990.43190.14330.21570.0654-0.06350.1720.00470.185726.3224-35.204255.0297
382.8781.47751.40613.9830.21842.4099-0.09560.03380.2847-0.00520.0361-0.13940.21080.56610.07130.14950.0291-0.05790.1935-0.01850.146226.1599-26.814756.7446
390.19780.17670.03022.91260.99990.8917-0.0631-0.17960.05610.69680.0942-0.35370.08630.0481-0.00250.19360.0236-0.06120.15850.00620.138719.0887-22.119460.8433
404.3722-0.5464-0.14512.5935-0.17762.19-0.05320.2789-0.42150.31610.2459-0.4587-0.2060.1862-0.15050.0627-0.0276-0.03590.1341-0.07490.197820.1822-14.887954.2488
412.7712.37070.96543.1822.13614.3038-0.0362-0.65850.62930.0667-0.30080.5126-0.2428-0.46910.18250.13540.04080.00040.2248-0.1110.2806-0.5675-23.279536.3313
420.3445-0.7213-0.10771.72710.4540.2897-0.0410.0306-0.00410.27390.0824-0.02940.1543-0.0076-0.02950.19880.0004-0.02940.1385-0.02060.1782.8554-37.51735.2115
432.23150.6725-0.08912.8822-1.41273.82450.24120.1403-0.4481-0.18240.15880.36350.8543-0.2959-0.27810.2239-0.0603-0.07910.1758-0.00150.2395-4.6288-37.793826.5664
447.8635-3.6911.95842.9555-0.971.0998-0.0345-0.0932-0.05470.06630.0521-0.00980.02710.04590.01140.1316-0.00110.00430.10610.0020.09278.7451-35.03633.348
453.43130.94192.5432.0481.00853.59970.10060.1978-0.2046-0.1446-0.03240.11610.23510.0061-0.03540.15950.0153-0.0450.1246-0.03310.12724.125-36.039625.8035
463.22640.4169-0.91524.4075-0.94131.28410.11110.2877-0.224-0.4138-0.08340.01070.1339-0.1812-0.03770.17110.0267-0.03340.1509-0.03590.07877.56-34.55924.3529
475.53741.10440.77914.82830.39925.466-0.00310.31880.0698-0.30620.099-0.5379-0.24970.3783-0.09160.1371-0.00830.02610.16-0.01830.14315.7967-22.032227.6278
480.8152-0.10520.65411.18210.14451.87760.00220.06980.0583-0.1811-0.01470.0956-0.11580.02610.0080.15040.0195-0.01130.1094-0.00440.10184.3246-21.407923.8497
495.5835-0.5398-2.59853.10981.50074.96720.13130.336-0.0565-0.4786-0.13410.05060.1271-0.0367-0.01090.20920.0566-0.03370.1597-0.00720.09084.0347-29.427516.1266
502.49940.1594-2.20992.974-1.98633.15950.1107-0.33120.35460.3117-0.16660.35950.0306-0.39160.02310.172-0.03190.00220.2118-0.04250.2439-6.5294-30.553729.3067
512.7851-1.4441.18022.9095-1.05274.10750.01220.1723-0.3143-0.0590.08990.58880.0742-0.5304-0.07880.1364-0.0130.00540.2312-0.02110.2582-0.4873-44.061845.9414
521.9968-0.09060.86840.19060.04590.5786-0.14440.09350.13540.158-0.01320.0227-0.02550.08930.09430.17380.0082-0.02690.12080.00550.145212.3863-38.493153.1351
532.0992-0.99980.05787.0228-0.34332.6892-0.0653-0.21380.11950.9047-0.04460.07550.03230.14210.10160.31550.01160.04040.1390.02270.156110.9995-46.712661.008
541.6151.2997-1.09421.9411-1.08982.2292-0.0607-0.0059-0.00620.09950.01570.00980.04290.03780.05640.14040.0156-0.00220.09780.00930.131312.7606-43.892147.5078
550.37410.2756-0.38560.9627-1.25263.3315-0.025-0.1171-0.1350.1704-0.05-0.00730.17720.29710.0260.24360.0342-0.01250.14280.04560.183116.284-50.742254.765
565.192-0.0205-1.27847.08590.94195.32480.12950.4356-0.6951-0.56450.0347-0.01280.14160.1297-0.16860.2098-0.0158-0.01510.1522-0.04240.189311.1559-50.635433.9561
573.1477-0.06631.58686.38322.31965.19180.04860.2022-0.84250.20760.3812-0.19410.48510.5166-0.19860.22490.0282-0.03440.1556-0.03350.32612.9352-57.220440.4153
580.8882-1.0630.65453.33570.72312.92580.0763-0.0589-0.17360.2417-0.17530.20920.3358-0.35910.12320.152-0.04760.00740.1309-0.02620.21163.3566-52.582340.6557
593.45981.1871.56041.9733-0.85543.17970.07240.2569-0.33220.1688-0.0391-0.00561.0948-0.1948-0.01650.398-0.04740.07930.10060.01240.24037.4764-59.640848.5169
603.4967-1.7035-0.55962.94921.16122.19320.1650.1050.14530.1489-0.197-0.34970.1798-0.1276-0.00950.28080.00650.04820.140.03480.20788.2282-52.142854.5272
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 453:459)A453 - 459
2X-RAY DIFFRACTION2(chain A and resid 460:470)A460 - 470
3X-RAY DIFFRACTION3(chain A and resid 471:479)A471 - 479
4X-RAY DIFFRACTION4(chain A and resid 480:490)A480 - 490
5X-RAY DIFFRACTION5(chain A and resid 491:503)A491 - 503
6X-RAY DIFFRACTION6(chain A and resid 504:508)A504 - 508
7X-RAY DIFFRACTION7(chain A and resid 509:513)A509 - 513
8X-RAY DIFFRACTION8(chain A and resid 514:522)A514 - 522
9X-RAY DIFFRACTION9(chain A and resid 523:535)A523 - 535
10X-RAY DIFFRACTION10(chain A and resid 536:552)A536 - 552
11X-RAY DIFFRACTION11(chain C and resid 453:460)C453 - 460
12X-RAY DIFFRACTION12(chain C and resid 461:468)C461 - 468
13X-RAY DIFFRACTION13(chain C and resid 469:474)C469 - 474
14X-RAY DIFFRACTION14(chain C and resid 475:486)C475 - 486
15X-RAY DIFFRACTION15(chain C and resid 487:499)C487 - 499
16X-RAY DIFFRACTION16(chain C and resid 500:508)C500 - 508
17X-RAY DIFFRACTION17(chain C and resid 509:513)C509 - 513
18X-RAY DIFFRACTION18(chain C and resid 514:535)C514 - 535
19X-RAY DIFFRACTION19(chain C and resid 536:546)C536 - 546
20X-RAY DIFFRACTION20(chain C and resid 547:552)C547 - 552
21X-RAY DIFFRACTION21(chain E and resid 452:461)E452 - 461
22X-RAY DIFFRACTION22(chain E and resid 462:470)E462 - 470
23X-RAY DIFFRACTION23(chain E and resid 471:475)E471 - 475
24X-RAY DIFFRACTION24(chain E and resid 476:482)E476 - 482
25X-RAY DIFFRACTION25(chain E and resid 483:487)E483 - 487
26X-RAY DIFFRACTION26(chain E and resid 488:500)E488 - 500
27X-RAY DIFFRACTION27(chain E and resid 501:511)E501 - 511
28X-RAY DIFFRACTION28(chain E and resid 512:529)E512 - 529
29X-RAY DIFFRACTION29(chain E and resid 530:540)E530 - 540
30X-RAY DIFFRACTION30(chain E and resid 541:552)E541 - 552
31X-RAY DIFFRACTION31(chain G and resid 452:457)G452 - 457
32X-RAY DIFFRACTION32(chain G and resid 458:469)G458 - 469
33X-RAY DIFFRACTION33(chain G and resid 470:477)G470 - 477
34X-RAY DIFFRACTION34(chain G and resid 478:490)G478 - 490
35X-RAY DIFFRACTION35(chain G and resid 491:502)G491 - 502
36X-RAY DIFFRACTION36(chain G and resid 503:508)G503 - 508
37X-RAY DIFFRACTION37(chain G and resid 509:513)G509 - 513
38X-RAY DIFFRACTION38(chain G and resid 514:521)G514 - 521
39X-RAY DIFFRACTION39(chain G and resid 522:536)G522 - 536
40X-RAY DIFFRACTION40(chain G and resid 537:552)G537 - 552
41X-RAY DIFFRACTION41(chain I and resid 453:460)I453 - 460
42X-RAY DIFFRACTION42(chain I and resid 461:470)I461 - 470
43X-RAY DIFFRACTION43(chain I and resid 471:480)I471 - 480
44X-RAY DIFFRACTION44(chain I and resid 481:488)I481 - 488
45X-RAY DIFFRACTION45(chain I and resid 489:502)I489 - 502
46X-RAY DIFFRACTION46(chain I and resid 503:507)I503 - 507
47X-RAY DIFFRACTION47(chain I and resid 508:515)I508 - 515
48X-RAY DIFFRACTION48(chain I and resid 516:535)I516 - 535
49X-RAY DIFFRACTION49(chain I and resid 536:546)I536 - 546
50X-RAY DIFFRACTION50(chain I and resid 547:552)I547 - 552
51X-RAY DIFFRACTION51(chain K and resid 452:461)K452 - 461
52X-RAY DIFFRACTION52(chain K and resid 462:470)K462 - 470
53X-RAY DIFFRACTION53(chain K and resid 471:478)K471 - 478
54X-RAY DIFFRACTION54(chain K and resid 479:496)K479 - 496
55X-RAY DIFFRACTION55(chain K and resid 497:507)K497 - 507
56X-RAY DIFFRACTION56(chain K and resid 508:514)K508 - 514
57X-RAY DIFFRACTION57(chain K and resid 515:519)K515 - 519
58X-RAY DIFFRACTION58(chain K and resid 520:529)K520 - 529
59X-RAY DIFFRACTION59(chain K and resid 530:540)K530 - 540
60X-RAY DIFFRACTION60(chain K and resid 541:552)K541 - 552

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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://pdbjlvh1.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