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- PDB-5vx3: Bcl-xL in complex with Bim-h3Pc-RT -

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基本情報

登録情報
データベース: PDB / ID: 5vx3
タイトルBcl-xL in complex with Bim-h3Pc-RT
要素
  • Bcl-2-like protein 1
  • Bcl-2-like protein 11
キーワードAPOPTOSIS / Bcl-2 Family / Pro-survival
機能・相同性
機能・相同性情報


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / apoptotic process in bone marrow cell / ear development / 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 / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / tube formation / mammary gland development / 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 / myeloid cell homeostasis / NFE2L2 regulating tumorigenic genes / cellular response to glucocorticoid stimulus / NRAGE signals death through JNK / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / thymocyte apoptotic process / hepatocyte apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / negative regulation of reproductive process / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of developmental process / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / germ cell development / T cell homeostasis / BH3 domain binding / B cell homeostasis / 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 / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / regulation of mitochondrial membrane potential / FLT3 Signaling / endomembrane system / negative regulation of autophagy / response to endoplasmic reticulum stress / thymus development / release of cytochrome c from mitochondria / cell-matrix adhesion / epithelial cell proliferation / regulation of cytokinesis / post-embryonic development / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / kidney development / cellular response to gamma radiation / RAS processing / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle membrane / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / channel activity / neuron apoptotic process / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / regulation of apoptotic process / microtubule binding / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane
類似検索 - 分子機能
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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 11 / Bcl-2-like protein 1
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: 1.945 Å
データ登録者Cowan, A.D. / Brouwer, J.M. / Colman, P.M. / Czabotar, P.E.
資金援助 オーストラリア, 3件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)1079706 オーストラリア
National Health and Medical Research Council (NHMRC, Australia)1058331 オーストラリア
National Health and Medical Research Council (NHMRC, Australia)1113133 オーストラリア
引用ジャーナル: Mol. Cell / 年: 2017
タイトル: Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design.
著者: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / ...著者: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / Call, M.J. / Smith, B.J. / Dewson, G. / Lessene, G. / Colman, P.M. / Czabotar, P.E.
履歴
登録2017年5月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年11月15日Provider: repository / タイプ: Initial release
改定 1.12017年11月29日Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22020年1月8日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32024年10月30日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Bcl-2-like protein 1
B: Bcl-2-like protein 11
C: Bcl-2-like protein 1
D: Bcl-2-like protein 11
E: Bcl-2-like protein 1
F: Bcl-2-like protein 11
G: Bcl-2-like protein 1
H: Bcl-2-like protein 11
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)85,44521
ポリマ－84,6388
非ポリマー80713
水7,476415
1
A: Bcl-2-like protein 1
B: Bcl-2-like protein 11
E: Bcl-2-like protein 1
F: Bcl-2-like protein 11
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,69210
ポリマ－42,3194
非ポリマー3726
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-48 kcal/mol
Surface area16110 Å2
手法PISA
2
C: Bcl-2-like protein 1
D: Bcl-2-like protein 11
G: Bcl-2-like protein 1
H: Bcl-2-like protein 11
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,75411
ポリマ－42,3194
非ポリマー4347
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint-49 kcal/mol
Surface area15860 Å2
手法PISA
単位格子
Length a, b, c (Å)125.661, 68.811, 102.830
Angle α, β, γ (deg.)90.00, 125.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11G-479-

HOH

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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: 17917.959 Da / 分子数: 4 / 断片: UNP residues 1-26 and 83-209 / 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 (大腸菌) / 参照: UniProt: Q07817
#2: タンパク質・ペプチド
Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


分子量: 3241.641 Da / 分子数: 4 / 断片: UNP residues 141-166 / Mutation: W147R, Y163T / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: O43521
#3: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 13 / 由来タイプ: 合成 / 式: C2H6O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 415 / 由来タイプ: 天然 / 式: H2O
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: 2.14 Å3/Da / 溶媒含有率: 42.58 %
結晶化温度: 273 K / 手法: 蒸気拡散法
詳細: 200 mM magnesium chloride, 20 % PEG 6000, and 100 mM sodium MES pH 6

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2015年4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: 0.9537 Å / 相対比: 1
反射解像度: 1.945→41.936 Å / Num. obs: 52409 / % possible obs: 99 % / 冗長度: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.09715 / Net I/σ(I): 8.4

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
XDSdata processing
XDS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 / 解像度: 1.945→41.936 Å / SU ML: 0.28 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 25.78
Rfactor反射数%反射
Rfree0.2429 2185 4.17 %
Rwork0.1939 --
obs0.196 52409 99.34 %
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: 1.945→41.936 Å
タンパク質核酸リガンド溶媒全体
原子数5371 0 52 415 5838
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0075559
X-RAY DIFFRACTIONf_angle_d0.8447489
X-RAY DIFFRACTIONf_dihedral_angle_d15.7273240
X-RAY DIFFRACTIONf_chiral_restr0.051771
X-RAY DIFFRACTIONf_plane_restr0.015980
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9445-1.98680.37381320.3222832X-RAY DIFFRACTION90
1.9868-2.0330.36971310.29033099X-RAY DIFFRACTION100
2.033-2.08390.28991440.25663159X-RAY DIFFRACTION100
2.0839-2.14020.29481330.23243122X-RAY DIFFRACTION100
2.1402-2.20320.25971300.21863172X-RAY DIFFRACTION100
2.2032-2.27430.26481400.21043139X-RAY DIFFRACTION100
2.2743-2.35560.26921320.20213130X-RAY DIFFRACTION100
2.3556-2.44990.25151410.1933172X-RAY DIFFRACTION100
2.4499-2.56140.23651290.18193154X-RAY DIFFRACTION100
2.5614-2.69640.21971440.18443112X-RAY DIFFRACTION100
2.6964-2.86530.25471280.19043211X-RAY DIFFRACTION100
2.8653-3.08650.24091420.18673124X-RAY DIFFRACTION100
3.0865-3.39690.24351390.18683173X-RAY DIFFRACTION100
3.3969-3.88820.2231360.17253162X-RAY DIFFRACTION100
3.8882-4.89750.18481450.1673204X-RAY DIFFRACTION100
4.8975-41.9460.25591390.19273259X-RAY DIFFRACTION100
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)
17.9365-0.28593.81875.5518-0.76092.001-0.01190.410.1201-0.50590.06030.3474-0.177-0.01720.06980.23150.00890.00250.2166-0.03360.1902-33.3321-17.596925.8228
23.9983-0.88921.95553.024-1.97368.38460.2229-0.09410.2271-0.1606-0.244-0.279-0.15880.5852-0.02230.18610.02680.07180.2184-0.01670.2163-23.6649-20.960628.3868
32.63071.00171.0116.75634.05739.04410.2307-0.3144-0.07510.7395-0.0483-0.19050.1712-0.0431-0.04750.3099-0.03560.02620.20220.05530.2213-20.4113-2.736135.6594
43.5871-1.02810.83543.8780.37832.5372-0.145-0.24840.37810.29940.1116-0.0363-0.4107-0.0030.04010.27010.00230.01440.1528-0.01840.1815-20.758710.554828.2113
52.9657-3.1569-2.5295.61821.33665.3265-0.01040.03790.3441-0.0560.04910.1223-0.3103-0.2866-0.0550.20270.0206-0.0160.1452-0.00760.1606-26.62137.410521.1033
68.4566-5.81976.28055.7588-4.60524.71760.3031-0.03720.2253-1.0327-0.0725-0.47270.42150.6078-0.09720.20760.05220.00190.2906-0.03480.3498-8.6942-3.204920.3158
78.57912.5029-1.38636.10442.54959.11520.0316-0.3376-0.75140.41960.6492-0.68940.5050.3633-0.60920.23980.0806-0.00960.24320.0090.3958-12.3908-9.873528.987
86.3015-4.71471.74356.9212-1.78864.6222-0.2477-0.15640.64111.23510.0245-0.8921-0.85730.44570.17040.5107-0.111-0.10540.4085-0.03240.2861-13.057611.124634.752
97.45090.25562.19244.50060.64316.29880.15910.18620.00090.10890.02210.34240.2544-0.2596-0.16860.22990.02140.03060.17560.00420.1876-16.179752.15753.1374
104.0965-6.1552-2.49799.59622.91426.23730.28750.06170.5439-0.7228-0.1373-0.8916-0.58840.2942-0.08260.2718-0.06550.04480.2180.02620.3493-5.205240.234511.2406
116.3264.1552-0.42083.15550.50892.48460.166-0.2231-0.943-0.178-0.036-1.68250.17740.5331-0.01340.55020.04090.08720.36350.05360.39783.82926.28869.2402
126.45974.72346.70977.92955.01247.0251-0.08431.1017-1.4022-0.7854-0.3337-1.3873-0.18620.56360.03740.66110.11810.00240.4337-0.08080.6617-3.609117.92716.7239
135.68062.2340.46815.97512.91513.75360.29620.3568-0.88640.0757-0.19130.02990.92520.08390.17470.36860.0072-0.02590.2014-0.02520.3137-14.250318.697513.3136
143.53830.44610.79670.88020.7445.19740.07190.0339-0.2432-0.0579-0.0139-0.31060.61270.3643-0.0490.35250.0030.06530.1407-0.00910.2512-8.671228.366314.2415
154.2516-0.5999-0.06825.26763.31632.4810.00680.3595-0.352-0.3208-0.1589-0.05470.3708-0.29580.18650.2679-0.0210.01750.1488-0.03970.1991-18.700926.65399.8313
162.56052.34580.09952.62831.71165.8269-0.0632-0.41540.05080.76810.18530.1830.04470.0024-0.13470.2767-0.0242-0.01260.2905-0.03190.273-13.37337.329427.0123
173.18072.1532-1.35032.4593-1.2626.7087-0.2516-0.43160.78110.32310.5571-0.6339-0.12950.5758-0.12630.4045-0.07270.00080.2561-0.0440.3829-6.455443.911120.5178
189.50735.08971.33583.62552.62387.67880.0141-0.4366-0.6915-0.38190.0065-1.33380.47130.4909-0.03010.27340.0159-0.0430.34440.07150.4213-0.859525.160418.3101
199.5964-4.6904-7.47883.76614.25735.7502-0.08240.232-0.4495-0.0347-0.2160.0924-0.0647-0.3070.3230.255-0.02930.00950.14780.01710.2057-25.3586-4.386223.5559
203.3052-0.1582-0.21523.86683.1882.6815-0.06730.0034-0.3348-0.157-0.03150.553-0.6959-0.7016-0.10810.30810.09050.00230.25680.00040.2928-36.64820.257927.9512
214.42141.7894-0.97832.61261.01872.24810.0144-0.13040.3270.34410.26890.7236-0.289-0.1071-0.42930.1555-0.00060.01740.2029-0.03410.2037-39.4577-14.211233.6201
222.0212-2.1272.47013.3852-3.67784.06-0.0088-0.22370.11560.27210.36210.40250.3859-0.5812-0.30270.4019-0.01790.0030.29630.07790.3147-39.406-27.886442.0935
235.948-1.4614-0.22573.6750.28523.34370.13460.1242-1.1024-0.2653-0.09630.42480.7216-0.2069-0.01190.3491-0.0739-0.01620.232-0.02140.3934-37.3037-36.69428.7291
242.7164-0.7003-0.3392.5179-0.50022.4622-0.1322-0.0628-0.3267-0.00590.0820.44340.3408-0.3273-0.03410.2214-0.0468-0.03250.2165-0.01930.2417-41.3405-26.451130.2496
255.1419-1.34120.15083.3318-0.36722.43060.18350.2577-0.5761-0.3234-0.06070.36130.2106-0.09030.0040.28110.0082-0.03780.2023-0.08750.2107-33.6225-28.797722.7073
265.2164-3.8276-0.43926.9542-0.14773.09220.0990.98920.0843-1.25780.05270.7363-0.0784-0.8796-0.05570.2974-0.0131-0.19150.5005-0.0060.4704-51.4374-18.269620.676
272.6434-1.2236-2.54342.7372.13522.92290.226-0.30360.71470.1081-0.16710.7254-0.394-0.5670.00860.2110.0414-0.05650.3555-0.08840.5032-47.499-10.64429.5734
285.9781-2.2242-0.58771.22721.62195.6994-0.0544-0.4725-0.78690.77570.0441.03820.5246-0.59-0.01460.263-0.11340.07610.37050.03630.4515-47.6762-29.406636.4882
296.9524-3.2959-6.0113.56343.75645.43230.15570.351-0.2765-0.3597-0.44260.1909-0.8054-0.41970.2160.24920.01630.02570.19520.00260.2386-15.966538.518210.4334
300.83832.5527-0.78437.6379-2.66960.9488-0.20520.1233-0.1916-0.51480.0436-0.30520.27170.15860.16220.30140.02280.0060.2077-0.01010.2055-12.017244.9998-5.4198
312.5347-1.9482-2.51143.813.10964.98910.0366-0.18160.353-0.33370.1425-0.1054-0.51510.3654-0.10760.4654-0.0158-0.02080.26160.02560.4028-7.155268.7469-3.0718
321.7537-0.09030.00362.99970.89333.1608-0.05620.13410.2948-0.4455-0.12570.4645-0.5571-0.17960.15220.23550.0292-0.05860.17510.0180.2503-17.423363.1292-3.4229
339.2551-3.07920.18632.73680.4437.89930.21710.407-0.425-0.7005-0.17010.51580.8664-0.1458-0.0520.4056-0.0101-0.13070.20860.01550.2571-21.842948.0906-13.1456
343.22170.58050.39876.69675.57856.4097-0.20940.36010.347-0.73380.07060.24880.16930.52640.08810.59620.0237-0.0330.43890.08910.1528-10.816663.8387-14.9718
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 156 )
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 186 )
7X-RAY DIFFRACTION7chain 'A' and (resid 187 through 196 )
8X-RAY DIFFRACTION8chain 'B' and (resid 84 through 104 )
9X-RAY DIFFRACTION9chain 'C' and (resid 0 through 25 )
10X-RAY DIFFRACTION10chain 'C' and (resid 26 through 100 )
11X-RAY DIFFRACTION11chain 'C' and (resid 101 through 105 )
12X-RAY DIFFRACTION12chain 'C' and (resid 106 through 112 )
13X-RAY DIFFRACTION13chain 'C' and (resid 113 through 130 )
14X-RAY DIFFRACTION14chain 'C' and (resid 131 through 156 )
15X-RAY DIFFRACTION15chain 'C' and (resid 157 through 177 )
16X-RAY DIFFRACTION16chain 'C' and (resid 178 through 186 )
17X-RAY DIFFRACTION17chain 'C' and (resid 187 through 196 )
18X-RAY DIFFRACTION18chain 'D' and (resid 85 through 106 )
19X-RAY DIFFRACTION19chain 'E' and (resid -4 through 20 )
20X-RAY DIFFRACTION20chain 'E' and (resid 21 through 25 )
21X-RAY DIFFRACTION21chain 'E' and (resid 26 through 100 )
22X-RAY DIFFRACTION22chain 'E' and (resid 101 through 105 )
23X-RAY DIFFRACTION23chain 'E' and (resid 106 through 130 )
24X-RAY DIFFRACTION24chain 'E' and (resid 131 through 156 )
25X-RAY DIFFRACTION25chain 'E' and (resid 157 through 177 )
26X-RAY DIFFRACTION26chain 'E' and (resid 178 through 186 )
27X-RAY DIFFRACTION27chain 'E' and (resid 187 through 197 )
28X-RAY DIFFRACTION28chain 'F' and (resid 85 through 106 )
29X-RAY DIFFRACTION29chain 'G' and (resid -4 through 20 )
30X-RAY DIFFRACTION30chain 'G' and (resid 21 through 100 )
31X-RAY DIFFRACTION31chain 'G' and (resid 101 through 118 )
32X-RAY DIFFRACTION32chain 'G' and (resid 119 through 177 )
33X-RAY DIFFRACTION33chain 'G' and (resid 178 through 197 )
34X-RAY DIFFRACTION34chain 'H' and (resid 84 through 106 )

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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