[日本語] English
万見
- PDB-5h77: Crystal structure of the PKA-protein A fusion protein -

+
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: 5h77
タイトルCrystal structure of the PKA-protein A fusion protein
要素cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
キーワードSIGNALING PROTEIN / IMMUNE SYSTEM / synthetic protein
機能・相同性
機能・相同性情報


cAMP-dependent protein kinase regulator activity / ROBO receptors bind AKAP5 / nucleotide-activated protein kinase complex / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / IgG binding / CREB1 phosphorylation through the activation of Adenylate Cyclase / cAMP-dependent protein kinase complex / PKA activation / ciliary base ...cAMP-dependent protein kinase regulator activity / ROBO receptors bind AKAP5 / nucleotide-activated protein kinase complex / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / IgG binding / CREB1 phosphorylation through the activation of Adenylate Cyclase / cAMP-dependent protein kinase complex / PKA activation / ciliary base / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / DARPP-32 events / cAMP binding / Hedgehog 'off' state / FCGR3A-mediated IL10 synthesis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / intracellular signal transduction / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / centrosome / protein-containing complex / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / Cyclic nucleotide-binding domain signature 2. / YSIRK type signal peptide / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold
類似検索 - ドメイン・相同性
cAMP-dependent protein kinase type II-alpha regulatory subunit / Immunoglobulin G-binding protein A
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Staphylococcus aureus (黄色ブドウ球菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.197 Å
データ登録者Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Lee, H. / Lee, J.O.
引用ジャーナル: Sci Rep / 年: 2017
タイトル: Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.
著者: Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Choi, J. / Lee, H. / Lee, J.O.
履歴
登録2016年11月17日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02017年6月28日Provider: repository / タイプ: Initial release
改定 1.12023年11月8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

-
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: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
B: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
C: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
D: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
E: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
F: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
G: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
H: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
I: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
J: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
K: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
L: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


分子量 (理論値)分子数
合計 (水以外)123,77412
ポリマ－123,77412
非ポリマー00
水00
1
A: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
B: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


分子量 (理論値)分子数
合計 (水以外)20,6292
ポリマ－20,6292
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-19 kcal/mol
Surface area11050 Å2
手法PISA
2
C: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
D: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


分子量 (理論値)分子数
合計 (水以外)20,6292
ポリマ－20,6292
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-21 kcal/mol
Surface area10970 Å2
手法PISA
3
E: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
F: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


分子量 (理論値)分子数
合計 (水以外)20,6292
ポリマ－20,6292
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-18 kcal/mol
Surface area10830 Å2
手法PISA
4
G: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
H: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


分子量 (理論値)分子数
合計 (水以外)20,6292
ポリマ－20,6292
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-20 kcal/mol
Surface area10780 Å2
手法PISA
5
I: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
J: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


分子量 (理論値)分子数
合計 (水以外)20,6292
ポリマ－20,6292
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-19 kcal/mol
Surface area11180 Å2
手法PISA
6
K: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
L: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


分子量 (理論値)分子数
合計 (水以外)20,6292
ポリマ－20,6292
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-19 kcal/mol
Surface area11210 Å2
手法PISA
単位格子
Length a, b, c (Å)71.588, 135.378, 88.988
Angle α, β, γ (deg.)90.00, 108.77, 90.00
Int Tables number4
Space group name H-MP1211

-
要素

#1: 抗体
cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A


分子量: 10314.522 Da / 分子数: 12 / 断片: UNP RESIDUES 5-41,UNP RESIDUES 220-268 / 変異: G222A, G240A / 由来タイプ: 組換発現
由来: (組換発現) Homo sapiens (ヒト), (組換発現) Staphylococcus aureus (黄色ブドウ球菌)
遺伝子: PRKAR2A, PKR2, PRKAR2, spa / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P13861, UniProt: P38507

-
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: 3.51 Å3/Da / 溶媒含有率: 64.99 %
結晶化温度: 296 K / 手法: 蒸気拡散法 / pH: 4.5
詳細: 0.1M sodium acetate pH 4.5, 0.68M sodium citrate pH 4.5

-
データ収集

回折平均測定温度: 80 K
放射光源由来: シンクロトロン / サイト: PAL/PLS / ビームライン: 7A (6B, 6C1) / 波長: 0.97934 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2016年3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: 0.97934 Å / 相対比: 1
反射解像度: 3.2→50 Å / Num. obs: 26459 / % possible obs: 99.4 % / 冗長度: 3.3 % / Net I/σ(I): 11.2
反射 シェル解像度: 3.2→3.31 Å / 冗長度: 3 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.1

-
解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155)精密化
HKL-2000データ削減
SCALEPACK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: 2IZX, 2SPZ

2izx

2spz


解像度: 3.197→42.419 Å / SU ML: 0.59 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 32.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2845 2003 7.58 %
Rwork0.2389 --
obs0.2424 26430 99.24 %
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: 3.197→42.419 Å
タンパク質核酸リガンド溶媒全体
原子数8143 0 0 0 8143
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0058351
X-RAY DIFFRACTIONf_angle_d0.9911340
X-RAY DIFFRACTIONf_dihedral_angle_d14.3265197
X-RAY DIFFRACTIONf_chiral_restr0.0531259
X-RAY DIFFRACTIONf_plane_restr0.0071534
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.197-3.27690.43471260.36331721X-RAY DIFFRACTION97
3.2769-3.36550.37231460.34271721X-RAY DIFFRACTION99
3.3655-3.46440.35121480.31351724X-RAY DIFFRACTION99
3.4644-3.57620.3951340.30341756X-RAY DIFFRACTION100
3.5762-3.7040.34991430.28461744X-RAY DIFFRACTION100
3.704-3.85220.35251530.27411745X-RAY DIFFRACTION100
3.8522-4.02740.29391360.25351746X-RAY DIFFRACTION100
4.0274-4.23950.28591460.23581757X-RAY DIFFRACTION100
4.2395-4.50480.27161500.20731743X-RAY DIFFRACTION100
4.5048-4.85220.20971400.19951733X-RAY DIFFRACTION100
4.8522-5.33970.23281370.21341754X-RAY DIFFRACTION100
5.3397-6.11040.28831550.25431752X-RAY DIFFRACTION100
6.1104-7.69090.30171440.24771768X-RAY DIFFRACTION100
7.6909-42.42320.20821450.16281763X-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)
11.0938-1.725-1.13723.49454.38538.4681-0.0680.78310.36030.5742-0.2504-0.2530.38250.80450.34540.40140.02020.02040.75530.36330.678368.1115-23.926420.2269
24.8982-1.95881.44631.4444-0.65310.4345-0.5337-1.90680.50320.52950.42810.50750.62250.7961-0.01711.2945-0.25160.25281.589-0.39420.777368.427-47.29616.5806
35.2285-2.8872-0.73782.49651.57915.57310.03061.70820.598-0.6069-1.0554-0.6785-0.0534-0.36080.21670.95840.40970.28241.65450.22980.622877.5135-37.66698.3004
43.8252-0.64830.53962.29131.63814.0551-0.03721.1668-0.6283-0.9843-0.554-0.29370.3710.70970.61630.92110.19170.24151.06970.0550.527868.1524-41.79910.7243
50.04820.08280.08680.14840.17640.4081-0.0621-0.10920.008-0.0698-0.07250.0528-0.14270.2012-0.04370.5272-0.16110.0210.87080.52280.794667.0271-10.4832.653
67.1055-0.0363-0.03882.2142.20362.1675-0.36850.3377-0.0365-0.6836-1.17610.4829-0.1518-1.03071.18130.37820.0677-0.09260.4493-0.11770.58858.0363-15.227914.7868
76.16774.9276-2.18834.6704-1.06431.64160.3910.37631.0371-0.8708-0.8055-0.4955-0.1651-0.3527-0.00030.49020.10830.0560.47750.32810.774372.4512-7.655711.5213
83.9563-0.57243.07942.9487-1.42747.01810.27691.31410.2542-0.73680.15-1.33591.00970.2124-0.30840.686-0.0280.09910.50350.07341.185282.1816-5.17084.8938
92.3361-2.6423-0.64053.20552.00226.3099-0.535-0.91260.67250.69050.1053-1.58250.84580.21240.26490.75530.119-0.05740.3792-0.15091.224686.8327-1.927714.8441
101.05080.6987-2.39719.236-7.17128.634-0.0231-0.1439-0.39510.8425-0.0007-0.0706-0.96460.16340.03240.4742-0.08780.06580.4135-0.05070.365855.735712.192526.5662
113.26553.093.13994.8542.25273.32140.49851.8355-0.07770.06080.2625-0.15420.04831.862-0.83490.761-0.08190.09690.947-0.01580.51358.663726.11339.4226
122.0807-1.4466-0.39633.24.82589.4738-0.40650.3604-0.7310.63380.3464-1.4228-0.40790.7320.30130.48670.04130.06360.68290.11960.638162.54641.322128.0289
139.53924.08476.54254.07426.04328.8965-0.48491.0612-0.9539-0.49790.7246-0.268-0.84330.6901-0.10410.436-0.04760.16140.5741-0.02620.426756.2536-0.069718.4409
142.83553.74470.37925.48230.72827.37270.03040.9115-0.4081-0.8708-0.8170.0468-0.1108-0.58530.40940.29040.0612-0.09910.8009-0.24260.707444.5073-8.304710.4597
156.06696.98930.23078.0630.43352.38250.46990.3983-0.24631.7148-0.25010.0344-0.1993-1.2977-0.04090.60380.1507-0.17080.9139-0.32370.78837.445-7.79116.917
163.18630.1361-0.80456.81082.0887.1345-0.021-0.09050.89290.2318-1.0484-0.8138-0.63320.42750.65421.0278-0.1281-0.00710.71160.21060.487662.4155-10.785344.811
172.1908-1.8893-1.41586.7331.56814.1974-0.3381-0.36950.12141.2988-0.09431.1896-0.46960.43260.3961.01370.04640.15670.49720.12650.672251.5459-13.631651.0625
181.413-0.7374-3.00880.66052.42069.1093-1.9803-0.17390.5337-0.3599-0.21622.15720.7111-1.80722.18760.8132-0.03060.05171.21620.12583.068930.4602-11.096448.4962
192.19750.46151.18568.35436.81525.8595-1.9514-0.2612-0.29930.7554-0.93560.57771.2048-0.99922.03041.17570.10640.40471.12050.37231.993836.275-15.819856.8332
202.62261.50420.47756.83294.42437.7144-1.35970.4372-0.1943-0.2412-0.8271.8521.663-1.19291.9880.9636-0.26540.46380.99350.03752.246940.2183-21.53248.2283
214.42210.8303-1.99860.7953-0.933.9756-1.9406-1.1362-3.76540.60310.0515-1.52841.68562.20292.05711.555-0.40430.48591.68590.15251.56627.8885-15.554743.3683
223.6057-5.25912.11779.835-1.61182.2505-0.09250.3746-0.0371-0.6005-0.0281-0.2480.61840.35740.28910.6712-0.0453-0.05120.54240.24130.537262.822-19.75639.2158
233.3923-2.58993.20832.9393-0.10078.3856-0.0732-0.30060.1706-0.06510.29010.30570.1685-0.556-0.46730.422-0.15240.01820.33390.16140.455363.1054-29.625152.119
243.96293.04694.61582.0317-0.71177.74510.607-0.16390.2761-0.8059-0.28220.42560.3448-0.9261-0.3130.73990.08680.01850.55210.12230.369159.3556-38.124658.9886
258.00360.49080.94234.4222-0.30324.94360.2101-0.73771.2536-0.02290.1605-0.4031-0.8116-0.2084-0.12340.70670.01240.07710.2832-0.03750.570966.6722-34.317267.1586
263.5559-2.18991.16366.4951-0.75325.3378-0.4874-0.55640.146-0.44640.30470.01340.3673-0.31280.22960.80680.3471-0.18850.8264-0.79971.210134.8389-27.1175-8.9752
274.9196-2.3260.54797.1608-2.30693.3884-1.161-1.16571.7905-0.05120.5869-1.0128-0.605-1.3065-0.58030.69080.5036-0.2511.4143-1.0126-0.30125.0714-31.1745-3.0716
283.07970.4735-0.56272.06661.97083.6260.1112-0.2576-0.10060.8779-0.1167-0.2120.2869-0.73760.00891.04060.14930.03041.55220.06690.453215.4781-41.89014.5029
29-0.001-0.0026-0.00140.00250.00520.00960.392-0.97840.36120.5293-0.07010.0561-0.2462-0.2538-0.15910.96390.1657-0.01691.7196-0.28110.696939.2798-17.3134-14.2891
309.8543-0.59971.36264.2977-0.10838.8105-0.2241-1.3971-0.62690.3604-0.3346-0.478-0.22090.64630.58780.51050.3562-0.30091.3705-0.4121.154540.3287-27.83313.6086
313.1305-0.3002-2.33293.9990.55413.37550.5293-0.3317-0.14620.1054-0.2169-0.186-0.29130.9799-0.42160.42290.5767-0.27851.2023-0.81251.061531.8061-18.1565.8849
326.4047-3.203-5.94391.653.04225.61140.7753-0.47271.95840.35420.6404-1.2908-1.56921.2141-1.29380.6178-0.08770.08581.2134-0.48221.324529.4333.41499.1664
331.48420.3768-0.70397.3641-0.00671.7121-0.1372-0.55490.66090.8920.2646-0.3028-0.03650.2466-0.01430.68760.4706-0.14630.4952-0.91261.325624.1175-5.761513.7706
343.7462-2.2271-0.25521.90681.15414.6443-0.15991.46950.57480.75620.833-0.72030.0268-0.1943-0.31810.54040.20350.03730.7592-0.30861.341322.8571-4.39993.4213
350.0041-0.00970.00430.1418-0.08860.06130.5547-0.334-0.11081.2387-0.05240.3247-0.40690.4245-0.08340.8347-0.2414-0.02150.9030.35630.753261.36481.968241.2837
363.9077-0.0629-5.2635.05820.54487.0506-1.2016-0.4177-1.35921.3250.05430.85040.54560.18041.19921.36760.03480.31080.53210.04320.654644.622-1.172553.5704
376.6183-0.3571-1.79913.70322.21924.7299-0.1158-2.5882-0.85581.59310.1187-0.79480.86941.7090.49352.08410.17640.26161.02730.54120.765754.64651.670561.6171
384.53980.13082.38190.78511.66844.5145-0.523-2.2412-0.16560.4560.55660.1062-0.12671.37910.19041.64210.5188-0.21274.19631.20271.392273.3025-6.614468.1545
394.41431.7058-3.00033.56973.51159.5358-0.1141-2.4313-1.59730.74121.2371-0.6539-0.60572.3868-0.91492.14880.163-0.39073.83540.3181.127466.14050.240374.0815
400.4483-0.0356-0.10910.0360.03760.0729-1.1779-2.0650.3039-0.33241.3146-0.0087-0.14771.6492-0.13082.409-0.6057-0.1722.1534-0.30861.138970.51995.783465.5055
412.2507-0.29942.33732.48852.33515.35260.20630.25950.1846-0.02960.01160.5155-0.6090.0906-0.02551.02650.08040.08730.45520.04270.535650.99267.858746.1568
423.0773-3.1707-0.71115.56551.9550.9449-0.22390.35-0.06230.47590.2629-0.2453-0.0074-0.3004-0.01521.5104-0.12170.11380.55880.15540.420348.150315.950255.0877
432.3535-1.0637-0.22357.46280.58848.12150.3435-0.64560.0391-0.099-0.404-0.18111.518-1.1420.09850.9454-0.12210.13570.6907-0.0370.38140.214925.423964.2871
443.6312-0.5688-0.33982.6021-0.27144.2639-0.08930.0211.0898-0.06430.5798-0.2289-0.65810.5956-0.53011.1031-0.285-0.07890.71830.00121.187319.9338-22.508855.034
453.5451-1.932-1.30733.311-2.93296.55270.8631-1.05030.3295-0.3954-0.8159-0.76240.30320.7594-0.06071.0291-0.1498-0.0381.14180.12811.726138.8848-36.274853.4749
469.48244.13072.53812.4560.07472.25590.6260.18730.53140.4473-0.110.4001-0.029-0.2767-0.66060.6738-0.03150.14910.7952-0.17480.91911.3693-27.130462.2962
479.66388.34046.74487.71015.6319.4573-0.06570.1447-0.61740.44720.5597-0.64070.03030.4847-0.55350.8247-0.01710.21230.5083-0.16470.669.6688-34.548751.7214
482.0163-3.48556.10677.6717-0.05644.32990.5725-0.9487-0.1775-1.39330.0893-0.55090.8182-0.0134-0.66550.9287-0.03940.26290.7806-0.10650.45274.7222-43.35640.1343
492.0063.25954.40236.40431.24886.57770.2817-0.66711.4271-0.3495-0.47180.0304-0.82360.72190.03231.0969-0.04090.3140.6066-0.16470.4330.6093-36.730734.5951
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 87 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 6 )
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 25 )
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 53 )
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 70 )
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 86 )
10X-RAY DIFFRACTION10chain 'C' and (resid 4 through 48 )
11X-RAY DIFFRACTION11chain 'C' and (resid 49 through 87 )
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 25 )
13X-RAY DIFFRACTION13chain 'D' and (resid 26 through 46 )
14X-RAY DIFFRACTION14chain 'D' and (resid 47 through 70 )
15X-RAY DIFFRACTION15chain 'D' and (resid 71 through 87 )
16X-RAY DIFFRACTION16chain 'E' and (resid 2 through 25 )
17X-RAY DIFFRACTION17chain 'E' and (resid 26 through 48 )
18X-RAY DIFFRACTION18chain 'E' and (resid 49 through 53 )
19X-RAY DIFFRACTION19chain 'E' and (resid 54 through 66 )
20X-RAY DIFFRACTION20chain 'E' and (resid 67 through 81 )
21X-RAY DIFFRACTION21chain 'E' and (resid 82 through 86 )
22X-RAY DIFFRACTION22chain 'F' and (resid 4 through 25 )
23X-RAY DIFFRACTION23chain 'F' and (resid 26 through 53 )
24X-RAY DIFFRACTION24chain 'F' and (resid 54 through 70 )
25X-RAY DIFFRACTION25chain 'F' and (resid 71 through 87 )
26X-RAY DIFFRACTION26chain 'G' and (resid 4 through 25 )
27X-RAY DIFFRACTION27chain 'G' and (resid 26 through 47 )
28X-RAY DIFFRACTION28chain 'G' and (resid 48 through 82 )
29X-RAY DIFFRACTION29chain 'H' and (resid 2 through 6 )
30X-RAY DIFFRACTION30chain 'H' and (resid 7 through 25 )
31X-RAY DIFFRACTION31chain 'H' and (resid 26 through 48 )
32X-RAY DIFFRACTION32chain 'H' and (resid 49 through 53 )
33X-RAY DIFFRACTION33chain 'H' and (resid 54 through 66 )
34X-RAY DIFFRACTION34chain 'H' and (resid 67 through 85 )
35X-RAY DIFFRACTION35chain 'I' and (resid 2 through 6 )
36X-RAY DIFFRACTION36chain 'I' and (resid 7 through 25 )
37X-RAY DIFFRACTION37chain 'I' and (resid 26 through 47 )
38X-RAY DIFFRACTION38chain 'I' and (resid 48 through 53 )
39X-RAY DIFFRACTION39chain 'I' and (resid 54 through 66 )
40X-RAY DIFFRACTION40chain 'I' and (resid 67 through 83 )
41X-RAY DIFFRACTION41chain 'J' and (resid 3 through 25 )
42X-RAY DIFFRACTION42chain 'J' and (resid 26 through 48 )
43X-RAY DIFFRACTION43chain 'J' and (resid 49 through 85 )
44X-RAY DIFFRACTION44chain 'K' and (resid 2 through 46 )
45X-RAY DIFFRACTION45chain 'K' and (resid 47 through 82 )
46X-RAY DIFFRACTION46chain 'L' and (resid 4 through 25 )
47X-RAY DIFFRACTION47chain 'L' and (resid 26 through 48 )
48X-RAY DIFFRACTION48chain 'L' and (resid 49 through 70 )
49X-RAY DIFFRACTION49chain 'L' and (resid 71 through 86 )

+
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://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