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- PDB-7xgg: Crystal structure of BCL-xL in complex with computationally desig... -

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基本情報

登録情報
データベース: PDB / ID: 7xgg
タイトルCrystal structure of BCL-xL in complex with computationally designed inhibitor protein
要素
  • BCL-xL and MCL-1 dual inhibitor
  • Bcl-2-like protein 1
キーワードAPOTOSIS / DE NOVO PROTEIN / computational design
機能・相同性
機能・相同性情報


apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of developmental process / apoptotic mitochondrial changes / germ cell development / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ovarian follicle development / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / regulation of mitochondrial membrane potential / negative regulation of autophagy / release of cytochrome c from mitochondria / epithelial cell proliferation / regulation of cytokinesis / cellular response to amino acid stimulus / cellular response to gamma radiation / RAS processing / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle membrane / channel activity / neuron apoptotic process / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / centrosome / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / identical protein binding / cytosol / cytoplasm
類似検索 - 分子機能
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
類似検索 - ドメイン・相同性
Bcl-2-like protein 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 多波長異常分散 / 解像度: 1.9 Å
データ登録者Oh, B.-H. / Kim, S.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Comput Struct Biotechnol J / 年: 2022
タイトル: Computational design of an apoptogenic protein that binds BCL-xL and MCL-1 simultaneously and potently.
著者: Kim, S. / Park, H.S. / Oh, B.H.
履歴
登録2022年4月4日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年7月20日Provider: repository / タイプ: Initial release
改定 1.12024年10月23日Group: Data collection / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
B: Bcl-2-like protein 1
A: BCL-xL and MCL-1 dual inhibitor
F: Bcl-2-like protein 1
D: BCL-xL and MCL-1 dual inhibitor
C: Bcl-2-like protein 1
E: Bcl-2-like protein 1


分子量 (理論値)分子数
合計 (水以外)116,5096
ポリマ－116,5096
非ポリマー00
水9,656536
1
B: Bcl-2-like protein 1
A: BCL-xL and MCL-1 dual inhibitor
C: Bcl-2-like protein 1


分子量 (理論値)分子数
合計 (水以外)58,2553
ポリマ－58,2553
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-21 kcal/mol
Surface area20390 Å2
手法PISA
2
F: Bcl-2-like protein 1
D: BCL-xL and MCL-1 dual inhibitor
E: Bcl-2-like protein 1


分子量 (理論値)分子数
合計 (水以外)58,2553
ポリマ－58,2553
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-19 kcal/mol
Surface area20630 Å2
手法PISA
単位格子
Length a, b, c (Å)60.612, 68.539, 80.517
Angle α, β, γ (deg.)100.890, 110.570, 108.730
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


分子量: 19827.191 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BCL2L1, BCL2L, BCLX / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q07817
#2: タンパク質 BCL-xL and MCL-1 dual inhibitor


分子量: 18600.221 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3)
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 536 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN
Has protein modificationY

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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: 2.39 Å3/Da / 溶媒含有率: 48.61 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 4% PEG 3,000(w/v), 0.1M Sodium acetate(pH4.5)

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: PAL/PLS / ビームライン: 5C (4A) / 波長: 0.97403 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2019年10月28日
放射プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97403 Å / 相対比: 1
反射解像度: 1.6→50 Å / Num. obs: 162032 / % possible obs: 96.7 % / 冗長度: 1.8 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.073 / Rrim(I) all: 0.103 / Χ2: 2.045 / Net I/σ(I): 3.1
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.10.32239870.8710.2170.3910.52495.3
1.93-1.973.30.28540390.9060.1880.3440.56595.9
1.97-2.013.30.24741090.9210.160.2950.61296.3
2.01-2.053.60.22540380.9530.1370.2640.67296.1
2.05-2.093.70.19640830.9650.1170.2290.75196.1
2.09-2.143.70.16941100.9720.1010.1970.8596.5
2.14-2.193.70.15340130.9770.0910.1780.93196.4
2.19-2.253.70.1440870.980.0830.1630.99796.4
2.25-2.323.70.12541090.9810.0750.1461.10596.8
2.32-2.393.70.11540390.9860.0690.1341.23896.1
2.39-2.483.70.11140850.9840.0670.131.40396.8
2.48-2.583.70.10340710.9870.0620.121.52296.6
2.58-2.73.70.09741360.9870.0580.1131.79897
2.7-2.843.70.09340180.9860.0560.1092.11796
2.84-3.023.50.08641300.9870.0530.1022.54396.8
3.02-3.253.40.08240720.9860.0520.0983.05396.7
3.25-3.5830.07440920.9860.0520.0924.39496.6
3.58-4.093.50.06941150.9890.0440.0825.00197.7
4.09-5.163.90.06541820.9930.0380.0755.14199.3
5.16-503.90.06542180.9960.0380.0765.11999.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874精密化
HKL-2000データスケーリング
PDB_EXTRACT3.27データ抽出
AutoSol位相決定
HKL-2000データ削減
精密化構造決定の手法: 多波長異常分散 / 解像度: 1.9→38.13 Å / SU ML: 0.17 / 交差検証法: THROUGHOUT / σ(F): 1.97 / 位相誤差: 19.16 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1967 3973 2.45 %
Rwork0.1657 158046 -
obs0.1665 162019 95.37 %
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
原子変位パラメータBiso max: 115.08 Å2 / Biso mean: 32.9394 Å2 / Biso min: 8.07 Å2
精密化ステップサイクル: final / 解像度: 1.9→38.13 Å
タンパク質核酸リガンド溶媒全体
原子数7318 0 0 536 7854
Biso mean---40.12 -
残基数----910
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.920.28381170.23154710482780
1.92-1.950.27231450.22395716586195
1.95-1.970.23891360.20835446558295
1.97-20.24821410.19315673581495
2-2.030.19251450.18615703584896
2.03-2.060.20621430.17875636577995
2.06-2.090.24531420.1745684582696
2.09-2.130.20691410.16875565570696
2.13-2.160.16261440.15915752589696
2.16-2.20.18641410.15275621576295
2.2-2.250.1821440.15035676582096
2.25-2.290.21121450.14645736588196
2.29-2.340.20261410.14995627576895
2.34-2.40.19051410.15275644578596
2.4-2.460.19931420.15935711585396
2.46-2.520.17981430.15615686582996
2.52-2.60.21731410.15255619576096
2.6-2.680.17521440.15395598574295
2.68-2.780.18171440.16235666581095
2.78-2.890.16911400.15395705584596
2.89-3.020.16911440.16135735587996
3.02-3.180.21961400.1665588572896
3.18-3.380.19521430.16785686582996
3.38-3.640.17981410.15755606574795
3.64-40.15751420.15515706584897
4-4.580.16291480.15445855600399
4.58-5.770.26681480.18155880602899
5.77-38.130.2191470.18955816596399
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)
13.44710.6117-0.06823.1341.46311.2182-0.0562-0.07630.2390.0807-0.19250.1809-0.558-0.44980.23640.17740.0366-0.02230.16490.00040.16721.626440.4252-13.9051
21.6728-1.9775-2.41254.3794.68335.64980.1284-0.48920.4840.7916-0.35270.9908-0.3488-1.24530.71250.4070.00730.05010.5281-0.07480.398615.468438.4673-19.3748
31.96520.265-0.41652.07090.79132.60410.04620.17110.0992-0.1386-0.10640.0473-0.3183-0.07310.080.13440.0116-0.02260.1520.03560.106432.49539.0753-16.8515
42.02410.69730.98831.72840.23972.2393-0.01780.0281-0.22470.080.0238-0.01110.0562-0.14210.01540.0830.01890.0270.1241-0.01060.126428.028727.8961-10.1718
52.23711.08941.09472.39320.98874.1724-0.02450.00930.003-0.0129-0.09310.18460.0355-0.22460.0960.09930.01350.04620.20630.00090.182519.082329.8009-10.2788
64.0361.439-0.91517.50790.29084.7678-0.0107-0.21240.29970.3225-0.1795-0.0958-0.8367-0.1463-0.03750.23680.0082-0.0660.1331-0.02260.132230.983140.89263.1003
75.93270.1011-0.67578.152-0.27233.45670.16260.02790.346-0.1723-0.079-0.3503-0.54660.1869-0.03750.21680.0173-0.01770.0953-0.0080.17934.359847.7655-6.3087
83.0208-0.85210.15673.6563-0.40191.77370.15010.1359-0.2433-0.3313-0.13670.14750.13560.0495-0.01840.10760.0486-0.02580.1755-0.01250.175747.728615.8189-13.6639
95.53271.68330.45333.11711.20142.12510.3677-0.4429-0.05940.671-0.36890.0851-0.0248-0.0309-0.02390.14770.0485-0.03210.18880.05240.193745.320722.9038-4.7249
103.5961-1.1320.47813.55510.17752.65580.1923-0.1308-0.69430.051-0.107-0.02490.2878-0.21950.05820.08560.0102-0.01250.14120.01210.202734.836221.2485-10.4965
112.91210.352-1.00442.7286-1.38084.520.092-0.131-0.48410.1006-0.17180.29020.6175-0.40110.11840.3504-0.0909-0.05020.21970.00440.2527.380828.171416.1455
125.1827-2.9371.95042.4913-0.85142.92510.06160.11130.4453-0.0327-0.1204-0.38510.0225-0.01520.12680.2877-0.02350.00460.14050.00710.208336.088737.308221.0687
133.418-1.5562-1.11893.74180.93134.91530.078-0.21680.22160.24630.0274-0.14920.46210.0194-0.08060.1761-0.037-0.01850.1109-0.01440.115434.557636.795724.6478
144.8426-1.0922-0.5713.46780.5083.61360.1899-0.2166-0.04850.175-0.16840.44570.4461-0.5055-0.01770.2893-0.1092-0.02840.21260.00810.189128.524632.130925.3216
154.02640.00360.57523.88540.23692.09240.11710.0827-0.24170.2532-0.0436-0.13390.14190.021-0.04330.1772-0.0125-0.00230.1122-0.03040.115338.00648.528731.3673
165.3117-0.45330.25083.7034-0.33783.31120.15260.7567-0.2221-0.3439-0.1342-0.19880.07510.21190.1410.2209-0.0230.06090.163-0.03970.166638.304254.708422.5711
176.4306-1.03310.48854.4274-0.43582.5366-0.14710.04090.05390.0745-0.0098-0.4972-0.02130.23840.03930.1027-0.02160.01250.11750.00740.15343.194461.990428.6719
184.24660.0105-2.70414.53590.77456.7910.07220.1765-0.0797-0.19970.0121-0.6120.01580.6385-0.02860.13060.03630.00730.2545-0.01340.171368.1418.5149-0.2488
192.89140.6736-1.10184.8055-0.18474.2860.10160.0781-0.2940.3314-0.1009-0.93960.71320.69260.13220.34240.0716-0.05860.3487-0.03230.319267.76650.89627.4357
202.37971.4744-1.92515.8365-0.5665.71960.1382-0.1287-0.42640.4471-0.2137-0.0955-0.56410.36880.10070.2164-0.0051-0.01370.2194-0.00730.139765.193717.57320.2132
212.14091.49310.4154.1941.60074.6026-0.3704-0.32231.17861.264-0.01541.1644-1.227-0.16830.40410.5076-0.0002-0.05990.3615-0.04170.588947.76438.2861-0.1246
221.39010.7904-0.27537.5346-4.25144.01980.07420.2227-0.0993-0.454-0.04530.46570.49130.13120.00240.21060.0213-0.01270.1484-0.03670.181854.8974-1.5926-9.7634
230.73210.5888-0.80014.3166-2.99275.6432-0.01890.1239-0.0081-0.09090.08820.20490.2077-0.0661-0.16070.0730.01130.00650.1498-0.00540.135457.78068.6679-7.0834
242.09231.2899-0.61814.2463-1.50583.1703-0.0540.008-0.13910.1339-0.0697-0.27740.06610.13690.02720.17070.08070.00160.169-0.04020.169663.0335-0.7962-4.5718
253.50212.3050.90465.6427-0.5753.104-0.03850.07160.332-0.19880.00210.1622-0.29710.1931-0.02280.0968-0.03610.03440.27830.02130.232768.217518.7945-12.0792
263.8763-0.56421.36442.68550.05512.0461-0.13980.19390.3557-0.1818-0.1142-0.2749-0.90420.1670.21440.3026-0.028-0.03780.1275-0.01340.192343.996784.303830.9849
273.08590.2349-2.02554.0275-3.09523.5201-0.26020.00860.7140.11150.1483-0.2819-0.63740.25590.18020.287-0.0793-0.04370.29310.03660.250349.987783.666940.7134
282.2906-0.34781.94960.3077-1.10914.3685-0.44040.22091.0388-0.4195-0.05270.0821-1.34040.62310.55170.7836-0.0416-0.0740.38160.01120.529950.003889.847532.6413
291.88460.1801-0.09024.0586-1.74043.16710.0024-0.04940.1650.1978-0.04520.0743-0.6157-0.09320.00270.17230.0072-0.00760.1313-0.02660.079934.57377.446233.6874
307.91812.5019-1.7831.8128-2.11784.86420.2771-0.5852-0.18230.31130.2312-0.47020.00880.27390.10630.2502-0.00120.00670.245-0.02130.179243.209266.79639.5374
311.53320.12490.44910.7151-0.67830.88240.2258-0.9106-0.24290.42340.0149-0.3293-0.28381.12590.16410.5260.0259-0.20820.6074-0.06830.381955.650467.101734.146
327.66460.8672.33563.48790.94775.9506-0.37930.29870.0843-0.20540.1029-0.6656-0.04760.7469-0.00030.19010.00940.02860.25740.04390.214550.214367.585224.4529
332.11520.37571.28180.98890.63314.3174-0.02520.0024-0.1391-0.0082-0.0001-0.1123-0.13260.21250.05560.1153-0.00720.01120.0930.01590.099942.626172.306327.9833
342.3884-0.32031.52451.58170.20394.8726-0.18160.17930.06130.0025-0.0682-0.2522-0.4150.81780.10920.1858-0.09740.00410.29810.07260.179352.612477.179427.8813
354.588-1.63540.74.3375-1.29055.7437-0.05510.17310.1658-0.116-0.03220.1453-0.6368-0.22350.17930.25020.0267-0.03880.1819-0.00680.107236.542278.89114.4236
364.83460.3418-0.12755.5584-1.0234.0955-0.00180.06850.06420.2723-0.04350.5252-0.8511-0.60860.13570.27560.1023-0.02630.1591-0.02030.152229.584682.244923.8796
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 23 )B6 - 23
2X-RAY DIFFRACTION2chain 'B' and (resid 24 through 42 )B24 - 42
3X-RAY DIFFRACTION3chain 'B' and (resid 43 through 74 )B43 - 74
4X-RAY DIFFRACTION4chain 'B' and (resid 75 through 119 )B75 - 119
5X-RAY DIFFRACTION5chain 'B' and (resid 120 through 140 )B120 - 140
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 149 )B141 - 149
7X-RAY DIFFRACTION7chain 'B' and (resid 150 through 160 )B150 - 160
8X-RAY DIFFRACTION8chain 'A' and (resid 4 through 78 )A4 - 78
9X-RAY DIFFRACTION9chain 'A' and (resid 79 through 120 )A79 - 120
10X-RAY DIFFRACTION10chain 'A' and (resid 121 through 165 )A121 - 165
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 44 )F1 - 44
12X-RAY DIFFRACTION12chain 'F' and (resid 45 through 93 )F45 - 93
13X-RAY DIFFRACTION13chain 'F' and (resid 94 through 119 )F94 - 119
14X-RAY DIFFRACTION14chain 'F' and (resid 120 through 160 )F120 - 160
15X-RAY DIFFRACTION15chain 'D' and (resid 4 through 78 )D4 - 78
16X-RAY DIFFRACTION16chain 'D' and (resid 79 through 124 )D79 - 124
17X-RAY DIFFRACTION17chain 'D' and (resid 125 through 165 )D125 - 165
18X-RAY DIFFRACTION18chain 'C' and (resid 4 through 23 )C4 - 23
19X-RAY DIFFRACTION19chain 'C' and (resid 24 through 43 )C24 - 43
20X-RAY DIFFRACTION20chain 'C' and (resid 44 through 62 )C44 - 62
21X-RAY DIFFRACTION21chain 'C' and (resid 63 through 75 )C63 - 75
22X-RAY DIFFRACTION22chain 'C' and (resid 76 through 93 )C76 - 93
23X-RAY DIFFRACTION23chain 'C' and (resid 94 through 119 )C94 - 119
24X-RAY DIFFRACTION24chain 'C' and (resid 120 through 140 )C120 - 140
25X-RAY DIFFRACTION25chain 'C' and (resid 141 through 159 )C141 - 159
26X-RAY DIFFRACTION26chain 'E' and (resid 6 through 22 )E6 - 22
27X-RAY DIFFRACTION27chain 'E' and (resid 23 through 29 )E23 - 29
28X-RAY DIFFRACTION28chain 'E' and (resid 30 through 44 )E30 - 44
29X-RAY DIFFRACTION29chain 'E' and (resid 45 through 68 )E45 - 68
30X-RAY DIFFRACTION30chain 'E' and (resid 69 through 74 )E69 - 74
31X-RAY DIFFRACTION31chain 'E' and (resid 75 through 81 )E75 - 81
32X-RAY DIFFRACTION32chain 'E' and (resid 82 through 93 )E82 - 93
33X-RAY DIFFRACTION33chain 'E' and (resid 94 through 119 )E94 - 119
34X-RAY DIFFRACTION34chain 'E' and (resid 120 through 140 )E120 - 140
35X-RAY DIFFRACTION35chain 'E' and (resid 141 through 149 )E141 - 149
36X-RAY DIFFRACTION36chain 'E' and (resid 150 through 160 )E150 - 160

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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