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- PDB-5jem: Complex of IRF-3 with CBP -

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基本情報

登録情報
データベース: PDB / ID: 5jem
タイトルComplex of IRF-3 with CBP
要素
  • CREB-binding protein
  • Interferon regulatory factor 3IRF3
キーワードIMMUNE SYSTEM (免疫系) / Innate Immunity (自然免疫系) / Signaling
機能・相同性
機能・相同性情報


IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway ...IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / positive regulation of type I interferon-mediated signaling pathway / MRF binding / NFE2L2 regulating MDR associated enzymes / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / 転写 (生物学) / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / toll-like receptor 4 signaling pathway / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / embryonic digit morphogenesis / DNA-binding transcription activator activity / immune system process / homeostatic process / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / Notch-HLH transcription pathway / cytoplasmic pattern recognition receptor signaling pathway / protein acetylation / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / acetyltransferase activity / positive regulation of interferon-alpha production / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / antiviral innate immune response / histone acetyltransferase complex / positive regulation of type I interferon production / Attenuation phase / regulation of cellular response to heat / histone acetyltransferase activity / lipopolysaccharide-mediated signaling pathway / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / ヒストンアセチルトランスフェラーゼ / TICAM1-dependent activation of IRF3/IRF7 / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of innate immune responses to cytosolic DNA / Regulation of lipid metabolism by PPARalpha / positive regulation of interferon-beta production / CD209 (DC-SIGN) signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / Formation of the beta-catenin:TCF transactivating complex / protein destabilization / Heme signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / chromatin DNA binding / ISG15 antiviral mechanism / cellular response to virus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / DNA-binding transcription repressor activity, RNA polymerase II-specific / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of protein localization to nucleus / transcription corepressor activity / cellular response to UV / rhythmic process / SARS-CoV-1 activates/modulates innate immune responses / Interferon gamma signaling
類似検索 - 分子機能
Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking domain / Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor ...Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking domain / Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / Tumour Suppressor Smad4 / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Coactivator CBP, KIX domain superfamily / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / SMAD/FHA domain superfamily / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / ブロモドメイン / Bromodomain profile. / bromo domain / ブロモドメイン / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / サンドイッチ / Orthogonal Bundle / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
Interferon regulatory factor 3 / CREB-binding protein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 解像度: 2.5 Å
データ登録者Zhao, B. / Li, P.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2016
タイトル: Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins.
著者: Zhao, B. / Shu, C. / Gao, X. / Sankaran, B. / Du, F. / Shelton, C.L. / Herr, A.B. / Ji, J.Y. / Li, P.
履歴
登録2016年4月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年6月15日Provider: repository / タイプ: Initial release
改定 1.12016年6月29日Group: Database references
改定 1.22024年3月6日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Interferon regulatory factor 3
C: CREB-binding protein
B: Interferon regulatory factor 3
D: CREB-binding protein
E: Interferon regulatory factor 3
F: CREB-binding protein
G: Interferon regulatory factor 3
H: CREB-binding protein


分子量 (理論値)分子数
合計 (水以外)116,1968
ポリマ－116,1968
非ポリマー00
水4,071226
1
A: Interferon regulatory factor 3
C: CREB-binding protein
B: Interferon regulatory factor 3
D: CREB-binding protein


分子量 (理論値)分子数
合計 (水以外)58,0984
ポリマ－58,0984
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-41 kcal/mol
Surface area21710 Å2
手法PISA
2
E: Interferon regulatory factor 3
F: CREB-binding protein
G: Interferon regulatory factor 3
H: CREB-binding protein


分子量 (理論値)分子数
合計 (水以外)58,0984
ポリマ－58,0984
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-39 kcal/mol
Surface area21480 Å2
手法PISA
単位格子
Length a, b, c (Å)85.230, 88.660, 92.810
Angle α, β, γ (deg.)90.00, 113.09, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Interferon regulatory factor 3 / IRF3 / IRF-3


分子量: 23774.992 Da / 分子数: 4 / 断片: UNP residues 189-398 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IRF3 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q14653
#2: タンパク質・ペプチド
CREB-binding protein /


分子量: 5274.103 Da / 分子数: 4 / 断片: UNP residues 2065-2111 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CREBBP, CBP / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q92793, ヒストンアセチルトランスフェラーゼ
#3: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 226 / 由来タイプ: 天然 / 式: H2O

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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: 2.78 Å3/Da / 溶媒含有率: 55.69 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M HEPES pH 7.5, 25% PEG 3350

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データ収集

回折平均測定温度: 120 K
放射光源由来: 回転陽極 / タイプ: RIGAKU MICROMAX-007 / 波長: 1.542 Å
検出器タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2015年10月25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: 1.542 Å / 相対比: 1
反射解像度: 2.5→36.992 Å / Num. obs: 42426 / % possible obs: 96.3 % / 冗長度: 3.5 % / Net I/σ(I): 6.2

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
MOSFLMデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化解像度: 2.5→36.992 Å / SU ML: 0.42 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 27.41
Rfactor反射数%反射
Rfree0.242 1985 4.68 %
Rwork0.192 --
obs0.1943 42378 96.05 %
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: 2.5→36.992 Å
タンパク質核酸リガンド溶媒全体
原子数7650 0 0 226 7876
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0037849
X-RAY DIFFRACTIONf_angle_d0.62410687
X-RAY DIFFRACTIONf_dihedral_angle_d14.5152871
X-RAY DIFFRACTIONf_chiral_restr0.0231159
X-RAY DIFFRACTIONf_plane_restr0.0031392
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.37821180.33082579X-RAY DIFFRACTION86
2.5625-2.63180.38341310.30942568X-RAY DIFFRACTION87
2.6318-2.70920.36281260.28142677X-RAY DIFFRACTION89
2.7092-2.79660.29341390.26372775X-RAY DIFFRACTION92
2.7966-2.89660.2821460.2632842X-RAY DIFFRACTION96
2.8966-3.01250.30591380.26442878X-RAY DIFFRACTION97
3.0125-3.14950.31841630.24182938X-RAY DIFFRACTION98
3.1495-3.31550.24711320.20573015X-RAY DIFFRACTION100
3.3155-3.5230.23091440.19132985X-RAY DIFFRACTION100
3.523-3.79480.26931580.17612997X-RAY DIFFRACTION100
3.7948-4.17620.19191520.16293002X-RAY DIFFRACTION100
4.1762-4.77940.20451360.14983023X-RAY DIFFRACTION100
4.7794-6.01740.20961530.15993030X-RAY DIFFRACTION100
6.0174-36.99560.19821490.16523084X-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)
17.0881-0.2782-2.47877.64080.40824.62570.1045-0.56840.82210.37340.0436-0.1338-0.68870.0983-0.1240.3902-0.0342-0.10860.32430.00590.3834-25.1657-7.19255.5507
25.9772-0.4130.50613.1861-0.47432.1739-0.08340.23550.0887-0.25420.0472-0.0335-0.1018-0.00110.03290.4060.00210.00170.25260.02510.3881-20.9538-7.8176-3.9329
35.60350.04110.48961.5258-0.12690.4081-0.06960.7524-0.6033-0.19270.05160.1149-0.0347-0.18190.03890.3386-0.0043-0.04270.3417-0.04690.4512-32.4327-16.9479-6.1792
46.6753-2.6943-1.38454.62851.74445.152-0.14220.72680.235-0.5050.2537-0.19070.11040.1249-0.04460.4559-0.1047-0.04730.6203-0.06010.5255-35.7107-40.5548-11.8113
57.5532-6.2263.75225.1671-3.25523.0615-0.8555-1.2729-1.91671.04841.81841.27570.178-0.7562-0.93890.6578-0.09190.0120.77420.09641.0803-51.0803-20.178710.8352
68.8883-1.81471.55132.1129-2.9444.47220.5295-0.3762-2.36270.07640.4548-0.95391.3146-0.7719-0.91650.66790.0609-0.07690.67960.11990.8434-39.6759-22.961710.6778
73.32071.66424.79842.62791.21037.9387-0.1759-0.61410.17530.1150.42130.2699-0.0705-0.5895-0.15830.42520.05890.02740.43130.04690.4826-44.3207-11.7398.131
87.0515-2.5519-5.45232.09811.83874.3382-0.491-0.4377-0.9031-0.2939-0.90360.43320.326-1.1471.13690.36930.0527-0.05810.8037-0.06290.6435-53.6279-21.0074-0.677
93.89331.28671.68292.8377-0.37294.3572-0.1008-0.33640.1170.25770.1086-0.24990.5198-0.0334-0.02390.40040.01170.10730.3198-0.05360.4569-15.5755-41.22863.8303
105.8319-4.8659-0.76114.7292.47086.4365-0.1073-1.9439-1.72262.83630.33342.28851.50340.4237-0.31721.6537-0.1451-0.13370.75820.09371.471-23.1877-54.71096.0826
112.4462-2.43420.22653.3234-0.72665.2474-0.2877-0.2884-0.04570.19620.29810.6199-0.0533-0.25330.06090.3172-0.05750.00390.4164-0.05770.6024-32.563-40.75131.1774
123.6511-3.18530.17994.5290.88664.2021-0.00060.2999-0.3559-0.08180.1171-0.130.47190.22-0.14380.4679-0.0240.03250.2931-0.03520.5364-15.1137-47.5554-6.7446
138.83765.38834.21026.11755.43767.3093-0.38120.64410.3429-1.65510.15450.4755-0.51090.21410.30650.53930.09130.12220.61080.02920.4943-16.3156-40.3286-11.6903
145.78153.36921.39575.73371.20582.2481-0.30151.14950.7034-0.63850.3389-0.0773-0.24280.2320.01140.3958-0.00630.12250.40480.08640.558-0.9624-33.6581-8.7134
153.2496-1.9101-0.32736.69461.74290.50850.53741.13940.4636-1.2591-0.5491-0.0897-0.05630.06320.02680.3743-0.05910.07710.47530.06860.4657-24.0417-35.5498-10.7489
160.19170.355-0.4622.03770.05652.62350.0327-0.15661.0973-0.253-0.2108-0.22370.15690.36250.19940.2722-0.00730.06560.2736-00.5798-6.5139-32.16940.3035
178.1922-2.32162.92654.9223-0.85923.06790.22610.5165-0.8711-0.7627-0.20820.4899-0.15850.421-0.07030.4169-0.04610.1850.51390.13810.6323-7.2786-10.0032-11.1376
185.616-0.7711-5.62011.69060.9615.6162-0.1512-2.02432.3886-0.36320.2580.0972-0.51350.4118-0.33750.57660.05510.01480.4824-0.11520.94853.2803-30.431410.0587
197.21772.7608-2.13385.6869-3.52827.5582-0.0120.09331.26110.3037-0.0547-0.4979-0.25440.70680.07230.32630.03090.03550.4402-0.01540.70536.3382-34.71952.5509
206.0599-0.74220.53478.39512.83936.98490.26630.324-0.1706-0.6081-0.0225-0.87260.0560.8815-0.21550.5466-0.0160.01580.61750.07210.3668-4.1645-35.780323.5481
212.9768-0.70010.37768.5825-0.57572.68960.0291-0.4807-0.01210.3155-0.0066-0.8733-0.01460.49570.07330.5860.0117-0.08160.6696-0.01220.4369-3.9553-31.963832.9006
223.49431.04660.8174.7076-0.88362.55640.0905-0.6554-0.07970.3758-0.1040.24930.2954-0.0440.03570.61220.0399-0.02280.52640.06640.2932-16.3659-40.037534.552
238.2781-0.4939-1.11795.94231.81615.5360.62-1.17290.91810.37160.33120.125-0.3831-0.844-0.77820.8343-0.02460.21190.80070.19690.6282-39.8823-35.860939.9489
244.31991.5683-2.18054.6037-5.15955.7751-0.02870.7041-0.8241-0.3292-0.031.13641.2513-1.4754-0.09791.0593-0.2057-0.04070.9362-0.06011.0008-24.8294-50.44117.0394
257.70114.2084-5.92399.7898-6.43428.18550.05950.1246-0.47540.07670.170.19341.4158-0.468-0.11291.0568-0.093-0.10370.4084-0.01940.4504-20.7171-55.684924.1999
266.1805-1.1307-1.25863.6222-3.65336.62750.45550.61120.1054-0.6232-0.04690.909-0.4271-1.0721-0.340.65170.1059-0.06620.6484-0.00550.4134-37.7043-18.335424.3328
272.6612-0.54720.87033.4097-0.61682.0042-0.0568-0.50880.03040.28220.14950.7776-0.1815-0.6427-0.12430.57440.0860.04850.6040.03120.4418-39.6869-23.475831.3127
284.1519-1.2626-2.84485.873-0.11214.2505-0.2515-1.94570.90621.16120.51290.0742-0.61930.3692-0.19930.9010.16970.10390.7244-0.04230.3919-33.6264-17.359640.2084
292.21010.90450.60193.76621.41441.4332-0.0893-0.50180.00760.51090.0505-0.1957-0.5164-0.120.04460.80290.1048-0.04010.563-0.03740.3039-25.7493-13.875635.4882
305.7577-0.63592.50414.4218-1.54263.01930.2705-0.9484-0.45340.42090.0297-0.121-0.2170.4731-0.40290.9609-0.0935-0.2610.7763-0.15870.6654-1.8804-18.2540.2316
313.73710.148-3.18452.29-1.40283.54431.15120.46790.0432-1.7444-0.6524-0.25242.0251-0.6241-0.59611.69870.006-0.31361.2573-0.01290.9271-17.38234.061119.3729
323.89672.36716.24084.94064.19532.01210.19980.86840.0709-1.25030.0303-1.389-1.87741.4924-0.49061.2531-0.1289-0.00260.9561-0.12090.7983-18.0808-6.98818.2576
337.45114.5514.47827.24835.30574.1913-0.5738-0.36620.78920.27530.49550.8255-2.32290.2850.12081.24880.10370.06560.4535-0.01950.443-27.8601-0.241222.0979
346.2158-1.58742.97845.9783-2.35765.6682-0.870.02181.35920.40910.1962-0.6005-1.22790.73540.43641.6348-0.1387-0.02980.5633-0.10170.8661-15.43565.059430.2984
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 196 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 316 )
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 382 )
4X-RAY DIFFRACTION4chain 'A' and (resid 383 through 398 )
5X-RAY DIFFRACTION5chain 'C' and (resid 2065 through 2072 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2073 through 2079 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2080 through 2092 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2093 through 2106 )
9X-RAY DIFFRACTION9chain 'B' and (resid 196 through 229 )
10X-RAY DIFFRACTION10chain 'B' and (resid 230 through 240 )
11X-RAY DIFFRACTION11chain 'B' and (resid 241 through 268 )
12X-RAY DIFFRACTION12chain 'B' and (resid 269 through 296 )
13X-RAY DIFFRACTION13chain 'B' and (resid 297 through 316 )
14X-RAY DIFFRACTION14chain 'B' and (resid 317 through 342 )
15X-RAY DIFFRACTION15chain 'B' and (resid 343 through 363 )
16X-RAY DIFFRACTION16chain 'B' and (resid 364 through 382 )
17X-RAY DIFFRACTION17chain 'B' and (resid 383 through 398 )
18X-RAY DIFFRACTION18chain 'D' and (resid 2065 through 2079 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2080 through 2106 )
20X-RAY DIFFRACTION20chain 'E' and (resid 196 through 240 )
21X-RAY DIFFRACTION21chain 'E' and (resid 241 through 316 )
22X-RAY DIFFRACTION22chain 'E' and (resid 317 through 382 )
23X-RAY DIFFRACTION23chain 'E' and (resid 383 through 398 )
24X-RAY DIFFRACTION24chain 'F' and (resid 2065 through 2079 )
25X-RAY DIFFRACTION25chain 'F' and (resid 2080 through 2106 )
26X-RAY DIFFRACTION26chain 'G' and (resid 199 through 240 )
27X-RAY DIFFRACTION27chain 'G' and (resid 241 through 296 )
28X-RAY DIFFRACTION28chain 'G' and (resid 297 through 316 )
29X-RAY DIFFRACTION29chain 'G' and (resid 317 through 382 )
30X-RAY DIFFRACTION30chain 'G' and (resid 383 through 398 )
31X-RAY DIFFRACTION31chain 'H' and (resid 2065 through 2071 )
32X-RAY DIFFRACTION32chain 'H' and (resid 2072 through 2079 )
33X-RAY DIFFRACTION33chain 'H' and (resid 2080 through 2092 )
34X-RAY DIFFRACTION34chain 'H' and (resid 2093 through 2106 )

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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