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- PDB-5j9t: 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: 5j9t
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 / SUMOylation of transcription cofactors ...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 / SUMOylation of transcription cofactors / positive regulation of triglyceride biosynthetic process / DNA-templated transcription elongation / histone H4 acetyltransferase activity / rDNA heterochromatin formation / histone H3K4me3 reader activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein-lysine-acetyltransferase activity / NuA4 histone acetyltransferase complex / histone acetyltransferase activity / Estrogen-dependent gene expression / positive regulation of macroautophagy / : / 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
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 ...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 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / Chromo-like domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
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: 2.7 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16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
H: Chromatin modification-related protein YNG2
A: Histone acetyltransferase ESA1
B: Chromatin modification-related protein EAF6
C: Enhancer of polycomb-like protein 1
D: Chromatin modification-related protein YNG2
I: Histone acetyltransferase ESA1
J: Chromatin modification-related protein EAF6
K: Enhancer of polycomb-like protein 1
L: Chromatin modification-related protein YNG2


分子量 (理論値)分子数
合計 (水以外)289,86612
ポリマ－289,86612
非ポリマー00
水5,405300
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)96,6224
ポリマ－96,6224
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15830 Å2
ΔGint-84 kcal/mol
Surface area38140 Å2
手法PISA
2
A: Histone acetyltransferase ESA1
B: Chromatin modification-related protein EAF6
C: Enhancer of polycomb-like protein 1
D: Chromatin modification-related protein YNG2


分子量 (理論値)分子数
合計 (水以外)96,6224
ポリマ－96,6224
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-88 kcal/mol
Surface area38390 Å2
手法PISA
3
I: Histone acetyltransferase ESA1
J: Chromatin modification-related protein EAF6
K: Enhancer of polycomb-like protein 1
L: Chromatin modification-related protein YNG2


分子量 (理論値)分子数
合計 (水以外)96,6224
ポリマ－96,6224
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16070 Å2
ΔGint-87 kcal/mol
Surface area38310 Å2
手法PISA
単位格子
Length a, b, c (Å)86.685, 137.582, 168.076
Angle α, β, γ (deg.)90.00, 97.63, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質 Histone acetyltransferase ESA1


分子量: 36556.883 Da / 分子数: 3 / 断片: UNP residues 141-445 / 変異: E338Q / 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: 33320.547 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
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 300 / 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: 3.43 Å3/Da / 溶媒含有率: 64.11 %
結晶化温度: 289 K / 手法: 蒸発脱水法
詳細: 100mM HEPES (pH 7.5), 6% 1,6-Hexanediol, 7% PEG 8000, 5% ethylene glycol, 10mM DTT.

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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12月27日
放射プロトコル: LAUE / 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: 2.7→30 Å / Num. obs: 106451 / % possible obs: 99.8 % / 冗長度: 3.4 % / Net I/σ(I): 12.9

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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
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.7→29.971 Å / SU ML: 0.35 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 24.64
Rfactor反射数%反射
Rfree0.2193 1998 1.88 %
Rwork0.1871 --
obs0.1877 106451 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: 2.7→29.971 Å
タンパク質核酸リガンド溶媒全体
原子数18581 0 0 300 18881
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00418961
X-RAY DIFFRACTIONf_angle_d0.70425520
X-RAY DIFFRACTIONf_dihedral_angle_d13.82211614
X-RAY DIFFRACTIONf_chiral_restr0.0432731
X-RAY DIFFRACTIONf_plane_restr0.0043297
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76750.35991330.2866982X-RAY DIFFRACTION94
2.7675-2.84220.32411440.27417490X-RAY DIFFRACTION100
2.8422-2.92580.34021420.26717477X-RAY DIFFRACTION100
2.9258-3.02020.33481430.25377473X-RAY DIFFRACTION100
3.0202-3.1280.26621440.23487525X-RAY DIFFRACTION100
3.128-3.25310.26761430.22957462X-RAY DIFFRACTION100
3.2531-3.4010.24131430.22157477X-RAY DIFFRACTION100
3.401-3.580.25761430.19817499X-RAY DIFFRACTION100
3.58-3.80390.20811430.17767467X-RAY DIFFRACTION100
3.8039-4.09690.19171440.16667545X-RAY DIFFRACTION100
4.0969-4.50790.14891440.14387494X-RAY DIFFRACTION100
4.5079-5.15740.17871440.14657487X-RAY DIFFRACTION100
5.1574-6.48690.23341430.19417508X-RAY DIFFRACTION99
6.4869-29.97260.17021450.15457567X-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)
12.8065-0.0558-0.20146.1502-2.56613.80480.1394-0.77930.03220.51820.10090.29760.27890.255-0.24890.53430.0225-0.03020.5999-0.02440.35392.8326-5.9184-17.7307
21.38730.42050.20791.3767-0.26721.8649-0.0317-0.05610.09150.0799-0.01950.01870.00930.06380.03160.27870.0313-0.00820.3135-0.00470.31120.8429-7.853-31.9591
32.0057-1.90141.83064.0849-1.79745.8921-0.64050.06321.27170.0188-0.32940.2192-1.1731-0.01790.77410.61590.0256-0.06440.4233-0.02610.6302-0.98319.0639-38.5764
43.2799-0.9467-0.61591.6683-0.42381.1799-0.0549-0.23410.05190.1830.00460.24850.0473-0.17580.02280.25570.00710.00920.3513-0.03260.3354-16.9236-7.4271-29.0817
51.3580.4415-1.01793.20520.75981.97260.00380.0372-0.2204-0.08080.01640.85040.054-0.5265-0.09050.3424-0.00480.00860.6323-0.07660.6575-36.9509-7.6953-27.2865
62.80171.8468-0.32574.5505-1.27282.0849-0.030.0404-0.72250.2011-0.06010.1964-0.1581-0.50880.03580.45380.04870.09360.5069-0.07140.7209-37.31851.1463-23.4816
72.7823-0.1020.15673.35640.56613.9497-0.09360.14160.30230.06450.15960.55380.249-0.3495-0.10930.35530.1049-0.02480.45950.01270.472-18.511-4.311-41.6713
8-0.0089-0.00820.0152-0.0065-0.0017-0.0074-0.6312-0.63250.23690.41680.1725-0.1445-0.25060.18370.33351.1625-0.2847-0.11531.13290.21631.177738.500223.8173-72.2048
97.55112.57521.05924.63660.7242.6162-0.411-0.05350.1674-0.0922-0.0215-0.41470.33730.69050.52270.6516-0.2357-0.08930.83130.09220.741726.198514.2472-75.5608
105.97533.85811.69287.21810.98563.0389-0.37340.87330.3114-1.14880.30430.09080.33440.14830.13650.4977-0.0704-0.03670.46050.04610.34159.18584.0822-75.9965
113.41381.24780.52475.62850.41691.62610.21650.0861-0.4906-0.37510.13060.3183-0.0389-0.1004-0.25070.5263-0.1692-0.0340.53230.11630.411-4.8341-8.5957-73.3317
121.8378-1.04840.76751.6695-0.32183.20140.0241-0.31570.1195-0.4357-0.34560.48150.3627-0.03280.25380.5178-0.0973-0.07060.5440.15840.8511-11.4881-9.5419-65.379
131.7234-1.76690.32191.8074-0.27692.7939-0.49270.1853-0.0816-0.04030.86140.1782-0.0487-0.33860.0140.4903-0.0948-0.04260.39380.03860.4594-4.94711.0339-67.9445
145.7777-0.72273.25742.0066-3.93072.010.62030.2460.4992-0.87730.14830.6498-0.3665-1.0783-0.54280.73540.0711-0.03590.67590.08040.5456-6.63888.6831-73.2388
151.6368-0.77710.47041.14310.17130.4071-0.01290.05770.51410.0421-0.0035-0.4002-0.02880.30120.00050.357-0.0143-0.00110.58050.02540.454616.6247-1.6078-37.966
162.49380.9043-1.91883.9711-2.26664.9917-0.19930.0966-0.2282-0.5035-0.0962-0.63750.71370.3530.2160.58520.17420.04940.614-0.0090.500926.8571-24.2757-40.1727
173.5787-1.5012-1.16772.67742.24845.68380.4327-0.3729-0.0739-0.03010.2691-1.01780.33091.2746-0.62190.4610.0344-0.04240.6850.02780.709314.9345-7.115-57.1463
181.48781.3669-0.52022.4736-1.14854.20150.09520.38760.1673-0.2321-0.1022-0.3637-0.18480.0324-0.09480.4120.14040.03240.73660.06090.563328.0547-12.3025-39.2236
192.59861.0341.16561.990.94452.58350.1113-0.0522-0.57410.07640.0287-0.33780.68580.2436-0.08920.44040.1159-0.04520.40680.0170.45646.1063-23.9852-27.0743
201.60870.86260.81482.33340.37993.03690.1767-0.26740.03330.39920.23750.28890.1634-0.4406-0.34420.5842-0.1034-0.09810.40470.06780.5473-8.1976-33.9864-54.702
210.6370.45230.11391.8614-1.23091.8872-0.28740.26620.0829-0.05310.182-0.5975-0.31960.40380.00510.4734-0.1701-0.0250.55250.02480.591214.90619.3586-70.1691
221.03421.21850.34381.45160.72734.854-0.1865-0.4293-0.77470.22480.3240.41840.47720.2099-0.21510.4904-0.0734-0.09180.40420.07430.5084-3.2474-30.7784-54.1129
232.54360.55980.30697.55061.45551.39160.0399-0.127-0.07730.65520.25470.06310.1519-0.4748-0.23910.3393-0.07020.02970.43580.020.3763-4.8875-12.2921-54.3072
243.66953.2004-0.58519.6575-2.47442.7209-0.239-0.03430.61880.43610.68450.0558-0.5948-0.5191-0.40940.5409-0.0069-0.04810.4398-0.00580.51081.916713.9579-63.4058
253.22121.4968-1.29581.6715-0.42051.08330.09790.39891.16560.45670.2679-0.2097-0.63420.0991-0.29951.1276-0.3484-0.08660.77890.23541.120315.777731-75.3602
260.33560.7729-0.04134.5092-2.43071.9542-0.2384-0.13460.956-0.1334-0.50360.0975-0.56240.10140.65551.036-0.234-0.06230.70480.01090.890514.652927.5319-63.4723
271.08260.90330.31153.7078-0.5571.3126-0.0924-0.1310.0129-0.05-0.0179-0.1918-0.18080.11230.08550.3101-0.0235-0.02720.3461-0.01160.33846.5459-6.534-58.0077
280.3239-0.893-1.00952.89681.61546.2373-0.28830.8824-1.1515-0.52080.2451-0.59871.46610.0789-0.06960.7589-0.01240.05120.5667-0.13650.6973.7596-34.6355-61.145
292.69250.15920.1482.621-0.57725.2260.1663-0.2837-0.41430.2099-0.2953-0.20451.02680.34820.31190.5449-0.00380.03510.43140.08040.5802-30.5191-4.688512.5639
302.00530.4672-0.37271.6839-0.36222.1397-0.12310.1602-0.21570.014-0.0012-0.22330.03860.11160.10330.2853-0.02190.03020.34380.03610.3098-27.93568.65155.9622
312.86970.10540.04220.2378-0.46893.2731-0.0453-0.2268-0.48840.1788-0.1873-0.39480.14980.36810.24740.31390.02510.05180.51250.11860.6544-10.95045.87679.3449
322.0807-0.60670.51772.06080.86351.8214-0.3575-0.2051-0.39960.06810.2710.3135-0.00820.71890.08040.42440.0638-0.02530.96450.18540.88336.02783.60389.1749
336.66896.39353.42546.10153.28431.7608-0.0119-0.26680.07410.14830.01250.01580.2381-0.0210.09740.76110.27640.22021.61470.21951.288819.32993.824819.9365
342.48490.62052.02721.6760.83543.81090.0235-0.5248-1.06350.10430.09180.11310.38770.3104-0.07350.57050.12140.04911.01650.0021.15538.7851-4.71724.5125
352.447-0.3307-0.21763.31250.15872.7257-0.21130.1067-0.1936-0.03750.1186-0.2644-0.05780.74450.03710.3573-0.01140.09660.71010.15320.6194-9.023214.1352-0.7818
360.11510.2778-0.6840.869-1.90834.3779-0.15490.36170.1320.2209-0.04280.2851-0.0864-0.28030.14231.43840.1161-0.41111.08710.04870.8485-55.897330.4901-43.0982
376.82512.10265.38552.09761.86126.0405-0.11210.52260.7615-0.6286-0.20870.5116-0.3141-0.00290.42390.8408-0.0245-0.12030.41890.0690.605-41.001637.4508-30.7932
380.50790.8825-0.15481.98241.15995.0570.1409-0.0910.4223-0.3641-0.1163-0.3791-0.46490.17950.01890.767-0.2309-0.03130.57230.12850.5383-24.109344.663-15.0799
392.7474-0.5454-1.66010.18380.25721.0942-0.1815-0.85330.15450.28390.3565-0.144-0.56150.2584-0.06530.6624-0.1006-0.01721.240.00270.4642-18.791437.9394-3.3402
401.78470.0669-0.60711.49731.48968.1665-0.028-0.3137-0.61040.02450.4724-0.5394-0.41350.3047-0.39520.75080.04790.08791.21180.09990.9202-14.436738.552-11.7981
410.412-0.335-0.83350.25980.66421.7210.1783-0.06130.2009-0.0758-0.6857-0.6392-0.23630.21120.37650.7524-0.19720.09890.61420.08820.3924-22.245335.2357-17.4359
422.0065-0.2061-2.81641.05850.10593.99170.47270.72380.7142-0.34120.0488-0.9159-0.44920.6735-0.34580.8262-0.1160.31931.03630.00550.954-19.714635.2417-26.9413
431.72320.1016-0.55060.68990.37021.00120.00270.3231-0.132-0.05940.02170.07850.1156-0.2192-0.03780.4026-0.05560.02330.4950.0340.3323-39.22428.55-2.3796
441.4932-0.3462-0.01662.1640.07892.8498-0.02660.24950.3099-0.02630.04740.1862-0.5624-0.4543-0.02990.43060.07560.06530.57250.14590.503-55.531820.37428.8482
453.1365-2.2862-0.82045.59190.56373.50240.1040.2768-0.3768-0.1174-0.17560.98370.0986-0.62120.15620.4788-0.0759-0.01770.55470.04970.5643-42.698228.7125-8.8183
461.9159-0.18951.1592.4941-1.04583.76960.01370.40470.1259-0.0050.15680.4407-0.5055-0.356-0.08490.4350.04890.04150.64570.15490.5291-56.778816.65546.8129
470.2431-0.1807-0.5130.31840.53182.3686-0.1052-0.95870.0760.8364-0.03280.3818-0.2634-0.24730.14260.57850.0640.05640.662-0.00020.3704-34.982712.181424.8308
481.6632-0.43870.90840.74480.62463.9126-0.0771-0.03140.15080.02880.07520.09990.0050.2359-0.07540.6082-0.1633-0.07720.5170.01740.5112-23.091642.582214.2259
490.9846-0.06570.53271.1249-0.41352.4833-0.13720.1680.0472-0.74170.00360.3637-0.2273-0.2140.07760.773-0.0766-0.16760.47920.02610.4214-40.737831.6651-32.9718
502.11411.5137-0.29067.27943.79562.01690.1569-0.5629-0.29850.49170.01290.39560.61440.4139-0.29680.5619-0.09-0.13810.46790.05630.4825-25.648936.35312.4957
511.87610.42282.33191.6442-0.38743.4582-0.06020.20990.13660.1415-0.1412-0.36190.30830.50770.11880.4273-0.11190.01640.47480.08970.3915-23.321827.8763-8.5598
525.50020.4485.13184.8615-2.61566.731-0.02620.03540.0319-0.1269-0.2233-0.33040.23221.1310.32450.6384-0.08080.09240.52780.04340.3913-25.772523.9765-26.1516
531.7866-0.60963.15610.2133-1.09515.61730.03180.2231-0.0602-1.2855-0.34640.2829-0.10570.35140.1191.0487-0.01050.02490.63680.04270.6061-32.238723.9061-40.0342
541.4829-1.2111.00162.1331-1.43562.7092-0.68510.38360.2367-0.95130.35940.2742-0.12190.18530.31071.5333-0.042-0.16860.8791-0.01280.6578-39.658222.473-51.2801
551.6829-0.05250.90841.81511.0744.46740.0702-0.0457-0.3292-0.4481-0.1959-0.03250.0286-0.24960.11450.5495-0.0614-0.00650.33550.04430.383-35.028524.2782-19.5048
566.26220.0379-0.78962.05363.2498.5929-0.1097-0.20970.74510.0977-0.78910.7753-0.665-0.39160.82450.7637-0.011-0.10150.5525-0.03240.5049-34.664742.892111.2461
572.43180.57632.12048.32042.16192.08180.0234-0.12210.4828-0.50850.41870.3514-0.4805-0.3091-0.32050.577-0.02280.07260.34450.07020.567-26.715899.1029-69.1353
581.84070.4884-0.12651.8955-0.21991.2148-0.09270.094-0.05740.03140.0602-0.1107-0.02910.04030.01520.30960.01020.01290.230.02960.2871-31.389482.8449-64.8089
592.83910.02370.89021.31020.14520.6394-0.1228-0.15750.12080.00930.0090.0451-0.1825-0.21130.10270.31470.05230.02070.27920.04680.284-50.847886.6662-65.449
602.1026-1.56531.10551.272-0.34783.4043-0.3347-0.5369-0.18720.22550.39220.2877-0.1868-1.45610.03490.46680.13980.12110.78520.08350.4439-67.087887.6816-64.2887
619.53951.2155-7.83681.5471-0.87682.00760.3174-0.04370.14640.4936-0.48280.55470.1882-0.23310.21270.86890.24350.09790.6908-0.13570.8136-77.186895.2783-60.078
622.1626-0.6811-1.09562.13211.29272.8374-0.0641-0.19630.1026-0.14560.15780.2082-0.13840.18830.02440.37850.09850.00860.6261-0.01320.4475-67.643686.8858-76.5164
633.75110.28251.06413.4990.65545.67070.214-0.1252-0.43340.262-0.13430.24750.0235-0.51260.20090.37150.04-0.02770.38270.06650.4578-50.151373.7135-61.3518
648.1593-0.1751-2.8261.88490.51958.4191-0.2897-0.67940.37480.2563-0.0803-0.0046-0.59590.33620.32090.64420.205-0.16780.622-0.17230.5568-4.24428.667-77.023
657.147-3.6851-2.43939.66993.72228.2408-0.0384-0.5658-0.0940.84360.70750.03610.29660.5582-0.80890.69460.2452-0.10970.4494-0.020.4258-15.433832.3567-65.7661
663.00080.781-0.97662.52540.56717.3971-0.2344-0.2309-0.65960.57340.3090.33120.99770.0347-0.04480.6620.0973-0.02860.35240.02550.4566-26.384537.0343-57.5724
673.6838-0.5579-0.78387.34694.54366.96590.3917-0.8307-0.1310.5383-0.0299-0.11260.5417-0.3697-0.22170.77990.05680.1350.42270.12610.4558-37.780447.5686-43.0533
684.3691-0.1089-0.59661.6213-1.74413.37460.1762-0.10870.34280.6074-0.26150.8848-0.1309-0.9447-0.05170.5714-0.01350.1550.55680.00380.6144-43.606255.7842-45.5935
693.4277-0.5579-1.86070.2974-0.5734.8921-0.62760.6077-0.42050.03320.46460.51471.2651-0.1480.20170.7547-0.07890.1020.4184-0.05630.3719-38.468346.8261-55.8893
70-0.00260.0028-0.0016-0.0020.003-0.001-0.03850.1549-0.12720.41530.49550.09750.34270.2433-0.42260.80650.0855-0.12211.1368-0.41670.9352-41.729641.3561-62.361
711.43460.5881-0.36340.7080.25731.3306-0.07610.1582-0.2846-0.0550.0242-0.41090.08510.30160.06140.4050.05920.07760.35920.0480.5525-17.875374.415-67.9662
721.5941-0.0924-0.17672.86490.62272.4365-0.1009-0.1804-0.31370.76640.1206-0.53190.21310.4820.04580.46260.0404-0.11420.56060.19170.7504-4.6679.5913-50.3879
732.5936-0.34611.39184.0078-1.03013.31830.36590.24740.02460.0024-0.2523-0.93930.10081.0051-0.13270.45830.0674-0.05570.6068-0.12210.668-16.810358.6577-55.6237
741.9906-1.2761-0.32512.7185-0.02311.56480.0264-0.2166-0.49150.06140.0145-0.45290.28340.274-0.02060.4318-0.01-0.12860.4260.10540.8236-4.542180.7096-56.1757
750.77991.41550.83863.0851.85151.1301-0.0414-0.82930.45931.2778-0.1537-0.7049-1.46680.6718-0.02530.6896-0.0617-0.21720.5352-0.05790.3917-25.196497.972-49.4736
761.8679-0.2179-0.22391.51060.71281.48260.2119-0.15550.1077-0.48750.05820.096-0.49650.0156-0.20240.58880.02120.13320.4421-0.01320.3573-35.4871.1322-30.9808
770.9166-1.0314-0.94222.46252.36972.7261-0.20.0317-0.11150.32270.35680.01350.54180.5411-0.20370.53760.0909-0.01590.4026-0.07880.3549-20.850337.523-68.0288
780.694-0.4198-1.25746.4309-1.98473.44930.2868-0.51350.7322-0.0430.0351-0.4655-0.48670.4197-0.30060.72790.02920.19610.6044-0.18110.4329-31.373.7059-32.6063
797.21664.70927.34893.45953.1842.0216-0.2999-0.00411.2051-0.4656-0.37440.529-1.121-0.28240.33470.56440.07640.05580.3738-0.04610.4959-34.990170.6939-43.4605
800.5222-0.7718-0.436.12544.92955.3797-0.10830.12370.0934-0.9201-0.33720.7741-0.5105-0.32460.19680.42420.0457-0.01940.29840.00960.3674-36.610456.7278-58.736
811.8842-0.4077-1.62468.06514.84216.1343-0.13780.6455-0.4779-0.1827-0.23410.5743-0.1037-0.18720.26960.43220.0335-0.01810.3855-0.07480.4202-33.377542.3667-74.0325
825.7879-3.15190.02336.0858-1.08093.4498-0.12260.2936-0.27730.3222-0.06860.78190.6352-0.10680.13090.56240.0011-0.01360.4004-0.10110.4017-27.246228.0653-81.7918
830.607-0.51-0.74572.06771.90722.8221-0.19320.115-0.0378-0.49610.13690.1902-0.51720.49160.01660.4366-0.0233-0.02480.3477-0.02750.3188-25.176447.4731-71.3373
845.61850.98132.36526.1218-0.03984.33750.2556-0.81450.18171.25310.3574-0.38010.32281.4831-0.20660.64110.05480.02830.7545-0.17440.4423-24.026466.8975-32.555
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 160:180)
2X-RAY DIFFRACTION2(chain A and resid 181:278)
3X-RAY DIFFRACTION3(chain A and resid 279:283)
4X-RAY DIFFRACTION4(chain A and resid 284:356)
5X-RAY DIFFRACTION5(chain A and resid 357:397)
6X-RAY DIFFRACTION6(chain A and resid 398:420)
7X-RAY DIFFRACTION7(chain A and resid 421:437)
8X-RAY DIFFRACTION8(chain B and resid 1:8)
9X-RAY DIFFRACTION9(chain B and resid 9:21)
10X-RAY DIFFRACTION10(chain B and resid 22:35)
11X-RAY DIFFRACTION11(chain B and resid 36:66)
12X-RAY DIFFRACTION12(chain B and resid 67:91)
13X-RAY DIFFRACTION13(chain B and resid 92:101)
14X-RAY DIFFRACTION14(chain B and resid 102:107)
15X-RAY DIFFRACTION15(chain C and resid 128:196)
16X-RAY DIFFRACTION16(chain C and resid 197:227)
17X-RAY DIFFRACTION17(chain C and resid 228:256)
18X-RAY DIFFRACTION18(chain C and resid 257:291)
19X-RAY DIFFRACTION19(chain C and resid 292:315)
20X-RAY DIFFRACTION20(chain C and resid 316:334)
21X-RAY DIFFRACTION21(chain C and resid 335:394)
22X-RAY DIFFRACTION22(chain D and resid 1:7)
23X-RAY DIFFRACTION23(chain D and resid 8:24)
24X-RAY DIFFRACTION24(chain D and resid 25:44)
25X-RAY DIFFRACTION25(chain D and resid 45:61)
26X-RAY DIFFRACTION26(chain D and resid 62:77)
27X-RAY DIFFRACTION27(chain D and resid 78:109)
28X-RAY DIFFRACTION28(chain D and resid 110:119)
29X-RAY DIFFRACTION29(chain E and resid 160:181)
30X-RAY DIFFRACTION30(chain E and resid 182:294)
31X-RAY DIFFRACTION31(chain E and resid 295:349)
32X-RAY DIFFRACTION32(chain E and resid 350:394)
33X-RAY DIFFRACTION33(chain E and resid 395:399)
34X-RAY DIFFRACTION34(chain E and resid 400:419)
35X-RAY DIFFRACTION35(chain E and resid 420:437)
36X-RAY DIFFRACTION36(chain F and resid 7:12)
37X-RAY DIFFRACTION37(chain F and resid 13:33)
38X-RAY DIFFRACTION38(chain F and resid 34:45)
39X-RAY DIFFRACTION39(chain F and resid 66:73)
40X-RAY DIFFRACTION40(chain F and resid 74:92)
41X-RAY DIFFRACTION41(chain F and resid 93:99)
42X-RAY DIFFRACTION42(chain F and resid 100:107)
43X-RAY DIFFRACTION43(chain G and resid 127:175)
44X-RAY DIFFRACTION44(chain G and resid 176:230)
45X-RAY DIFFRACTION45(chain G and resid 231:258)
46X-RAY DIFFRACTION46(chain G and resid 259:291)
47X-RAY DIFFRACTION47(chain G and resid 292:315)
48X-RAY DIFFRACTION48(chain G and resid 316:340)
49X-RAY DIFFRACTION49(chain G and resid 341:399)
50X-RAY DIFFRACTION50(chain H and resid 1:13)
51X-RAY DIFFRACTION51(chain H and resid 14:29)
52X-RAY DIFFRACTION52(chain H and resid 30:37)
53X-RAY DIFFRACTION53(chain H and resid 38:50)
54X-RAY DIFFRACTION54(chain H and resid 51:68)
55X-RAY DIFFRACTION55(chain H and resid 69:101)
56X-RAY DIFFRACTION56(chain H and resid 102:118)
57X-RAY DIFFRACTION57(chain I and resid 161:170)
58X-RAY DIFFRACTION58(chain I and resid 171:294)
59X-RAY DIFFRACTION59(chain I and resid 295:361)
60X-RAY DIFFRACTION60(chain I and resid 362:393)
61X-RAY DIFFRACTION61(chain I and resid 394:400)
62X-RAY DIFFRACTION62(chain I and resid 401:420)
63X-RAY DIFFRACTION63(chain I and resid 421:437)
64X-RAY DIFFRACTION64(chain J and resid 1:14)
65X-RAY DIFFRACTION65(chain J and resid 15:21)
66X-RAY DIFFRACTION66(chain J and resid 22:34)
67X-RAY DIFFRACTION67(chain J and resid 35:66)
68X-RAY DIFFRACTION68(chain J and resid 67:92)
69X-RAY DIFFRACTION69(chain J and resid 93:102)
70X-RAY DIFFRACTION70(chain J and resid 103:104)
71X-RAY DIFFRACTION71(chain K and resid 128:181)
72X-RAY DIFFRACTION72(chain K and resid 182:228)
73X-RAY DIFFRACTION73(chain K and resid 229:259)
74X-RAY DIFFRACTION74(chain K and resid 260:296)
75X-RAY DIFFRACTION75(chain K and resid 297:315)
76X-RAY DIFFRACTION76(chain K and resid 316:340)
77X-RAY DIFFRACTION77(chain K and resid 341:396)
78X-RAY DIFFRACTION78(chain L and resid 1:7)
79X-RAY DIFFRACTION79(chain L and resid 8:16)
80X-RAY DIFFRACTION80(chain L and resid 17:33)
81X-RAY DIFFRACTION81(chain L and resid 34:44)
82X-RAY DIFFRACTION82(chain L and resid 45:57)
83X-RAY DIFFRACTION83(chain L and resid 58:100)
84X-RAY DIFFRACTION84(chain L and resid 101:119)

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万見について

-
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

-
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