[日本語] English
万見
- PDB-4riq: Crystal structure of DPY-30 dimerization/docking domain in comple... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 4riq
タイトルCrystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI)
要素
  • Protein dpy-30 homolog
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
キーワードTransferase/Protein Binding / histone / chromatin / methylation / dimerization/docking module / allosteric regulator / Ash2L / WDR5 / RbBP5 / MLL1 / MLL2 / MLL3 / MLL4 / SET1A / SET1B / Transferase-Protein Binding complex
機能・相同性
機能・相同性情報


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / hemopoiesis / MLL1 complex / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / hemopoiesis / MLL1 complex / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / trans-Golgi network / PKMTs methylate histone lysines / beta-catenin binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / transcription cis-regulatory region binding / DNA damage response / positive regulation of cell population proliferation / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding
類似検索 - 分子機能
: / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / : / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / cAMP-dependent Protein Kinase, Chain A / Histone methyltransferase complex subunit ASH2 ...: / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / : / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / cAMP-dependent Protein Kinase, Chain A / Histone methyltransferase complex subunit ASH2 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily / Up-down Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Protein dpy-30 homolog / Set1/Ash2 histone methyltransferase complex subunit ASH2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 分子置換 / 解像度: 2.231 Å
データ登録者Tremblay, V. / Couture, J.-F.
引用ジャーナル: Structure / 年: 2014
タイトル: Molecular Basis for DPY-30 Association to COMPASS-like and NURF Complexes.
著者: Tremblay, V. / Zhang, P. / Chaturvedi, C.P. / Thornton, J. / Brunzelle, J.S. / Skiniotis, G. / Shilatifard, A. / Brand, M. / Couture, J.F.
履歴
登録2014年10月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年12月17日Provider: repository / タイプ: Initial release
改定 1.12024年2月28日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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

-
集合体

登録構造単位
A: Protein dpy-30 homolog
B: Protein dpy-30 homolog
C: Set1/Ash2 histone methyltransferase complex subunit ASH2
D: Protein dpy-30 homolog
E: Protein dpy-30 homolog
F: Set1/Ash2 histone methyltransferase complex subunit ASH2
G: Protein dpy-30 homolog
H: Protein dpy-30 homolog
I: Set1/Ash2 histone methyltransferase complex subunit ASH2
J: Protein dpy-30 homolog
K: Protein dpy-30 homolog
L: Set1/Ash2 histone methyltransferase complex subunit ASH2
M: Protein dpy-30 homolog
N: Protein dpy-30 homolog
O: Set1/Ash2 histone methyltransferase complex subunit ASH2
P: Protein dpy-30 homolog
Q: Protein dpy-30 homolog
R: Set1/Ash2 histone methyltransferase complex subunit ASH2
S: Protein dpy-30 homolog
T: Protein dpy-30 homolog
U: Set1/Ash2 histone methyltransferase complex subunit ASH2
V: Protein dpy-30 homolog
X: Set1/Ash2 histone methyltransferase complex subunit ASH2
Z: Protein dpy-30 homolog
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,00832
ポリマ－125,23924
非ポリマー7698
水41423
1
D: Protein dpy-30 homolog
E: Protein dpy-30 homolog
F: Set1/Ash2 histone methyltransferase complex subunit ASH2
ヘテロ分子

A: Protein dpy-30 homolog
B: Protein dpy-30 homolog
C: Set1/Ash2 histone methyltransferase complex subunit ASH2
J: Protein dpy-30 homolog
K: Protein dpy-30 homolog
L: Set1/Ash2 histone methyltransferase complex subunit ASH2
V: Protein dpy-30 homolog
X: Set1/Ash2 histone methyltransferase complex subunit ASH2
Z: Protein dpy-30 homolog
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,00416
ポリマ－62,62012
非ポリマー3844
水1267
タイプ名称対称操作数
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area20880 Å2
ΔGint-238 kcal/mol
Surface area21200 Å2
手法PISA
2
G: Protein dpy-30 homolog
H: Protein dpy-30 homolog
I: Set1/Ash2 histone methyltransferase complex subunit ASH2
ヘテロ分子

M: Protein dpy-30 homolog
N: Protein dpy-30 homolog
O: Set1/Ash2 histone methyltransferase complex subunit ASH2
P: Protein dpy-30 homolog
Q: Protein dpy-30 homolog
R: Set1/Ash2 histone methyltransferase complex subunit ASH2
S: Protein dpy-30 homolog
T: Protein dpy-30 homolog
U: Set1/Ash2 histone methyltransferase complex subunit ASH2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,00416
ポリマ－62,62012
非ポリマー3844
水1629
タイプ名称対称操作数
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Buried area20540 Å2
ΔGint-238 kcal/mol
Surface area20960 Å2
手法PISA
単位格子
Length a, b, c (Å)56.270, 56.270, 95.090
Angle α, β, γ (deg.)90.08, 89.90, 115.39
Int Tables number1
Space group name H-MP1

-
要素

#1: タンパク質
Protein dpy-30 homolog / Dpy-30-like protein / Dpy-30L


分子量: 6300.285 Da / 分子数: 16 / 断片: UNP RESIDUES 45-99 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DPY30 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9C005
#2: タンパク質・ペプチド
Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein


分子量: 3054.341 Da / 分子数: 8 / 断片: UNP residues 603-618 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ASH2L, ASH2L1 / プラスミド: parallel vector / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Rosetta / 参照: UniProt: Q9UBL3
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 8 / 由来タイプ: 合成 / 式: SO4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 23 / 由来タイプ: 天然 / 式: H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.17 Å3/Da / 溶媒含有率: 43.37 %
結晶化温度: 323 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5
詳細: 0.2M MgCl2, 25% PEG 3350, 0.1M Tris pH 8.5 and 10 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 323K

-
データ収集

回折平均測定温度: 200 K
放射光源由来: 回転陽極 / タイプ: RIGAKU MICROMAX-007 HF / 波長: 1.5418 Å
検出器タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2013年4月10日
放射モノクロメーター: GRAPHITE / 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: 1.5418 Å / 相対比: 1
反射解像度: 2.231→28.79 Å / Num. obs: 47679 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
反射 シェル解像度: 2.231→2.33 Å / % possible all: 93.5

-
解析

ソフトウェア
名称バージョン分類
StructureStudioデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.4_1496)精密化
d*TREKデータ削減
d*TREKデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 2.231→28.675 Å / SU ML: 0.38 / σ(F): 1.99 / 位相誤差: 39.48 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2839 2414 5.07 %RANDOM
Rwork0.2357 ---
all0.2432 ---
obs0.2382 45135 92.78 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.231→28.675 Å
タンパク質核酸リガンド溶媒全体
原子数7344 0 40 23 7407
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0067596
X-RAY DIFFRACTIONf_angle_d1.11710443
X-RAY DIFFRACTIONf_dihedral_angle_d11.6622678
X-RAY DIFFRACTIONf_chiral_restr0.041300
X-RAY DIFFRACTIONf_plane_restr0.0061317
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.231-2.27680.43231010.38391884X-RAY DIFFRACTION66
2.2768-2.32630.39461420.37292725X-RAY DIFFRACTION93
2.3263-2.38040.39391170.35082640X-RAY DIFFRACTION93
2.3804-2.43990.41421340.35452706X-RAY DIFFRACTION93
2.4399-2.50580.37331410.34942667X-RAY DIFFRACTION93
2.5058-2.57950.39331540.32522662X-RAY DIFFRACTION94
2.5795-2.66270.43571430.35382655X-RAY DIFFRACTION94
2.6627-2.75780.41391490.31242709X-RAY DIFFRACTION94
2.7578-2.86810.31641350.31192722X-RAY DIFFRACTION95
2.8681-2.99850.37931690.31762731X-RAY DIFFRACTION95
2.9985-3.15640.37781530.3012696X-RAY DIFFRACTION95
3.1564-3.35390.31311480.25492735X-RAY DIFFRACTION96
3.3539-3.61240.33151400.22972702X-RAY DIFFRACTION96
3.6124-3.97510.27961200.21352834X-RAY DIFFRACTION96
3.9751-4.54830.23791630.17362705X-RAY DIFFRACTION97
4.5483-5.72290.24131560.18112752X-RAY DIFFRACTION96
5.7229-28.67750.18631490.2012640X-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)
13.59661.8615-1.92114.50283.42628.196-0.75510.18790.8663-1.7840.3511-0.9791-0.31691.18380.18720.81140.00850.09850.65360.05040.65860.83515.4258-85.5625
22.54-0.22880.78492.28871.94155.55830.2671-0.81741.15180.0487-0.0013-0.71-0.94220.5731-0.2370.5806-0.17140.00330.7845-0.23220.94643.078712.7156-66.5822
39.7368-6.2764-2.73589.82031.32850.7888-1.179-0.16241.36460.3249-0.0508-0.2804-0.3579-0.0370.06860.9368-0.2059-0.04280.7969-0.17041.370610.627316.3539-74.6099
44.1149-0.56693.52923.4523-2.61794.4856-1.0050.83590.4820.87950.5659-0.58440.45622.45960.52330.65790.0916-0.07950.926-0.16550.6042-4.37534.1069-57.0038
56.7389-2.02372.25.3805-2.69449.79020.1643-0.3971.0817-0.16870.5356-0.2162-1.6029-0.4058-0.73180.5249-0.05550.08920.3993-0.05830.7749-6.848610.5693-71.2912
64.0955-3.45090.58565.85594.61058.92620.18260.50271.3866-0.8309-0.90540.2037-1.2359-0.43550.58340.83040.0222-0.01910.55560.04751.326-3.758518.3282-76.5879
78.69363.39810.72852.4451-0.54257.43520.2359-0.4346-0.73970.4363-0.36970.31110.80310.50420.22920.53560.0301-0.0120.6676-0.10490.63830.38690.4447-67.7387
86.2597-0.6742-0.97995.21590.29162.04560.3355-0.37650.58290.1191-0.59660.12041.450.26420.05260.6203-0.03850.07310.5808-0.03430.6714-7.9712.077-76.9647
99.95542.50283.56973.1094-1.23313.1193-0.18680.6092-0.46080.1295-0.2198-0.2631-0.4448-0.78720.09420.69990.0589-0.05080.6815-0.08580.8013-13.62522.3447-84.7871
105.55392.58186.14633.76480.17419.5556-0.3819-0.98010.44191.133-0.12350.3610.4917-0.59360.03520.719-0.0839-0.0030.89410.0650.57227.1877-0.092-53.9766
113.6016-1.3110.3682.37941.13777.05150.14870.3782-0.151-0.2912-0.19030.5338-0.6391-1.3498-0.05870.46610.062-0.06290.6869-0.06850.543323.39493.1443-73.9015
123.45415.0711-0.48277.8097-0.69140.08490.45310.3033-0.23030.1215-0.37710.31210.0698-0.1066-0.22110.5490.1796-0.04891.1172-0.13320.776114.83684.4809-69.7436
132.11031.39811.22622.48811.6561.17430.70241.50030.3934-0.8053-0.4212-0.7641-1.8714-0.7218-0.16821.02390.18130.11310.7711-0.02510.641231.98831.5813-89.0133
142.32840.9591-1.22539.30026.20045.57860.27080.33390.5594-0.2061-0.702-0.2599-0.4091-0.40430.43590.45070.0396-0.01240.64770.13380.605132.85833.5607-77.5693
153.67290.69670.81125.2804-2.03859.8561-0.1568-0.42590.8104-0.0251-0.02530.243-0.8885-0.57150.08080.65940.1061-0.11170.6201-0.12870.670727.152411.528-65.68
163.4769-3.6612-3.82473.90953.9274.18940.06480.0425-1.5536-0.1128-0.9280.6114-0.3291-1.4890.42380.6135-0.0101-0.01680.7436-0.01340.631729.2435-6.1164-75.0643
177.7813-0.59772.862.18424.11319.8394-1.18470.421-0.2713-0.49420.35780.9035-0.37010.17760.68160.414-0.0095-0.03410.44850.09260.558536.5198-0.612-66.1774
187.4481-0.7165-4.10172.11962.11643.84770.0896-0.55171.3184-0.07160.2423-0.016-0.83830.0177-0.89690.6413-0.05520.12070.72440.02430.73741.77143.0335-57.4386
197.8208-0.3898-2.16180.5342-0.19591.2398-0.3605-0.0461-0.21041.175-0.5357-0.9957-0.34521.01461.04730.6665-0.0287-0.02680.72860.04970.6924-9.4798-2.319-9.3923
202.6509-0.86571.54151.4817-1.71894.22730.13470.31850.0166-0.6356-0.6412-0.7640.57941.01840.30090.56150.08640.11750.86960.14660.6546-5.224-6.7757-29.4083
219.48612.2938-4.6282.70550.89984.18440.8645-0.91341.58920.5905-1.2965-1.23860.59252.02710.14340.57320.1074-0.00091.50270.27670.77653.1622-5.153-19.6149
221.804-1.69960.71594.04423.27166.52680.6730.9833-0.6311-2.27970.09140.9007-0.8122.427-0.55410.8610.2254-0.07391.1479-0.10670.638-14.9911-2.8893-40.5854
233.3404-0.60632.41764.0369-1.6637.98360.12650.1534-0.0908-0.0531-0.67270.22260.4038-0.09490.5230.46670.0377-0.00110.5508-0.02670.637-16.1591-7.1657-27.8867
242.9065-1.8151-1.61876.22890.50091.9959-0.4576-0.4123-0.9510.35420.0060.35621.61191.42890.40730.70750.09420.13010.69510.11770.639-9.8687-14.3459-18.0559
252.3745-1.53051.74854.2353-5.03186.0835-0.5715-0.21051.1382-0.5668-0.355-1.07070.29410.7641.04260.71750.10740.02230.75240.05680.6628-12.60943.7824-27.3648
266.7524-0.5982-0.95434.4254-0.00691.1846-0.56610.48980.2182-0.07120.7238-0.16060.6382-0.4328-0.2370.5616-0.065-0.0350.6349-0.04520.6244-20.1337-1.8419-18.2766
273.6061-0.7202-2.96243.53130.74482.4325-0.2224-1.1505-0.4080.40661.8858-1.08170.9366-0.3925-1.44480.67630.0084-0.1230.67320.09070.7473-25.1398-5.7351-9.2496
286.9492-0.59031.59566.90771.86119.21160.05150.30841.0558-0.62330.1678-1.16890.49890.7047-0.25250.53610.09630.18410.61820.02590.69415.3841-8.7735-84.2866
291.99732.43053.88736.72692.63278.72930.17481.53880.9046-0.03340.1901-0.02640.2357-0.1665-0.04880.6160.03780.03040.60780.01380.5438-10.9848-14.0174-91.1036
304.756-3.1494-0.49474.2611.7363.77960.35090.37160.0029-1.0344-0.60420.5601-0.0471-0.12930.13450.81190.0488-0.10480.5646-0.02770.593-8.3349-20.8788-92.0114
319.3274-4.5967-1.5318.4796-2.14376.45380.4105-0.64840.0550.5481-0.8380.2436-0.0479-0.41910.42730.6118-0.08120.02070.556-0.05140.5217-19.6119-15.7845-83.0315
326.78261.1987-0.54445.57021.18237.35780.2529-0.1717-0.95370.4787-0.1481-0.50450.6981.12010.02660.58450.1006-0.07880.57540.00190.53441.1266-17.2364-79.0799
335.57132.7916-1.78632.4409-2.56516.36270.61980.13550.14790.2661-0.1550.49950.90320.6617-0.54530.92960.14490.05550.5370.00950.4288-2.29-24.1684-82.7482
343.5648-3.3305-4.3683.18044.19245.44510.45680.5584-0.5521-0.8704-0.64120.97581.5218-0.92010.52110.7960.0538-0.02280.6783-0.00120.6268-12.6035-6.7465-85.6371
359.5249-3.86186.50993.4931-2.62944.57490.3911-0.91240.6556-0.0614-0.4129-0.41610.9189-0.76930.46820.5831-0.113-0.08850.67740.040.5702-4.3956-8.1527-75.0302
364.36671.7835-2.8947.0123-5.14294.42941.0566-1.00581.3463-0.8887-0.5924-0.73710.99783.1232-0.82810.7380.12190.02680.9774-0.00130.68593.6715-8.0662-66.6313
377.99672.38541.69172.70630.28428.244-0.36280.3342-1.2763-1.9986-0.0840.3176-0.5719-0.64540.54240.87760.0162-0.10340.6311-0.09510.696315.1668-8.246-38.3393
385.2289-0.76861.70513.3376-2.14463.45540.3158-1.376-1.3755-0.1690.4190.36161.0139-0.8446-0.76950.5272-0.0453-0.00330.74730.20670.910313.9189-13.3584-18.0541
394.7637-0.0080.29692.72561.00420.35-0.73680.0622-0.85590.21740.48020.6714-0.65950.06260.38260.8978-0.162-0.11940.63260.26621.04359.536-19.0825-23.4409
406.3021-0.7831-1.29656.95094.0753.905-1.3447-0.685-2.01340.48031.9581.5475-0.2452-1.0601-0.50150.59690.03220.11230.91080.18290.934920.4364-8.6956-7.1405
414.1737-2.7205-0.00752.4288-0.53414.35280.1685-0.0715-1.1883-0.3510.03460.25891.08960.3931-0.10780.6745-0.0117-0.03320.45410.07020.877420.9739-15.2398-26.6451
426.6026-2.5065-0.00042.01574.2831.98640.33660.35540.4311-0.82761.081-0.10252.15651.6202-0.78461.01360.0627-0.02110.55420.4292.016927.146-22.2641-22.0702
439.90677.0428-1.24058.0189-0.32076.70210.0082-0.57911.08690.4175-0.32920.9529-0.0285-0.07190.29060.60560.0351-0.07780.77680.08530.699114.2909-2.0807-18.4868
446.3457-2.8825-4.27763.58021.7652.91-0.0252-0.1379-1.4961-0.1136-0.14660.7591-1.260.08390.40940.52270.00930.02130.55240.07680.659623.2257-4.3198-27.3904
452.0697-2.2514-2.23999.08332.84153.0697-0.78890.38670.2131-0.52480.1051-0.20730.0503-0.39050.75390.64920.1055-0.11140.81880.00360.651230.2961-4.6533-37.178
462.42184.0019-2.54837.5014-2.81714.31760.977-0.2355-0.44450.9221-0.4142-1.1875-0.12330.8168-0.66650.73310.1216-0.10880.8483-0.10420.667241.519111.6422-9.5774
472.4016-1.37431.11939.4971-1.16929.1233-0.6369-1.0960.67641.11540.50410.9918-0.123-1.23640.22810.75170.08760.08690.7792-0.06540.568423.09112.1486-3.0047
485.83971.9604-0.04063.02481.54092.64511.2721-0.4359-0.07990.6735-0.5135-0.12830.60820.4725-0.75371.03970.0958-0.03340.7805-0.04490.570929.532818.55-0.9345
494.77460.14942.17862.54711.47967.5980.2183-0.82190.05740.1841-0.26520.7735-0.9822-0.08840.25570.71860.18070.04590.90580.03720.577917.68668.5347-10.7517
504.9823.2365-0.37844.69630.74426.1777-0.75550.24550.6177-1.14110.6398-0.6739-1.45660.05040.11220.9654-0.07990.09710.5397-0.06380.597535.552218.4542-14.9572
516.3576-3.3856-1.34469.6943-1.52155.7536-0.1718-0.35760.8817-1.12750.2378-0.4157-1.4526-0.6632-0.11471.27220.11660.07160.5791-0.06610.5230.438623.5142-10.9467
522.3701-1.8229-1.93143.17993.16133.330.6182-2.1665-1.0598-0.07131.32870.8837-0.7586-2.1074-2.49380.66790.07730.0661.09310.12040.688527.52791.9872-7.7964
535.4545-2.3845-4.12218.8004-2.37545.40890.59390.5615-0.0584-0.378-0.54530.2483-1.6917-1.67190.18740.77090.070.0610.8489-0.07430.566331.67957.0942-13.9523
545.4467-4.7885-2.4727.19192.37022.1851-0.30120.1792-0.5392-0.9224-0.02920.4024-0.6541-0.23840.28050.91030.014-0.03680.75520.050.730738.782410.4463-23.7753
554.39763.31144.17523.84032.09494.7814-0.9458-0.9519-0.79640.04070.33120.6172-1.0859-0.56640.07460.52820.0617-0.05640.66780.05980.79858.61884.5194-33.3392
566.94350.2208-2.49834.4159-1.43786.24850.08130.0481-0.2837-0.934-0.15820.04740.1031-0.3050.05250.68760.0841-0.04270.5862-0.00450.457421.11159.6407-41.2601
578.2527-2.9658-0.03764.8244-2.04875.50490.12220.61840.3329-0.906-0.1993-0.36720.03770.08250.09970.76270.02820.08840.53570.05820.47624.36318.7145-44.4229
586.2186-0.859-0.51072.0408-3.9738.46560.47990.0471.0374-0.167-1.0942-0.91260.55991.86910.6670.48260.00050.0160.81090.17860.682840.544213.3932-37.1132
592.2689-2.512-0.67524.4266-0.06843.7319-0.1501-0.01530.11610.28840.2193-0.0977-0.23430.1160.08390.6904-0.0379-0.01030.58880.01920.514128.117214.0571-32.3434
604.71612.1607-0.89918.0852-2.09885.5095-0.08430.460.38430.17210.28160.6191-1.0888-0.7738-0.1080.72690.20080.0150.60120.01970.573815.414519.1784-34.2537
612.7362-0.1872.79629.1799-4.89765.2190.0750.33030.5796-0.3262-0.7595-1.089-0.41290.77630.46180.56840.00240.02510.48050.06530.505528.494.4085-37.0345
623.5936-4.00490.74187.82522.27993.030.4759-0.964-0.2992-0.4904-0.64130.3632-1.53670.5086-0.05270.694-0.04380.00680.6999-0.05120.688320.94175.9511-27.1285
634.3159-0.6838-1.78344.91575.23216.04411.4481-0.6486-0.2108-0.5067-1.19481.2071-0.9811-4.3289-0.4760.64080.15720.04771.01540.03030.647412.96555.7157-19.1691
649.0975-0.3583.23955.3653-2.07499.34950.1881-0.70870.37630.2942-0.3230.69880.9509-0.7958-0.02310.72310.02050.09640.59640.01580.599-23.9542-14.6695-56.181
654.24120.83772.99615.66732.2528.5610.1872-0.334-0.77971.43470.3514-1.34171.83781.7041-0.23340.83730.2186-0.15240.98460.04670.6431-2.8177-16.3721-51.0535
664.32511.99241.22622.545-1.08492.07720.41140.10470.28181.01370.09360.4575-0.7267-1.0199-0.69631.0930.08210.05790.75660.13650.5712-14.1551-20.7028-47.3153
675.50592.96655.31772.19663.28195.68120.41140.2278-0.00950.29210.5194-0.10821.240.9071-0.9640.63860.15050.02250.88060.06390.7159-12.2399-5.9439-56.9561
684.09415.2966-0.14349.2941-2.85673.05121.2591-0.21350.1127-0.1549-0.49230.8590.78020.8419-0.85450.5760.0213-0.07360.5895-0.00880.5498-18.1796-11.2053-66.5325
690.9116-0.50630.75691.43370.05712.5060.60950.5721-0.5742-0.46710.23790.24842.0091-2.9265-0.37690.8613-0.3403-0.07370.9335-0.15860.5499-24.1643-14.3116-73.8641
703.97116.6955-4.21041.9955-7.14494.47350.1578-0.0907-0.69982.0635-1.4458-3.2019-0.61590.36820.810.61430.2579-0.17821.2537-0.24860.88714.1784-9.5855-56.9851
714.09972.5790.26577.471-0.78444.0011-0.0148-0.0570.0079-0.26910.17590.11290.93360.5008-0.12030.78340.13120.0250.64020.00110.4693-10.4879-15.8592-61.6394
721.10380.2077-2.53955.45371.60678.6396-0.4045-0.6215-0.5780.26130.1967-0.14592.2961-0.71850.08361.2127-0.0161-0.03480.70190.1480.6692-17.6241-26-57.7288
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 48:59)
2X-RAY DIFFRACTION2(chain A and resid 60:88)
3X-RAY DIFFRACTION3(chain A and resid 89:96)
4X-RAY DIFFRACTION4(chain B and resid 49:55)
5X-RAY DIFFRACTION5(chain B and resid 56:74)
6X-RAY DIFFRACTION6(chain B and resid 75:95)
7X-RAY DIFFRACTION7(chain C and resid 505:515)
8X-RAY DIFFRACTION8(chain C and resid 516:521)
9X-RAY DIFFRACTION9(chain C and resid 522:528)
10X-RAY DIFFRACTION10(chain D and resid 46:55)
11X-RAY DIFFRACTION11(chain D and resid 56:86)
12X-RAY DIFFRACTION12(chain D and resid 87:96)
13X-RAY DIFFRACTION13(chain E and resid 47:52)
14X-RAY DIFFRACTION14(chain E and resid 53:66)
15X-RAY DIFFRACTION15(chain E and resid 67:95)
16X-RAY DIFFRACTION16(chain F and resid 505:513)
17X-RAY DIFFRACTION17(chain F and resid 514:521)
18X-RAY DIFFRACTION18(chain F and resid 522:528)
19X-RAY DIFFRACTION19(chain G and resid 47:61)
20X-RAY DIFFRACTION20(chain G and resid 62:90)
21X-RAY DIFFRACTION21(chain G and resid 91:96)
22X-RAY DIFFRACTION22(chain H and resid 47:53)
23X-RAY DIFFRACTION23(chain H and resid 54:69)
24X-RAY DIFFRACTION24(chain H and resid 70:95)
25X-RAY DIFFRACTION25(chain I and resid 505:513)
26X-RAY DIFFRACTION26(chain I and resid 514:522)
27X-RAY DIFFRACTION27(chain I and resid 523:528)
28X-RAY DIFFRACTION28(chain J and resid 47:64)
29X-RAY DIFFRACTION29(chain J and resid 65:74)
30X-RAY DIFFRACTION30(chain J and resid 75:95)
31X-RAY DIFFRACTION31(chain K and resid 47:61)
32X-RAY DIFFRACTION32(chain K and resid 62:79)
33X-RAY DIFFRACTION33(chain K and resid 80:95)
34X-RAY DIFFRACTION34(chain L and resid 505:513)
35X-RAY DIFFRACTION35(chain L and resid 514:523)
36X-RAY DIFFRACTION36(chain L and resid 524:528)
37X-RAY DIFFRACTION37(chain M and resid 47:60)
38X-RAY DIFFRACTION38(chain M and resid 61:81)
39X-RAY DIFFRACTION39(chain M and resid 82:96)
40X-RAY DIFFRACTION40(chain N and resid 48:53)
41X-RAY DIFFRACTION41(chain N and resid 54:89)
42X-RAY DIFFRACTION42(chain N and resid 90:95)
43X-RAY DIFFRACTION43(chain O and resid 505:511)
44X-RAY DIFFRACTION44(chain O and resid 512:521)
45X-RAY DIFFRACTION45(chain O and resid 522:528)
46X-RAY DIFFRACTION46(chain P and resid 51:64)
47X-RAY DIFFRACTION47(chain P and resid 65:79)
48X-RAY DIFFRACTION48(chain P and resid 80:95)
49X-RAY DIFFRACTION49(chain Q and resid 47:61)
50X-RAY DIFFRACTION50(chain Q and resid 62:78)
51X-RAY DIFFRACTION51(chain Q and resid 79:95)
52X-RAY DIFFRACTION52(chain R and resid 505:511)
53X-RAY DIFFRACTION53(chain R and resid 512:517)
54X-RAY DIFFRACTION54(chain R and resid 518:528)
55X-RAY DIFFRACTION55(chain S and resid 48:54)
56X-RAY DIFFRACTION56(chain S and resid 55:75)
57X-RAY DIFFRACTION57(chain S and resid 76:95)
58X-RAY DIFFRACTION58(chain T and resid 47:53)
59X-RAY DIFFRACTION59(chain T and resid 54:69)
60X-RAY DIFFRACTION60(chain T and resid 70:95)
61X-RAY DIFFRACTION61(chain U and resid 506:514)
62X-RAY DIFFRACTION62(chain U and resid 515:523)
63X-RAY DIFFRACTION63(chain U and resid 524:528)
64X-RAY DIFFRACTION64(chain V and resid 47:69)
65X-RAY DIFFRACTION65(chain V and resid 70:81)
66X-RAY DIFFRACTION66(chain V and resid 82:95)
67X-RAY DIFFRACTION67(chain X and resid 505:515)
68X-RAY DIFFRACTION68(chain X and resid 516:521)
69X-RAY DIFFRACTION69(chain X and resid 522:528)
70X-RAY DIFFRACTION70(chain Z and resid 47:52)
71X-RAY DIFFRACTION71(chain Z and resid 53:74)
72X-RAY DIFFRACTION72(chain Z and resid 75:93)

+
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

-
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

+
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

+
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

+
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。

-
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