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- PDB-6fj5: New Insights into the Role of DNA Shape on Its Recognition by p53... -

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基本情報

登録情報
データベース: PDB / ID: 6fj5
タイトルNew Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-AGG-HG)
要素
  • Cellular tumor antigen p53
  • DNA
キーワードTRANSCRIPTION / P53 / TRANSCRIPTION FACTOR / DNA BINDING / DNA RECOGNITION / HOOGSTEEN BASE-PAIRING / TRANSCRIPTION REGULATION / APOPTOSIS / BIOLOGICAL RHYTHMS / CELL CYCLE / NUCLEUS / TUMOR SUPPRESSOR / ANTIGEN NY-CO-13 / PHOSPHOPROTEIN
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
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
DNA / DNA (> 10) / Cellular tumor antigen p53
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: 2.051 Å
データ登録者Golovenko, D. / Rozenberg, H. / Shakked, Z.
引用ジャーナル: Structure / 年: 2018
タイトル: New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins.
著者: Golovenko, D. / Brauning, B. / Vyas, P. / Haran, T.E. / Rozenberg, H. / Shakked, Z.
履歴
登録2018年1月20日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年6月27日Provider: repository / タイプ: Initial release
改定 1.12019年1月2日Group: Data collection / Database references / Structure summary
カテゴリ: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct.title
改定 1.22024年1月17日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
F: DNA
G: DNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)104,03124
ポリマ－102,9016
非ポリマー1,13118
水13,241735
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
  • 根拠: native gel electrophoresis
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-29 kcal/mol
Surface area40960 Å2
手法PISA
単位格子
Length a, b, c (Å)68.517, 98.024, 73.171
Angle α, β, γ (deg.)90.000, 93.390, 90.000
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: 22505.582 Da / 分子数: 4 / 断片: P53 DNA BINDING DOMAIN, UNP residues 94-293 / 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: PET27-B / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P04637
#2: DNA鎖 DNA


分子量: 6439.159 Da / 分子数: 2 / 断片: DNA / 由来タイプ: 合成 / 詳細: SYNTHESISED BY IDT / 由来: (合成) synthetic construct (人工物)
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 断片: ZN / 由来タイプ: 合成 / 式: Zn
#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: 14 / 断片: 1,2-ETHANEDIOL / 由来タイプ: 合成 / 式: C2H6O2
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 735 / 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: 2.38 Å3/Da / 溶媒含有率: 48.4 % / Mosaicity: 0.222 °
結晶化温度: 292 K / 手法: 蒸発脱水法 / pH: 7
詳細: 0.1 M Sodium formate pH 7.0, 12% w/v Polyethylene glycol 3,350

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID29 / 波長: 0.8856 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年7月21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: 0.8856 Å / 相対比: 1
反射解像度: 2.05→50 Å / Num. obs: 59807 / % possible obs: 99 % / Observed criterion σ(I): -3 / 冗長度: 4.8 % / Rmerge(I) obs: 0.186 / Rsym value: 0.186 / Net I/av σ(I): 10.087 / Net I/σ(I): 3.1
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsDiffraction-ID% possible all
2.05-2.094.50.475199.3
2.09-2.124.60.466199
2.12-2.164.50.43199.3
2.16-2.214.60.409199.3
2.21-2.264.40.365198.7
2.26-2.314.30.36197.9
2.31-2.3750.35199.6
2.37-2.435.10.333199.7
2.43-2.55.10.322199.5
2.5-2.585.10.306199.5
2.58-2.685.10.275199.3
2.68-2.7850.253199.1
2.78-2.914.70.226199.1
2.91-3.064.50.193198.1
3.06-3.255.20.173199.7
3.25-3.5150.142199.3
3.51-3.864.80.126198.7
3.86-4.424.30.106196.8
4.42-5.564.80.11199.3
5.56-504.60.108198.3

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation2.05 Å49.01 Å
Translation2.05 Å49.01 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
PHASER2.5.7位相決定
HKL-2000データ収集
HKL-2000データスケーリング
PDB_EXTRACT3.2データ抽出
HKL-2000データ削減
精密化構造決定の手法: 分子置換
開始モデル: 1TSR

1tsr


解像度: 2.051→49.012 Å / SU ML: 0.29 / 交差検証法: FREE R-VALUE / σ(F): 1.41 / 位相誤差: 32.31
詳細: Translational non-crystallographic symmetry (tNCS) correction
Rfactor反射数%反射Selection details
Rfree0.2438 2001 3.37 %Random selection
Rwork0.1987 ---
obs0.2002 59381 98.17 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 120.41 Å2 / Biso mean: 23.7163 Å2 / Biso min: 4.4 Å2
精密化ステップサイクル: final / 解像度: 2.051→49.012 Å
タンパク質核酸リガンド溶媒全体
原子数6103 820 60 735 7718
Biso mean--22.71 29.28 -
残基数----836
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0097271
X-RAY DIFFRACTIONf_angle_d1.02810006
X-RAY DIFFRACTIONf_chiral_restr0.061105
X-RAY DIFFRACTIONf_plane_restr0.0071170
X-RAY DIFFRACTIONf_dihedral_angle_d21.0694284
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0511-2.10230.30591320.24414057418997
2.1023-2.15920.27361480.23584107425599
2.1592-2.22270.36711500.22734124427499
2.2227-2.29450.25911290.22214065419498
2.2945-2.37650.26011530.21634118427199
2.3765-2.47160.26511420.210341294271100
2.4716-2.58410.26341470.2144131427899
2.5841-2.72030.28391430.20434142428599
2.7203-2.89070.22991550.20574074422999
2.8907-3.11390.24441370.19244115425298
3.1139-3.42720.21741460.1834126427299
3.4272-3.92290.23381390.17234118425798
3.9229-4.94180.19641400.16834114425498
4.9418-49.0260.21021400.19873960410093
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)
10.41770.2193-0.21330.31680.15660.39980.0612-0.1165-0.02590.05460.01660.00470.1486-0.34840.0080.2154-0.02790.03510.3363-0.01870.2031-11.87492.8762-21.3417
20.7039-0.21730.68261.0369-0.26990.6528-0.03170.1684-0.0676-0.1922-0.05030.0166-0.00710.1489-0.13820.20550.17860.02590.05320.12960.1601-6.59273.4809-19.5167
30.16030.02430.25590.4707-0.11380.4692-0.0144-0.0787-0.089-0.1570.07920.2124-0.0313-0.14221.40920.02420.11540.0178-0.0021-0.02460.1219-18.998413.8355-12.3346
40.4795-0.1556-0.06852.11252.21932.34990.1597-0.0370.03690.00070.1678-0.4155-0.26150.282.02460.1867-0.0151-0.0190.05040.01050.1068-8.180822.5693-7.4917
51.9-0.5873-0.16770.2293-0.04360.24640.05710.14110.36780.26680.01360.0138-0.1128-0.03750.40530.12850.01650.03910.04780.01060.1766-11.154120.2573-19.7202
60.89180.11580.75391.1682-0.07360.73590.06870.1170.0269-0.02820.02950.0395-0.03090.14550.00070.1634-0.01040.03060.15620.01730.1719-10.70289.3247-18.2782
70.3927-0.20590.15830.56380.20980.26030.0859-0.14230.0079-0.0845-0.17780.1640.3744-0.0358-0.22780.22450.00230.02640.1409-0.04060.1099-13.9791-7.805-5.369
80.8051-0.14790.06480.9898-0.21560.05610.1750.1548-0.0729-0.49460.02960.0204-0.0172-0.28440.58060.32640.0358-0.07720.18460.00120.132717.32355.5597-28.1564
90.43420.0452-0.09080.21440.20.2275-0.0204-0.15880.09640.1284-0.08890.07730.16440.087-0.79330.17120.10490.12060.2193-0.00910.199631.8228-2.1247-8.6852
100.10280.0079-0.05150.04950.03020.320.0408-0.0343-0.0101-0.0264-0.0315-0.1388-0.03540.3274-0.01980.229-0.0507-0.00420.2165-0.04690.165127.66563.482-19.5076
110.2528-0.2290.12580.45070.03690.73620.0673-0.14710.3046-0.0746-0.0428-0.0002-0.19840.00730.00010.2405-0.01910.02250.3061-0.01340.206921.422617.0358-12.1075
120.06390.0807-0.06180.37560.04570.1114-0.06740.44390.3665-0.3503-0.01910.3181-0.48080.0498-0.00190.31250.0276-0.07230.28280.04790.25616.118822.3439-20.3423
130.6128-0.3224-0.56370.9380.19310.55270.0815-0.0889-0.2789-0.19280.0714-0.11860.17050.16280.07970.16540.0634-0.02630.3029-0.07430.17831.595810.9689-27.3856
140.7756-0.10640.5510.88670.15990.791-0.08110.01950.0858-0.05480.0267-0.08360.0068-0.1051-0.02440.17840.0361-0.02440.16960.00950.116721.42518.888-15.865
150.0425-0.0282-0.03440.56820.02940.2148-0.058-0.0191-0.04660.02950.01420.11230.22740.0184-0.92160.29130.0486-0.07590.09720.15320.354820.2843-7.7988-5.3835
162.27220.6994-0.54612.21160.05440.61660.1078-0.44490.08030.23440.0277-0.5946-0.25270.18550.03360.25190.0441-0.02010.2029-0.06530.22117.63327.747533.407
170.1508-0.143-0.0120.14840.02340.0181-0.0418-0.0191-0.04290.0371-0.00590.07190.0232-0.0115-0.21090.08370.01720.03760.12290.03680.47713.16938.562123.2195
181.4595-0.09960.05181.20030.27090.6946-0.02320.02420.1473-0.00340.0308-0.0601-0.1876-0.0081-0.00010.21420.0059-0.01960.1976-0.01210.231812.557925.922519.2721
190.8331-0.56690.44580.3974-0.3040.23440.0188-0.43420.00420.00930.1855-0.0113-0.1613-0.2246-0.0370.2647-0.0403-0.00310.3189-0.01250.25683.464831.23430.5882
200.53680.36390.3260.8038-0.11040.3625-0.17470.0334-0.1806-0.06880.0914-0.03090.042-0.01030.00120.176-0.0146-0.01080.2142-0.03740.171613.248319.394216.2731
210.4633-0.34510.54180.398-0.15481.1145-0.1297-0.26980.5780.0812-0.12590.0446-0.38770.0304-0.33680.2735-0.06810.03520.2112-0.08680.440215.537532.096528.8707
220.5643-0.2563-0.00930.335-0.11320.34280.0504-0.1591-0.12640.3537-0.03720.02790.1336-0.0375-0.04680.3069-0.03910.04440.1850.02220.241815.021211.582525.2189
230.2027-0.28760.01870.4214-0.02680.00380.0426-0.36560.12310.3138-0.0223-0.1074-0.01360.0827-0.22890.2992-0.1493-0.00160.3908-0.05990.1966-16.617627.729533.4157
240.13140.11230.03120.20330.09460.06510.0294-0.1407-0.00880.1939-0.16470.06890.0575-0.0687-0.58510.2702-0.20660.07080.3001-0.08280.2884-31.05518.569723.2281
251.22860.0273-0.08091.11290.09720.83910.0749-0.02360.0576-0.0386-0.1130.0732-0.0356-0.0504-0.2190.1539-0.03530.00720.11890.00630.1188-21.579823.671919.6336
261.2214-0.11770.45731.2318-0.26891.26450.0045-0.19140.13110.0983-0.0228-0.0080.1209-0.0316-0.06070.0965-0.01430.00330.1356-0.02770.1697-21.897223.568822.9117
270.21120.0197-0.10370.14450.06670.1098-0.0533-0.0407-0.06090.0458-0.1414-0.12650.07370.1403-2.05130.0196-0.09590.14980.04570.11820.0154-17.0240.36189.2185
280.231-0.0933-0.24130.1516-0.00080.30910.0999-0.3093-0.44430.1291-0.15590.16920.15330.1403-0.00240.3462-0.0523-0.1810.38550.07270.551517.23080.35479.2102
290.24990.02530.05030.53240.17110.26240.04640.0476-0.13160.0195-0.0221-0.06530.21010.11520.09790.1950.02340.0618-0.0159-0.05070.095718.21990.19298.8216
300.1410.0014-0.19380.3980.01270.25770.34640.2442-0.1798-0.2465-0.4230.31830.06270.0157-0.00060.3473-0.0238-0.12080.43810.0430.4344-16.04340.19578.8335
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 94 through 123 )A94 - 123
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 155 )A124 - 155
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 180 )A156 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 194 )A181 - 194
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 213 )A195 - 213
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 277 )A214 - 277
7X-RAY DIFFRACTION7chain 'A' and (resid 278 through 292 )A278 - 292
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 112 )B94 - 112
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 123 )B113 - 123
10X-RAY DIFFRACTION10chain 'B' and (resid 124 through 155 )B124 - 155
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 203 )B156 - 203
12X-RAY DIFFRACTION12chain 'B' and (resid 204 through 213 )B204 - 213
13X-RAY DIFFRACTION13chain 'B' and (resid 214 through 228 )B214 - 228
14X-RAY DIFFRACTION14chain 'B' and (resid 229 through 277 )B229 - 277
15X-RAY DIFFRACTION15chain 'B' and (resid 278 through 292 )B278 - 292
16X-RAY DIFFRACTION16chain 'C' and (resid 94 through 113 )C94 - 113
17X-RAY DIFFRACTION17chain 'C' and (resid 114 through 123 )C114 - 123
18X-RAY DIFFRACTION18chain 'C' and (resid 124 through 213 )C124 - 213
19X-RAY DIFFRACTION19chain 'C' and (resid 214 through 229 )C214 - 229
20X-RAY DIFFRACTION20chain 'C' and (resid 230 through 250 )C230 - 250
21X-RAY DIFFRACTION21chain 'C' and (resid 251 through 263 )C251 - 263
22X-RAY DIFFRACTION22chain 'C' and (resid 264 through 292 )C264 - 292
23X-RAY DIFFRACTION23chain 'D' and (resid 94 through 113 )D94 - 113
24X-RAY DIFFRACTION24chain 'D' and (resid 114 through 123 )D114 - 123
25X-RAY DIFFRACTION25chain 'D' and (resid 124 through 194 )D124 - 194
26X-RAY DIFFRACTION26chain 'D' and (resid 195 through 292 )D195 - 292
27X-RAY DIFFRACTION27chain 'F' and (resid 1 through 10 )F1 - 10
28X-RAY DIFFRACTION28chain 'F' and (resid 11 through 20 )F11 - 20
29X-RAY DIFFRACTION29chain 'G' and (resid 1 through 10 )G1 - 10
30X-RAY DIFFRACTION30chain 'G' and (resid 11 through 20 )G11 - 20

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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