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- PDB-6w89: Structure of DNMT3A (R882H) in complex with CGA DNA -

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基本情報

登録情報
データベース: PDB / ID: 6w89
タイトルStructure of DNMT3A (R882H) in complex with CGA DNA
要素
  • (DNA (cytosine-5)-methyltransferase ...) x 2
  • CGA DNA (25-MER)
キーワードTRANSFERASE/DNA / DNA methylation / DNMT3A(R882H) / AML / epigenetics / TRANSFERASE / TRANSFERASE-DNA complex
機能・相同性
機能・相同性情報


epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / genomic imprinting / DNA (cytosine-5-)-methyltransferase activity ...epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / genomic imprinting / DNA (cytosine-5-)-methyltransferase activity / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / autosome genomic imprinting / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / XY body / cellular response to ethanol / response to vitamin A / response to ionizing radiation / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / hepatocyte apoptotic process / negative regulation of gene expression, epigenetic / male meiosis I / chromosome, centromeric region / catalytic complex / heterochromatin / DNA methylation / enzyme activator activity / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / stem cell differentiation / cellular response to amino acid stimulus / placenta development / response to cocaine / response to lead ion / euchromatin / RMTs methylate histone arginines / nuclear matrix / response to toxic substance / neuron differentiation / transcription corepressor activity / response to estradiol / spermatogenesis / methylation / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / chromatin binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site ...DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Vaccinia Virus protein VP39 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
CITRIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (cytosine-5)-methyltransferase 3-like / DNA (cytosine-5)-methyltransferase 3A
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.499 Å
データ登録者Anteneh, H. / Song, J.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 米国
引用ジャーナル: Nat Commun / 年: 2020
タイトル: Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation.
著者: Anteneh, H. / Fang, J. / Song, J.
履歴
登録2020年3月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年4月15日Provider: repository / タイプ: Initial release
改定 1.12020年5月20日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22023年10月18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
改定 1.32024年12月25日Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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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: DNA (cytosine-5)-methyltransferase 3A
B: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3A
C: DNA (cytosine-5)-methyltransferase 3-like
E: CGA DNA (25-MER)
F: CGA DNA (25-MER)
G: DNA (cytosine-5)-methyltransferase 3A
H: DNA (cytosine-5)-methyltransferase 3-like
J: DNA (cytosine-5)-methyltransferase 3A
I: DNA (cytosine-5)-methyltransferase 3-like
K: CGA DNA (25-MER)
L: CGA DNA (25-MER)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)260,54420
ポリマ－258,23712
非ポリマー2,3068
水4,666259
1
A: DNA (cytosine-5)-methyltransferase 3A
B: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3A
C: DNA (cytosine-5)-methyltransferase 3-like
E: CGA DNA (25-MER)
F: CGA DNA (25-MER)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,27210
ポリマ－129,1196
非ポリマー1,1534
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
2
G: DNA (cytosine-5)-methyltransferase 3A
H: DNA (cytosine-5)-methyltransferase 3-like
J: DNA (cytosine-5)-methyltransferase 3A
I: DNA (cytosine-5)-methyltransferase 3-like
K: CGA DNA (25-MER)
L: CGA DNA (25-MER)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,27210
ポリマ－129,1196
非ポリマー1,1534
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)187.559, 187.559, 82.398
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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要素

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DNA (cytosine-5)-methyltransferase ... , 2種, 8分子 ADGJBCHI

#1: タンパク質
DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / DNA methyltransferase HsaIIIA / M.HsaIIIA


分子量: 32696.668 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DNMT3A / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase
#2: タンパク質
DNA (cytosine-5)-methyltransferase 3-like


分子量: 24163.705 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DNMT3L / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9UJW3

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DNA鎖 , 1種, 4分子 EFKL

#3: DNA鎖
CGA DNA (25-MER)


分子量: 7698.969 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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非ポリマー , 3種, 267分子

#4: 化合物
ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C6H8O7
#5: 化合物
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-アデノシルホモシステイン


分子量: 384.411 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C14H20N6O5S
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 259 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationN

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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: 3.24 Å3/Da / 溶媒含有率: 62.09 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M Sodium Citrate pH 4.2, 1% PEG8000

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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: SSRL / ビームライン: BL12-2 / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2019年1月26日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.499→37.72 Å / Num. obs: 110518 / % possible obs: 98.5 % / 冗長度: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.4
反射 シェル解像度: 2.5→2.59 Å / Num. unique obs: 110518 / CC1/2: 0.726

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
PDB_EXTRACT3.25データ抽出
HKL-3000データ削減
HKL-3000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: 5YX2

5yx2


解像度: 2.499→37.72 Å / SU ML: 0.32 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 31.32 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2404 2010 1.82 %
Rwork0.196 108507 -
obs0.1968 110517 98.5 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 251.83 Å2 / Biso mean: 90.5492 Å2 / Biso min: 30 Å2
精密化ステップサイクル: final / 解像度: 2.499→37.72 Å
タンパク質核酸リガンド溶媒全体
原子数14612 2019 156 259 17046
Biso mean--73.97 68.76 -
残基数----1989
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 (%)
2.4993-2.56170.381320.3422728793
2.5617-2.6310.31351380.3105747895
2.631-2.70840.38241450.2969760197
2.7084-2.79580.33611370.2835773798
2.7958-2.89570.31591470.2592779699
2.8957-3.01160.28381480.23517910100
3.0116-3.14860.27521460.22417850100
3.1486-3.31450.29031390.21957831100
3.3145-3.5220.29181440.2081777099
3.522-3.79370.20081460.17917871100
3.7937-4.1750.2121440.17177855100
4.175-4.77810.18581400.14977850100
4.7781-6.0160.21891480.1727859100
6.016-37.720.21411560.1765781299
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)
15.37341.22680.81025.2372-0.32933.17190.07030.0326-0.0401-0.1366-0.1220.30640.29220.07060.02940.4196-0.04480.13130.43130.00370.3228229.008-35.15311.6306
23.00631.33450.38311.81670.32362.17850.1335-0.56690.32220.7173-0.29080.73590.1887-0.34210.18210.6273-0.12880.29070.5956-0.06240.6587220.1151-33.35516.7138
34.37045.36970.17467.6219-1.09341.33190.3369-0.82420.45261.0356-0.43430.487-0.0391-0.15650.15620.5714-0.06430.16860.565-0.04480.3993238.2756-19.991120.6393
43.69551.92230.15435.2175-0.63852.1563-0.0187-0.1830.3740.00240.00230.29640.16620.02040.05410.3467-0.00660.08480.4449-0.03330.2892238.6309-21.643610.6216
59.63162.06640.7621.8174-0.18842.25120.1294-0.7109-0.3660.7971-0.41251.44160.4598-0.36990.18720.8103-0.24360.42491.018-0.08561.4968193.1271-49.7320.1827
65.7290.88841.94533.7723-1.54124.25750.2738-0.2298-0.10220.5534-0.12531.11240.1023-0.3702-0.05630.6682-0.16340.48830.7352-0.1381.2767201.5283-41.065616.9551
79.12732.74133.2010.93030.70781.4775-0.51240.74411.0281-0.11230.9030.5312-0.6348-0.7154-0.39130.6818-0.08020.24981.02810.08451.3238197.1854-34.0524.7272
83.4053-3.20372.32973.0415-2.13694.76990.41391.22070.6044-0.9210.51041.19120.3654-1.035-0.70620.6591-0.19620.18721.1940.06171.5635193.1052-40.76975.4419
99.3753.12344.42836.2752-1.92669.23140.53881.47292.342-0.61721.26381.06771.009-0.8295-1.46751.1043-0.020.14071.45790.61852.033187.3488-27.59623.7733
102.8521-0.3545-0.77894.3159-0.0313.1863-0.04481.1758-0.54230.14220.736-0.76980.2072-0.6989-0.340.7193-0.25690.13851.3608-0.05921.5411185.7372-47.962413.6128
115.50311.38120.23465.80170.82562.2575-0.0672-0.03910.25410.1111-0.0715-0.2679-0.02470.32410.11380.4038-0.0187-0.00470.45150.10210.3069263.0416-1.8730.555
122.26930.64021.00322.03391.01672.3189-0.32830.53330.7595-0.38660.07510.0762-0.37150.31850.28730.5244-0.1293-0.06820.60770.30840.6775260.58427.1575-14.3747
138.46384.3284-0.58114.79240.30732.522-0.47170.8320.2611-0.60840.24780.29930.12920.1140.19440.5383-0.0352-0.03990.50820.13610.3129247.2632-11.0203-18.2905
143.11821.91781.06174.10770.33653.2396-0.11540.17820.2509-0.2011-0.02280.37730.11920.08680.08860.39740.00170.01520.34570.07490.3355249.0386-11.3906-8.3202
152.52431.0130.61021.1550.6771.0053-0.52040.94450.5577-0.62020.34980.0192-0.88441.12520.1321.2671-0.9504-0.27341.14261.03512.4314276.457333.5694-18.2778
162.38340.2112-0.99214.3705-0.01434.798-0.09880.56181.3946-0.22540.0368-0.3835-1.36980.5538-0.01931.0889-0.33-0.170.81680.38861.5382266.990828.2988-13.5858
179.12462.01490.03923.88040.21794.04360.8716-0.81060.54481.6767-0.51920.3014-1.67140.4957-0.3771.8791-0.52030.14230.9986-0.00881.8571266.545839.2753-4.7012
184.83421.0231-4.61485.4275-2.436.6065-0.10470.15690.44720.25740.64251.6151-0.0823-1.3546-0.51550.64050.0869-0.05890.89770.31391.287232.3841.6164-10.4388
192.09373.5469-2.83477.5311-6.0286.31180.4284-0.9617-0.13550.9865-0.5970.7501-0.92790.1954-0.01391.3045-0.09930.5921.1578-0.21251.8058220.8668-10.282625.9369
206.02120.7942-0.53759.0877-6.95228.20560.3864-1.10390.64211.30390.22550.3343-1.965-0.31140.14770.9645-0.02010.42280.7093-0.31671.1608226.3392-14.413825.6535
211.35651.5897-1.95166.1425-5.66875.4910.38710.28970.76990.5105-0.02151.2499-1.6874-0.6062-0.59211.47710.23070.05220.8690.05731.653224.661-1.03284.2926
226.97263.1372-5.09975.0906-1.44963.8941-0.83811.2642-0.4511-0.60110.434-0.45570.3538-0.9887-0.06280.9622-0.0545-0.19910.98990.26051.528238.85575.8096-24.9642
233.7486-0.64360.32077.31470.58853.2983-0.02650.1805-0.3965-0.1321-0.03840.02030.120.24720.10750.46380.0140.05680.34990.10170.3396238.8015-90.036-12.1084
241.1949-0.37430.10173.85430.50922.3675-0.2913-0.411-0.49490.72220.05180.4850.42510.05550.25910.68030.06720.17860.48280.2210.6598232.8252-96.7532.944
251.9721-3.64430.42288.53450.12060.8647-0.2337-0.3694-0.08180.73790.19910.32090.11650.01440.03480.58810.00120.10970.51950.12210.3752232.6198-75.23166.5555
262.436-0.95670.57874.98480.24472.207-0.0642-0.26040.09360.4053-0.0390.56140.09970.04680.12770.481-0.01460.08970.39130.06340.3928229.9123-74.1593-1.5549
270.99721.20331.35577.9192-0.46182.8832-0.13360.1833-0.88550.45570.16690.29560.51630.2027-0.26491.14850.04280.37410.64490.24531.6465234.928-131.14692.5424
281.08442.75980.87949.19550.12942.6920.2767-0.554-1.03842.0377-0.33570.74650.364-0.2538-0.22721.42090.02510.36320.83740.37411.3562231.562-124.574512.3697
291.93621.21871.26086.9512-0.22444.1551-0.1006-0.1464-0.7638-0.17890.27860.73090.6192-0.3479-0.12980.8535-0.00630.32970.52960.24361.285227.8295-116.71850.0134
303.9436-1.58372.94144.5322-1.98964.10011.08771.5212-1.2961-2.29570.49780.98041.1357-0.0333-0.58491.5074-0.1125-0.30990.76010.06731.5293224.4574-125.0884-10.9343
313.8297-2.24122.61534.394-2.74833.2962-0.2526-1.0373-0.9484-1.13010.64691.93250.7378-1.2478-1.11351.0442-0.1722-0.22891.06190.48522.9219209.1796-121.2714-4.0947
322.4993-2.68531.01915.5585-2.13774.22710.0327-0.334-0.7468-1.02870.63320.06981.4341-0.3542-0.55461.3424-0.04170.10640.6324-0.01371.8714230.0615-134.8648-0.8296
334.7149-1.2345-0.27525.71861.16452.6624-0.0703-0.12250.40040.0747-0.04610.0262-0.31260.20440.14470.414-0.0174-0.08410.3570.05830.3251226.8838-43.8716-13.1652
341.2898-0.4807-0.18312.13160.68092.5025-0.12180.3120.3561-0.6048-0.10320.6578-0.4996-0.13330.32850.68060.0223-0.27340.43450.08820.7185217.8642-41.499-28.0999
351.606-1.1951-0.80958.35240.43051.871-0.02330.3971-0.0907-1.0075-0.17930.3028-0.07310.16110.1930.56610.0236-0.16060.51570.06420.339226.8859-62.1323-32.0067
362.8059-0.27190.28893.98131.47273.2392-0.03330.2009-0.1687-0.3522-0.07660.4130.06110.18230.02710.40760.0337-0.08320.420.05070.3634228.1875-61.0523-22.117
376.37834.63762.42714.97452.2892.60010.3621-0.32210.8378-1.4494-0.55010.5191-1.9307-0.91510.34882.30330.611-1.02990.34870.44412.3998200.752-12.2128-31.3363
381.525-1.3198-0.91253.6674-2.51034.9148-0.06040.69281.4859-0.50360.36851.4595-0.7547-0.797-0.23071.30020.2274-0.49450.7450.18031.6665205.0519-25.9846-33.0404
391.0913-0.0685-1.96489.38851.04813.97460.3012-0.24991.0790.1048-0.109-0.44-2.25140.37160.28742.0462-0.0128-0.59860.82910.01391.818215.8324-14.4219-24.7786
400.9817-1.4075-0.50072.9654-1.20474.3116-0.5553-0.78891.18710.59930.41951.2158-1.6057-1.62790.01061.12550.4414-0.30731.014-0.13221.8282198.2082-26.7436-18.2616
411.80321.9433-0.70014.49221.9352.7153-0.9742-1.0520.78680.04930.43311.6-0.8953-0.99020.34871.54470.58670.08881.30210.19062.034190.2277-21.1815-20.67
424.3703-1.6691-1.79497.0257-2.61438.46730.20480.5589-1.2396-1.0248-0.60990.70540.5751-0.8864-0.08690.72570.0316-0.39720.6478-0.05750.9148213.6563-60.6599-37.019
432.2754-0.83610.66934.5704-3.90013.92310.0927-1.0998-1.4453-0.28141.02241.42050.919-1.035-0.66760.8779-0.2553-0.19951.27290.35091.762205.5661-73.2331-16.5701
444.87860.3515-2.25670.93230.09146.4056-0.2562-0.4128-0.49321.69460.2889-0.1818-1.1665-0.6934-0.44171.3405-0.00230.45170.90210.42242.1631214.7181-84.765913.3737
455.9483-1.32696.33545.7093-3.41548.65170.2348-0.74150.4081.1654-0.04770.8695-0.6168-1.51350.23090.84190.01580.46290.78850.08381.1481219.5078-82.162512.0899
463.6928-1.94395.1313.882-4.8788.8377-0.435-0.1058-0.30230.05840.74991.4409-0.5865-1.8431-0.32930.82710.0308-0.09351.29410.05731.6268206.9965-76.6448-9.3835
474.7922-3.1803-2.91215.19-2.24127.32430.03980.38860.4655-1.52370.06650.61890.8299-0.1301-0.41960.92540.0381-0.4750.8371-0.11171.3899208.1642-60.8821-38.6635
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 628 through 698 )A628 - 698
2X-RAY DIFFRACTION2chain 'A' and (resid 699 through 784 )A699 - 784
3X-RAY DIFFRACTION3chain 'A' and (resid 785 through 849 )A785 - 849
4X-RAY DIFFRACTION4chain 'A' and (resid 850 through 912 )A850 - 912
5X-RAY DIFFRACTION5chain 'B' and (resid 178 through 228 )B178 - 228
6X-RAY DIFFRACTION6chain 'B' and (resid 229 through 291 )B229 - 291
7X-RAY DIFFRACTION7chain 'B' and (resid 292 through 318 )B292 - 318
8X-RAY DIFFRACTION8chain 'B' and (resid 319 through 332 )B319 - 332
9X-RAY DIFFRACTION9chain 'B' and (resid 333 through 353 )B333 - 353
10X-RAY DIFFRACTION10chain 'B' and (resid 354 through 380 )B354 - 380
11X-RAY DIFFRACTION11chain 'D' and (resid 628 through 698 )D628 - 698
12X-RAY DIFFRACTION12chain 'D' and (resid 699 through 784 )D699 - 784
13X-RAY DIFFRACTION13chain 'D' and (resid 785 through 849 )D785 - 849
14X-RAY DIFFRACTION14chain 'D' and (resid 850 through 912 )D850 - 912
15X-RAY DIFFRACTION15chain 'C' and (resid 185 through 199 )C185 - 199
16X-RAY DIFFRACTION16chain 'C' and (resid 200 through 324 )C200 - 324
17X-RAY DIFFRACTION17chain 'C' and (resid 325 through 378 )C325 - 378
18X-RAY DIFFRACTION18chain 'E' and (resid 423 through 438 )E423 - 438
19X-RAY DIFFRACTION19chain 'E' and (resid 439 through 446 )E439 - 446
20X-RAY DIFFRACTION20chain 'F' and (resid 423 through 428 )F423 - 428
21X-RAY DIFFRACTION21chain 'F' and (resid 429 through 438 )F429 - 438
22X-RAY DIFFRACTION22chain 'F' and (resid 439 through 447 )F439 - 447
23X-RAY DIFFRACTION23chain 'G' and (resid 629 through 698 )G629 - 698
24X-RAY DIFFRACTION24chain 'G' and (resid 699 through 784 )G699 - 784
25X-RAY DIFFRACTION25chain 'G' and (resid 785 through 839 )G785 - 839
26X-RAY DIFFRACTION26chain 'G' and (resid 840 through 912 )G840 - 912
27X-RAY DIFFRACTION27chain 'H' and (resid 178 through 206 )H178 - 206
28X-RAY DIFFRACTION28chain 'H' and (resid 207 through 228 )H207 - 228
29X-RAY DIFFRACTION29chain 'H' and (resid 229 through 319 )H229 - 319
30X-RAY DIFFRACTION30chain 'H' and (resid 320 through 339 )H320 - 339
31X-RAY DIFFRACTION31chain 'H' and (resid 340 through 360 )H340 - 360
32X-RAY DIFFRACTION32chain 'H' and (resid 361 through 380 )H361 - 380
33X-RAY DIFFRACTION33chain 'J' and (resid 628 through 698 )J628 - 698
34X-RAY DIFFRACTION34chain 'J' and (resid 699 through 784 )J699 - 784
35X-RAY DIFFRACTION35chain 'J' and (resid 785 through 849 )J785 - 849
36X-RAY DIFFRACTION36chain 'J' and (resid 850 through 912 )J850 - 912
37X-RAY DIFFRACTION37chain 'I' and (resid 184 through 206 )I184 - 206
38X-RAY DIFFRACTION38chain 'I' and (resid 207 through 270 )I207 - 270
39X-RAY DIFFRACTION39chain 'I' and (resid 271 through 280 )I271 - 280
40X-RAY DIFFRACTION40chain 'I' and (resid 281 through 332 )I281 - 332
41X-RAY DIFFRACTION41chain 'I' and (resid 333 through 378 )I333 - 378
42X-RAY DIFFRACTION42chain 'K' and (resid 423 through 428 )K423 - 428
43X-RAY DIFFRACTION43chain 'K' and (resid 429 through 438 )K429 - 438
44X-RAY DIFFRACTION44chain 'K' and (resid 439 through 447 )K439 - 447
45X-RAY DIFFRACTION45chain 'L' and (resid 423 through 428 )L423 - 428
46X-RAY DIFFRACTION46chain 'L' and (resid 429 through 438 )L429 - 438
47X-RAY DIFFRACTION47chain 'L' and (resid 439 through 447 )L439 - 447

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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