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- PDB-7bre: The crystal structure of MLL2 in complex with ASH2L and RBBP5 -

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基本情報

登録情報
データベース: PDB / ID: 7bre
タイトルThe crystal structure of MLL2 in complex with ASH2L and RBBP5
要素
  • Histone-lysine N-methyltransferase 2B
  • Retinoblastoma-binding protein 5
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
キーワードPROTEIN BINDING / Histone methyltransferase / MLL2 complex / MLL2 / RBBP5 / ASH2L / histone methylation / epigenetics / non-histone substrate / P53
機能・相同性
機能・相同性情報


[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / hemopoiesis / MLL1 complex / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / beta-catenin binding / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / methylation / histone binding / transcription cis-regulatory region binding / positive regulation of cell population proliferation / DNA damage response / positive regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
類似検索 - 分子機能
KMT2B, ePHD domain / : / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / Methyltransferase, trithorax / : / FY-rich, N-terminal ...KMT2B, ePHD domain / : / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / PHD-finger / 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 / Bromodomain-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily
類似検索 - ドメイン・相同性
S-ADENOSYL-L-HOMOCYSTEINE / Retinoblastoma-binding protein 5 / Set1/Ash2 histone methyltransferase complex subunit ASH2 / Histone-lysine N-methyltransferase 2B
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: 2.803 Å
データ登録者Li, Y. / Zhao, L. / Chen, Y.
資金援助 中国, 2件
組織認可番号国
National Natural Science Foundation of China (NSFC)31970576 中国
National Natural Science Foundation of China (NSFC)31900934 中国
引用ジャーナル: Structure / 年: 2020
タイトル: Crystal Structure of MLL2 Complex Guides the Identification of a Methylation Site on P53 Catalyzed by KMT2 Family Methyltransferases.
著者: Li, Y. / Zhao, L. / Tian, X. / Peng, C. / Gong, F. / Chen, Y.
履歴
登録2020年3月28日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年7月22日Provider: repository / タイプ: Initial release
改定 1.12020年8月5日Group: Database references / カテゴリ: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22020年10月21日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.32023年11月29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: Set1/Ash2 histone methyltransferase complex subunit ASH2
B: Histone-lysine N-methyltransferase 2B
E: Histone-lysine N-methyltransferase 2B
D: Set1/Ash2 histone methyltransferase complex subunit ASH2
C: Retinoblastoma-binding protein 5
F: Retinoblastoma-binding protein 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)86,67910
ポリマ－85,7806
非ポリマー9004
水00
1
A: Set1/Ash2 histone methyltransferase complex subunit ASH2
B: Histone-lysine N-methyltransferase 2B
C: Retinoblastoma-binding protein 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,3405
ポリマ－42,8903
非ポリマー4502
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: Histone-lysine N-methyltransferase 2B
D: Set1/Ash2 histone methyltransferase complex subunit ASH2
F: Retinoblastoma-binding protein 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,3405
ポリマ－42,8903
非ポリマー4502
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)79.075, 66.195, 83.734
Angle α, β, γ (deg.)90.000, 93.230, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質 Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein


分子量: 20597.355 Da / 分子数: 2 / 断片: UNP residues 286-402 and UNP residues 445-504 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ASH2L, ASH2L1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): Rosetta / 参照: UniProt: Q9UBL3
#2: タンパク質 Histone-lysine N-methyltransferase 2B / Lysine N-methyltransferase 2B / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / Trithorax ...Lysine N-methyltransferase 2B / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / Trithorax homolog 2 / WW domain-binding protein 7 / WBP-7


分子量: 19037.148 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MLL2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): Rosetta
参照: UniProt: Q9UMN6, [histone H3]-lysine4 N-trimethyltransferase
#3: タンパク質・ペプチド Retinoblastoma-binding protein 5 / RBBP-5 / Retinoblastoma-binding protein RBQ-3


分子量: 3255.321 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RBBP5 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): Rosetta / 参照: UniProt: Q15291
#4: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#5: 化合物 ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-アデノシルホモシステイン


タイプ: L-peptide linking / 分子量: 384.411 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C14H20N6O5S
研究の焦点であるリガンドがあるかN
配列の詳細Authors made a construct of ASH2L (Q9UBL3-3) that delete a loop deletion from 402-445, and the loop ...Authors made a construct of ASH2L (Q9UBL3-3) that delete a loop deletion from 402-445, and the loop is replaced by a linker sequence (ISGRGS).

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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: 2.32 Å3/Da / 溶媒含有率: 46.92 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL19U1 / 波長: 0.9785 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2015年12月28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: 0.9785 Å / 相対比: 1
反射解像度: 2.8→50 Å / Num. obs: 21457 / % possible obs: 100 % / 冗長度: 6.7 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.066 / Rrim(I) all: 0.173 / Χ2: 0.631 / Net I/σ(I): 3.4 / Num. measured all: 142941
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.96.30.64221200.7930.2760.70.477100
2.9-3.026.60.52421480.8690.2210.570.495100
3.02-3.156.50.40121220.920.170.4360.527100
3.15-3.3270.31621300.9540.1280.3410.543100
3.32-3.536.90.23221140.9640.0960.2510.592100
3.53-3.86.50.1721440.9780.0720.1850.643100
3.8-4.186.90.1321540.9890.0530.140.73100
4.18-4.796.80.121340.9920.0410.1090.801100
4.79-6.036.70.09421750.9920.0390.1020.682100
6.03-506.40.08122160.9970.0340.0880.80199.9

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解析

ソフトウェア
名称バージョン分類
HKL-3000データスケーリング
PHENIX1.17精密化
PDB_EXTRACT3.25データ抽出
HKL-3000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3TOJ,5F6E

3toj

5f6e


解像度: 2.803→37.833 Å / SU ML: 0.34 / 交差検証法: THROUGHOUT / σ(F): 1.38 / 位相誤差: 26.25
Rfactor反射数%反射
Rfree0.2646 1096 5.13 %
Rwork0.2185 --
obs0.2209 21376 99.57 %
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 max: 122.34 Å2 / Biso mean: 52.2977 Å2 / Biso min: 13.43 Å2
精密化ステップサイクル: final / 解像度: 2.803→37.833 Å
タンパク質核酸リガンド溶媒全体
原子数5813 0 54 0 5867
Biso mean--49.21 --
残基数----723
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.803-2.93040.30671390.2767248799
2.9304-3.08490.30361410.26512530100
3.0849-3.2780.27641150.24692543100
3.278-3.5310.31931380.23682525100
3.531-3.8860.25831310.21272551100
3.886-4.44750.27931490.19272535100
4.4475-5.60050.20321450.18472542100
5.6005-37.830.25041380.2199256798
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)
13.9556-2.3293-0.39575.15420.16375.96070.10450.1219-0.92890.9338-0.16130.77380.5148-0.86450.20920.3126-0.03380.05380.2251-0.04240.284125.3627-7.861496.9135
24.1897-0.5321-0.54784.32661.20474.34360.10920.05820.03110.9577-0.20220.847-0.0131-0.21120.27030.34160.02450.03250.2207-0.0010.251821.66153.170697.3615
33.8581-2.1456-1.17755.43650.76931.79750.07720.0866-0.301-0.53510.0310.30480.1425-0.2673-0.07050.2120.0264-0.00940.219-0.00850.233333.1059-2.825690.7333
43.04770.69551.13590.8948-0.32222.87520.0234-0.3128-0.0519-0.90060.3770.5626-0.55920.1932-0.22680.3371-0.03980.03670.1368-0.02840.270930.514410.162792.4691
50.7868-1.5863-0.47165.38830.6381.4869-0.46240.36820.02190.92350.0259-0.47310.07490.11510.44170.20660.0519-0.01990.26560.0350.200537.3823.0427103.3456
61.94720.7874-0.54911.33430.7632.2070.16680.05360.1454-0.321-0.1455-0.55530.12760.06940.03260.3206-0.0139-0.0270.11380.04060.171741.11385.709689.0797
72.43870.0046-1.78482.8651-0.44651.4753-0.07040.29010.0712-0.145-0.010.00290.0598-0.14940.04490.3102-0.0277-0.07680.1812-0.00360.139135.52681.509387.8914
83.0099-0.91160.0914.32651.33711.8405-0.00620.39750.5207-1.0915-0.07650.3305-0.3675-0.15350.1150.69460.09410.00050.1991-0.09210.307437.8586-9.109982.8949
92.5582.68470.31052.15570.52352.3454-0.0486-0.16740.3486-0.0474-0.02440.4906-0.2765-0.6030.0950.45470.0761-0.01040.318-0.09620.57169.022215.3769129.17
101.1175-0.54520.81242.19871.364.0590.0205-0.51660.1448-0.1221-0.1266-0.0301-0.3881-0.3944-0.08330.3037-0.06330.1650.2578-0.1240.339421.67721.3815135.3392
110.81370.374-0.89671.87442.10734.75970.40960.04530.3844-0.18080.0734-0.5238-0.44140.8149-0.41870.48850.0701-0.04760.1679-0.02660.37735.460116.7381114.2215
120.7566-0.6881-0.86693.8024-2.34.1559-0.18570.4468-0.62950.0758-0.28430.1304-0.56330.01790.34530.45350.0798-0.00860.2581-0.17470.553929.112916.6366119.7736
134.9935-1.04640.1474.20221.3212.75190.0191-0.014-0.27110.0852-0.0413-0.294-0.04090.3467-0.02320.3941-0.08380.03980.23170.02010.271627.934813.4736134.0648
148.0433-1.9746-3.03150.48410.71123.6886-0.67110.5376-0.79390.1310.4025-0.35730.49950.67450.08940.64380.1426-0.16640.4648-0.00110.448128.05868.1407126.4257
153.91444.36640.36125.43042.54098.2518-0.79610.47540.38490.44420.2768-0.00150.41750.62710.43170.40970.0595-0.00150.47540.0460.902518.0971-7.7702125.3876
160.1112-0.30360.42632.6078-2.31462.6529-0.3888-1.0016-1.1933-1.06560.0962-0.02190.71770.70740.35520.8320.3070.06960.84050.25890.69077.0415-20.9545132.0533
174.4821-0.5919-1.70163.34540.69024.4962-0.7566-0.8551-0.96280.1729-0.0756-0.11731.33340.67960.57260.481-0.04720.19740.94080.42890.469-4.7002-19.0806137.1048
180.91580.50780.43591.6622-0.15230.3586-0.7138-0.332-0.02210.1154-0.1192-0.25920.09590.6361-0.13580.46150.0777-0.22030.70320.07490.44768.6001-13.6799133.2369
190.14670.7223-0.05433.9568-1.09661.11730.1797-0.4929-0.24630.8003-0.01490.59050.5174-0.5489-0.37340.388-0.0255-0.09050.5320.16680.5787-10.3326-10.519113.6463
203.2579-1.52712.11261.55950.76825.0476-0.0171-0.34170.17370.35560.05880.16860.1798-0.1118-0.22040.29010.02160.02240.32610.02060.4551-5.066-7.2991119.9745
213.1943-0.3672-1.92030.7733-0.73776.3428-0.33510.102-0.3566-0.3264-0.06580.14321.4999-0.28330.1280.6666-0.0956-0.28770.38050.21020.4897-2.4127-14.1346118.4212
229.8728-1.8533-1.02077.402-5.81845.2228-0.302-0.29820.46250.14020.24380.16690.26460.6921-0.0080.3156-0.045-0.14250.45470.04050.372-3.2351-11.5407134.4527
236.55290.2818-0.52085.8352-0.3974.5924-0.2511-1.01910.6821-0.13830.2298-0.50710.3353-0.10660.08010.27450.0534-0.03880.4-0.03540.42177.0348-8.3598131.5221
248.30842.1892-5.29425.81220.84074.3230.80570.51250.7555-0.084-0.01530.3731-0.5896-0.5881-0.63880.41320.1877-0.12250.8385-0.18410.6248-8.9319-4.1817130.499
254.93390.0063-4.66978.849-0.35047.6493-0.0982-0.52630.86930.14420.57960.61870.675-0.4108-0.39380.4409-0.0772-0.16990.623-0.00310.6033-13.8582-5.5498138.134
261.00751.9585-0.79894.1091-1.10291.23990.32050.25781.38120.2103-0.5989-0.5815-0.29350.70970.44780.382-0.06260.02730.72120.1851.40890.359113.503799.4391
273.2347-0.43391.3920.3198-0.01591.20790.38441.29111.0613-0.4464-0.311-0.7752-0.3980.94980.2174-0.48770.2898-0.16070.97090.49570.90023.81534.324697.8367
281.0152-0.8850.74940.8146-0.63090.55040.02290.78141.5872-0.4613-0.3227-0.6882-0.20960.31030.2580.25560.03620.02180.48580.37990.9901-8.963513.254892.7499
292.03130.53070.81940.4727-0.65052.58520.42841.31990.4584-0.5495-0.2081-0.76040.33520.86080.01060.42660.19510.00160.75180.16550.7296-3.3526-1.637791.1806
305.25950.06282.86252.3396-2.43954.18990.0319-0.34690.59-0.1756-0.28420.06390.1612-0.42010.17270.19090.03720.05420.231-0.07970.2902-12.24751.273398.4902
315.5607-0.528-1.16323.8451.26642.08850.51630.7762-0.911-0.214-0.72320.08530.70420.96990.28940.3540.1906-0.00870.610.03340.4121-14.0072-3.222589.9726
322.54711.68351.44091.73340.56522.4271-0.41680.81231.1829-0.4338-0.4434-0.28990.03431.0452-0.04320.50190.06290.11530.62510.3640.5991-13.67610.335586.7641
334.3155-1.04210.53374.1013-0.28762.58050.33470.16451.1652-0.0205-0.6481-0.233-0.83880.26240.48810.42580.03650.02010.39450.12280.7903-22.181513.02788.5111
342.9634-0.08160.43880.940.08131.9471-0.15980.72540.7095-0.1314-0.4555-0.6119-0.02680.33690.53070.2620.02740.02030.52590.1410.5748-11.74554.899691.8541
353.07080.4755-2.13091.4014-0.71221.59250.11520.36420.2887-0.0992-0.00380.06840.1979-0.7857-0.2190.1719-0.35960.44361.510.82610.177-4.507612.89980.9021
360.21120.2735-0.17591.1990.41110.5628-0.46580.94430.6456-0.4394-0.6697-0.5901-0.82360.76570.74030.6708-0.1313-0.29090.89980.80731.2463-11.87917.807383.3985
375.1193-3.6032-5.69172.87252.8832.0001-0.1124-0.5140.36320.41510.2129-0.87271.3433-1.3734-0.03211.2691-0.0304-0.20310.59880.02190.647623.927528.853120.8116
389.7312-1.82980.8051.98031.23762.4031.001-0.08-0.31570.623-0.33290.3947-0.3716-0.6982-0.7040.4443-0.10240.13470.3142-0.10570.618221.244720.1155113.4672
392.0969-0.75521.82835.35050.90782.09480.66040.52050.6955-0.3275-0.33450.8018-1.2602-0.229-0.39190.37160.10040.01640.34810.06840.499430.09618.7223102.2417
407.9911-1.78150.84322.71583.46875.86820.50320.53451.0787-0.1322-0.0475-0.0229-1.55791.1619-0.38320.4164-0.1045-0.02290.41740.02720.705438.456316.8932103.0676
412.7716-1.19494.11571.7403-2.26858.17690.60360.3141-0.2498-0.0485-0.0862-0.49810.22140.0774-0.44241.53150.5769-0.05991.13990.16080.49214.1714-20.9914118.5403
422.9239-0.3953.03947.3601-2.33863.9009-0.164-0.0782-0.0586-0.48650.1245-0.42990.46220.1661-0.08630.74750.29140.19440.2030.30870.7632.0855-13.0173110.0191
435.1359-0.94451.04214.63422.03692.29870.09820.7496-1.3716-0.11790.6425-0.18282.41060.1115-0.7720.8415-0.0245-0.21520.4609-0.0740.5123-7.0263-10.6869101.5451
445.87450.7315-2.45260.73530.4417.00490.18711.1817-0.9174-0.61680.41940.6722.1851-0.9779-0.41370.5698-0.1801-0.25220.49580.15660.8566-14.638-9.0195101.382
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 285 through 294 )A285 - 294
2X-RAY DIFFRACTION2chain 'A' and (resid 295 through 313 )A295 - 313
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 335 )A314 - 335
4X-RAY DIFFRACTION4chain 'A' and (resid 336 through 347 )A336 - 347
5X-RAY DIFFRACTION5chain 'A' and (resid 348 through 362 )A348 - 362
6X-RAY DIFFRACTION6chain 'A' and (resid 363 through 451 )A363 - 451
7X-RAY DIFFRACTION7chain 'A' and (resid 452 through 493 )A452 - 493
8X-RAY DIFFRACTION8chain 'A' and (resid 494 through 503 )A494 - 503
9X-RAY DIFFRACTION9chain 'B' and (resid 2551 through 2581 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 2582 through 2606 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 2607 through 2624 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 2625 through 2646 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 2647 through 2715 )B0
14X-RAY DIFFRACTION14chain 'E' and (resid 2551 through 2558 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 2559 through 2568 )E0
16X-RAY DIFFRACTION16chain 'E' and (resid 2569 through 2581 )E0
17X-RAY DIFFRACTION17chain 'E' and (resid 2582 through 2591 )E0
18X-RAY DIFFRACTION18chain 'E' and (resid 2592 through 2606 )E0
19X-RAY DIFFRACTION19chain 'E' and (resid 2607 through 2624 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 2625 through 2636 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 2637 through 2646 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 2647 through 2658 )E0
23X-RAY DIFFRACTION23chain 'E' and (resid 2659 through 2686 )E0
24X-RAY DIFFRACTION24chain 'E' and (resid 2687 through 2698 )E0
25X-RAY DIFFRACTION25chain 'E' and (resid 2699 through 2715 )E0
26X-RAY DIFFRACTION26chain 'D' and (resid 286 through 295 )D286 - 295
27X-RAY DIFFRACTION27chain 'D' and (resid 296 through 313 )D296 - 313
28X-RAY DIFFRACTION28chain 'D' and (resid 314 through 332 )D314 - 332
29X-RAY DIFFRACTION29chain 'D' and (resid 333 through 347 )D333 - 347
30X-RAY DIFFRACTION30chain 'D' and (resid 348 through 372 )D348 - 372
31X-RAY DIFFRACTION31chain 'D' and (resid 373 through 390 )D373 - 390
32X-RAY DIFFRACTION32chain 'D' and (resid 391 through 398 )D391 - 398
33X-RAY DIFFRACTION33chain 'D' and (resid 399 through 451 )D399 - 451
34X-RAY DIFFRACTION34chain 'D' and (resid 452 through 481 )D452 - 481
35X-RAY DIFFRACTION35chain 'D' and (resid 482 through 492 )D482 - 492
36X-RAY DIFFRACTION36chain 'D' and (resid 493 through 503 )D493 - 503
37X-RAY DIFFRACTION37chain 'C' and (resid 336 through 340 )C336 - 340
38X-RAY DIFFRACTION38chain 'C' and (resid 341 through 345 )C341 - 345
39X-RAY DIFFRACTION39chain 'C' and (resid 346 through 350 )C346 - 350
40X-RAY DIFFRACTION40chain 'C' and (resid 351 through 355 )C351 - 355
41X-RAY DIFFRACTION41chain 'F' and (resid 337 through 341 )F337 - 341
42X-RAY DIFFRACTION42chain 'F' and (resid 342 through 346 )F342 - 346
43X-RAY DIFFRACTION43chain 'F' and (resid 347 through 351 )F347 - 351
44X-RAY DIFFRACTION44chain 'F' and (resid 352 through 355 )F352 - 355

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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