[日本語] English
万見
- PDB-6m64: Crystal structure of SMAD2 in complex with CBP -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 6m64
タイトルCrystal structure of SMAD2 in complex with CBP
要素
  • CBP
  • Mothers against decapentaplegic homolog 2
キーワードSIGNALING PROTEIN / TGF-beta / Complex / Transcription factor
機能・相同性
機能・相同性情報


zygotic specification of dorsal/ventral axis / homomeric SMAD protein complex / activin responsive factor complex / paraxial mesoderm morphogenesis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / endoderm formation / heteromeric SMAD protein complex ...zygotic specification of dorsal/ventral axis / homomeric SMAD protein complex / activin responsive factor complex / paraxial mesoderm morphogenesis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / endoderm formation / heteromeric SMAD protein complex / pericardium development / co-SMAD binding / odontoblast differentiation / determination of left/right asymmetry in lateral mesoderm / FOXO-mediated transcription of cell cycle genes / regulation of transforming growth factor beta receptor signaling pathway / secondary palate development / trophoblast cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / Transcriptional regulation of pluripotent stem cells / embryonic foregut morphogenesis / Germ layer formation at gastrulation / transforming growth factor beta receptor binding / primary miRNA processing / peptide lactyltransferase (CoA-dependent) activity / pulmonary valve morphogenesis / Formation of definitive endoderm / SMAD protein signal transduction / type I transforming growth factor beta receptor binding / NFE2L2 regulating ER-stress associated genes / Signaling by Activin / embryonic cranial skeleton morphogenesis / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / activin receptor signaling pathway / Formation of axial mesoderm / positive regulation of BMP signaling pathway / Signaling by NODAL / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / response to cholesterol / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes / I-SMAD binding / pancreas development / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / aortic valve morphogenesis / negative regulation of ossification / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / anterior/posterior pattern specification / ureteric bud development / NOTCH3 Intracellular Domain Regulates Transcription / insulin secretion / endocardial cushion morphogenesis / negative regulation of transcription by RNA polymerase I / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / embryonic digit morphogenesis / organ growth / protein-lysine-acetyltransferase activity / protein acetylation / homeostatic process / Notch-HLH transcription pathway / Formation of paraxial mesoderm / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / acetyltransferase activity / FOXO-mediated transcription of cell death genes / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / R-SMAD binding / TGF-beta receptor signaling activates SMADs / mesoderm formation / histone acetyltransferase complex / negative regulation of cell differentiation / anatomical structure morphogenesis / cell fate commitment / canonical NF-kappaB signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucose / Attenuation phase / phosphatase binding / positive regulation of epithelial to mesenchymal transition / positive regulation of double-strand break repair via homologous recombination / cellular response to nutrient levels / histone acetyltransferase activity / histone acetyltransferase
類似検索 - 分子機能
MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain ...MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / SMAD-like domain superfamily / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / SMAD/FHA domain superfamily / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
類似検索 - ドメイン・相同性
Mothers against decapentaplegic homolog 2 / CREB-binding protein
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: 1.45 Å
データ登録者Miyazono, K. / Ito, T. / Wada, H. / Tanokura, M.
資金援助 日本, 3件
組織認可番号国
Japan Society for the Promotion of Science (JSPS)15K14708 日本
Japan Society for the Promotion of Science (JSPS)17K19581 日本
Japan Society for the Promotion of Science (JSPS)23228003 日本
引用ジャーナル: Sci.Signal. / 年: 2020
タイトル: Structural basis for transcriptional coactivator recognition by SMAD2 in TGF-beta signaling.
著者: Miyazono, K.I. / Ito, T. / Fukatsu, Y. / Wada, H. / Kurisaki, A. / Tanokura, M.
履歴
登録2020年3月13日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年11月25日Provider: repository / タイプ: Initial release
改定 1.12020年12月30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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22023年11月29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

-
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

-
集合体

登録構造単位
A: Mothers against decapentaplegic homolog 2
B: CBP
C: Mothers against decapentaplegic homolog 2
D: CBP
E: Mothers against decapentaplegic homolog 2
F: CBP


分子量 (理論値)分子数
合計 (水以外)79,8096
ポリマ－79,8096
非ポリマー00
水11,782654
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 area10130 Å2
ΔGint-47 kcal/mol
Surface area27770 Å2
手法PISA
単位格子
Length a, b, c (Å)68.371, 70.803, 165.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
要素

#1: タンパク質 Mothers against decapentaplegic homolog 2 / Mothers against DPP homolog 2 / JV18-1 / Mad-related protein 2 / hMAD-2 / SMAD family member 2 / hSMAD2


分子量: 23481.596 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SMAD2, MADH2, MADR2 / プラスミド: pET48 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15796
#2: タンパク質・ペプチド CBP


分子量: 3121.352 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pET48 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q92793*PLUS
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 654 / 由来タイプ: 天然 / 式: H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.5 Å3/Da / 溶媒含有率: 50.87 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.2 / 詳細: 0.1 M HEPES pH 7.2, 0.2 M NaCl and 31% PEG3350

-
データ収集

回折平均測定温度: 95 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Photon Factory / ビームライン: AR-NE3A / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2018年12月1日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 1.45→47.14 Å / Num. obs: 142487 / % possible obs: 100 % / 冗長度: 13 % / CC1/2: 1 / Rpim(I) all: 0.019 / Rsym value: 0.046 / Net I/σ(I): 24.7
反射 シェル解像度: 1.45→1.47 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6970 / CC1/2: 0.807 / Rpim(I) all: 0.412 / Rsym value: 0.988

-
解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829: ???)精密化
XDSデータ削減
XDSデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5ZOJ

5zoj


解像度: 1.45→36.673 Å / SU ML: 0.14 / 交差検証法: FREE R-VALUE / σ(F): 0.45 / 位相誤差: 19.51
Rfactor反射数%反射
Rfree0.1893 13995 5.1 %
Rwork0.1693 --
obs0.1703 142379 99.99 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 1.45→36.673 Å
タンパク質核酸リガンド溶媒全体
原子数5190 0 0 654 5844
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0135343
X-RAY DIFFRACTIONf_angle_d1.2867270
X-RAY DIFFRACTIONf_dihedral_angle_d14.6091946
X-RAY DIFFRACTIONf_chiral_restr0.106781
X-RAY DIFFRACTIONf_plane_restr0.01957
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.28434540.26848710X-RAY DIFFRACTION100
1.4665-1.48380.32274650.26088628X-RAY DIFFRACTION100
1.4838-1.50180.27784440.25368729X-RAY DIFFRACTION100
1.5018-1.52090.28294300.24298698X-RAY DIFFRACTION100
1.5209-1.54090.25025550.22878670X-RAY DIFFRACTION100
1.5409-1.5620.24654950.22018608X-RAY DIFFRACTION100
1.562-1.58430.21754690.20788663X-RAY DIFFRACTION100
1.5843-1.60790.22545370.20048633X-RAY DIFFRACTION100
1.6079-1.63310.22044630.19618684X-RAY DIFFRACTION100
1.6331-1.65980.21494830.19358666X-RAY DIFFRACTION100
1.6598-1.68850.23174780.1928705X-RAY DIFFRACTION100
1.6885-1.71920.23045330.18198529X-RAY DIFFRACTION100
1.7192-1.75220.23114770.18288741X-RAY DIFFRACTION100
1.7522-1.7880.17964310.17398712X-RAY DIFFRACTION100
1.788-1.82690.21013910.17748754X-RAY DIFFRACTION100
1.8269-1.86940.20394560.17678724X-RAY DIFFRACTION100
1.8694-1.91610.20575010.17688632X-RAY DIFFRACTION100
1.9161-1.96790.19974900.17378683X-RAY DIFFRACTION100
1.9679-2.02580.19274990.16928621X-RAY DIFFRACTION100
2.0258-2.09120.20344860.17198691X-RAY DIFFRACTION100
2.0912-2.16590.19454000.16688700X-RAY DIFFRACTION100
2.1659-2.25260.16954510.16088693X-RAY DIFFRACTION100
2.2526-2.35520.19064170.16588790X-RAY DIFFRACTION100
2.3552-2.47930.20794110.16738694X-RAY DIFFRACTION100
2.4793-2.63460.20854490.1768726X-RAY DIFFRACTION100
2.6346-2.83790.20484080.17118747X-RAY DIFFRACTION100
2.8379-3.12340.19164370.17568696X-RAY DIFFRACTION100
3.1234-3.5750.17494700.15768683X-RAY DIFFRACTION100
3.575-4.50290.15114980.14618645X-RAY DIFFRACTION100
4.5029-36.6730.16395170.15298642X-RAY DIFFRACTION100
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)
16.25556.69855.50377.81746.04154.8481-0.16770.30810.1826-0.05160.4308-0.2039-0.33930.6056-0.1210.2132-0.04880.03480.3061-0.00520.2416-10.423712.7364-12.8108
22.48150.2196-0.26683.0591-0.41181.8679-0.06610.0476-0.0549-0.08360.0014-0.08090.09190.08050.07220.15210.0111-0.01370.1498-0.02380.1425-27.5886-0.9864-20.9842
36.56123.90330.91578.8169-0.27572.88580.01470.07550.1046-0.3045-0.08960.68150.0038-0.10010.06440.13980.0476-0.0080.1904-0.06030.1267-36.22122.3146-20.0761
41.8797-0.05940.29420.62090.28781.9337-0.0186-0.14780.2520.0604-0.06860.1456-0.0068-0.10640.10490.17310.0152-0.00890.1649-0.05770.2613-36.253411.3823-8.7577
54.52760.04796.35240.9977-0.37838.8882-0.2101-0.22690.5020.0578-0.14570.0614-0.2148-0.13340.4010.16310.02940.00410.1848-0.07670.2658-24.417317.7101-1.5697
66.1094.02465.50892.58283.63374.72630.183-0.0907-0.04510.0714-0.0621-0.1190.136-0.1996-0.19450.1772-0.00590.00360.2133-0.05660.2226-23.79716.3568-1.4115
72.4896-1.42810.73117.0946-3.42012.1006-0.1405-0.25050.00520.47180.07020.55710.0758-0.30310.02890.2165-0.04690.04080.2121-0.05930.2251-40.2036-2.5175-6.3359
83.84692.97612.48592.65331.90831.6593-0.07-0.08290.1058-0.0324-0.0196-0.0354-0.0326-0.05890.09830.16550.0088-0.00510.1706-0.04240.2052-17.7769.3892-6.169
91.9054-3.1071-0.79196.79660.7830.9278-0.5645-0.335-0.40122.45880.357-0.28080.84870.25210.20870.94080.0811-0.02120.3865-0.0160.3784-9.8076-2.679412.0806
107.0727-0.46365.08983.0777-0.32983.6614-0.11890.08590.32720.0741-0.02390.1576-0.25570.15130.21780.1954-0.0079-0.01870.1914-0.06830.2744-12.691922.98380.6902
113.1687-2.42510.86076.9605-1.19282.19220.1220.28770.328-0.4949-0.1155-0.0946-0.11690.1247-0.01990.2372-0.0017-0.02490.1848-0.02020.191-20.5868-6.2855-31.3191
122.62610.8802-0.33276.9435-2.04184.08880.0561-0.00520.16170.27630.078-0.1787-0.12480.0066-0.13320.12610.0014-0.04010.1521-0.03550.1373-15.3564-14.0401-25.5689
137.02780.88630.05063.3638-5.38899.4452-0.15830.30790.2884-0.10530.2447-0.4307-0.0810.2212-0.0760.18450.0222-0.01870.2686-0.06460.2003-4.783-14.4843-27.5938
144.362.7819-2.644.7469-2.7456.50230.3317-0.218-0.32540.4077-0.0628-0.03020.36950.3223-0.25750.25950.0383-0.10640.1895-0.03710.1957-11.4721-23.5405-18.3654
156.5192-6.73855.35589.0698-6.38016.2420.24930.6730.2165-0.373-0.4479-0.48160.16010.58370.16180.25990.0345-0.01370.2955-0.05320.1687-15.3378-21.1953-37.4776
167.8773-0.8130.644.40050.98281.63520.04640.0848-0.0076-0.227-0.01090.17160.045-0.0678-0.03690.2245-0.0102-0.04910.1709-0.02420.1443-27.9468-25.6785-35.6153
174.6358-5.8424-1.44228.45350.51372.40640.34430.2206-0.2369-0.704-0.15970.38780.059-0.0558-0.16610.2969-0.0063-0.09240.2063-0.02670.1598-33.2406-13.1433-41.6698
184.3507-2.28364.57883.2242-3.69435.47530.03490.0931-0.41110.06120.14250.4895-0.2547-0.1942-0.21420.2617-0.0193-0.03420.18010.00910.229-33.017-13.5768-30.4723
192.12970.303-2.44336.28261.99127.87930.15140.0297-0.46950.0488-0.19140.44660.9413-0.58130.04010.381-0.0409-0.0830.22250.0070.239-25.911-29.7971-22.4624
202.7876-3.44962.11635.6262-2.85142.1685-0.0237-0.0837-0.0909-0.00140.13080.2243-0.0385-0.1898-0.0590.22490.0069-0.03950.2128-0.01370.1433-31.7971-5.1842-32.4094
217.9475-4.3113-1.44996.7057-0.77188.21270.13340.5108-0.1183-0.5001-0.2291-0.08090.37670.02860.06510.2890.0009-0.0670.1880.01790.1563-35.7213-1.6825-45.9351
222.8231-0.3834-2.2831.16591.77057.81860.01190.23620.0652-0.09830.1703-0.15180.06040.1157-0.1750.15690.0224-0.04030.1329-0.02370.1699-6.3929-6.0036-14.0757
232.15691.4258-1.61885.4905-3.00266.1387-0.0185-0.00830.1350.03710.15630.17250.1606-0.2408-0.110.13120.0033-0.030.1283-0.0490.1768-14.27950.0822-1.9829
248.9744-2.3264-6.94992.73093.4967.13350.1965-0.24120.42240.12140.4015-0.58480.01970.6172-0.64970.19390.0436-0.0820.2583-0.12130.31013.136-2.9335-3.3631
251.4066-0.8793-1.01610.85470.96462.7035-0.1207-0.2094-0.08930.53220.4585-0.360.70480.7104-0.2970.37520.1611-0.15960.3757-0.13980.36986.0892-17.3697-5.8336
264.0532-5.0647-4.20678.06857.9268.4459-0.14110.2812-0.36260.7010.0520.20471.037-0.08770.15760.37480.0164-0.06710.2377-0.07150.2816-1.7935-20.7842-12.3131
275.4511-4.00312.68383.5316-3.70267.3562-0.022-0.4969-0.55620.66250.0826-0.16640.79070.2941-0.04720.43570.0624-0.04040.24950.0010.3157-9.783-16.24854.9082
281.398-0.5989-0.72660.92440.95313.82530.04950.415-0.31320.11270.049-0.07660.52130.0796-0.04440.22930.0305-0.06950.2354-0.11470.2608-0.2347-17.3469-19.6215
290.37061.54540.99987.17123.69463.21640.19291.0675-0.5171-0.41170.2724-0.75380.04770.8313-0.60890.2730.1076-0.05030.6061-0.32220.596713.9869-17.7782-24.1969
308.56263.44596.91975.09123.42929.4406-0.1966-0.27340.62140.123-0.4690.7738-0.269-0.83810.56550.1901-0.0167-0.01620.3314-0.11940.503319.8797-0.7088-14.711
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 274 )
2X-RAY DIFFRACTION2chain 'A' and (resid 275 through 322 )
3X-RAY DIFFRACTION3chain 'A' and (resid 323 through 341 )
4X-RAY DIFFRACTION4chain 'A' and (resid 342 through 380 )
5X-RAY DIFFRACTION5chain 'A' and (resid 381 through 400 )
6X-RAY DIFFRACTION6chain 'A' and (resid 401 through 418 )
7X-RAY DIFFRACTION7chain 'A' and (resid 419 through 436 )
8X-RAY DIFFRACTION8chain 'A' and (resid 437 through 455 )
9X-RAY DIFFRACTION9chain 'A' and (resid 456 through 467 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1950 through 1968 )
11X-RAY DIFFRACTION11chain 'C' and (resid 267 through 280 )
12X-RAY DIFFRACTION12chain 'C' and (resid 281 through 300 )
13X-RAY DIFFRACTION13chain 'C' and (resid 301 through 309 )
14X-RAY DIFFRACTION14chain 'C' and (resid 310 through 332 )
15X-RAY DIFFRACTION15chain 'C' and (resid 333 through 354 )
16X-RAY DIFFRACTION16chain 'C' and (resid 355 through 380 )
17X-RAY DIFFRACTION17chain 'C' and (resid 381 through 400 )
18X-RAY DIFFRACTION18chain 'C' and (resid 401 through 418 )
19X-RAY DIFFRACTION19chain 'C' and (resid 419 through 436 )
20X-RAY DIFFRACTION20chain 'C' and (resid 437 through 460 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1950 through 1969 )
22X-RAY DIFFRACTION22chain 'E' and (resid 266 through 300 )
23X-RAY DIFFRACTION23chain 'E' and (resid 301 through 332 )
24X-RAY DIFFRACTION24chain 'E' and (resid 333 through 354 )
25X-RAY DIFFRACTION25chain 'E' and (resid 355 through 400 )
26X-RAY DIFFRACTION26chain 'E' and (resid 401 through 418 )
27X-RAY DIFFRACTION27chain 'E' and (resid 419 through 436 )
28X-RAY DIFFRACTION28chain 'E' and (resid 437 through 458 )
29X-RAY DIFFRACTION29chain 'F' and (resid 1951 through 1971 )
30X-RAY DIFFRACTION30chain 'F' and (resid 1972 through 1977 )

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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