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- PDB-6dj9: Structure of the USP15 DUSP domain in complex with a high-affinit... -

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基本情報

登録情報
データベース: PDB / ID: 6dj9
タイトルStructure of the USP15 DUSP domain in complex with a high-affinity Ubiquitin Variant (UbV)
要素
  • Ubiquitin Variant UbV 15.D
  • Ubiquitin carboxyl-terminal hydrolase 15
キーワードSIGNALING PROTEIN / deubiquitination / Ubv / high-affinity / strand-exchange / dimerization
機能・相同性
機能・相同性情報


regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling ...regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling / protein deubiquitination / SMAD binding / BMP signaling pathway / transforming growth factor beta receptor signaling pathway / Downregulation of TGF-beta receptor signaling / negative regulation of transforming growth factor beta receptor signaling pathway / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : ...Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / Ubiquitin-like domain superfamily
類似検索 - ドメイン・相同性
Ubiquitin carboxyl-terminal hydrolase 15
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: 3.1 Å
データ登録者Singer, A.U. / Teyra, J. / Boehmelt, G. / Lenter, M. / Sicheri, F. / Sidhu, S.S.
引用ジャーナル: Structure / 年: 2019
タイトル: Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15.
著者: Teyra, J. / Singer, A.U. / Schmitges, F.W. / Jaynes, P. / Kit Leng Lui, S. / Polyak, M.J. / Fodil, N. / Krieger, J.R. / Tong, J. / Schwerdtfeger, C. / Brasher, B.B. / Ceccarelli, D.F.J. / ...著者: Teyra, J. / Singer, A.U. / Schmitges, F.W. / Jaynes, P. / Kit Leng Lui, S. / Polyak, M.J. / Fodil, N. / Krieger, J.R. / Tong, J. / Schwerdtfeger, C. / Brasher, B.B. / Ceccarelli, D.F.J. / Moffat, J. / Sicheri, F. / Moran, M.F. / Gros, P. / Eichhorn, P.J.A. / Lenter, M. / Boehmelt, G. / Sidhu, S.S.
履歴
登録2018年5月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年1月23日Provider: repository / タイプ: Initial release
改定 1.12019年2月13日Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22019年4月17日Group: Data collection / Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.32023年10月11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

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集合体

登録構造単位
A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
C: Ubiquitin carboxyl-terminal hydrolase 15
D: Ubiquitin carboxyl-terminal hydrolase 15
E: Ubiquitin carboxyl-terminal hydrolase 15
F: Ubiquitin carboxyl-terminal hydrolase 15
G: Ubiquitin Variant UbV 15.D
H: Ubiquitin Variant UbV 15.D
I: Ubiquitin Variant UbV 15.D
J: Ubiquitin Variant UbV 15.D
K: Ubiquitin Variant UbV 15.D
L: Ubiquitin Variant UbV 15.D


分子量 (理論値)分子数
合計 (水以外)153,00512
ポリマ－153,00512
非ポリマー00
水00
1
G: Ubiquitin Variant UbV 15.D
L: Ubiquitin Variant UbV 15.D


  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration, In fact no evidence for this hexameric assembly. Gel filtration is more consistent with a tetrameric complex of USP15 and Ubv, aka A+D+K+H, B+E+G+L, and C+F+I+J
  • 19 kDa, 2 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)19,0272
ポリマ－19,0272
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-31 kcal/mol
Surface area9870 Å2
手法PISA
2
H: Ubiquitin Variant UbV 15.D

K: Ubiquitin Variant UbV 15.D


分子量 (理論値)分子数
合計 (水以外)19,0272
ポリマ－19,0272
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation6_654x-y+1,x,z-1/21
Buried area3930 Å2
ΔGint-32 kcal/mol
Surface area9610 Å2
手法PISA
3
I: Ubiquitin Variant UbV 15.D
J: Ubiquitin Variant UbV 15.D


分子量 (理論値)分子数
合計 (水以外)19,0272
ポリマ－19,0272
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-31 kcal/mol
Surface area9400 Å2
手法PISA
4
A: Ubiquitin carboxyl-terminal hydrolase 15
D: Ubiquitin carboxyl-terminal hydrolase 15

A: Ubiquitin carboxyl-terminal hydrolase 15
D: Ubiquitin carboxyl-terminal hydrolase 15

A: Ubiquitin carboxyl-terminal hydrolase 15
D: Ubiquitin carboxyl-terminal hydrolase 15


分子量 (理論値)分子数
合計 (水以外)95,9226
ポリマ－95,9226
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area12690 Å2
ΔGint-78 kcal/mol
Surface area42550 Å2
手法PISA
5
B: Ubiquitin carboxyl-terminal hydrolase 15
F: Ubiquitin carboxyl-terminal hydrolase 15

B: Ubiquitin carboxyl-terminal hydrolase 15
F: Ubiquitin carboxyl-terminal hydrolase 15

B: Ubiquitin carboxyl-terminal hydrolase 15
F: Ubiquitin carboxyl-terminal hydrolase 15


分子量 (理論値)分子数
合計 (水以外)95,9226
ポリマ－95,9226
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area11870 Å2
ΔGint-90 kcal/mol
Surface area43750 Å2
手法PISA
6
C: Ubiquitin carboxyl-terminal hydrolase 15
E: Ubiquitin carboxyl-terminal hydrolase 15

C: Ubiquitin carboxyl-terminal hydrolase 15
E: Ubiquitin carboxyl-terminal hydrolase 15

C: Ubiquitin carboxyl-terminal hydrolase 15
E: Ubiquitin carboxyl-terminal hydrolase 15


分子量 (理論値)分子数
合計 (水以外)95,9226
ポリマ－95,9226
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area11840 Å2
ΔGint-85 kcal/mol
Surface area43800 Å2
手法PISA
単位格子
Length a, b, c (Å)152.410, 152.410, 125.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
詳細The biological assembly from PISA is a dimer of Ubvs -- this is observed by gel filtration (chains HK, GL and IJ). Then in turn we expect the individual USP15 domains to bind to the Ubv dimers, yielding the following tetrameric complexes -- the tetrameric complexes are observed by gel filtration

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要素

#1: タンパク質
Ubiquitin carboxyl-terminal hydrolase 15 / Deubiquitinating enzyme 15 / Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 ...Deubiquitinating enzyme 15 / Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 / Unph-2 / Unph4


分子量: 15987.022 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: USP15, KIAA0529 / プラスミド: pHH0103
詳細 (発現宿主): expressed as a fusion with an N-terminal 6His affinity TAG, GST and TEV cleavage site
発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#2: タンパク質
Ubiquitin Variant UbV 15.D


分子量: 9513.738 Da / 分子数: 6 / 由来タイプ: 組換発現
詳細: The following is a variant of ubiquitin selected by phage display to bind to the USP15 N-terminus
由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pHH0103
詳細 (発現宿主): expressed as a fusion with an N-terminal 6His affinity TAG, GST and TEV cleavage site
発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21

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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: 2.75 Å3/Da / 溶媒含有率: 55.24 % / 解説: small 'teardrop' shape
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5
詳細: 16% PEG6K, 100 mM Sodium Citrate, pH 5.0, 100 mM MgCl2, cryoprotected in 20% PEG6K, 100 mM Sodium Citrate, pH 5.0, 100 mM MgCl2, 30% ethylene glycol
Temp details: room temperature

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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: APS / ビームライン: 24-ID-E / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2017年10月23日 / 詳細: mirrors
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: 0.97918 Å / 相対比: 1
反射解像度: 2.93→90.935 Å / Num. obs: 69830 / % possible obs: 100 % / 冗長度: 5.3 % / Biso Wilson estimate: 90.34 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.049 / Rrim(I) all: 0.113 / Net I/σ(I): 8.8
反射 シェル解像度: 2.93→3.09 Å / 冗長度: 5.4 % / Rmerge(I) obs: 1.463 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 10150 / Rpim(I) all: 0.694 / Rrim(I) all: 1.621 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.13_2998: ???)精密化
MOSFLMデータ削減
SCALA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: PDB 4A3O

4a3o


解像度: 3.1→90.935 Å / SU ML: 0 / 交差検証法: FREE R-VALUE / σ(F): 269.39 / 位相誤差: 31.61
詳細: In the collection statistics there were 69830 unique reflections, versus 30123 reflections in refinement. This is because data was processed (Scala) as P3, but Phaser identified the optimal ...詳細: In the collection statistics there were 69830 unique reflections, versus 30123 reflections in refinement. This is because data was processed (Scala) as P3, but Phaser identified the optimal solution in P63, which was what the structure was refined as.
Rfactor反射数%反射
Rfree0.2672 2200 7.3 %
Rwork0.2533 --
obs0.2548 30123 99.98 %
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: 3.1→90.935 Å
タンパク質核酸リガンド溶媒全体
原子数9737 0 0 0 9737
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0039972
X-RAY DIFFRACTIONf_angle_d0.6513497
X-RAY DIFFRACTIONf_dihedral_angle_d7.916381
X-RAY DIFFRACTIONf_chiral_restr0.0441469
X-RAY DIFFRACTIONf_plane_restr0.0051712
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1003-3.16770.37731410.33761738X-RAY DIFFRACTION92
3.1677-3.24130.36011340.33511737X-RAY DIFFRACTION93
3.2413-3.32240.28341360.31691729X-RAY DIFFRACTION93
3.3224-3.41210.30191380.32331742X-RAY DIFFRACTION93
3.4121-3.51250.34131350.30991723X-RAY DIFFRACTION93
3.5125-3.62580.31081370.30091736X-RAY DIFFRACTION93
3.6258-3.75520.33521370.30471736X-RAY DIFFRACTION93
3.7552-3.90540.31591360.28081744X-RAY DIFFRACTION93
3.9054-4.0830.25761370.26111732X-RAY DIFFRACTION93
4.083-4.2980.27221380.25641744X-RAY DIFFRACTION93
4.298-4.56690.22351370.22151748X-RAY DIFFRACTION93
4.5669-4.91880.21121370.22551740X-RAY DIFFRACTION93
4.9188-5.41250.26131380.22911751X-RAY DIFFRACTION93
5.4125-6.19280.26491370.25011742X-RAY DIFFRACTION93
6.1928-7.79140.24171390.23751761X-RAY DIFFRACTION93
7.7914-38.10540.24481420.21631798X-RAY DIFFRACTION93
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)
16.9540.19821.4844.4014-0.96082.4282-0.2601-0.75571.05630.2612-0.3180.9975-0.61820.32930.58670.9308-0.0275-0.15821.4624-0.48651.889644.6947129.0994-6.0548
28.31972.4424-0.32082.3618-1.6415.11150.0599-1.8984-0.1503-0.1383-0.6365-1.01910.26221.12210.56350.62990.1435-0.17540.860.07941.142450.2001137.4801-14.28
38.5464-2.3949-2.613.89783.14539.4772-0.20270.8052-0.8268-0.4774-0.8428-1.53650.7522.10920.9720.88840.18910.37080.9440.27551.19462.0106129.3161-26.6515
47.58070.33990.69475.7591.81668.29-0.13140.4915-0.3327-1.6094-1.40510.11440.12640.36031.0070.84230.13060.14460.57920.14830.669442.62133.7268-22.3745
56.1154-0.35840.5326.44961.71517.2946-1.0382-1.30370.02010.17850.9248-0.4667-0.8868-0.47930.21870.79920.1293-0.20130.8543-0.04280.763237.5862140.6928-15.5842
60.5029-0.7899-0.77622.29361.39661.2636-0.29730.2853-0.6044-0.78290.44680.1170.28770.41920.14172.4033-0.30390.7540.7694-0.10550.468737.5315124.1048-32.376
73.9962-0.48520.14840.4944-0.8122.5619-0.17180.7609-1.5423-0.0348-0.28340.44260.2629-0.0815-0.161.25570.24080.49920.6402-0.62071.96243.5548129.7685-36.8203
82.49720.2371-0.14450.3103-0.67052.07290.0097-0.2574-1.3425-0.71470.29980.1798-0.40560.1891-0.0631.63950.24510.30430.60670.03941.130748.2989129.8755-23.2515
98.8719-2.1405-1.54370.73640.08584.299-0.65540.0662-2.15740.1925-0.2984-0.78731.3565-0.27720.8241.37650.04120.27190.42780.07521.22347.3565124.7327-25.8434
104.6142-2.0078-2.82373.84930.69131.8348-1.3726-0.1193-1.7168-0.8817-0.477-2.38351.06940.50211.52031.19120.0140.19581.04130.53471.283381.9331142.6494-46.6862
116.13893.44643.79833.04853.10433.2331-0.3859-0.8753-0.24341.16480.03490.52010.74-1.77520.37080.77810.00090.10341.0190.12440.959517.6728108.0443-10.5452
122.23541.56363.36751.37982.13296.4660.8626-0.91230.55850.3322-0.36950.2450.8634-1.1835-0.26731.1517-0.1958-0.02480.95720.0041.18656.475598.8063-22.9892
132.29010.8963.02540.72140.57774.5396-0.0221-0.22161.3356-0.2782-0.34480.25180.0575-0.48690.47880.54440.00530.06231.2502-0.12691.069120.5457112.979-19.4548
143.35330.80673.01940.50231.26313.9228-0.39830.40530.7151-0.20790.25470.564-0.30560.14590.820.89380.16450.03070.9352-0.05730.766529.358118.5379-12.3523
151.61680.2508-1.94645.86211.04622.7933-1.11160.16311.4513-1.21710.42330.272-0.927-1.24260.370.91550.2358-0.45931.04850.2741.443414.5869117.2682-28.7946
165.6645-2.60124.03856.7883-2.64884.3206-0.3034-1.78160.95380.80191.06281.6342-0.6923-1.3093-0.36060.54750.07950.20691.1757-0.21731.17359.9469114.3901-17.976
170.31390.1632-0.35490.0845-0.22320.5612-0.30170.05490.71160.0274-0.10850.47850.0576-0.55630.12810.6981-0.1526-0.14641.17270.10021.27414.554102.2283-32.1495
182.4256-2.2261-1.05323.12212.4412.4182-0.5219-0.4711-0.67850.1417-0.10410.82670.52480.97160.62461.14680.16570.17641.1478-0.09521.03367.823670.2128-45.0203
193.6977-0.2873-0.82688.0958-6.44977.8557-0.17410.1228-1.0026-0.11310.5350.9171-0.4683-0.2752-0.1520.61620.0399-0.0260.7274-0.17631.31977.1502155.9372-15.4032
206.26830.5372-2.91180.1538-0.94138.4121-0.7029-0.1275-1.2490.3083-0.5488-1.01150.0317-0.37151.30580.7175-0.2615-0.05381.30260.25290.958913.5746147.794-20.785
213.1011.844-1.09122.6767-0.69262.24110.16990.01461.22350.81040.03150.27780.41121.2805-0.03940.56220.13550.22051.2169-0.01271.280511.2079138.8748-14.7136
226.6656.7004-4.83788.27-2.14158.4233-0.2445-0.8219-2.35210.0923-1.69891.1044-0.66613.56071.89280.8824-0.18850.30761.6455-0.30561.694923.5867150.4171-31.8814
236.0362-1.41473.03765.1430.07151.6602-0.19940.3882-0.0371-3.42010.1904-1.955-1.14491.8846-0.17311.2772-0.21830.54560.8966-0.07541.214612.906150.6984-34.944
244.1785-2.522-4.01375.1579-2.33089.9170.7578-0.5731.06561.43340.4091-0.2235-0.6487-0.0533-1.04770.8447-0.2440.08120.6602-0.10851.198114.9604155.5502-17.8385
251.9758-1.47850.61733.2153-2.39551.69650.5462-0.58320.3866-0.1885-0.6638-0.3539-0.62310.8147-0.13560.7372-0.2088-0.02321.28140.19131.1118.5981157.5691-25.5633
266.12175.57740.69856.6013-1.01067.1853-0.44920.4740.6687-1.40591.9522.6062-0.7791-1.3158-1.19060.9914-0.02610.07351.24710.79631.9998-6.4986171.8742-43.8159
271.1143-0.2183-0.56830.30730.21280.61580.18970.2716-0.02750.25670.2828-0.42140.25930.7018-0.30411.3955-0.245-0.34662.708-1.97222.0821-22.1371179.0322-45.2562
284.61686.056.15149.31497.80658.2311-0.69180.1718-0.5217-0.127-0.4225-0.2996-0.56350.87361.06790.98560.1760.13980.90570.39831.092450.8771126.621-71.4052
293.58582.51963.14111.8382.35116.303-1.02140.370.7304-0.1716-0.05280.491-0.4218-0.53131.09470.92890.1231-0.04660.7958-0.08541.08546.7723126.8729-62.7705
301.60711.84920.00743.02231.60212.9725-0.01310.58240.95780.3052-0.0657-0.2509-1.1246-1.4902-0.28592.20141.21521.38280.9004-0.07672.102534.7882131.719-66.5434
319.70131.83121.23741.8131.22789.89430.4170.10711.49320.9866-0.9074-0.1135-1.67490.13290.75161.29890.10640.10760.5880.23581.237548.327133.896-55.3531
322.232-0.0377-2.20044.7551.37022.5270.33510.49351.40240.0885-1.0832-0.2381-1.2596-0.05130.79971.1308-0.3055-0.35071.02770.31141.119550.8231138.3587-58.4278
338.4931-4.87690.16796.6735-1.35466.2076-0.3981-1.6599-0.28560.66880.403-0.30970.51360.34740.05750.7976-0.0741-0.04490.6050.1560.737184.3354119.1174-37.1746
344.14184.07490.74219.2621-0.12576.462-3.01721.07260.54-1.23641.40340.37460.7821-0.12611.57351.3141-0.18270.24150.6629-0.13861.462318.5126154.2135-72.1828
357.19731.0729-7.23181.9977-0.60267.44692.1273-2.26490.80190.5405-1.0411-1.0132-0.5160.1446-1.19280.8109-0.10450.10531.6825-0.16191.90858.8623162.0924-58.4837
364.24430.9642-1.7154.7308-1.68412.23730.06151.1614-0.7410.7507-1.3062-0.8273-0.39770.23921.11390.8373-0.2884-0.27932.1911-0.16451.238119.0648147.7381-59.5812
370.9666-1.527-1.23122.55311.56234.157-0.48450.14141.1391-0.1683-0.25290.4804-0.12290.7140.44260.7849-0.179-0.07981.41650.13451.257929.6253149.1665-67.7714
385.9663-1.9226-2.80511.60740.60921.4628-0.8510.74150.34460.67570.35231.3360.3540.22280.3590.5849-0.0784-0.01850.92540.40062.579617.8764140.206-59.9565
391.6067-1.05041.00543.06121.39692.3915-1.1238-0.558-0.02220.29770.12810.45131.2328-0.73910.8832.0625-0.31931.60881.4065-1.42912.974412.1676141.4568-44.6576
409.77-6.34825.3728.1936-2.01373.50480.94381.1408-1.9015-0.6685-0.32331.2764-0.73150.9461-0.56780.7471-0.0318-0.20021.4512-0.10930.648619.7481150.646-48.2903
412.89660.377-2.47715.55650.25455.9208-0.28630.4401-0.5446-0.1735-0.08582.40440.364-0.8190.32760.7301-0.0474-0.04491.6536-0.52171.490410.7707151.3114-60.8053
421.6529-0.0623-2.05713.6257-1.18842.9817-1.27390.9487-0.958-1.3794-0.50442.00132.6017-1.32741.26312.4499-0.7030.00021.6547-0.38741.308710.4607140.5647-63.0503
430.50090.28181.57435.5417-0.20324.9593-0.75161.1878-0.66161.0762-0.6163-0.5724-0.02220.13581.30581.00170.1053-0.11711.13-0.51921.91114.601155.0998-49.1649
445.4222-0.5931.06470.9682-2.08474.49140.221-0.0046-1.91610.9405-0.60982.23170.4739-1.17660.73720.9613-0.30190.72341.2829-0.52991.76317.2064177.2578-36.131
456.82392.10451.7135.88796.11796.4593-0.02290.40870.3149-0.2143-0.93712.0065-0.3435-0.86861.47010.9652-0.0654-0.18351.2782-0.1990.81266.0864193.1945-34.7841
460.062-0.11030.33549.17480.79976.4402-0.31920.33550.4521-0.60760.11711.27690.37810.8003-0.13540.55070.1260.04510.9030.11211.45111.7289113.8204-72.1542
470.5675-0.33240.68493.9215-0.56661.7423-0.0958-0.1450.31531.45180.40261.21721.25950.3986-0.46241.88180.20620.57740.67090.08781.65369.0333102.0216-56.9903
484.7336-2.03890.96552.89540.83456.2569-0.80060.48961.0330.7162-1.1541-0.15430.91760.83311.30610.63870.08530.18870.68740.15651.247415.2417118.8308-59.7471
490.097-0.55160.11353.8143-0.46898.91420.02830.4965-0.0913-0.0717-0.91430.6011-0.6101-0.30910.84540.57580.2275-0.0250.97910.09771.23337.3415126.3394-67.3784
503.1199-1.08432.25014.6471-4.89949.01270.22010.8816-0.55650.3789-1.0072-0.2079-0.83682.44570.66920.3245-0.1470.00330.97550.00432.259723.5888121.6165-57.2709
515.5771-3.8945-4.16142.82313.10173.51810.3644-0.6353-0.4520.819-1.5622-2.73080.06211.45260.83010.7899-0.1049-0.14221.00880.66391.697816.8725116.1086-45.3193
523.20422.1127-1.00331.5972-0.12612.44840.83180.6021-0.8785-1.0489-0.2628-1.936-0.60750.3758-0.19531.00060.29610.65261.13390.34861.61417.3553110.7411-62.4421
538.76685.39231.14573.36161.11694.0518-1.05782.40611.50490.5819-0.6365-0.5793-0.12430.23391.43720.8142-0.3214-0.33011.15580.4451.828628.1752112.9417-58.0949
546.9224.1563-5.90462.5679-3.64965.0845-1.14660.3832-0.3993-1.1480.49720.3760.2158-0.48180.50941.5844-0.119-0.11080.6240.08281.36398.448698.2976-43.7075
559.8377-1.2737-3.10352.2289-2.07814.2621-0.6226-0.3279-1.2090.50150.0696-0.2442-0.63-0.19070.37391.12890.10790.17281.1986-0.06130.9212-16.131386.3473-34.4318
564.71192.13241.2844.14493.63358.524-0.12390.008-1.11070.99781.01780.9583-0.82561.3182-0.90410.91650.4012-0.10211.03390.12180.796837.154112.55340.537
571.906-2.1191.00855.50232.94566.1049-0.34352.9965-0.3781-2.0494-1.4194-1.0387-0.32170.21010.14662.0940.40011.34792.0043-0.09381.177441.6418107.7939-27.1133
584.61640.67751.29813.0445-3.83565.8530.71090.97-0.3562-0.3393-1.0726-1.52320.3211.97390.60170.6703-0.07120.22621.79070.07851.260746.4925102.746-20.1615
590.1063-0.97180.17638.8764-1.61160.29130.3168-0.58780.7168-2.632-0.9034-0.38430.47092.41010.58721.5612-0.14560.16051.2667-0.07821.126944.038992.3032-22.4025
603.8557-1.2265-0.12824.0323-2.72852.12431.2431-1.15641.6665-0.8639-1.58111.08141.2635-1.74570.36071.6403-0.0808-0.20810.9051-0.59331.340934.673798.3479-27.8577
610.78632.1455-1.01637.069-1.44783.0941.75981.8155-0.2748-0.2867-1.50170.409-0.7990.68010.0230.74580.18670.09821.1712-0.23760.835543.361102.5108-14.4043
625.1276-0.57243.83477.4508-0.56628.64270.3653-0.7376-0.46121.22622.1038-1.36380.5296-0.3375-2.38920.82120.12260.13450.6245-0.14281.122840.1755109.1911-60.8812
639.12990.29770.36196.31651.14040.21280.30640.9085-0.9216-2.1181-1.02991.2026-0.18130.37780.75761.27380.2265-0.04370.9551-0.31170.710134.353107.2036-83.4291
642.044-1.1827-3.34783.4192.66125.67110.57271.37710.665-1.303-0.9770.4511-0.36980.01420.23552.040.3168-1.69692.77921.7462.746333.0342120.0953-96.3031
652.9306-2.622-0.76345.9545-4.01016.397-1.03140.6646-0.34-0.38430.49221.4926-0.5115-2.74430.03781.0150.2905-0.24122.3204-0.03740.719725.9243114.9626-86.3782
662.8547-3.16693.27955.9092-3.93594.1741-0.2191.4573-0.50950.93640.82241.0828-0.9695-1.9344-0.27330.98010.521-0.02362.0910.15180.702429.1667120.0522-79.3829
673.69381.2223-0.73724.21642.89967.2062-0.22820.2161-0.0162-2.45620.4120.3073-1.2987-0.1288-0.05531.6105-0.03980.10460.85170.24021.189637.0373125.582-85.2298
686.4089-0.6409-3.68063.09464.5497.90890.124-0.3905-0.21750.09550.601-0.5701-0.3382.0326-0.7911.01840.06090.06911.26880.33721.117242.2714120.0893-90.0543
691.31591.8022-0.57874.82070.12072.07670.59440.30650.48480.3119-0.18320.23430.24520.3136-0.21910.757-0.29470.20882.5593-0.02350.837330.0247120.0885-75.0137
706.70071.46712.33658.6901-1.09796.92490.4181-2.32820.49650.4745-0.72871.08581.80490.70550.33370.44090.02720.15621.31760.18080.9981.8133131.55220.2564
712.6169-0.95331.7419.96180.01621.7565-0.28671.4617-0.082-1.35950.3994-0.80261.0291-0.7524-0.12790.9592-0.23670.2211.373-0.06881.283-5.85130.5036-27.3248
725.9962-2.36944.49485.04670.63035.8250.2346-0.0243-1.6121-0.6880.45740.85172.3176-1.294-0.50641.4415-0.6657-0.03511.4373-0.07560.863-11.6564125.5274-20.7359
735.2051-4.07783.57137.2018-6.31096.68870.0711.33451.4109-0.2466-0.3347-1.1239-1.030.43960.18520.9972-0.0145-0.07830.96790.05431.0341-11.6602139.6686-23.7942
745.2658-5.27272.71649.62831.1474.81620.06530.07220.12080.60120.59181.27031.5523-0.9083-0.42720.9882-0.21590.17430.74230.03560.8568-12.8881129.7072-12.0894
752.96151.5632-1.07117.1071-3.35852.0959-0.43520.1053-0.65920.6646-0.013-0.03030.64430.38860.39820.810.21680.23710.89320.0410.96023.1539129.2061-1.59
761.32470.1211-0.15471.94330.06770.48471.0147-0.2035-1.3093-0.30860.61270.35240.2160.96970.1244-0.0031.9902-1.1691-0.25881.52562.649411.1556131.6104-1.9702
779.0290.4009-2.23620.2166-0.29884.66910.96240.1321-0.68450.4402-1.16180.1848-0.59920.72820.19621.303-0.0660.00320.77990.02610.940910.6449138.89297.9231
783.9367-1.79490.30263.45023.32275.5489-1.0624-0.1164-0.71980.0160.54860.8663-0.01260.94710.51930.6932-0.05710.04210.6996-0.11870.946410.2191130.7014-5.4846
796.91062.5792-3.0626.45262.56475.09680.0018-0.8430.28690.6975-0.06280.7503-0.5769-0.77430.14740.51080.09760.03390.8681-0.06280.650734.1814152.2493-2.4133
802.85120.7904-1.88023.4991-2.80193.36060.9053-1.80061.58950.7930.71870.25240.48870.6975-0.30670.54070.19420.51642.0795-0.01821.772232.5225141.8175-0.2837
817.0846-0.01935.8651.18920.44844.9873-0.13850.3037-0.48550.50630.28410.35650.77491.2004-0.11870.85470.02-0.00141.514-0.15240.572937.0601144.27981.2553
824.59562.340.0138.30323.97832.21710.5608-0.58310.1977-1.995-0.4837-0.4420.0302-0.667-0.15561.10420.2224-0.1920.6315-0.23851.043239.0986108.9839-19.7856
836.4869-1.7702-2.91833.725-1.35686.0606-0.153-2.01180.25751.3908-0.0934-0.1754-1.62051.16740.17411.2612-0.2978-0.12671.1013-0.16690.795237.8158117.71857.267
841.9948-0.12320.98981.51211.36542.29160.864-0.9691.17680.5704-0.7547-0.972-1.46641.00640.27131.1618-0.5192-0.57690.9994-0.18212.160936.8571122.6828-2.1665
852.16053.94393.31618.43143.76049.3317-0.31341.0506-1.46691.3238-1.06160.1215-0.8059-2.56280.86981.5544-0.40480.32891.3408-0.58771.213124.671119.55492.6003
867.31723.2546-0.19338.9614-5.96724.5961-0.3743-1.0834-0.33040.4965-0.107-1.1605-0.1458-0.97920.52550.9695-0.14690.1270.951-0.09030.808128.0444111.47088.453
870.9014-0.3081.57358.9571-1.59355.0726-0.13150.325-0.3698-0.5897-0.1878-0.616-0.40340.24460.30240.83910.02360.1271.1551-0.30080.955633.5984121.6772-7.3392
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 21 )
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 28 )
4X-RAY DIFFRACTION4chain 'A' and (resid 29 through 45 )
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 65 )
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 75 )
7X-RAY DIFFRACTION7chain 'A' and (resid 77 through 86 )
8X-RAY DIFFRACTION8chain 'A' and (resid 87 through 101 )
9X-RAY DIFFRACTION9chain 'A' and (resid 102 through 121 )
10X-RAY DIFFRACTION10chain 'A' and (resid 122 through 134 )
11X-RAY DIFFRACTION11chain 'B' and (resid 6 through 20 )
12X-RAY DIFFRACTION12chain 'B' and (resid 21 through 29 )
13X-RAY DIFFRACTION13chain 'B' and (resid 30 through 51 )
14X-RAY DIFFRACTION14chain 'B' and (resid 52 through 59 )
15X-RAY DIFFRACTION15chain 'B' and (resid 60 through 88 )
16X-RAY DIFFRACTION16chain 'B' and (resid 89 through 109 )
17X-RAY DIFFRACTION17chain 'B' and (resid 110 through 124 )
18X-RAY DIFFRACTION18chain 'B' and (resid 125 through 133 )
19X-RAY DIFFRACTION19chain 'C' and (resid 7 through 28 )
20X-RAY DIFFRACTION20chain 'C' and (resid 29 through 45 )
21X-RAY DIFFRACTION21chain 'C' and (resid 46 through 65 )
22X-RAY DIFFRACTION22chain 'C' and (resid 66 through 78 )
23X-RAY DIFFRACTION23chain 'C' and (resid 79 through 88 )
24X-RAY DIFFRACTION24chain 'C' and (resid 89 through 103 )
25X-RAY DIFFRACTION25chain 'C' and (resid 104 through 121 )
26X-RAY DIFFRACTION26chain 'C' and (resid 122 through 126 )
27X-RAY DIFFRACTION27chain 'C' and (resid 127 through 132 )
28X-RAY DIFFRACTION28chain 'D' and (resid 6 through 21 )
29X-RAY DIFFRACTION29chain 'D' and (resid 22 through 57 )
30X-RAY DIFFRACTION30chain 'D' and (resid 58 through 65 )
31X-RAY DIFFRACTION31chain 'D' and (resid 66 through 101 )
32X-RAY DIFFRACTION32chain 'D' and (resid 102 through 121 )
33X-RAY DIFFRACTION33chain 'D' and (resid 122 through 134 )
34X-RAY DIFFRACTION34chain 'E' and (resid 6 through 16 )
35X-RAY DIFFRACTION35chain 'E' and (resid 17 through 29 )
36X-RAY DIFFRACTION36chain 'E' and (resid 30 through 44 )
37X-RAY DIFFRACTION37chain 'E' and (resid 45 through 59 )
38X-RAY DIFFRACTION38chain 'E' and (resid 60 through 69 )
39X-RAY DIFFRACTION39chain 'E' and (resid 70 through 82 )
40X-RAY DIFFRACTION40chain 'E' and (resid 83 through 88 )
41X-RAY DIFFRACTION41chain 'E' and (resid 89 through 101 )
42X-RAY DIFFRACTION42chain 'E' and (resid 102 through 111 )
43X-RAY DIFFRACTION43chain 'E' and (resid 112 through 121 )
44X-RAY DIFFRACTION44chain 'E' and (resid 122 through 126 )
45X-RAY DIFFRACTION45chain 'E' and (resid 127 through 134 )
46X-RAY DIFFRACTION46chain 'F' and (resid 2 through 18 )
47X-RAY DIFFRACTION47chain 'F' and (resid 19 through 29 )
48X-RAY DIFFRACTION48chain 'F' and (resid 30 through 45 )
49X-RAY DIFFRACTION49chain 'F' and (resid 46 through 57 )
50X-RAY DIFFRACTION50chain 'F' and (resid 58 through 76 )
51X-RAY DIFFRACTION51chain 'F' and (resid 77 through 88 )
52X-RAY DIFFRACTION52chain 'F' and (resid 89 through 104 )
53X-RAY DIFFRACTION53chain 'F' and (resid 105 through 114 )
54X-RAY DIFFRACTION54chain 'F' and (resid 115 through 124 )
55X-RAY DIFFRACTION55chain 'F' and (resid 125 through 134 )
56X-RAY DIFFRACTION56chain 'G' and (resid 0 through 11 )
57X-RAY DIFFRACTION57chain 'G' and (resid 12 through 24 )
58X-RAY DIFFRACTION58chain 'G' and (resid 25 through 51 )
59X-RAY DIFFRACTION59chain 'G' and (resid 52 through 56 )
60X-RAY DIFFRACTION60chain 'G' and (resid 57 through 66 )
61X-RAY DIFFRACTION61chain 'G' and (resid 67 through 76 )
62X-RAY DIFFRACTION62chain 'H' and (resid 0 through 9 )
63X-RAY DIFFRACTION63chain 'H' and (resid 10 through 19 )
64X-RAY DIFFRACTION64chain 'H' and (resid 20 through 24 )
65X-RAY DIFFRACTION65chain 'H' and (resid 25 through 39 )
66X-RAY DIFFRACTION66chain 'H' and (resid 40 through 46 )
67X-RAY DIFFRACTION67chain 'H' and (resid 47 through 58 )
68X-RAY DIFFRACTION68chain 'H' and (resid 59 through 69 )
69X-RAY DIFFRACTION69chain 'H' and (resid 70 through 77 )
70X-RAY DIFFRACTION70chain 'I' and (resid 0 through 11 )
71X-RAY DIFFRACTION71chain 'I' and (resid 12 through 24 )
72X-RAY DIFFRACTION72chain 'I' and (resid 25 through 46 )
73X-RAY DIFFRACTION73chain 'I' and (resid 47 through 69 )
74X-RAY DIFFRACTION74chain 'I' and (resid 70 through 77 )
75X-RAY DIFFRACTION75chain 'J' and (resid 1 through 36 )
76X-RAY DIFFRACTION76chain 'J' and (resid 37 through 51 )
77X-RAY DIFFRACTION77chain 'J' and (resid 52 through 66 )
78X-RAY DIFFRACTION78chain 'J' and (resid 67 through 77 )
79X-RAY DIFFRACTION79chain 'K' and (resid 0 through 36 )
80X-RAY DIFFRACTION80chain 'K' and (resid 37 through 57 )
81X-RAY DIFFRACTION81chain 'K' and (resid 58 through 76 )
82X-RAY DIFFRACTION82chain 'L' and (resid 0 through 11 )
83X-RAY DIFFRACTION83chain 'L' and (resid 12 through 35 )
84X-RAY DIFFRACTION84chain 'L' and (resid 36 through 46 )
85X-RAY DIFFRACTION85chain 'L' and (resid 47 through 57 )
86X-RAY DIFFRACTION86chain 'L' and (resid 58 through 69 )
87X-RAY DIFFRACTION87chain 'L' and (resid 70 through 77 )

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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

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