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- PDB-5j3x: Structure of c-CBL Y371F -

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基本情報

登録情報
データベース: PDB / ID: 5j3x
タイトルStructure of c-CBL Y371F
要素E3 ubiquitin-protein ligase CBL
キーワードLIGASE / UBIQUITIN LIGASE / RING E3
機能・相同性
機能・相同性情報


regulation of platelet-derived growth factor receptor-alpha signaling pathway / regulation of Rap protein signal transduction / phosphatidylinositol 3-kinase regulatory subunit binding / flotillin complex / Regulation of KIT signaling / ubiquitin-dependent endocytosis / Interleukin-6 signaling / response to starvation / mast cell degranulation / negative regulation of T cell activation ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / regulation of Rap protein signal transduction / phosphatidylinositol 3-kinase regulatory subunit binding / flotillin complex / Regulation of KIT signaling / ubiquitin-dependent endocytosis / Interleukin-6 signaling / response to starvation / mast cell degranulation / negative regulation of T cell activation / response to testosterone / TGF-beta receptor signaling activates SMADs / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of T cell receptor signaling pathway / protein monoubiquitination / protein K63-linked ubiquitination / protein autoubiquitination / positive regulation of epidermal growth factor receptor signaling pathway / ephrin receptor binding / cellular response to platelet-derived growth factor stimulus / phosphotyrosine residue binding / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / response to activity / InlB-mediated entry of Listeria monocytogenes into host cell / response to gamma radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / sperm end piece / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / Constitutive Signaling by EGFRvIII / cellular response to nerve growth factor stimulus / Spry regulation of FGF signaling / Negative regulation of MET activity / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / SH3 domain binding / positive regulation of receptor-mediated endocytosis / male gonad development / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / cilium / protein ubiquitination / cadherin binding / membrane raft / focal adhesion / calcium ion binding / DNA damage response / symbiont entry into host cell / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / zinc ion binding / plasma membrane / cytosol
類似検索 - 分子機能
Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. ...Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Prokaryotic RING finger family 4 / Adaptor protein Cbl, N-terminal domain superfamily / Transcription Elongation Factor S-II; Chain A / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SH2 domain / SHC Adaptor Protein / UBA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Zinc finger RING-type profile. / SH2 domain superfamily / Zinc finger, RING-type / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
E3 ubiquitin-protein ligase CBL
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.822 Å
データ登録者Huang, D.T. / Buetow, L. / Dou, H.
資金援助 英国, 2件
組織認可番号国
European Research Council647849 英国
Cancer Research UK 英国
引用ジャーナル: Bmc Biol. / 年: 2016
タイトル: Casitas B-lineage lymphoma linker helix mutations found in myeloproliferative neoplasms affect conformation.
著者: Buetow, L. / Tria, G. / Ahmed, S.F. / Hock, A. / Dou, H. / Sibbet, G.J. / Svergun, D.I. / Huang, D.T.
履歴
登録2016年3月31日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年9月21日Provider: repository / タイプ: Initial release
改定 1.12024年1月10日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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: E3 ubiquitin-protein ligase CBL
B: E3 ubiquitin-protein ligase CBL
C: E3 ubiquitin-protein ligase CBL
D: E3 ubiquitin-protein ligase CBL
E: E3 ubiquitin-protein ligase CBL
F: E3 ubiquitin-protein ligase CBL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)271,36624
ポリマ－270,3416
非ポリマー1,02518
水1,69394
1
A: E3 ubiquitin-protein ligase CBL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2284
ポリマ－45,0571
非ポリマー1713
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase CBL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2284
ポリマ－45,0571
非ポリマー1713
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase CBL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2284
ポリマ－45,0571
非ポリマー1713
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase CBL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2284
ポリマ－45,0571
非ポリマー1713
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: E3 ubiquitin-protein ligase CBL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2284
ポリマ－45,0571
非ポリマー1713
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: E3 ubiquitin-protein ligase CBL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2284
ポリマ－45,0571
非ポリマー1713
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)147.842, 149.040, 344.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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要素

#1: タンパク質
E3 ubiquitin-protein ligase CBL / Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / Signal ...Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / Signal transduction protein CBL


分子量: 45056.824 Da / 分子数: 6 / 断片: UNP residues 47-435 / 変異: Y371F / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CBL, CBL2, RNF55 / プラスミド: pGEX4T1 TEV / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P22681, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ（ペプチド合成）
#2: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 12 / 由来タイプ: 組換発現 / 式: Zn
#3: 化合物
ChemComp-CA / CALCIUM ION


分子量: 40.078 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Ca
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 94 / 由来タイプ: 天然 / 式: H2O

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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: 3.22 Å3/Da / 溶媒含有率: 61.79 %
結晶化温度: 281.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: Equal volume protein at 10 mg/mL + well containing 3.0-3.1 M sodium formate 0.1 M Tris-HCl, pH 8.5 5 mM DTT

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I04 / 波長: 0.9763 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2010年10月21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: 0.9763 Å / 相対比: 1
反射解像度: 2.82→105 Å / Num. obs: 91407 / % possible obs: 99.9 % / 冗長度: 4.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.7
反射 シェル解像度: 2.82→2.9 Å / 冗長度: 4.7 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
XDSデータ削減
xia2データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2Y1M

2y1m


解像度: 2.822→50.371 Å / SU ML: 0.4 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.95
Rfactor反射数%反射
Rfree0.2541 4533 4.98 %
Rwork0.2124 --
obs0.2145 90968 99.57 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.822→50.371 Å
タンパク質核酸リガンド溶媒全体
原子数18172 0 18 94 18284
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00218727
X-RAY DIFFRACTIONf_angle_d0.54425445
X-RAY DIFFRACTIONf_dihedral_angle_d10.4256731
X-RAY DIFFRACTIONf_chiral_restr0.0212787
X-RAY DIFFRACTIONf_plane_restr0.0043244
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.822-2.85410.4421560.38742852X-RAY DIFFRACTION100
2.8541-2.88760.38151280.35912850X-RAY DIFFRACTION100
2.8876-2.92290.37061420.33452890X-RAY DIFFRACTION99
2.9229-2.95980.33141760.32992800X-RAY DIFFRACTION100
2.9598-2.99880.33911370.30682905X-RAY DIFFRACTION99
2.9988-3.03990.35521500.32796X-RAY DIFFRACTION99
3.0399-3.08330.33421380.29972913X-RAY DIFFRACTION100
3.0833-3.12930.37471480.27972822X-RAY DIFFRACTION100
3.1293-3.17820.27651560.26342886X-RAY DIFFRACTION100
3.1782-3.23030.35021550.26762843X-RAY DIFFRACTION100
3.2303-3.2860.34091580.2592873X-RAY DIFFRACTION100
3.286-3.34570.29581280.25652826X-RAY DIFFRACTION99
3.3457-3.41010.2951370.24912895X-RAY DIFFRACTION100
3.4101-3.47960.28641480.23922855X-RAY DIFFRACTION100
3.4796-3.55530.28551510.24112865X-RAY DIFFRACTION99
3.5553-3.6380.24241350.23312895X-RAY DIFFRACTION100
3.638-3.72890.28891410.21782895X-RAY DIFFRACTION100
3.7289-3.82970.26491570.21232833X-RAY DIFFRACTION99
3.8297-3.94240.27881310.21142891X-RAY DIFFRACTION100
3.9424-4.06960.24321450.1992890X-RAY DIFFRACTION100
4.0696-4.21490.23731580.18882901X-RAY DIFFRACTION100
4.2149-4.38360.21911570.18372898X-RAY DIFFRACTION100
4.3836-4.5830.22981740.17722851X-RAY DIFFRACTION100
4.583-4.82440.22671500.182891X-RAY DIFFRACTION100
4.8244-5.12640.22121770.18152880X-RAY DIFFRACTION100
5.1264-5.52180.22631450.18662939X-RAY DIFFRACTION100
5.5218-6.07660.22251460.20972881X-RAY DIFFRACTION99
6.0766-6.95390.24091920.2042929X-RAY DIFFRACTION100
6.9539-8.75380.25151450.17562987X-RAY DIFFRACTION100
8.7538-50.37940.18261720.16193003X-RAY DIFFRACTION98
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)
12.6150.34260.29561.6856-1.16582.3383-0.2341-0.25490.2158-0.19580.28080.0198-0.05010.1602-0.03040.7055-0.1054-0.01190.9269-0.15610.36-9.5841-67.36335.5797
23.98750.1942-0.89062.44970.01643.64580.1660.5364-0.3324-0.0361-0.0690.36890.2157-0.4611-0.17040.6069-0.103-0.04180.7992-0.06370.4319-21.0501-73.45569.6788
35.05571.0331-0.6372.1855-0.2713.44460.2579-0.02440.3788-0.17830.078-0.1603-0.4670.5858-0.32340.6626-0.2055-0.02530.8173-0.10340.5248-6.4469-62.295410.7562
42.14260.6166-0.19611.14590.14863.0132-0.0775-0.03830.01690.0191-0.01640.10110.16640.11780.06570.719-0.2742-0.08080.8314-0.11960.1484-9.5652-71.217816.406
51.9417-0.1546-0.21051.3691-0.09081.38070.2666-0.3019-0.1270.6258-0.14220.1905-0.0459-0.1285-0.10910.8181-0.3286-0.06430.8038-0.05640.4322-11.8283-68.689334.3607
61.4406-1.07560.61771.60230.37022.03360.4609-0.2671-0.8370.6-0.3071-0.60340.270.2231-0.160.7784-0.3417-0.29710.75930.1221.08278.431-81.318531.9132
71.9419-4.13310.00068.7955-0.0009-0.0003-0.1256-0.7525-0.39631.25640.01930.48720.234-1.08710.11291.1879-0.5366-0.30671.53760.01360.8015-2.1621-75.463550.5879
81.9401-0.60570.31871.4816-0.86111.65480.2997-0.0033-0.14840.2655-0.15660.0794-0.0391-0.0166-0.06920.8469-0.3517-0.10210.8594-0.04860.88190.9401-51.150227.7783
91.05930.6391-0.93732.52830.22942.25970.0969-0.28280.3427-0.3579-0.2040.3823-0.088-0.00030.07010.949-0.1123-0.3570.9490.00931.018666.5685-66.790180.7266
102.25950.7234-0.27982.9414-0.19592.93920.0277-0.51690.31860.30010.12930.0655-0.65980.4198-0.16170.7966-0.1636-0.3040.82780.03031.112372.6994-55.347376.8932
112.0291.5756-0.94751.52830.13392.9371-0.39210.33890.6593-0.08390.17880.2370.2609-0.31450.15610.8541-0.1903-0.35960.76990.11040.869861.4657-69.275975.5609
121.54770.0917-0.66932.9693-0.81312.5394-0.27520.1370.4767-0.19090.0519-0.16010.07490.01580.20520.8288-0.2191-0.3880.71120.1240.688670.1284-66.368469.7931
131.8304-0.3911-0.34950.57680.25411.2685-0.39910.58081.0927-0.43090.31710.3491-0.24340.11660.07681.0178-0.418-0.52370.9220.4311.08267.0303-63.480151.9315
141.8981-0.60630.35531.61070.12251.2874-0.290.34790.08-0.08790.2142-0.11320.02710.01520.13330.8806-0.4262-0.31520.87460.25070.79579.7059-83.981453.4178
151.6034-2.3271-0.70383.97181.22170.37640.36631.58991.1334-1.69410.05350.1883-0.917-0.8399-0.4111.3829-0.4542-0.29131.26870.35240.748367.5864-74.605136.7694
161.0599-0.0791-0.58561.1095-0.12821.7291-0.1998-0.08330.7885-0.04590.2832-0.1258-0.0931-0.2496-0.0131.0371-0.4074-0.46551.07550.17071.307649.0938-76.731260.3983
172.56590.23080.05811.7002-0.63622.4619-0.368-0.17970.3926-0.55390.0010.20220.01170.45320.31211.2992-0.4862-0.63431.16580.53641.114635.62-84.882833.636
184.927-0.0853-2.51471.8-0.37392.15090.05290.140.8283-0.4262-0.10310.2087-0.28340.48620.00281.2974-0.5626-0.73241.28510.56811.33547.8983-80.100532.7323
192.9353-0.70960.43611.2521-0.05551.42140.17060.1635-0.42160.0455-0.17870.18550.1406-0.1924-0.18711.2679-0.6649-0.64381.33490.52940.92235.1065-93.090134.9131
201.41340.18590.73270.67230.03911.0376-0.13860.20460.147-0.07560.1471-0.1473-0.08370.04250.21351.0367-0.6592-0.77641.2250.5120.900243.9034-88.887640.9595
210.7497-0.2939-0.2362.09290.16890.7527-0.15880.28790.0929-0.59390.1828-0.35930.130.010.03491.0899-0.4709-0.35641.01490.27950.710855.9562-101.787646.3026
221.347-0.6418-0.78021.79390.22872.11870.0168-0.29260.63990.3447-0.0285-0.00370.3826-0.46750.01950.9731-0.445-0.43190.97820.18850.913343.0181-96.63865.7066
230.1162-0.4848-0.66314.40234.43655.27010.306-0.0135-0.4933-0.35020.6089-0.75580.81311.5754-0.81271.024-0.2404-0.37351.07020.25181.089957.174-113.359961.2229
241.37391.2350.39621.4056-0.37312.1652-0.40320.20890.2858-1.21960.38140.62990.2432-0.2452-0.06791.676-0.9173-0.65071.16820.51521.092436.5228-113.403239.4847
253.2186-0.45370.55353.06070.45092.6821-0.39930.04670.0025-1.0440.2236-0.1934-0.298-0.1360.25571.122-0.3317-0.04230.90990.00030.812743.3962-142.052449.7289
263.5307-0.15950.52363.32561.42561.8357-0.39260.2690.096-0.67330.756-0.43811.0768-0.0396-0.28421.014-0.2957-0.11140.96580.12280.727150.8467-132.47854.929
272.0129-0.0063-0.9213.36680.93230.8309-0.10130.2150.00650.11940.06380.0561.2031-0.37540.09991.2853-0.3838-0.15810.93050.08920.421736.78-143.613253.839
282.49030.19210.38581.53960.50791.7321-0.6086-0.44930.3802-0.42360.1295-0.0836-0.4170.18370.38671.0336-0.36-0.36360.82210.18240.663538.1839-132.47253.4907
292.1360.8983-0.34131.52260.55941.3638-0.1184-0.00031.2505-0.06460.31481.0032-0.10960.093-0.16450.8486-0.2775-0.35650.83980.18471.184728.1571-123.712565.9517
301.18840.2324-0.51320.2195-0.22630.3225-0.01030.68550.8565-0.72170.59280.85570.0424-0.35710.3781.5259-1.0815-0.97621.09870.9722.046417.1828-120.305344.7247
312.3431-0.1764-0.5630.18-0.56812.6329-0.1982-0.6540.74780.5524-0.0272-0.1379-0.8395-0.35790.20711.1944-0.2482-0.23750.92260.21361.600210.5478-117.010566.2981
324.0291-0.42870.25423.3398-0.81270.8429-0.39610.13980.7355-0.25680.1065-0.0996-0.20040.04360.23450.7975-0.3002-0.27320.8790.23380.808318.9351-145.351264.2612
331.4545-0.1718-0.28541.85020.62480.46890.113-0.46550.13340.8607-0.41240.12250.3682-0.87460.15261.312-0.6402-0.05391.2475-0.11720.79029.0046-35.830751.9944
341.7484-0.2259-0.36423.3325-1.02591.69830.0229-0.183-0.3360.79540.0470.80730.6042-0.5392-0.01381.7573-0.83450.11521.2808-0.11640.95445.5606-50.450554.2176
351.54930.3826-0.92812.57251.00271.15960.4685-0.59460.24020.2311-0.2081-0.5254-0.25360.1225-0.11831.5815-0.6492-0.19041.11910.03960.984318.3964-37.581551.3211
361.6475-0.1856-0.16932.0577-0.00361.75870.155-0.3519-0.16710.3078-0.23510.27020.6731-0.0499-0.00311.4542-0.8138-0.0871.03130.04440.796213.9106-45.882245.3913
370.88920.19140.16181.1611-0.22791.46340.2979-0.5052-1.22620.9268-0.6126-1.0216-0.01310.19620.24751.1558-0.5078-0.43540.99480.28951.383726.3889-57.497738.8478
381.9105-0.20340.28021.21690.03622.2238-0.04470.3019-0.5293-0.1410.0407-0.1681-0.23730.27790.04090.8366-0.3624-0.14690.8808-0.01310.959221.0758-44.602220.1965
391.6667-0.4269-0.21880.2902-0.42912.01560.4808-0.5343-0.66070.9074-0.6032-0.0823-0.1083-0.14550.1981.3868-0.9908-0.62981.29990.37431.472638.4093-39.393645.0849
400.0787-0.05760.17820.0421-0.12940.40280.1489-0.4366-0.78620.1684-0.4621-0.64030.35121.00270.3061.24150.11890.08041.82390.27352.8761-8.7127-128.657719.2909
412.5433-0.74130.09731.3893-0.6431.6148-0.1256-0.864-0.42920.7311-0.4189-0.9052-0.05681.08210.50981.1782-0.2036-0.52771.51180.62362.2977-7.1862-117.40239.3778
421.93651.56411.9171.26011.54331.97720.1096-0.246-1.53370.2306-0.4462-0.22610.17440.35740.06520.9958-0.2949-0.22130.95850.38823.1569-17.5395-126.783728.954
431.92890.10450.11511.6246-0.68020.6471-0.1736-0.0489-0.38640.5943-0.3269-0.9330.01210.4170.2571.096-0.359-0.42610.86310.51852.986-6.2872-112.454630.8302
441.33220.021-0.31240.5712-0.21111.4966-0.244-0.1086-0.09660.0045-0.2178-0.3371-0.24610.1860.13570.9184-0.4913-0.69770.86620.39812.416-17.3166-113.88731.2054
452.57781.05890.31471.3092-0.34831.7050.1898-0.0315-1.4890.2211-0.2701-1.16490.269-0.00980.15290.7061-0.2584-0.11070.75390.01451.0667-26.6171-103.212219.8539
461.1074-0.4143-0.93511.74010.41641.10580.9119-1.0028-0.65671.1487-0.6903-0.4453-0.0483-0.0828-0.07481.2212-0.8101-0.40051.18170.26590.9799-29.6171-92.921240.435
472.2803-1.1786-0.39161.76940.19392.12160.3428-0.0924-1.1810.0628-0.1220.01480.27130.0915-0.21210.7472-0.2517-0.27770.77380.05751.3615-6.6508-93.24220.8374
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 175 )
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 267 )
6X-RAY DIFFRACTION6chain 'A' and (resid 268 through 350 )
7X-RAY DIFFRACTION7chain 'A' and (resid 351 through 356 )
8X-RAY DIFFRACTION8chain 'A' and (resid 360 through 435 )
9X-RAY DIFFRACTION9chain 'B' and (resid 47 through 82 )
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 112 )
11X-RAY DIFFRACTION11chain 'B' and (resid 113 through 145 )
12X-RAY DIFFRACTION12chain 'B' and (resid 146 through 175 )
13X-RAY DIFFRACTION13chain 'B' and (resid 176 through 267 )
14X-RAY DIFFRACTION14chain 'B' and (resid 268 through 350 )
15X-RAY DIFFRACTION15chain 'B' and (resid 351 through 364 )
16X-RAY DIFFRACTION16chain 'B' and (resid 365 through 435 )
17X-RAY DIFFRACTION17chain 'C' and (resid 47 through 82 )
18X-RAY DIFFRACTION18chain 'C' and (resid 83 through 112 )
19X-RAY DIFFRACTION19chain 'C' and (resid 113 through 145 )
20X-RAY DIFFRACTION20chain 'C' and (resid 146 through 175 )
21X-RAY DIFFRACTION21chain 'C' and (resid 176 through 267 )
22X-RAY DIFFRACTION22chain 'C' and (resid 268 through 350 )
23X-RAY DIFFRACTION23chain 'C' and (resid 351 through 364 )
24X-RAY DIFFRACTION24chain 'C' and (resid 365 through 435 )
25X-RAY DIFFRACTION25chain 'D' and (resid 47 through 82 )
26X-RAY DIFFRACTION26chain 'D' and (resid 83 through 112 )
27X-RAY DIFFRACTION27chain 'D' and (resid 113 through 145 )
28X-RAY DIFFRACTION28chain 'D' and (resid 146 through 175 )
29X-RAY DIFFRACTION29chain 'D' and (resid 176 through 267 )
30X-RAY DIFFRACTION30chain 'D' and (resid 268 through 350 )
31X-RAY DIFFRACTION31chain 'D' and (resid 351 through 364 )
32X-RAY DIFFRACTION32chain 'D' and (resid 365 through 435 )
33X-RAY DIFFRACTION33chain 'E' and (resid 51 through 82 )
34X-RAY DIFFRACTION34chain 'E' and (resid 83 through 112 )
35X-RAY DIFFRACTION35chain 'E' and (resid 113 through 145 )
36X-RAY DIFFRACTION36chain 'E' and (resid 146 through 175 )
37X-RAY DIFFRACTION37chain 'E' and (resid 176 through 267 )
38X-RAY DIFFRACTION38chain 'E' and (resid 268 through 354 )
39X-RAY DIFFRACTION39chain 'E' and (resid 359 through 435 )
40X-RAY DIFFRACTION40chain 'F' and (resid 50 through 54 )
41X-RAY DIFFRACTION41chain 'F' and (resid 55 through 82 )
42X-RAY DIFFRACTION42chain 'F' and (resid 83 through 112 )
43X-RAY DIFFRACTION43chain 'F' and (resid 113 through 145 )
44X-RAY DIFFRACTION44chain 'F' and (resid 146 through 175 )
45X-RAY DIFFRACTION45chain 'F' and (resid 176 through 267 )
46X-RAY DIFFRACTION46chain 'F' and (resid 268 through 356 )
47X-RAY DIFFRACTION47chain 'F' and (resid 359 through 435 )

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る