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- PDB-5y6o: Crystal structure of DAXX N-terminal four-helix bundle domain (4H... -

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基本情報

登録情報
データベース: PDB / ID: 5y6o
タイトルCrystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX
要素Death domain-associated protein 6,Transcriptional regulator ATRX
キーワードGENE REGULATION / Histone chaperone / Gene repressor
機能・相同性
機能・相同性情報


post-embryonic forelimb morphogenesis / cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / positive regulation of nuclear cell cycle DNA replication / chromosome, subtelomeric region / cellular response to sodium arsenite / chromosome organization involved in meiotic cell cycle ...post-embryonic forelimb morphogenesis / cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / positive regulation of nuclear cell cycle DNA replication / chromosome, subtelomeric region / cellular response to sodium arsenite / chromosome organization involved in meiotic cell cycle / Sertoli cell development / chromo shadow domain binding / DNA translocase activity / cellular response to hydroxyurea / meiotic spindle organization / condensed chromosome, centromeric region / histone H3K9me2/3 reader activity / protein localization to chromosome, telomeric region / nuclear androgen receptor binding / nuclear chromosome / androgen receptor signaling pathway / seminiferous tubule development / forebrain development / : / cellular response to cadmium ion / positive regulation of telomere maintenance / replication fork processing / extrinsic apoptotic signaling pathway via death domain receptors / chromosome, centromeric region / regulation of protein ubiquitination / cellular response to unfolded protein / protein kinase activator activity / subtelomeric heterochromatin formation / pericentric heterochromatin / heterochromatin / transcription regulator inhibitor activity / JNK cascade / heat shock protein binding / SUMOylation of transcription cofactors / Inhibition of DNA recombination at telomere / cellular response to copper ion / DNA damage response, signal transduction by p53 class mediator / molecular condensate scaffold activity / helicase activity / PML body / chromatin DNA binding / multicellular organism growth / HCMV Early Events / p53 binding / Regulation of TP53 Degradation / transcription corepressor activity / nucleosome assembly / cellular response to heat / chromatin organization / regulation of gene expression / spermatogenesis / regulation of apoptotic process / histone binding / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / chromosome, telomeric region / nuclear body / chromatin remodeling / negative regulation of gene expression / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / protein kinase binding / nucleolus / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
類似検索 - 分子機能
ATRX, ADD domain / : / Cysteine Rich ADD domain / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / ADD domain ...ATRX, ADD domain / : / Cysteine Rich ADD domain / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / ADD domain / ADD domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, FYVE/PHD-type / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Transcriptional regulator ATRX / Death domain-associated protein 6
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: 3.1 Å
データ登録者Huang, H. / Patel, D.J.
引用ジャーナル: Nat Commun / 年: 2017
タイトル: Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX
著者: Huang, H. / Patel, D.J.
履歴
登録2017年8月13日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02017年10月25日Provider: repository / タイプ: Initial release
改定 1.12023年11月22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

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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: Death domain-associated protein 6,Transcriptional regulator ATRX
B: Death domain-associated protein 6,Transcriptional regulator ATRX
C: Death domain-associated protein 6,Transcriptional regulator ATRX
D: Death domain-associated protein 6,Transcriptional regulator ATRX
E: Death domain-associated protein 6,Transcriptional regulator ATRX
F: Death domain-associated protein 6,Transcriptional regulator ATRX
G: Death domain-associated protein 6,Transcriptional regulator ATRX
H: Death domain-associated protein 6,Transcriptional regulator ATRX
I: Death domain-associated protein 6,Transcriptional regulator ATRX


分子量 (理論値)分子数
合計 (水以外)123,1819
ポリマ－123,1819
非ポリマー00
水00
1
A: Death domain-associated protein 6,Transcriptional regulator ATRX
B: Death domain-associated protein 6,Transcriptional regulator ATRX
C: Death domain-associated protein 6,Transcriptional regulator ATRX


分子量 (理論値)分子数
合計 (水以外)41,0603
ポリマ－41,0603
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-31 kcal/mol
Surface area17930 Å2
手法PISA
2
D: Death domain-associated protein 6,Transcriptional regulator ATRX
E: Death domain-associated protein 6,Transcriptional regulator ATRX
F: Death domain-associated protein 6,Transcriptional regulator ATRX


分子量 (理論値)分子数
合計 (水以外)41,0603
ポリマ－41,0603
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-33 kcal/mol
Surface area17980 Å2
手法PISA
3
G: Death domain-associated protein 6,Transcriptional regulator ATRX
H: Death domain-associated protein 6,Transcriptional regulator ATRX
I: Death domain-associated protein 6,Transcriptional regulator ATRX


分子量 (理論値)分子数
合計 (水以外)41,0603
ポリマ－41,0603
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-32 kcal/mol
Surface area17570 Å2
手法PISA
単位格子
Length a, b, c (Å)78.666, 78.666, 503.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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要素

#1: タンパク質
Death domain-associated protein 6,Transcriptional regulator ATRX / Daxx / hDaxx / ETS1-associated protein 1 / EAP1 / Fas death domain-associated protein / ATP- ...Daxx / hDaxx / ETS1-associated protein 1 / EAP1 / Fas death domain-associated protein / ATP-dependent helicase ATRX / X-linked helicase II / X-linked nuclear protein / XNP / Znf-HX


分子量: 13686.805 Da / 分子数: 9 / 断片: UNP residues 50-144,UNP residues 1265-1288 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DAXX, BING2, DAP6, ATRX, RAD54L, XH2 / プラスミド: RSFDuet
詳細 (発現宿主): A modified RSFDuet plasmid with an N-terminal 6xHis-SUMO tag.
発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-CodonPlus(DE3)-RIL / 参照: UniProt: Q9UER7, UniProt: P46100, DNA helicase

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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: 3.65 Å3/Da / 溶媒含有率: 69.61 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.8
詳細: The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using ...詳細: The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.

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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: APS / ビームライン: 24-ID-C / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年2月10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: 0.9795 Å / 相対比: 1
反射解像度: 3.1→167.74 Å / Num. obs: 34423 / % possible obs: 99.9 % / 冗長度: 8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.033 / Rrim(I) all: 0.097 / Net I/σ(I): 14.4
反射 シェル解像度: 3.1→3.27 Å / 冗長度: 6.9 % / Rmerge(I) obs: 1.344 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4917 / CC1/2: 0.615 / Rpim(I) all: 0.527 / Rrim(I) all: 1.449 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.8.2_1309精密化
XDSdata processing
pointless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: 2KZS

2kzs


解像度: 3.1→83.869 Å / SU ML: 0.55 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.44
Rfactor反射数%反射
Rfree0.2972 1730 5.05 %
Rwork0.2238 --
obs0.2274 34234 99.64 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 72.9 Å2
精密化ステップサイクル: LAST / 解像度: 3.1→83.869 Å
タンパク質核酸リガンド溶媒全体
原子数7467 0 0 0 7467
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.017595
X-RAY DIFFRACTIONf_angle_d1.43410248
X-RAY DIFFRACTIONf_dihedral_angle_d18.9582826
X-RAY DIFFRACTIONf_chiral_restr0.0991179
X-RAY DIFFRACTIONf_plane_restr0.0071310
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.19130.39331460.35072568X-RAY DIFFRACTION97
3.1913-3.29430.38141400.32932661X-RAY DIFFRACTION100
3.2943-3.4120.37761500.32792683X-RAY DIFFRACTION100
3.412-3.54870.39011290.30692611X-RAY DIFFRACTION100
3.5487-3.71020.34431490.26612677X-RAY DIFFRACTION100
3.7102-3.90580.26991180.2372715X-RAY DIFFRACTION100
3.9058-4.15050.32451500.22522683X-RAY DIFFRACTION100
4.1505-4.47090.31051270.20982684X-RAY DIFFRACTION100
4.4709-4.92080.25011690.19012727X-RAY DIFFRACTION100
4.9208-5.63270.27761600.2022738X-RAY DIFFRACTION100
5.6327-7.09610.35361490.2492778X-RAY DIFFRACTION100
7.0961-83.89980.25221430.18892979X-RAY DIFFRACTION99
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)
11.0317-1.77180.7765.93962.88859.22290.57650.41110.4484-0.84920.22060.0144-0.979-0.66-0.44750.3368-0.0661-0.03640.3250.01080.553715.97591.477314.1362
24.68310.01250.02136.6959-3.33517.48160.703-1.14620.31180.56490.1851-0.6076-1.54160.4486-0.62420.6891-0.05460.10980.8506-0.32650.305920.10045.01423.3333
37.17664.9121-1.42653.8829-2.53225.0256-0.58270.2337-0.6944-1.26570.685-1.09890.6036-0.2982-0.07550.62450.15810.1910.7219-0.0330.671821.6326-4.772915.2854
42.9774-0.8167-1.36674.45891.8962.2403-0.1717-0.45470.3274-0.38130.5182-0.4098-0.90310.8523-0.39950.96850.012-0.05870.724-0.18170.419417.789217.505524.3811
53.33290.79810.59746.47021.1234.69190.35081.280.3162-0.5030.0928-0.70180.28470.3388-0.24240.71540.03590.15140.72140.0130.2179-4.59120.5549.6395
62.8452-2.0622-3.59327.1812.04068.79710.0752-1.4049-0.3530.88520.344-0.76650.79790.4489-0.48620.47120.1611-0.1080.5010.04650.3464-0.86520.6422.318
73.5065-4.5972-1.9962.01582.49126.27320.65950.8363-0.56-1.6666-0.90621.9271-0.2897-0.82640.24160.51360.08280.05260.8264-0.0920.3902-11.8162-0.741915.6856
87.0733-3.42782.33662.69060.87255.25820.6463-0.3923-0.18170.78320.1627-0.85231.15540.7555-0.70090.7531-0.00120.170.83110.09770.206314.2522-8.195329.2416
90.64090.40140.350.3033-0.02972.921-0.22510.7683-0.6589-0.4350.391-0.58320.47340.31190.20191.0308-0.06660.33211.4167-0.87890.31424.709419.60447.2784
100.84831.6183-1.23344.4568-0.54355.8085-0.12190.3507-0.7009-0.00850.0512-0.1624-0.19090.59090.12660.4335-0.0490.19740.6244-0.19750.66333.122717.770818.3887
116.04331.98011.89883.8254-0.54853.6256-0.32670.71260.564-0.75710.56641.4969-1.3535-0.8127-0.161.12490.2546-0.09780.43980.09780.6637-5.524229.333311.8282
120.687-0.4037-0.7431.00940.73440.9079-0.22860.29680.6028-0.73540.585-0.8748-0.60580.5318-0.15051.5527-0.54440.5540.6886-0.33191.1299.196328.5756.0038
136.0059-2.2074.76325.5555-3.93554.78980.27520.57180.4324-0.7906-0.7543-0.99240.17120.57210.5470.7376-0.19190.26670.4516-0.18110.965411.35425.745815.5149
144.59075.0565-3.62736.1133-4.76013.91780.16220.13810.185-0.74020.15380.5417-0.90910.0301-0.28380.97830.2252-0.02610.7711-0.78710.7837-9.08525.143121.823
155.41053.16291.9815.4697-0.0398.70180.0582-0.4384-0.39580.80770.47450.37950.9108-1.0919-0.31060.7751-0.02360.31750.81570.04490.4728-8.87443.063130.7357
162.3535-2.55541.29063.8819-1.7564.2759-0.4993-1.1366-0.61881.14130.11431.27420.30010.0320.47380.8207-0.23890.24991.3630.00060.744915.463453.702444.3437
177.16765.2893-2.03234.2748-0.54343.0108-0.54870.6620.8986-0.44860.47562.0784-0.7714-0.0751-0.15171.2948-0.6917-0.33340.78050.38880.85977.576559.817629.4174
184.60220.07640.06095.4447-0.38496.80910.2293-0.32580.05160.23290.349-0.3133-0.93711.0281-0.60870.9357-0.35350.04840.9184-0.04090.379320.756458.654839.9259
191.3249-0.0981-0.55850.3854-0.5731.25560.2147-0.1085-0.1151-0.37650.6715-0.1128-0.14590.09290.33190.7582-0.88250.75851.6644-0.0041.517928.380243.839531.6123
204.6988-0.5113.24663.8745-1.30588.27330.611.6404-0.7872-0.2922-0.6708-0.33180.7156-0.1364-0.12451.12850.03180.22080.874-0.09930.453310.529437.062124.9796
215.85091.0618-0.80657.11831.27173.858-0.3625-1.9201-0.52861.2073-0.52680.0308-0.33120.09060.26340.9250.1529-0.1740.80830.07280.2654-4.078453.124547.4843
225.16530.9763-0.8245.3025-2.75571.45430.41410.81521.0494-0.8711-0.2607-0.7018-0.65470.5298-0.21670.2729-0.06760.17820.62540.31850.4759-1.411156.487335.5003
231.68852.2364-2.23277.7571-7.00457.73210.25920.15410.17930.255-0.08470.0852-1.3048-0.6104-0.12520.73780.1239-0.02031.334-0.66040.5005-7.606767.235147.8316
246.5241.80230.88995.3287-0.59285.44230.5789-0.0877-0.04410.0281-0.29150.83050.1896-0.7037-0.24650.77220.2937-0.12510.5443-0.08040.327-13.200353.366141.9894
250.03770.4087-0.26774.5162-2.31083.3645-0.2235-0.6088-0.38290.47540.50990.79490.0376-0.08590.21430.79490.4011-0.1411.01720.69880.69870.016173.745138.1919
261.2482-0.0622-0.34011.8085-2.43043.43080.26120.18010.0117-0.2096-0.0262-0.1209-0.33390.56740.56091.6954-0.90210.0051.30790.42480.157317.973464.392326.3786
273.79241.8541-2.18177.9437-3.97242.7332-0.4457-0.0457-0.11081.15520.4561-0.33710.1096-0.1148-0.0680.95060.0134-0.01830.6121-0.13390.42113.290735.117841.0805
282.4181-0.97661.6885.9092-2.82992.82690.53890.7459-0.91440.3619-0.2244-0.60330.8782.4983-0.26460.755-0.0238-0.01461.0447-0.08550.522311.704629.698738.7122
292.5302-0.43631.63651.3314-0.56562.06630.1461-0.25590.083-0.0550.3970.20070.2494-0.16050.27941.1517-0.2336-0.37151.1134-0.75190.0555-12.336336.655630.7879
303.4638-2.27450.47064.06180.38854.37150.2725-0.2333-0.3413-0.20710.40220.38040.2997-1.5044-0.70571.07380.1368-0.23291.3038-0.00120.176-9.853955.921326.7123
312.0641-2.7163-2.36113.88662.15276.16350.4352-0.0660.3737-1.45860.1683-0.50620.80990.6579-0.28961.3044-0.21930.3430.4363-0.00730.6461-4.411734.066563.6114
326.51154.9660.81026.8373.52532.8670.3985-0.27720.3556-0.54170.05840.84170.1052-0.6621-0.5340.57490.0186-0.07320.41410.20240.6417-3.043341.229780.45
337.32613.0913.69754.93835.03745.18940.3083-0.4163-1.18381.55320.3206-0.77462.20460.6039-0.62460.76590.10090.01170.50210.07530.5331-2.56230.043376.9502
348.73423.32831.36219.18555.14064.78220.37090.7814-0.9993-0.19610.4434-0.6711.4790.486-0.6361.26720.2814-0.03311.0509-0.43240.6967-5.67922.491465.2292
358.3606-1.7260.78742.69192.00032.04770.0338-0.15860.176-0.69810.57911.5164-0.126-0.572-0.51060.9413-0.19720.18190.53490.13210.5118-14.093736.88766.3675
364.4739-2.26782.0932.2792-0.38054.057-0.2341-0.6885-0.87450.51710.12750.42061.42130.1915-0.05981.06010.04620.130.72250.23430.36042.076229.404977.5084
375.9707-2.60912.21324.7901-1.34470.8776-0.43530.6808-0.58130.63810.19750.0331-0.7105-0.40080.1810.84150.2356-0.11650.7267-0.1470.33643.29152.531773.3129
386.7327-1.2035-5.49574.64770.68658.64550.10190.0741.5247-0.75890.4605-0.1752-0.77080.3816-0.59291.2614-0.0671-0.13760.52050.00870.42743.650562.506871.9294
396.28311.8625-1.91810.6691-0.76631.13020.0883-0.49641.1786-0.16520.4923-0.006-0.53160.676-0.24660.77570.1491-0.02760.5858-0.17730.3687.787659.000680.4631
404.17751.06151.3472.209-1.06741.55790.4807-0.532-0.54750.29010.33421.204-0.3381-1.0776-0.32790.9246-0.04840.34551.054-0.34830.3115-11.943837.755484.7303
412.47880.4246-0.7253.3887-0.14944.36310.58770.2989-0.1365-0.9886-0.2749-0.1246-0.36850.8345-0.3011.01450.2303-0.0321.02990.00830.447818.679636.933165.1244
422.1238-1.07710.70223.3746-2.88623.57910.38910.4827-0.4331-0.4888-0.491-0.29010.6650.3408-0.2831.22090.6506-0.03280.7333-0.05570.132418.794728.115469.7084
430.653-0.493-0.85962.2472-0.44581.79160.5247-0.20520.31870.7257-0.3043-0.58510.25240.8614-0.11551.05620.1348-0.2351.7545-0.18170.326812.846651.829986.6209
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 133 )
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 164 )
5X-RAY DIFFRACTION5chain 'B' and (resid 56 through 77 )
6X-RAY DIFFRACTION6chain 'B' and (resid 78 through 93 )
7X-RAY DIFFRACTION7chain 'B' and (resid 94 through 136 )
8X-RAY DIFFRACTION8chain 'B' and (resid 137 through 164 )
9X-RAY DIFFRACTION9chain 'C' and (resid 57 through 80 )
10X-RAY DIFFRACTION10chain 'C' and (resid 81 through 93 )
11X-RAY DIFFRACTION11chain 'C' and (resid 94 through 102 )
12X-RAY DIFFRACTION12chain 'C' and (resid 103 through 118 )
13X-RAY DIFFRACTION13chain 'C' and (resid 119 through 135 )
14X-RAY DIFFRACTION14chain 'C' and (resid 136 through 146 )
15X-RAY DIFFRACTION15chain 'C' and (resid 147 through 164 )
16X-RAY DIFFRACTION16chain 'D' and (resid 58 through 77 )
17X-RAY DIFFRACTION17chain 'D' and (resid 78 through 82 )
18X-RAY DIFFRACTION18chain 'D' and (resid 83 through 136 )
19X-RAY DIFFRACTION19chain 'D' and (resid 137 through 146 )
20X-RAY DIFFRACTION20chain 'D' and (resid 147 through 165 )
21X-RAY DIFFRACTION21chain 'E' and (resid 58 through 77 )
22X-RAY DIFFRACTION22chain 'E' and (resid 78 through 93 )
23X-RAY DIFFRACTION23chain 'E' and (resid 94 through 102 )
24X-RAY DIFFRACTION24chain 'E' and (resid 103 through 136 )
25X-RAY DIFFRACTION25chain 'E' and (resid 137 through 147 )
26X-RAY DIFFRACTION26chain 'E' and (resid 148 through 165 )
27X-RAY DIFFRACTION27chain 'F' and (resid 58 through 103 )
28X-RAY DIFFRACTION28chain 'F' and (resid 104 through 136 )
29X-RAY DIFFRACTION29chain 'F' and (resid 137 through 148 )
30X-RAY DIFFRACTION30chain 'F' and (resid 149 through 163 )
31X-RAY DIFFRACTION31chain 'G' and (resid 57 through 73 )
32X-RAY DIFFRACTION32chain 'G' and (resid 74 through 82 )
33X-RAY DIFFRACTION33chain 'G' and (resid 83 through 92 )
34X-RAY DIFFRACTION34chain 'G' and (resid 93 through 102 )
35X-RAY DIFFRACTION35chain 'G' and (resid 103 through 119 )
36X-RAY DIFFRACTION36chain 'G' and (resid 120 through 165 )
37X-RAY DIFFRACTION37chain 'H' and (resid 57 through 93 )
38X-RAY DIFFRACTION38chain 'H' and (resid 94 through 119 )
39X-RAY DIFFRACTION39chain 'H' and (resid 120 through 136 )
40X-RAY DIFFRACTION40chain 'H' and (resid 137 through 164 )
41X-RAY DIFFRACTION41chain 'I' and (resid 58 through 118 )
42X-RAY DIFFRACTION42chain 'I' and (resid 119 through 135 )
43X-RAY DIFFRACTION43chain 'I' and (resid 136 through 164 )

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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