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- PDB-7b4c: Structural basis of reactivation of oncogenic p53 mutants by a sm... -

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基本情報

登録情報
データベース: PDB / ID: 7b4c
タイトルStructural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C mutant bound to MQ: R273C-MQ (II)
要素Cellular tumor antigen p53
キーワードTRANSCRIPTION / P53 / TUMOR SUPPRESSOR / DNA BINDING PROTEIN / PROTEIN DNA COMPLEX / MICHAEL ACCEPTOR / MICHAEL REACTION / PROTEIN-DRUG COMPLEX / PROTEIN-DNA-DRUG COMPLEX / LOOP-SHEET-HELIX MOTIF / DNA TARGET / ACTIVATOR / HOOGSTEEN BASE-PAIRING
機能・相同性
機能・相同性情報


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / T cell lineage commitment / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / positive regulation of execution phase of apoptosis / Transcriptional Regulation by VENTX / replicative senescence / cellular response to UV-C / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to actinomycin D / neuroblast proliferation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / type II interferon-mediated signaling pathway / hematopoietic stem cell differentiation / Pyroptosis / chromosome organization / viral process / embryonic organ development / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / negative regulation of proteolysis / Regulation of TP53 Activity through Acetylation / mitotic G1 DNA damage checkpoint signaling / gastrulation / 14-3-3 protein binding / response to salt stress / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex
類似検索 - 分子機能
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one / (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one / Cellular tumor antigen p53
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: 1.71 Å
データ登録者Degtjarik, O. / Rozenberg, H. / Shakked, Z.
資金援助1件
組織認可番号国
Aprea Therapeutics AB
引用ジャーナル: Nat Commun / 年: 2021
タイトル: Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ).
著者: Degtjarik, O. / Golovenko, D. / Diskin-Posner, Y. / Abrahmsen, L. / Rozenberg, H. / Shakked, Z.
履歴
登録2020年12月2日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年12月8日Provider: repository / タイプ: Initial release
改定 1.12021年12月15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 1.22024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _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: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,50321
ポリマ－89,8064
非ポリマー1,69717
水9,800544
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • tetramer
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint3 kcal/mol
Surface area36380 Å2
手法PISA
単位格子
Length a, b, c (Å)68.881, 71.083, 84.923
Angle α, β, γ (deg.)90.000, 90.033, 90.000
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


分子量: 22451.531 Da / 分子数: 4 / 断片: p53 human DNA binding domain / 変異: R273C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TP53, P53 / プラスミド: pET-27-b / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P04637

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非ポリマー , 6種, 561分子

#2: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn
#3: 化合物
ChemComp-QNN / (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one


分子量: 139.195 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C8H13NO / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物 ChemComp-QN8 / (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one


分子量: 139.195 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H13NO / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H10O3
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 544 / 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Y
Has protein modificationY
非ポリマーの詳細Two enantiomers, QNN and QN8 are produced by addition reaction of the michael acceptor compound "2- ...Two enantiomers, QNN and QN8 are produced by addition reaction of the michael acceptor compound "2-methylenequinuclidin-3-one" with cysteine or lysine. As such, QNN and QN8 bind covalently to the thiol group of cysteine or amino group of lysine. The chiral definitions of QNN and QN8 bound to cysteines are reversed to that of the pseudo free ligands.

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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: 46.87 % / Mosaicity: 0.912 °
結晶化温度: 292 K / 手法: 蒸発脱水法 / pH: 6.1 / 詳細: 0.2M Sodium Fluoride, 20% w/v PEG 3350

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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: ESRF / ビームライン: ID23-1 / 波長: 0.972 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年3月2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: 0.972 Å / 相対比: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.64
11-h,-k,l20.36
反射解像度: 1.709→50 Å / Num. obs: 87231 / % possible obs: 98.4 % / 冗長度: 6 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Χ2: 0.962 / Net I/σ(I): 6.1
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
1.71-1.745.60.62643260.8230.2870.690.76497
1.74-1.775.60.50942150.8810.2320.5610.79596.4
1.77-1.816.20.49543030.9140.2120.540.79997.8
1.81-1.846.20.43642950.9270.1860.4750.79897.9
1.84-1.886.20.37443600.9460.160.4080.83797.9
1.88-1.936.10.31643200.9630.1360.3450.8797.9
1.93-1.976.10.26143280.970.1130.2850.90597.9
1.97-2.0360.22843460.9690.10.2490.95598.2
2.03-2.095.50.1843190.9810.0820.1981.00298.4
2.09-2.155.80.15743440.9850.070.1720.99498
2.15-2.236.30.14543570.9880.0610.1571.04898.5
2.23-2.326.20.12943580.9890.0550.141.05198.7
2.32-2.436.20.11243740.9920.0480.1221.05298.8
2.43-2.556.10.09943790.9930.0430.1081.0498.8
2.55-2.715.60.08843410.9920.040.0971.09998.5
2.71-2.926.30.07944050.9940.0340.0861.08599.3
2.92-3.226.30.0744310.9950.030.0761.04199.5
3.22-3.686.10.06344570.9950.0280.0691.04299.6
3.68-4.645.90.05544310.9960.0240.061.00199.1
4.64-5060.05345420.9970.0230.0581.01699.4

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
REFMAC5.8.0266精密化
PDB_EXTRACT3.25データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 4IBQ

4ibq


解像度: 1.71→42.75 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.957 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0197 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor反射数%反射Selection details
Rfree0.1819 4332 5 %RANDOM
Rwork0.1488 ---
obs0.1505 82878 98.25 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso max: 82.72 Å2 / Biso mean: 30.458 Å2 / Biso min: 13.55 Å2
Baniso -1Baniso -2Baniso -3
1--14.78 Å2-0 Å2-9.96 Å2
2--25.33 Å20 Å2
3----10.55 Å2
精密化ステップサイクル: final / 解像度: 1.71→42.75 Å
タンパク質核酸リガンド溶媒全体
原子数5917 0 104 548 6569
Biso mean--41.24 35.14 -
残基数----765
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0136641
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176020
X-RAY DIFFRACTIONr_angle_refined_deg1.9341.6739090
X-RAY DIFFRACTIONr_angle_other_deg1.5821.59413936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2085873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78520.313351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.267151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9961565
X-RAY DIFFRACTIONr_chiral_restr0.1010.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027843
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021569
LS精密化 シェル解像度: 1.71→1.754 Å / Rfactor Rfree error: 0
Rfactor反射数%反射
Rfree0.222 296 -
Rwork0.177 5912 -
obs--95.17 %
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)
14.324-2.9076-1.86811.90727.14289.6506-0.1619-0.1554-0.24140.19370.1319-0.12050.7220.01170.030.18010.00270.10040.15750.03850.09414.6305-7.605823.1646
23.8254-0.34351.10.66780.01631.3816-0.01390.09590.1316-0.05710.0411-0.01630.0124-0.0144-0.02710.11530.01360.08870.0914-0.00460.1487-3.4410.50258.729
32.8544-0.04220.31675.21593.13164.9780.0338-0.2354-0.20080.2978-0.13740.12510.3277-0.11250.10360.10980.01170.09460.16070.03790.11388.948-6.72615.0739
43.7904-2.08181.08798.6412-4.667211.51720.15590.2887-0.2638-0.109-0.1302-0.2750.0760.3742-0.02570.12520.04610.09630.2078-0.08950.191514.0134-11.96671.5717
52.7097.15324.725920.756215.549613.4785-0.53390.3369-0.0657-1.50440.5772-0.2766-1.1230.2815-0.04330.309-0.10960.0410.58760.14860.397918.55082.0321-1.1999
63.55670.2128-0.6113.48591.70793.7106-0.02860.03160.054-0.07910.063-0.2068-0.04110.3473-0.03440.0746-0.00740.08540.1547-0.00080.125616.3508-1.322810.2299
73.4676-1.1787-2.10234.92984.00986.46060.02090.05260.4381-0.1609-0.13570.1921-0.2917-0.14130.11490.0890.01150.05850.09270.01090.17533.91034.754610.0283
82.137-0.6673-1.04486.27736.97810.3480.06480.3229-0.3201-0.2053-0.0254-0.0198-0.0260.1121-0.03940.10940.03320.06650.1132-0.00740.15276.8236-10.07167.4012
93.6166-0.41181.46430.83830.17733.41720.13220.1852-0.2032-0.0269-0.04330.07110.22470.098-0.08890.13950.0030.10850.0772-0.01710.12881.4631-5.06989.8975
1013.42062.2188-8.749517.933215.459352.6779-0.02050.0652-1.31810.2247-0.13720.14272.0867-1.47360.15770.1852-0.0612-0.02160.2056-0.06910.5528-12.29-11.89790.8975
1119.6772-12.6751-16.39189.30811.091313.9067-0.8397-0.004-1.06370.8740.2906-0.01640.88470.11810.54910.54780.0245-0.01370.2135-0.0050.81532.8897-15.163656.3265
127.6877-1.72122.48741.4301-1.88052.6556-0.0664-0.5565-0.47360.09040.07440.0894-0.0309-0.115-0.00790.15670.0060.11430.10640.01660.1924-6.5591-1.385558.1188
135.1989-0.0486-0.37570.566-0.05761.5234-0.0440.1134-0.32990.0231-0.0140.0676-0.0196-0.20550.0580.11780.00820.11250.1088-0.00080.1318-1.315-1.959251.7179
144.3487-0.0732-1.27778.4307-6.618610.4880.11620.383-0.48620.0321-0.5587-0.3959-0.18070.75770.44250.10620.01090.05620.2112-0.05220.145312.6242-4.933439.1516
1511.53696.12621.558823.920511.706620.5645-0.11330.25110.89-0.50680.1811-0.3137-1.27980.1123-0.06770.11920.00660.04090.2088-0.0030.188616.14014.661844.5962
166.3951-0.57840.00853.64921.85144.6154-0.0374-0.1601-0.21170.09590.0155-0.0612-0.11130.17050.02190.1001-0.0080.08660.14130.02320.114412.9108-0.897953.124
1728.0476-13.2598-0.372519.01862.88814.03270.3459-0.64151.6981-0.0383-0.37710.1359-0.8653-0.25350.03120.32390.02880.13310.3152-0.11870.2368-0.17429.253865.9366
183.67160.242-0.83121.77050.92295.5945-0.06070.1696-0.0745-0.1326-0.08120.0808-0.1295-0.14120.14180.10560.01960.07950.08560.00310.12852.68441.057146.3938
193.67850.3516-1.35540.4661-0.3194.7019-0.0295-0.1455-0.7677-0.05-0.09840.01220.4145-0.22440.12790.1672-0.00570.10730.1270.03940.29752.7229-7.270352.6132
208.11493.2116-0.46654.16370.19566.2692-0.08880.81-0.6767-0.362-0.0384-0.00890.50480.31310.12720.17660.02320.0710.4496-0.08270.1765-12.5508-2.313738.9121
214.67391.2053-0.97521.4373-1.05411.4698-0.05920.34240.5774-0.0628-0.01380.0643-0.04920.18590.0730.14770.00110.02450.20660.06310.1985-38.27198.126946.4121
227.502-0.77771.55094.5579-2.13493.8742-0.0096-0.4030.0725-0.03360.08820.08230.1087-0.0145-0.07860.0909-0.00380.07740.236-0.00990.1058-42.7673.017757.5243
234.84370.63070.58980.54040.12763.9093-0.14070.19310.5243-0.08540.02670.0721-0.116-0.09340.1140.08480.02950.06640.18080.04710.1593-31.44366.94850.7081
244.4555-1.9667-2.9781.49070.74927.202-0.2784-0.283-0.13590.0380.0437-0.32130.57010.58730.23470.16150.0060.10370.29710.01140.2925-19.9791-0.517463.1769
257.91430.3899-0.56483.06520.14724.6985-0.07160.2443-0.17430.0415-0.0245-0.11630.31010.0530.09610.09890.03510.09410.22490.02480.11-21.62240.466752.4034
265.5357-0.04331.55432.06752.07026.76760.05920.49640.2124-0.0212-0.0886-0.09810.2572-0.1360.02930.12330.02080.10420.31570.09610.1175-25.4553.753945.1134
276.42740.99521.70951.00350.98917.2119-0.0682-0.1856-0.1306-0.0530.0426-0.04710.0216-0.03120.02550.10870.00810.1010.17410.04190.1009-31.94081.146156.6763
284.1103-0.3736-0.2751.5590.78564.4359-0.05290.12390.75680.00460.09730.0405-0.2160.1339-0.04440.097-0.01080.04810.16050.04850.2194-30.647710.807950.4924
298.8448-0.01321.14751.8583-0.84451.3805-0.0295-1.11870.37220.25420.00450.02970.08670.02130.0250.13660.02370.06290.3482-0.06050.0917-42.17963.867263.6085
3013.93470.7451.745811.1761-7.64629.28970.1115-1.21231.36370.91840.25430.6563-1.4867-1.4688-0.36580.20370.04950.09770.3131-0.10710.2389-50.00249.803964.4763
311.3612-0.44582.60676.35013.77098.9865-0.3161-0.04390.1617-0.3190.3059-0.4715-0.9904-0.38980.01020.18490.09340.06430.5321-0.00330.1242-28.816910.9693-4.308
326.07570.95930.11460.54310.19740.312-0.00170.0766-0.32930.0632-0.02350.0248-0.0050.06450.02520.119-0.01620.10440.2345-0.03310.1797-37.67071.572211.8106
3317.6874.21845.48514.4613.01473.67790.41640.8952-1.4218-0.32-0.32720.25080.172-0.4355-0.08920.22090.0086-0.06440.4567-0.15040.2784-31.144-4.8082-7.288
343.00490.0131-0.12412.99271.12891.46130.0709-0.02680.44520.1124-0.00950.1038-0.18120.0835-0.06140.1194-0.01110.1090.24210.0190.1677-23.376912.560411.3963
351.3112-2.7528-0.425412.441712.653421.0795-0.4236-0.11710.031.66740.4817-0.18261.59620.7675-0.05810.33190.1390.12480.6080.12910.4294-15.55550.44220.3029
364.3940.0488-1.46364.77320.43053.38790.06130.0366-0.12460.0996-0.1336-0.10410.0684-0.08720.07230.0642-0.00220.0650.17760.0210.094-17.77232.93498.6146
3710.19656.06521.96648.35095.95055.26120.2375-0.5276-0.76520.6033-0.71740.3130.5668-0.50630.47990.2894-0.1270.0160.4943-0.07840.5163-32.5938-10.8637-1.2612
384.23910.0087-0.82852.41550.8222.96560.0972-0.05130.13050.1795-0.14650.1381-0.1674-0.06680.04930.0963-0.01050.08280.19380.00130.0947-27.68527.34212.6787
394.8965-0.4448-3.89441.06810.66325.43750.14010.09260.14280.0458-0.12410.1334-0.1508-0.1648-0.0160.0701-0.01890.05860.2198-0.02140.0892-32.16756.41418.9857
405.1767-2.99384.41317.1703-3.88237.605-0.2454-0.40690.9860.49830.1933-0.184-0.6758-0.36130.05220.1589-0.00040.19090.2127-0.09570.5798-46.814211.353517.4575
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A96 - 109
2X-RAY DIFFRACTION2A110 - 149
3X-RAY DIFFRACTION3A150 - 168
4X-RAY DIFFRACTION4A169 - 179
5X-RAY DIFFRACTION5A180 - 188
6X-RAY DIFFRACTION6A189 - 220
7X-RAY DIFFRACTION7A221 - 241
8X-RAY DIFFRACTION8A242 - 258
9X-RAY DIFFRACTION9A259 - 283
10X-RAY DIFFRACTION10A284 - 288
11X-RAY DIFFRACTION11B97 - 102
12X-RAY DIFFRACTION12B103 - 120
13X-RAY DIFFRACTION13B121 - 168
14X-RAY DIFFRACTION14B169 - 182
15X-RAY DIFFRACTION15B183 - 192
16X-RAY DIFFRACTION16B193 - 219
17X-RAY DIFFRACTION17B220 - 227
18X-RAY DIFFRACTION18B228 - 245
19X-RAY DIFFRACTION19B246 - 275
20X-RAY DIFFRACTION20B276 - 288
21X-RAY DIFFRACTION21C96 - 120
22X-RAY DIFFRACTION22C121 - 135
23X-RAY DIFFRACTION23C136 - 173
24X-RAY DIFFRACTION24C174 - 188
25X-RAY DIFFRACTION25C189 - 208
26X-RAY DIFFRACTION26C209 - 227
27X-RAY DIFFRACTION27C228 - 244
28X-RAY DIFFRACTION28C245 - 270
29X-RAY DIFFRACTION29C271 - 283
30X-RAY DIFFRACTION30C284 - 288
31X-RAY DIFFRACTION31D95 - 108
32X-RAY DIFFRACTION32D109 - 145
33X-RAY DIFFRACTION33D146 - 154
34X-RAY DIFFRACTION34D155 - 179
35X-RAY DIFFRACTION35D180 - 188
36X-RAY DIFFRACTION36D189 - 219
37X-RAY DIFFRACTION37D220 - 229
38X-RAY DIFFRACTION38D230 - 258
39X-RAY DIFFRACTION39D259 - 281
40X-RAY DIFFRACTION40D282 - 289

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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