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- PDB-4lo9: Human p53 Core Domain Mutant N235K -

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基本情報

登録情報
データベース: PDB / ID: 4lo9
タイトルHuman p53 Core Domain Mutant N235K
要素Cellular tumor antigen p53
キーワードAPOPTOSIS / Beta Sandwich / Tumor Suppressor / DNA Binding / Nuclear
機能・相同性
機能・相同性情報


negative regulation of helicase 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 / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase 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 / 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 / positive regulation of mitochondrial membrane permeability / mRNA transcription / positive regulation of programmed necrotic cell death / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / 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 / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / B cell lineage commitment / 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 / 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 / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / replicative senescence / general transcription initiation factor binding / cellular response to UV-C / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of execution phase of apoptosis / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / hematopoietic stem cell differentiation / Pyroptosis / viral process / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / hematopoietic progenitor cell differentiation / glial cell proliferation / negative regulation of fibroblast proliferation / core promoter sequence-specific DNA binding / positive regulation of cardiac muscle cell apoptotic process / negative regulation of stem cell proliferation / cellular response to glucose starvation / mitophagy / cis-regulatory region sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / gastrulation / response to salt stress / mitotic G1 DNA damage checkpoint signaling / 14-3-3 protein binding / negative regulation of proteolysis / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex / cellular response to ionizing radiation
類似検索 - 分子機能
Immunoglobulin-like - #720 / 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 ...Immunoglobulin-like - #720 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
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: 2.5 Å
データ登録者Wallentine, B.D. / Wang, Y. / Luecke, H.
引用ジャーナル: Acta Crystallogr.,Sect.D / 年: 2013
タイトル: Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue.
著者: Wallentine, B.D. / Wang, Y. / Tretyachenko-Ladokhina, V. / Tan, M. / Senear, D.F. / Luecke, H.
履歴
登録2013年7月12日登録サイト: RCSB / 処理サイト: RCSB
置き換え2013年7月31日ID: 2QXB
改定 1.02013年7月31日Provider: repository / タイプ: Initial release
改定 1.12013年10月2日Group: Database references
改定 1.22014年1月15日Group: Database references
改定 1.32019年7月17日Group: Data collection / Refinement description / カテゴリ: software
Item: _software.classification / _software.name / _software.version
改定 1.42023年9月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)98,6698
ポリマ－98,4084
非ポリマー2624
水4,540252
1
A: Cellular tumor antigen p53
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,6672
ポリマ－24,6021
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: Cellular tumor antigen p53
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,6672
ポリマ－24,6021
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
C: Cellular tumor antigen p53
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,6672
ポリマ－24,6021
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: Cellular tumor antigen p53
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,6672
ポリマ－24,6021
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)69.164, 69.213, 83.851
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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


分子量: 24601.955 Da / 分子数: 4 / 断片: p53 Core Domain (UNP residues 94-312) / 変異: N235K / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: P53, TP53 / プラスミド: Pse420 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P04637
#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: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 252 / 由来タイプ: 天然 / 式: H2O

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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: 2.04 Å3/Da / 溶媒含有率: 39.69 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(100 mM HEPES, 30 % (w/v) polyethylene ...詳細: 2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(100 mM HEPES, 30 % (w/v) polyethylene glycol (PEG) 6000, pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 4.2.2 / 波長: 1.5418 Å
検出器検出器: CCD / 日付: 2005年6月22日
詳細: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
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: 1.5418 Å / 相対比: 1
反射解像度: 2.5→53.378 Å / Num. obs: 27431 / % possible obs: 99.2 % / 冗長度: 3.58 % / Rsym value: 0.107 / Net I/σ(I): 7.9
反射 シェル解像度: 2.5→2.59 Å / 冗長度: 3.38 % / Mean I/σ(I) obs: 3.5 / % possible all: 96.7

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.8.2_1309)精密化
CNS精密化
Blu-Iceデータ収集
d*TREKデータ削減
d*TREKデータスケーリング
CNS位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB Entry 2OCJ

2ocj


解像度: 2.5→53.378 Å / SU ML: 0.34 / σ(F): 1.36 / 位相誤差: 25.77 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2466 3712 7.28 %Random
Rwork0.1762 ---
obs0.1813 27431 94.7 %-
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 mean: 26.19 Å2
精密化ステップサイクル: LAST / 解像度: 2.5→53.378 Å
タンパク質核酸リガンド溶媒全体
原子数6096 0 4 252 6352
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0096240
X-RAY DIFFRACTIONf_angle_d1.1578460
X-RAY DIFFRACTIONf_dihedral_angle_d11.9062380
X-RAY DIFFRACTIONf_chiral_restr0.047920
X-RAY DIFFRACTIONf_plane_restr0.0061120
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53160.35521270.27251546X-RAY DIFFRACTION81
2.5316-2.5650.30541320.24311708X-RAY DIFFRACTION91
2.565-2.60010.34651320.23911653X-RAY DIFFRACTION93
2.6001-2.63720.27081250.22761763X-RAY DIFFRACTION93
2.6372-2.67660.35831440.21641660X-RAY DIFFRACTION92
2.6766-2.71840.26271300.21261705X-RAY DIFFRACTION91
2.7184-2.7630.30491370.21391725X-RAY DIFFRACTION93
2.763-2.81060.34011430.22171729X-RAY DIFFRACTION94
2.8106-2.86170.29211400.21091799X-RAY DIFFRACTION94
2.8617-2.91680.30331270.21081666X-RAY DIFFRACTION94
2.9168-2.97630.26041330.19481780X-RAY DIFFRACTION95
2.9763-3.0410.28421470.21721745X-RAY DIFFRACTION95
3.041-3.11170.29991290.19461721X-RAY DIFFRACTION95
3.1117-3.18960.31991460.19141762X-RAY DIFFRACTION95
3.1896-3.27580.25171420.17891749X-RAY DIFFRACTION95
3.2758-3.37220.26041490.17841804X-RAY DIFFRACTION96
3.3722-3.4810.2381360.1781738X-RAY DIFFRACTION96
3.481-3.60540.24711360.16881802X-RAY DIFFRACTION95
3.6054-3.74970.20251420.16931718X-RAY DIFFRACTION94
3.7497-3.92030.24771290.16831783X-RAY DIFFRACTION97
3.9203-4.12690.2781430.16771790X-RAY DIFFRACTION97
4.1269-4.38540.19071450.1311824X-RAY DIFFRACTION98
4.3854-4.72380.17051490.13361774X-RAY DIFFRACTION98
4.7238-5.19880.19971320.13271882X-RAY DIFFRACTION99
5.1988-5.95020.22871380.14611794X-RAY DIFFRACTION99
5.9502-7.49330.22391350.16891844X-RAY DIFFRACTION99
7.4933-53.38990.14941440.14081834X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.4973-3.7721-4.79396.19065.68525.698-0.28640.0757-0.16570.36150.5522-0.36490.6860.0650.00010.3897-0.019-0.00420.30290.05990.3331.343-9.108542.707
23.4068-1.81771.85592.8514-0.1931.4027-0.13170.03810.53740.05960.0410.0461-0.1923-0.2412-0.12360.2156-0.11870.04050.52860.11180.3705-8.94425.400630.4549
35.983-1.96030.24691.38760.95133.0742-0.05410.26890.20450.0682-0.4801-0.3319-0.33970.18580.35820.2874-0.007-0.01420.35220.06190.216-6.04241.596125.9931
44.71170.39032.34254.8552-2.74699.6753-0.159-0.60260.03140.28340.19930.5259-0.1025-0.1265-0.10810.27510.12880.05940.34-0.04860.3199-0.54274.903343.719
53.3349-1.5974-1.28042.4742-2.02574.60570.07880.4413-0.6-0.4539-0.0345-0.07270.1002-0.30160.25380.18780.0197-0.02980.451-0.02890.35575.6102-8.44130.1976
62.0731.2195-0.81324.4345-5.73377.74830.20130.4091-0.2551-0.0941-0.24850.2133-0.11140.38470.14320.30690.10390.0560.5971-0.09240.322611.7381-4.787220.7357
73.74094.35471.54077.3118-0.0967.1537-0.21461.59690.0089-0.10790.68160.0282-0.23610.5659-0.32440.1401-0.051-0.01890.52810.01970.323215.21025.703723.0877
88.16360.6740.84248.35042.16057.1703-0.04320.28140.0734-0.11360.0373-0.4177-0.40490.0980.11930.1832-0.1063-0.02540.3240.02080.188614.2921.264133.4778
91.8945-0.7643-3.19423.74762.37776.08650.58680.61020.6776-0.346-0.73710.3863-0.8739-1.4345-0.33390.30870.1394-0.06660.4842-0.12570.45833.36487.892442.6399
104.3306-0.7624-1.6283.4438-2.31953.6442-0.09050.95080.0846-0.5815-0.1977-0.02130.06830.19550.17830.18010.0018-0.02080.5908-0.01720.30793.45870.255423.6491
112.85330.88711.52281.58070.59544.4237-0.00880.31420.1676-0.0797-0.08410.04950.01390.16420.05190.17560.04280.03170.36660.03340.29572.6509-3.320435.3872
125.3542-2.1325-2.75216.2295-3.82649.3073-0.0890.8898-0.3517-0.0539-0.0122-0.4961.4382-0.00440.04790.3878-0.0413-0.07960.7049-0.1340.367-13.8428-2.123219.8368
137.2834-3.91921.40028.0669-5.0483.4378-0.1396-0.86640.5561-0.0402-0.1198-0.0405-0.69420.56980.01320.42930.0223-0.0380.3244-0.1570.362833.345350.336362.8187
148.3992-3.8859-3.83756.77641.60211.7671-0.0439-0.33670.0257-0.00610.4279-0.26910.47390.6045-0.29160.18480.021-0.04670.24530.00950.287544.026736.089948.9259
155.81190.076-1.46780.5239-0.20782.7706-0.07780.2037-0.1893-0.0677-0.1255-0.34930.0676-0.2769-0.00010.2435-0.0338-0.00010.37960.00940.274640.143640.239945.8595
166.3710.7399-0.30292.09720.44462.93150.0689-0.6750.3517-0.0109-0.068-0.16360.0402-0.22740.07540.20810.055-0.00090.2435-0.06620.278331.860743.958357.4397
176.00211.71650.53568.78024.01796.1490.08010.53310.9330.1418-0.5575-0.08220.2223-0.52830.34790.28860.0033-0.09780.61250.20040.436722.718447.197340.6798
186.4682.2130.79716.5046-0.06943.4064-0.03950.4171-0.1101-0.1270.1062-0.0625-0.0198-0.98290.24320.2073-0.10170.01820.6262-0.03620.287219.152736.541242.8779
198.1085-2.43551.6695.6391-3.60848.4345-0.1166-0.11420.45760.4148-0.05230.3502-0.1721-0.13950.20530.1828-0.05920.03320.3409-0.06030.324420.18341.004353.2988
207.799-6.9886.69578.1946-6.41815.82730.3846-0.0954-0.4661-0.077-0.01520.32360.452-0.2207-0.44030.2775-0.02440.02860.53340.01840.334631.297533.8161.8548
216.5017-2.95383.62784.33110.03323.45310.10620.6470.2901-0.2872-0.14350.3053-0.02580.02140.210.1848-0.01180.06490.4283-0.00940.301130.735842.397442.6662
221.7101-0.0089-1.45062.50281.30738.9621-0.1092-0.0467-0.0478-0.0781-0.27980.0564-0.3302-0.25230.28520.1070.0307-0.01260.2365-0.06640.318631.859645.421455.2569
236.62722.4682.1452.69372.29976.46-0.09711.3591.10110.24840.14760.5704-0.69220.9624-0.0830.4101-0.02510.08750.61890.17920.39948.174244.434339.5913
242.34391.5791.37447.345.24944.97830.6583-0.6787-0.48090.0814-0.0197-0.58750.8561-0.84430.72480.5301-0.11710.10010.97590.156-0.09625.081-5.104887.4823
255.87380.4135-0.18327.8925-1.90080.4647-0.0183-0.01290.35140.30760.29220.44540.2479-0.2081-0.09190.2220.02610.03650.4589-0.01620.251-6.59332.707371.6559
264.7078-0.14780.72822.48661.82743.9284-0.2096-0.48210.15310.05080.18780.1108-0.2546-0.37540.03930.26650.01320.01310.4640.0360.27074.57713.492177.7858
272.1268-2.35160.98645.2131-1.13834.56690.02690.2828-1.0915-0.0497-0.1307-0.04940.38940.5085-0.12150.26440.0318-0.08540.40870.00390.539610.4844-12.899269.609
282.27960.76111.27112.73913.44975.48650.08420.9347-0.1985-0.58970.2988-0.5241-0.7040.8396-0.30580.32570.04150.08970.6179-0.01770.368217.58781.462.5573
297.12181.6922-1.39143.77734.09217.75530.19030.63951.0668-1.0505-0.09960.6307-1.0593-0.2280.1280.3208-0.0246-0.06930.40250.14860.391213.23269.874773.2251
307.68950.6963-2.70582.10761.93215.9753-0.201-0.0772-0.68170.2065-0.1542-0.56560.34620.07430.23250.23260.031-0.00690.25340.02570.295620.8216-4.472576.8276
312.4168-3.1027-3.90384.82224.30416.67160.50930.89160.7764-0.2692-0.3723-0.2185-0.285-1.1466-0.22540.23630.0398-0.04920.494-0.00030.48796.529711.026982.2658
326.0607-2.59020.02614.5057-2.01731.15430.11480.2692-0.2695-0.9647-0.05830.1340.09320.24190.12090.2514-0.0932-0.07330.5093-0.03460.34396.5219-2.677166.0338
332.17390.52350.2812.33671.01065.2023-0.2348-0.1602-0.1966-0.07160.53780.0154-0.70370.8964-0.2640.29260.02950.02810.65750.11470.269810.3723-0.734184.0322
342.6348-0.05820.98521.61470.92577.18790.20790.4988-0.11440.0364-0.04180.37410.93210.5656-0.20880.1993-0.03080.00620.5430.10670.37222.0803-3.156974.6267
353.25272.3392-2.37355.1338-3.57723.3078-0.4030.7727-1.36360.1187-0.1812-0.52390.2388-0.80030.34150.29180.0016-0.07320.7176-0.17360.5336-10.8582-5.397464.3151
365.9159-0.632-3.67482.71431.00546.81070.2126-0.16990.01450.2062-0.1271-0.0851-0.3565-0.06710.04430.2399-0.0194-0.06260.3327-0.00830.211936.338643.114.0111
374.7566-0.668-1.22652.59160.46123.7151-0.01480.1189-0.1689-0.05780.12580.105-0.0443-0.023-0.03490.20.0551-0.00840.3382-0.02460.208429.716442.159312.8448
383.52362.4011-0.77116.1952-1.17796.4328-0.04571.02170.1593-0.2148-0.22410.2738-0.0472-0.58760.21510.16330.0418-0.02820.53080.01560.345717.579842.8365.1771
395.55160.6176-1.3551.5871-0.75643.5245-0.00040.42420.1114-0.1712-0.0994-0.0847-0.0926-0.14690.13530.25160.0244-0.01340.3056-0.00730.24731.150642.8169.1855
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 96:108)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 109:123)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 124:139)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 140:155)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 156:168)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 169:180)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 181:194)
8X-RAY DIFFRACTION8CHAIN A AND (RESID 195:213)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 214:228)
10X-RAY DIFFRACTION10CHAIN A AND (RESID 229:250)
11X-RAY DIFFRACTION11CHAIN A AND (RESID 251:277)
12X-RAY DIFFRACTION12CHAIN A AND (RESID 278:289)
13X-RAY DIFFRACTION13CHAIN B AND (RESID 96:109)
14X-RAY DIFFRACTION14CHAIN B AND (RESID 110:123)
15X-RAY DIFFRACTION15CHAIN B AND (RESID 124:140)
16X-RAY DIFFRACTION16CHAIN B AND (RESID 141:168)
17X-RAY DIFFRACTION17CHAIN B AND (RESID 169:180)
18X-RAY DIFFRACTION18CHAIN B AND (RESID 181:194)
19X-RAY DIFFRACTION19CHAIN B AND (RESID 195:213)
20X-RAY DIFFRACTION20CHAIN B AND (RESID 214:229)
21X-RAY DIFFRACTION21CHAIN B AND (RESID 230:250)
22X-RAY DIFFRACTION22CHAIN B AND (RESID 251:277)
23X-RAY DIFFRACTION23CHAIN B AND (RESID 278:289)
24X-RAY DIFFRACTION24CHAIN C AND (RESID 96:109)
25X-RAY DIFFRACTION25CHAIN C AND (RESID 110:131)
26X-RAY DIFFRACTION26CHAIN C AND (RESID 132:163)
27X-RAY DIFFRACTION27CHAIN C AND (RESID 164:176)
28X-RAY DIFFRACTION28CHAIN C AND (RESID 177:194)
29X-RAY DIFFRACTION29CHAIN C AND (RESID 195:203)
30X-RAY DIFFRACTION30CHAIN C AND (RESID 204:213)
31X-RAY DIFFRACTION31CHAIN C AND (RESID 214:229)
32X-RAY DIFFRACTION32CHAIN C AND (RESID 230:250)
33X-RAY DIFFRACTION33CHAIN C AND (RESID 251:263)
34X-RAY DIFFRACTION34CHAIN C AND (RESID 264:277)
35X-RAY DIFFRACTION35CHAIN C AND (RESID 278:289)
36X-RAY DIFFRACTION36CHAIN D AND (RESID 96:131)
37X-RAY DIFFRACTION37CHAIN D AND (RESID 132:168)
38X-RAY DIFFRACTION38CHAIN D AND (RESID 169:213)
39X-RAY DIFFRACTION39CHAIN D AND (RESID 214:289)

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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