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- PDB-5j9u: Crystal structure of the NuA4 core complex -

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基本情報

登録情報
データベース: PDB / ID: 5j9u
タイトルCrystal structure of the NuA4 core complex
要素
  • Chromatin modification-related protein EAF6
  • Chromatin modification-related protein YNG2
  • Enhancer of polycomb-like protein 1
  • Histone acetyltransferase ESA1
キーワードTRANSFERASE / NuA4 / nucleosome / histone / acetylation
機能・相同性
機能・相同性情報


PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / positive regulation of triglyceride biosynthetic process ...PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / positive regulation of triglyceride biosynthetic process / SUMOylation of transcription cofactors / DNA-templated transcription elongation / histone H4 acetyltransferase activity / rDNA heterochromatin formation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / histone H3K4me3 reader activity / protein-lysine-acetyltransferase activity / NuA4 histone acetyltransferase complex / : / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone acetyltransferase activity / histone acetyltransferase / 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 / meiotic cell cycle / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / nucleosome / regulation of cell cycle / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / zinc ion binding / nucleus / cytosol
類似検索 - 分子機能
N-acetyl transferase-like / Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Enhancer of polycomb protein / : / MYST, zinc finger domain ...N-acetyl transferase-like / Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Enhancer of polycomb protein / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / Chromo-like domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Zinc finger, PHD-type, conserved site / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Aminopeptidase / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Zinc finger, FYVE/PHD-type / Arc Repressor Mutant, subunit A / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Chromatin modification-related protein YNG2 / Enhancer of polycomb-like protein 1 / Chromatin modification-related protein EAF6 / Histone acetyltransferase ESA1
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.95 Å
データ登録者Chen, Z.C. / Xu, P.
引用ジャーナル: Mol Cell / 年: 2016
タイトル: The NuA4 Core Complex Acetylates Nucleosomal Histone H4 through a Double Recognition Mechanism.
著者: Peng Xu / Chengmin Li / Zhihong Chen / Shuanying Jiang / Shilong Fan / Jiawei Wang / Junbiao Dai / Ping Zhu / Zhucheng Chen /
要旨: NuA4 catalyzes the acetylation of nucleosomes at histone H4, which is a well-established epigenetic event, controlling many genomic processes in Saccharomyces cerevisiae. Here we report the crystal ...NuA4 catalyzes the acetylation of nucleosomes at histone H4, which is a well-established epigenetic event, controlling many genomic processes in Saccharomyces cerevisiae. Here we report the crystal structures of the NuA4 core complex and a cryoelectron microscopy structure with the nucleosome. The structures show that the histone-binding pocket of the enzyme is rearranged, suggesting its activation. The enzyme binds the histone tail mainly through the target lysine residue, with a preference for a small residue at the -1 position. The complex engages the nucleosome at the dish face and orients its catalytic pocket close to the H4 tail to achieve selective acetylation. The combined data reveal a space-sequence double recognition mechanism of the histone tails by a modifying enzyme in the context of the nucleosome.
履歴
登録2016年4月11日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02016年10月26日Provider: repository / タイプ: Initial release
改定 1.12024年10月23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 / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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集合体

登録構造単位
E: Histone acetyltransferase ESA1
F: Chromatin modification-related protein EAF6
G: Enhancer of polycomb-like protein 1
A: Histone acetyltransferase ESA1
I: Histone acetyltransferase ESA1
N: Enhancer of polycomb-like protein 1
C: Enhancer of polycomb-like protein 1
D: Chromatin modification-related protein YNG2
B: Chromatin modification-related protein EAF6
J: Chromatin modification-related protein EAF6
H: Chromatin modification-related protein YNG2
K: Chromatin modification-related protein YNG2


分子量 (理論値)分子数
合計 (水以外)315,41312
ポリマ－315,41312
非ポリマー00
水00
1
E: Histone acetyltransferase ESA1
F: Chromatin modification-related protein EAF6
G: Enhancer of polycomb-like protein 1
H: Chromatin modification-related protein YNG2


分子量 (理論値)分子数
合計 (水以外)105,1384
ポリマ－105,1384
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18610 Å2
ΔGint-104 kcal/mol
Surface area41700 Å2
手法PISA
2
A: Histone acetyltransferase ESA1
C: Enhancer of polycomb-like protein 1
D: Chromatin modification-related protein YNG2
B: Chromatin modification-related protein EAF6


分子量 (理論値)分子数
合計 (水以外)105,1384
ポリマ－105,1384
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18200 Å2
ΔGint-105 kcal/mol
Surface area41540 Å2
手法PISA
3
I: Histone acetyltransferase ESA1
N: Enhancer of polycomb-like protein 1
J: Chromatin modification-related protein EAF6
K: Chromatin modification-related protein YNG2


分子量 (理論値)分子数
合計 (水以外)105,1384
ポリマ－105,1384
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18150 Å2
ΔGint-105 kcal/mol
Surface area41470 Å2
手法PISA
単位格子
Length a, b, c (Å)217.909, 189.889, 173.558
Angle α, β, γ (deg.)90.00, 113.61, 90.00
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質 Histone acetyltransferase ESA1


分子量: 36557.867 Da / 分子数: 3 / 断片: UNP residues 141-445) / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: ESA1, YOR244W, O5257 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q08649, histone acetyltransferase
#2: タンパク質 Chromatin modification-related protein EAF6 / ESA1-associated factor 6


分子量: 12915.704 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: EAF6, YJR082C, J1854 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P47128
#3: タンパク質 Enhancer of polycomb-like protein 1


分子量: 41835.215 Da / 分子数: 3 / 断片: UNP residues 50-400 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: EPL1, YFL024C / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P43572
#4: タンパク質 Chromatin modification-related protein YNG2 / ESA1-associated factor 4 / ING1 homolog 2


分子量: 13828.894 Da / 分子数: 3 / 断片: UNP residues 1-120 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: YNG2, EAF4, NBN1, YHR090C / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P38806
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: 5.22 Å3/Da / 溶媒含有率: 76.42 %
結晶化温度: 298 K / 手法: 蒸発脱水法
詳細: 100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol

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データ収集

回折平均測定温度: 173 K
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL17U / 波長: 0.987 Å
検出器タイプ: ADSC QUANTUM 4r / 検出器: CCD / 日付: 2014年4月20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: 0.987 Å / 相対比: 1
反射解像度: 2.95→30 Å / Num. obs: 106917 / % possible obs: 78.4 % / 冗長度: 2.8 % / Net I/σ(I): 10.3

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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
HKL-2000データスケーリング
autoSHARP位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.95→29.686 Å / SU ML: 0.37 / 交差検証法: FREE R-VALUE / σ(F): 1.41 / 位相誤差: 27.94
Rfactor反射数%反射
Rfree0.2462 1993 1.86 %
Rwork0.2157 --
obs0.2162 106917 78.84 %
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: 2.95→29.686 Å
タンパク質核酸リガンド溶媒全体
原子数19676 0 0 0 19676
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00320089
X-RAY DIFFRACTIONf_angle_d0.69427054
X-RAY DIFFRACTIONf_dihedral_angle_d14.64312290
X-RAY DIFFRACTIONf_chiral_restr0.0432902
X-RAY DIFFRACTIONf_plane_restr0.0043485
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.02370.3552450.29672362X-RAY DIFFRACTION25
3.0237-3.10540.3007720.2913831X-RAY DIFFRACTION40
3.1054-3.19670.3447940.29754946X-RAY DIFFRACTION52
3.1967-3.29970.29261160.29256093X-RAY DIFFRACTION64
3.2997-3.41750.34751400.28477389X-RAY DIFFRACTION78
3.4175-3.55410.31811640.26978633X-RAY DIFFRACTION91
3.5541-3.71560.31761710.24559005X-RAY DIFFRACTION94
3.7156-3.91110.25011720.22759027X-RAY DIFFRACTION95
3.9111-4.15550.23681710.21319001X-RAY DIFFRACTION95
4.1555-4.47540.21521700.18958958X-RAY DIFFRACTION94
4.4754-4.92390.22891700.17938927X-RAY DIFFRACTION94
4.9239-5.63220.22271700.19339003X-RAY DIFFRACTION95
5.6322-7.080.22391710.22528969X-RAY DIFFRACTION94
7.08-29.68720.19361670.17058780X-RAY DIFFRACTION91
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)
13.00692.7510.24675.36990.36192.17750.01370.4223-0.2261-0.37960.1412-0.40060.33050.0845-0.12080.38060.06030.07920.31960.01070.481910.620959.465976.184
21.3929-0.4829-0.22982.00131.5224.353-0.02640.3370.0165-0.41720.0823-0.42480.14930.1527-0.07410.2119-0.06230.09730.23820.0420.362511.22374.202571.1775
32.06270.3242-0.39742.37420.15781.4027-0.0667-0.20430.03120.0792-0.05050.10430.1275-0.03130.08180.1442-0.04440.01480.22590.04620.28955.181573.700884.7501
44.62123.69448.06288.37996.08162.00090.09870.10250.1474-0.4921-0.1202-1.0879-0.44141.77150.03120.2902-0.10530.26660.48010.17260.785718.815485.686175.2348
53.0757-0.2232-0.68331.89480.41712.9358-0.1565-0.5492-0.27310.2342-0.0741-0.2353-0.020.11970.21940.2455-0.0442-0.05470.26020.01150.395413.002376.948495.5073
65.5765-1.2371-4.50033.1540.09735.47480.233-0.75690.95630.4984-0.08390.1671-0.7180.2205-0.14940.74-0.1883-0.21770.7758-0.16590.67717.887188.779114.4374
74.7996-1.8330.19133.7921-2.45735.004-0.1044-0.48330.01070.4736-0.0071-0.46540.04090.43170.11570.6185-0.0756-0.21460.7397-0.01910.540916.774178.6229114.4927
81.9150.04360.20980.6254-0.54251.84110.1421-0.13660.15160.3529-0.0806-0.3042-0.12750.5298-0.12620.4848-0.0452-0.11180.4378-0.13490.702914.721584.3905101.7375
91.66841.5415-0.06632.3529-0.81580.6162-0.02610.7108-0.2932-0.53280.0037-0.2630.17960.02310.02351.3893-0.3402-0.1251.1442-0.06780.87299.6205111.893827.974
103.45161.5561-5.40611.1184-3.45172.0060.03240.50410.2847-0.19120.010.1737-0.3273-0.2011-0.11440.6106-0.1502-0.23920.60050.01630.5328-2.6522112.794951.121
118.42542.1828-2.3347.3554-0.63670.64490.0495-0.070.46680.2399-0.05090.3644-0.4415-0.182-0.02440.50410.02940.08590.2450.0480.5907-13.2629108.761973.419
128.76011.5167-6.2851.59321.44289.3217-0.0331-0.17760.51630.207-0.02520.7202-0.5991-0.70650.09010.8161-0.0266-0.10870.9321-0.09120.7694-16.7295100.702984.0851
132.00265.5006-0.56762.0013-3.23112.00180.3879-1.2183-0.23271.5299-0.38550.37380.0414-0.04060.00130.688-0.1346-0.07920.5722-0.06090.4396-10.677196.649583.8105
140.00060.00230.01120.00580.03120.14920.2977-0.4849-0.12610.8514-0.4676-0.2171-0.24740.2050.14760.8341-0.085-0.05370.8606-0.27790.9974-11.3245104.461886.1924
158.05592.3954-2.39158.1896-4.48475.28850.008-0.53250.48410.4105-0.0174-0.018-0.59130.2379-0.03410.47570.00060.01290.1823-0.1050.565-2.8597108.967175.0078
168.3354.5893-5.97822.7721-2.91044.8790.3446-0.10472.1158-0.0001-0.1571-0.6927-1.86120.8363-0.20521.001-0.1081-0.01790.649-0.05091.10430.0368116.461272.0426
172.39371.4518-1.26832.94920.26551.18190.34530.1771-0.20340.3422-0.3463-0.85980.36890.91560.09680.60420.0809-0.26420.77760.08531.049440.586352.848192.4373
182.00182.00091.99982.00311.99952.00020.4084-0.3628-0.76690.6674-0.03990.29140.71890.0872-0.35790.4102-0.0589-0.08510.64520.19660.869330.223364.606395.0482
191.0060.09370.22961.02640.45310.57690.05320.2017-0.005-0.3711-0.049-0.5075-0.02460.28080.01540.3793-0.03790.13620.32960.04410.57513.105773.922167.6454
203.21522.0326-0.69444.4599-2.00332.3944-0.10790.77990.2273-0.53850.20780.365-0.0240.0295-0.06110.5884-0.0379-0.04930.5545-0.0070.3891-7.679166.511453.3889
216.63670.9653.73254.8945-1.58958.24180.26581.1936-1.0668-1.097-0.1777-0.22651.02570.4499-0.05370.59180.01550.02350.5105-0.14170.745-3.830789.958857.9971
221.3934-0.43210.06375.3367-2.34573.9979-0.07240.41610.1173-0.78070.29230.08520.00310.1089-0.14720.6899-0.05570.02220.4674-0.03290.3516-2.609365.581352.0821
234.1604-1.9854-0.57892.70920.19351.25620.05750.003-0.0820.0974-0.05950.6733-0.0287-0.4085-0.00140.3726-0.04650.0450.39960.00680.7129-8.698861.754282.4344
242.88231.4964-1.96872.0908-1.55463.0124-0.08250.32740.0147-0.25830.07420.1419-0.4030.0249-0.0150.4163-0.0781-0.11120.3754-0.00510.2862-3.991104.479458.7641
252.00149.5911-0.77282.0018-0.65418.15990.1582-0.189-1.17950.3168-0.0658-0.19320.8211-0.15-0.09040.2594-0.0309-0.02740.36150.05280.4499-18.544381.732881.9085
267.00331.7627-1.48731.2938-2.16834.0880.0251-0.2922-0.32040.2039-0.0388-0.09540.0025-0.01840.0280.23830.00610.01010.28330.01630.4924-3.953892.440378.7595
278.36256.852-4.91266.3784-3.69133.02020.1636-0.17280.09790.313-0.1943-0.1342-0.47950.403-0.01360.5269-0.1536-0.13430.36310.01370.54948.9701107.213667.3915
281.0427-0.54320.9955.1604-2.47115.0842-0.01970.1072-0.01050.00670.09350.214-0.0669-0.1767-0.08070.4956-0.1921-0.02870.5470.1050.485516.2406122.488647.7792
293.38274.3662-2.84467.1181-4.50083.0112-0.00260.022-0.1907-0.1359-0.0377-0.3102-0.08380.44360.04630.4611-0.116-0.03510.55860.01480.285717.1268109.532452.9917
301.9997-1.1480.26485.68020.26235.18210.0344-0.0574-0.25350.0162-0.0602-0.2244-0.0240.14070.04910.2713-0.1976-0.09810.2863-0.00490.3342-2.324894.06966.6852
312.00369.902-0.72638.78440.38951.5544-0.1460.4089-0.2757-0.3410.038-0.23450.23580.09980.05130.2524-0.02530.05660.29310.02920.3956-18.895784.733171.8825
322.00324.70370.24127.3849-1.03749.89420.10370.2225-0.241-0.0222-0.11890.39830.1148-0.22250.0610.17840.01860.14860.49350.09880.7216-30.044483.530775.7983
331.6147-1.35650.31252.3421-2.08067.43590.0858-0.23050.4140.219-0.0071-0.0186-0.3443-0.0304-0.0550.394-0.04850.06140.4111-0.1210.4684-10.021581.1316110.0685
341.40281.37871.31352.00041.99982.001-0.33730.24370.8293-0.79780.27040.0152-1.34650.46130.09820.918-0.0761-0.08270.7256-0.02540.555-12.165687.1029108.7162
350.5554-0.11510.06561.3967-0.23830.59790.2194-0.46880.25060.35950.0154-0.3107-0.3102-0.0159-0.00710.4995-0.0365-0.16580.5356-0.5168-1.3721-16.331970.4962119.9133
361.99981.9985-0.0442.0001-6.59362.0015-0.3211-1.50330.3311.020.6402-0.63250.22860.621-0.33190.8628-0.0499-0.09410.8198-0.13910.223-16.134972.6744136.2798
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485.05051.0589-3.35620.80641.47872.002-0.0906-0.3753-0.38050.32560.2072-0.09720.49590.2932-0.08571.1057-0.17910.00150.93650.1540.2596-39.912750.2631138.8202
493.57752.35780.53172.3251-0.01910.703-0.1298-0.23510.19410.1362-0.1917-0.2049-0.2150.22430.17390.8696-0.0404-0.29691.1017-0.10340.66717.437681.2954123.24
500.24080.25560.03391.0697-0.23280.7666-0.0092-0.4340.31160.33850.1149-0.0416-0.3856-0.0702-0.06630.7388-0.01560.03720.7699-0.17220.3865-24.62782.5062124.2202
511.52050.1973-0.58520.76111.6026.69760.0088-0.15980.29540.09050.02910.2687-0.1892-0.81630.02770.43980.02380.02810.75680.04050.5544-38.293986.6353105.8932
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581.71060.30212.49491.74783.21858.1797-0.03460.0154-0.0004-0.08730.0705-0.1135-0.31110.4239-0.03180.6124-0.0853-0.01750.62030.12210.3226-31.032555.9406123.029
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601.03971.83563.14443.31256.16152.0007-0.0555-0.57620.19160.5530.0164-0.5033-0.18590.23820.05460.97950.01070.05110.9774-0.00660.3665-39.963864.7693152.811
617.8920.0308-5.38660.284-0.28643.9241-0.15980.0199-0.35920.08250.0190.21840.3972-0.27430.1381.2686-0.09410.22871.454-0.0340.3156-50.296669.6181162.2167
621.2228-1.807-0.42482.86950.84530.37140.00380.07580.0004-0.0968-0.0316-0.11490.04670.1058-0.01831.48460.11130.20871.5353-0.13540.1809-51.630377.9417166.4788
631.0073-0.6281-0.86621.34650.62290.740.033-0.58370.25510.49460.0742-0.032-0.05960.2692-0.1130.9584-0.25810.11351.0145-0.0644-0.0065-39.985369.6012140.4357
644.78371.79442.35045.5143.22538.9642-0.14150.02360.1386-0.3092-0.10580.2109-0.352-0.07130.18670.35910.05730.04190.36080.00050.2647-42.259756.1468107.358
654.13923.36365.34143.15874.57577.02060.05930.4415-0.2477-0.40060.08690.2594-0.0377-0.0808-0.13580.6979-0.08980.1140.5296-0.08640.7506-23.913342.2414105.8239
662.8497-1.33611.1445.16290.05341.8729-0.1861-0.8226-0.39140.68750.18260.220.2781-0.21080.03720.48550.04460.02850.41010.06710.4386-5.607934.37111.0008
671.28850.2521-0.47721.5055-0.14921.3378-0.0544-0.1681-0.23630.1928-0.0417-0.04290.12150.08620.05320.28920.0814-0.02240.22240.03840.4742-1.171530.408296.0879
682.28480.37410.22841.4531-0.30981.4544-0.22120.00780.11040.098-0.0807-0.6134-0.12550.26070.23660.2710.052-0.02250.27610.04560.586215.879541.729295.2698
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700.94430.86110.10945.2647-0.44611.14280.0077-0.24340.15920.5779-0.1469-0.4135-0.02020.44510.12530.4791-0.0023-0.26310.6830.17151.480537.921949.428899.7448
712.0048-2.43575.71332.1629-3.34935.78130.0065-0.3562-0.32750.21980.0807-0.43990.25250.1016-0.15850.29330.09780.00030.5925-0.16631.098823.138630.142191.2424
720.7160.62820.99692-0.97493.74680.08650.3927-0.268-0.2125-0.15160.4992-0.0444-0.30170.07160.38480.0307-0.00460.31220.03050.3915-1.291344.028979.7138
731.67821.915-2.87552.1864-3.28274.92730.0993-1.0346-0.63110.95120.04290.9630.6324-1.1915-0.14611.0195-0.05820.10231.0262-0.10481.221-18.0139-28.842377.9313
741.66770.2409-0.77350.0351-0.11350.3583-0.14270.1836-0.87980.1385-0.0160.83010.9358-1.06330.16830.4506-0.0787-0.0170.50540.08250.945-16.0617-21.914172.1839
754.11555.4830.40712.0105-1.89181.0471-0.06360.126-0.105-0.42150.27880.21050.1689-0.2929-0.12210.4495-0.0112-0.08210.3622-0.13531.002-10.3361-4.88164.5631
762.41623.805-1.32626.9596-1.58461.0001-0.13970.3457-0.148-0.49770.05210.05460.17520.02170.05030.46440.0762-0.01390.4103-0.14440.6759-3.84814.771558.0089
776.00680.54093.09181.99990.99364.8038-0.06280.3480.6746-0.51990.1053-0.3172-0.75320.2872-0.03810.57810.00320.15440.4492-0.17980.8399-2.659728.905760.2409
782.04080.45890.33223.314-2.33941.8660.10690.21060.9474-0.45880.1019-0.8046-0.85220.4605-0.20690.498-0.13810.16240.7752-0.12681.1039-0.240737.238865.9675
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875.3453-3.38440.71172.0023-6.37844.0925-0.0481-0.2270.11550.44710.0203-0.2381-0.08820.11170.00490.42870.0873-0.11970.3502-0.12590.6519-0.67411.534778.9376
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960.7813-0.58920.29755.7733-1.03310.6246-0.0580.0789-0.4569-0.0460.24030.06040.0613-0.0669-0.06560.24180.02360.01930.3251-0.05540.6258-9.11097.411168.1596
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 154:187)
2X-RAY DIFFRACTION2(chain A and resid 188:232)
3X-RAY DIFFRACTION3(chain A and resid 233:277)
4X-RAY DIFFRACTION4(chain A and resid 278:284)
5X-RAY DIFFRACTION5(chain A and resid 285:356)
6X-RAY DIFFRACTION6(chain A and resid 357:372)
7X-RAY DIFFRACTION7(chain A and resid 373:397)
8X-RAY DIFFRACTION8(chain A and resid 398:445)
9X-RAY DIFFRACTION9(chain B and resid 1:11)
10X-RAY DIFFRACTION10(chain B and resid 12:34)
11X-RAY DIFFRACTION11(chain B and resid 35:45)
12X-RAY DIFFRACTION12(chain B and resid 46:68)
13X-RAY DIFFRACTION13(chain B and resid 69:75)
14X-RAY DIFFRACTION14(chain B and resid 76:89)
15X-RAY DIFFRACTION15(chain B and resid 90:101)
16X-RAY DIFFRACTION16(chain B and resid 102:106)
17X-RAY DIFFRACTION17(chain C and resid 59:72)
18X-RAY DIFFRACTION18(chain C and resid 73:77)
19X-RAY DIFFRACTION19(chain C and resid 118:179)
20X-RAY DIFFRACTION20(chain C and resid 180:227)
21X-RAY DIFFRACTION21(chain C and resid 231:259)
22X-RAY DIFFRACTION22(chain C and resid 260:293)
23X-RAY DIFFRACTION23(chain C and resid 294:321)
24X-RAY DIFFRACTION24(chain C and resid 322:395)
25X-RAY DIFFRACTION25(chain D and resid 1:11)
26X-RAY DIFFRACTION26(chain D and resid 12:23)
27X-RAY DIFFRACTION27(chain D and resid 24:41)
28X-RAY DIFFRACTION28(chain D and resid 42:61)
29X-RAY DIFFRACTION29(chain D and resid 62:84)
30X-RAY DIFFRACTION30(chain D and resid 85:99)
31X-RAY DIFFRACTION31(chain D and resid 100:111)
32X-RAY DIFFRACTION32(chain D and resid 112:120)
33X-RAY DIFFRACTION33(chain E and resid 153:186)
34X-RAY DIFFRACTION34(chain E and resid 187:193)
35X-RAY DIFFRACTION35(chain E and resid 194:277)
36X-RAY DIFFRACTION36(chain E and resid 278:282)
37X-RAY DIFFRACTION37(chain E and resid 283:366)
38X-RAY DIFFRACTION38(chain E and resid 367:391)
39X-RAY DIFFRACTION39(chain E and resid 392:396)
40X-RAY DIFFRACTION40(chain E and resid 397:445)
41X-RAY DIFFRACTION41(chain F and resid 1:11)
42X-RAY DIFFRACTION42(chain F and resid 12:17)
43X-RAY DIFFRACTION43(chain F and resid 18:25)
44X-RAY DIFFRACTION44(chain F and resid 26:34)
45X-RAY DIFFRACTION45(chain F and resid 35:66)
46X-RAY DIFFRACTION46(chain F and resid 67:74)
47X-RAY DIFFRACTION47(chain F and resid 75:89)
48X-RAY DIFFRACTION48(chain F and resid 90:102)
49X-RAY DIFFRACTION49(chain G and resid 58:125)
50X-RAY DIFFRACTION50(chain G and resid 126:179)
51X-RAY DIFFRACTION51(chain G and resid 180:224)
52X-RAY DIFFRACTION52(chain G and resid 225:259)
53X-RAY DIFFRACTION53(chain G and resid 260:292)
54X-RAY DIFFRACTION54(chain G and resid 293:340)
55X-RAY DIFFRACTION55(chain G and resid 341:390)
56X-RAY DIFFRACTION56(chain G and resid 391:399)
57X-RAY DIFFRACTION57(chain H and resid 1:8)
58X-RAY DIFFRACTION58(chain H and resid 9:24)
59X-RAY DIFFRACTION59(chain H and resid 25:34)
60X-RAY DIFFRACTION60(chain H and resid 35:41)
61X-RAY DIFFRACTION61(chain H and resid 42:54)
62X-RAY DIFFRACTION62(chain H and resid 55:69)
63X-RAY DIFFRACTION63(chain H and resid 70:98)
64X-RAY DIFFRACTION64(chain H and resid 99:120)
65X-RAY DIFFRACTION65(chain I and resid 154:162)
66X-RAY DIFFRACTION66(chain I and resid 163:192)
67X-RAY DIFFRACTION67(chain I and resid 193:285)
68X-RAY DIFFRACTION68(chain I and resid 286:366)
69X-RAY DIFFRACTION69(chain I and resid 367:393)
70X-RAY DIFFRACTION70(chain I and resid 394:416)
71X-RAY DIFFRACTION71(chain I and resid 417:430)
72X-RAY DIFFRACTION72(chain I and resid 431:445)
73X-RAY DIFFRACTION73(chain J and resid 1:5)
74X-RAY DIFFRACTION74(chain J and resid 6:12)
75X-RAY DIFFRACTION75(chain J and resid 13:30)
76X-RAY DIFFRACTION76(chain J and resid 31:41)
77X-RAY DIFFRACTION77(chain J and resid 42:70)
78X-RAY DIFFRACTION78(chain J and resid 71:86)
79X-RAY DIFFRACTION79(chain J and resid 87:93)
80X-RAY DIFFRACTION80(chain J and resid 94:102)
81X-RAY DIFFRACTION81(chain K and resid 1:20)
82X-RAY DIFFRACTION82(chain K and resid 21:39)
83X-RAY DIFFRACTION83(chain K and resid 40:49)
84X-RAY DIFFRACTION84(chain K and resid 50:57)
85X-RAY DIFFRACTION85(chain K and resid 58:64)
86X-RAY DIFFRACTION86(chain K and resid 65:74)
87X-RAY DIFFRACTION87(chain K and resid 75:85)
88X-RAY DIFFRACTION88(chain K and resid 86:120)
89X-RAY DIFFRACTION89(chain N and resid 58:69)
90X-RAY DIFFRACTION90(chain N and resid 70:76)
91X-RAY DIFFRACTION91(chain N and resid 77:179)
92X-RAY DIFFRACTION92(chain N and resid 180:226)
93X-RAY DIFFRACTION93(chain N and resid 227:257)
94X-RAY DIFFRACTION94(chain N and resid 258:289)
95X-RAY DIFFRACTION95(chain N and resid 290:321)
96X-RAY DIFFRACTION96(chain N and resid 322:395)

+
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

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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

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