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- PDB-7b48: 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: 7b48
タイトルStructural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to MQ: R273H-MQ (II)
要素Cellular tumor antigen p53P53遺伝子
キーワードTRANSCRIPTION (転写 (生物学)) / P53 (P53遺伝子) / TUMOR SUPPRESSOR (がん抑制遺伝子) / DNA BINDING PROTEIN (DNA結合タンパク質) / 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 / 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 / Activation of NOXA and translocation to mitochondria / 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 / 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / 転写 (生物学) / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of neuroblast proliferation / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / rRNA transcription / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / マイトファジー / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / ヘイフリック限界 / chromosome organization / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of reactive oxygen species metabolic process / MDM2/MDM4 family protein binding / embryonic organ development / glial cell proliferation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / negative regulation of fibroblast proliferation / cardiac muscle cell apoptotic process / response to salt stress / transcription initiation-coupled chromatin remodeling / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation
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
酢酸塩 / DI(HYDROXYETHYL)ETHER / (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one / P53遺伝子
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: 2.05 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

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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)91,29521
ポリマ－89,9464
非ポリマー1,34917
水8,449469
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
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint16 kcal/mol
Surface area36370 Å2
手法PISA
単位格子
Length a, b, c (Å)69.249, 72.003, 85.233
Angle α, β, γ (deg.)90.000, 90.066, 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 / P53遺伝子 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


分子量: 22486.535 Da / 分子数: 4 / 断片: p53 human DNA binding domain / 変異: R273H / 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, 486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: 2 / 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 / エチレングリコール


分子量: 62.068 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン / 酢酸塩


分子量: 59.044 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H3O2
#6: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル / ジエチレングリコール


分子量: 106.120 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C4H10O3
#7: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 469 / 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
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: 2.46 Å3/Da / 溶媒含有率: 50.01 % / Mosaicity: 0.64 °
結晶化温度: 292 K / 手法: 蒸発脱水法 / pH: 6.1 / 詳細: 0.2M Li Acetate, 2.0% w/v Agarose, 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: ID23-2 / 波長: 0.8729 Å
検出器タイプ: DECTRIS PILATUS3 2M / 検出器: PIXEL / 日付: 2016年7月22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: 0.8729 Å / 相対比: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.756
11-h,-k,l20.244
反射解像度: 2.05→39 Å / Num. obs: 49698 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / 冗長度: 3.1 % / CC1/2: 0.986 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.073 / Rrim(I) all: 0.136 / Χ2: 1.094 / Net I/σ(I): 10.18
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
2.05-2.0930.25421270.910.1620.3030.68381.1
2.09-2.123.10.25922110.9260.1610.3070.68884.5
2.12-2.1630.2523420.9210.1570.2970.73988.7
2.16-2.2130.27623630.9150.1750.3280.78392.4
2.21-2.263.10.22225340.9250.1410.2640.77695.1
2.26-2.313.20.23825460.9340.1510.2830.83296.3
2.31-2.373.20.22525070.9370.1420.2670.82596.8
2.37-2.433.10.18825740.9550.120.2250.93496.6
2.43-2.52.90.17425020.9510.1160.2110.99696
2.5-2.582.90.16125190.9510.1070.1951.08295.9
2.58-2.683.20.15725420.9620.0980.1861.07296.3
2.68-2.783.10.1425340.9610.090.1671.14196.2
2.78-2.9130.12724910.9620.0820.1521.28195.3
2.91-3.063.30.12325720.9720.0770.1461.34497.6
3.06-3.253.30.11425570.9750.0710.1351.48397.2
3.25-3.53.20.10625480.9790.0670.1261.4696.6
3.5-3.863.20.09825730.9780.0630.1171.44296
3.86-4.4130.08825230.9810.0580.1061.40895.6
4.41-5.562.90.08425300.9820.0560.1021.36694.7
5.56-393.10.08326030.9880.0540.11.30595.1

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解析

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

4ibs


解像度: 2.05→36.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2257 / WRfactor Rwork: 0.1744 / FOM work R set: 0.8089 / SU B: 7.979 / SU ML: 0.127 / SU R Cruickshank DPI: 0.0447 / SU Rfree: 0.0383 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.038 / 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
Rfree0.2275 2400 4.8 %RANDOM
Rwork0.1762 ---
obs0.1787 47284 93.9 %-
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: 76.41 Å2 / Biso mean: 31.036 Å2 / Biso min: 3.48 Å2
Baniso -1Baniso -2Baniso -3
1--7.59 Å2-0 Å2-4.02 Å2
2--11 Å20 Å2
3----3.41 Å2
精密化ステップサイクル: final / 解像度: 2.05→36.67 Å
タンパク質核酸リガンド溶媒全体
原子数5955 0 77 477 6509
Biso mean--36.83 33.37 -
残基数----766
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136283
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175694
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.6658535
X-RAY DIFFRACTIONr_angle_other_deg1.441.57813145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0195790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80520.583343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.253151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7041562
X-RAY DIFFRACTIONr_chiral_restr0.0970.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021466
LS精密化 シェル解像度: 2.05→2.101 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.297 91 -
Rwork0.174 2947 -
all-3038 -
obs--78.04 %
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)
121.8898-1.1436-2.38831.55890.55730.4548-0.13180.3771-0.478-0.28690.1284-0.26060.07910.05350.00330.40820.00440.11460.26830.02870.09056.483-22.807-23.724
27.6101-0.11910.98485.65263.328512.3446-0.0739-0.3679-0.0626-0.0527-0.08950.03560.0112-0.12770.16340.0717-0.00190.06880.2131-0.01520.0691.208-11.235-16.551
31.7475-0.35810.63130.3934-0.15031.98650.00040.05930.084-0.0363-0.02220.0388-0.0484-0.0160.02190.0623-0.00250.05680.2997-0.00640.0847-0.102-8.967-32.109
40.7672-2.03820.75865.7373-0.94724.45610.0880.0113-0.0691-0.1423-0.01890.14050.54880.0453-0.0690.1640.04910.07870.2855-0.04330.1529.97-26.568-36.425
58.0619-8.1845-4.075827.27518.56553.09590.71790.022-0.1967-0.2017-0.5726-0.8638-0.2372-0.107-0.14530.315-0.11740.12290.7969-0.05920.186316.398-16.599-48.784
60.2934-0.19860.10720.1397-0.07240.04030.14880.0932-0.0669-0.1355-0.09770.01090.05640.0423-0.05110.5034-0.19360.17670.7698-0.02380.466218.261-5.789-44.167
71.82170.68880.93991.77021.82182.6076-0.05430.08250.1601-0.25440.1096-0.0725-0.23440.2705-0.05530.0847-0.01450.06760.36250.00740.085116.073-8.328-34.647
81.9316-0.2289-0.1261.08980.92171.95830.04420.0730.1936-0.0638-0.0253-0.1008-0.0970.139-0.01890.05910.0040.06210.28050.00580.09258.756-8.11-30.774
91.375-1.63291.03943.93092.23187.78070.25820.1168-0.1681-0.2495-0.0072-0.03380.31670.3328-0.2510.14310.01640.03520.2821-0.07420.18516.537-22.538-40.903
106.12760.17311.42740.014-0.03353.45870.0427-0.204-0.2239-0.00310.0318-0.00280.33940.3599-0.07460.12260.04120.05930.35290.01040.073810.821-11.763-18.69
114.3232-0.87991.03581.6349-1.89913.02380.10180.2623-0.2645-0.2058-0.0920.10020.2318-0.0636-0.00970.1013-0.01250.04490.2677-0.05860.0764-3.651-15.248-40.934
1214.19816.7974-2.32878.98456.380710.4528-0.22340.4132-1.3353-0.025-0.3002-0.34940.27-0.56370.52360.122-0.0525-0.02710.3673-0.07490.5389-12.375-21.163-41.927
133.055-3.6881-4.42678.04616.869314.1079-0.0425-0.269-0.44410.230.111-0.21220.3206-0.3351-0.06840.1121-0.03810.0710.21580.13280.37890.493-20.07520.326
1410.6287-4.36723.45311.947-0.97322.4354-0.1639-0.3988-0.54630.05020.20940.2712-0.1207-0.0469-0.04560.08070.00660.03680.25230.01660.1722-9.188-8.30112.521
157.2992-1.1237-2.1393.2133-1.22452.4528-0.11840.477-0.22050.03020.1228-0.1135-0.0277-0.0647-0.00450.07740.00540.06250.4184-0.09160.0811-10.06-9.6783.036
163.72870.5545-1.28540.7373-0.05081.4758-0.0109-0.0711-0.18330.08350.02960.1045-0.07-0.0793-0.01870.08310.02450.0820.2420.00140.10591.386-9.96813.049
176.33531.47365.111610.2122-1.78945.02940.47150.3724-0.7238-0.31420.1575-0.11510.51630.2799-0.6290.2403-0.02620.10660.2201-0.1470.3336.175-26.8360.385
183.08060.5903-1.60720.1713-0.34210.87840.13450.1194-0.16410.079-0.1837-0.0735-0.16670.04580.04920.2189-0.09090.02380.73180.03830.141214.2-7.682-3.479
193.6088-0.0276-0.51233.33111.04762.6423-0.09410.0427-0.14080.04390.0194-0.0739-0.01790.13730.07470.0517-0.0080.0420.2779-0.00070.080713.448-10.5939.293
2017.2541-2.65931.83741.3155-0.87954.45670.1584-0.63591.98770.0801-0.3412-0.2448-0.55790.2550.18280.40570.09730.1020.5855-0.03760.2621-0.385-0.25823.621
212.2437-0.7701-1.71.0141.89326.0967-0.11670.2433-0.01750.09440.00220.06250.1747-0.28710.11440.084900.04110.2687-0.00130.07882.487-8.7163.721
221.20960.871-0.95451.63581.430912.569-0.11520.2008-0.3949-0.04270.0688-0.00520.602-0.31040.04640.0932-0.01210.03330.2225-0.07570.32512.266-18.1434.421
234.64-0.55140.51330.2724-0.05591.4495-0.08870.223-0.56930.01310.02640.06040.0391-0.07490.06220.0712-0.01010.07450.2131-0.04890.1336-1.568-13.798.579
248.131110.5423-4.135222.80320.90226.4107-0.07460.7502-0.06970.20170.0803-0.12570.2989-0.9635-0.00570.2670.0566-0.00840.4948-0.11780.1605-16.859-17.569-2.434
255.3027-0.7331-1.16071.0005-1.32732.7159-0.19770.67480.04020.21540.33450.0766-0.2626-0.8524-0.13680.11760.1160.00450.7746-0.09820.0507-32.139-2.665-46.704
263.38590.6858-0.21610.1398-0.04080.3794-0.02620.0149-0.25790.0015-0.0056-0.0437-0.03190.08920.03180.071-0.01940.07260.4037-0.04530.1165-38.166-7.663-29.326
273.26553.0473.864815.28647.280411.37770.11540.0961-0.2349-0.0862-0.48231.1667-0.2204-0.12320.36690.0926-0.0126-0.04660.4052-0.130.2525-35.682-13.373-49.084
282.2674-0.47-1.06086.08263.43422.48280.0970.20880.0526-0.3805-0.16320.2458-0.2822-0.06620.06620.05790.02820.03070.38380.02530.073-25.415-1.112-39.115
293.28870.2426-0.10832.7168-0.60612.27240.1389-0.17380.04760.0376-0.1636-0.37460.19570.1420.02460.062-0.040.01250.3734-0.02750.0676-19.4190.53-25.114
307.8411-4.2502-0.51169.3178-4.43895.5692-0.2611-0.30020.3580.38370.0287-0.2927-0.09980.31470.23240.0943-0.04320.01950.2693-0.01730.0529-17.081-4.436-27.349
313.43660.3624-0.87352.52971.39251.4336-0.00490.43-0.16420.0226-0.1125-0.06440.069-0.2550.11740.0386-0.0020.04460.412800.0896-19.585-8.343-36.838
323.21780.21980.26822.72753.20186.201-0.10980.2343-0.60120.211-0.13090.18590.0749-0.2350.24070.0541-0.03560.07180.3763-0.06560.1924-30.606-12.684-33.259
333.7319-2.67950.80444.048-5.381711.14770.297-0.24640.5590.18840.0731-0.1776-0.66070.1487-0.37010.402-0.08360.0970.3393-0.09580.1322-27.5786.169-22.471
343.0908-0.4394-4.59221.55121.84847.78350.02620.15590.0881-0.10740.02190.0879-0.1209-0.1987-0.04810.06430.0561-0.00580.4277-0.0080.0229-24.889-4.216-45.815
354.64331.0769-2.37120.9172-2.54327.4305-0.01030.11410.09470.0074-0.1267-0.01050.04280.1190.13690.0652-0.03520.06530.3524-0.05020.0728-35.514-1.96-27.613
364.4126-1.3061.208211.0484-0.83673.253-0.0109-0.38620.5560.2999-0.0042-0.0114-0.4265-0.24060.01510.0899-0.03180.05430.3019-0.05070.1487-45.80.946-23.591
372.34662.59212.42593.81021.66628.10090.02610.38910.17030.11650.27540.0578-0.2534-0.085-0.30160.05820.0466-0.03560.37530.1890.2199-33.5374.964-0.724
384.5091.22290.45830.4560.37912.0568-0.035-0.15590.0737-0.0684-0.0330.0548-0.01880.03510.0680.07350.01790.02890.28950.00080.0885-44.187-6.91512.026
393.02340.1517-0.57890.9363-0.37192.2111-0.09910.36130.1073-0.05010.0146-0.05820.1741-0.12070.08440.0396-0.00720.03320.36260.02320.0455-33.563-7.6944.02
405.3731-2.2039-2.815315.92440.13611.54580.1620.37330.64720.46210.21510.1365-0.1322-0.2278-0.37710.18980.04390.01250.2005-0.0460.4519-31.0949.66917.506
411.48010.5419-1.04593.1975-2.53743.82250.0981-0.39860.49790.1256-0.2216-0.1954-0.07250.84610.12360.0849-0.01360.02710.4556-0.02810.2468-23.065-0.62621.511
420.12440.2294-0.35490.9416-3.535418.36880.05460.0163-0.22860.07820.0627-0.3359-0.27280.353-0.11730.11930.0402-0.0040.4611-0.06430.5305-18.489-12.07919.336
433.6490.3594-0.23061.73161.10842.5177-0.04770.18380.0943-0.0239-0.0303-0.05250.06650.06080.0780.0381-0.00330.03940.30650.02150.0676-21.291-5.6269.136
443.46740.89740.87670.2761-0.21665.0179-0.07140.2648-0.1944-0.0340.085-0.04150.2680.0636-0.01360.1060.02580.04860.2972-0.00880.0897-33.375-10.5537.553
453.036-0.27590.80032.88434.777716.9499-0.0904-0.16310.58240.13450.06270.18430.1473-0.11290.02770.0396-0.01040.0250.1902-0.01050.1951-31.6471.91415.175
4615.16258.7767-4.09785.0812-2.3781.17120.2910.13240.79150.17390.09320.4775-0.1606-0.0767-0.38430.1912-0.00820.17390.53830.2310.5486-25.1880.424-5.532
474.29680.782-1.09781.28610.04470.55170.0183-0.32410.37620.17080.00030.0513-0.054-0.1214-0.01860.0920.0487-0.03730.3421-0.05290.1157-40.87-3.80617.255
4813.8063-11.47932.239617.46582.44022.73230.0163-0.48860.3478-0.2921-0.11250.0187-0.1763-0.32510.09620.44870.17820.06550.5146-0.06970.4974-51.1831.18921.331
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A97 - 102
2X-RAY DIFFRACTION2A103 - 110
3X-RAY DIFFRACTION3A111 - 162
4X-RAY DIFFRACTION4A163 - 175
5X-RAY DIFFRACTION5A176 - 181
6X-RAY DIFFRACTION6A182 - 188
7X-RAY DIFFRACTION7A189 - 208
8X-RAY DIFFRACTION8A209 - 241
9X-RAY DIFFRACTION9A242 - 254
10X-RAY DIFFRACTION10A255 - 267
11X-RAY DIFFRACTION11A268 - 283
12X-RAY DIFFRACTION12A284 - 288
13X-RAY DIFFRACTION13B97 - 109
14X-RAY DIFFRACTION14B110 - 117
15X-RAY DIFFRACTION15B118 - 133
16X-RAY DIFFRACTION16B134 - 164
17X-RAY DIFFRACTION17B165 - 172
18X-RAY DIFFRACTION18B173 - 188
19X-RAY DIFFRACTION19B189 - 219
20X-RAY DIFFRACTION20B220 - 227
21X-RAY DIFFRACTION21B228 - 246
22X-RAY DIFFRACTION22B247 - 257
23X-RAY DIFFRACTION23B258 - 284
24X-RAY DIFFRACTION24B285 - 289
25X-RAY DIFFRACTION25D97 - 111
26X-RAY DIFFRACTION26D112 - 145
27X-RAY DIFFRACTION27D146 - 150
28X-RAY DIFFRACTION28D151 - 167
29X-RAY DIFFRACTION29D168 - 188
30X-RAY DIFFRACTION30D189 - 194
31X-RAY DIFFRACTION31D195 - 223
32X-RAY DIFFRACTION32D224 - 239
33X-RAY DIFFRACTION33D240 - 251
34X-RAY DIFFRACTION34D252 - 267
35X-RAY DIFFRACTION35D268 - 279
36X-RAY DIFFRACTION36D280 - 288
37X-RAY DIFFRACTION37C96 - 109
38X-RAY DIFFRACTION38C110 - 133
39X-RAY DIFFRACTION39C134 - 161
40X-RAY DIFFRACTION40C162 - 169
41X-RAY DIFFRACTION41C170 - 179
42X-RAY DIFFRACTION42C180 - 188
43X-RAY DIFFRACTION43C189 - 219
44X-RAY DIFFRACTION44C220 - 244
45X-RAY DIFFRACTION45C245 - 257
46X-RAY DIFFRACTION46C258 - 266
47X-RAY DIFFRACTION47C267 - 283
48X-RAY DIFFRACTION48C284 - 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