[日本語] English
万見
- PDB-3qhe: Crystal structure of the complex between the armadillo repeat dom... -

+
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: 3qhe
タイトルCrystal structure of the complex between the armadillo repeat domain of adenomatous polyposis coli and the tyrosine-rich domain of Sam68
要素
  • Adenomatous polyposis coli protein
  • KH domain-containing, RNA-binding, signal transduction-associated protein 1
キーワードsignaling protein/splicing / Armadillo repeat superhelix / Regulation of Wnt signaling / tumor suppressor protein / adaptor protein / RNA-binding protein / signaling protein-splicing protein complex / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / signaling protein-splicing complex
機能・相同性
機能・相同性情報


regulation of RNA export from nucleus / Grb2-Sos complex / APC truncation mutants are not K63 polyubiquitinated / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly ...regulation of RNA export from nucleus / Grb2-Sos complex / APC truncation mutants are not K63 polyubiquitinated / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of protein localization to centrosome / bicellular tight junction assembly / pattern specification process / negative regulation of microtubule depolymerization / catenin complex / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / heart valve development / regulation of microtubule-based process / microtubule plus-end binding / poly(A) binding / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / protein kinase regulator activity / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / poly(U) RNA binding / endocardial cushion morphogenesis / regulation of alternative mRNA splicing, via spliceosome / molecular function inhibitor activity / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / dynein complex binding / regulation of RNA splicing / mitotic cytokinesis / positive regulation of translational initiation / bicellular tight junction / lateral plasma membrane / signaling adaptor activity / SH2 domain binding / protein tyrosine kinase binding / adherens junction / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / Degradation of beta-catenin by the destruction complex / kinetochore / SH3 domain binding / Wnt signaling pathway / G1/S transition of mitotic cell cycle / ruffle membrane / mRNA processing / positive regulation of protein catabolic process / G2/M transition of mitotic cell cycle / Ovarian tumor domain proteases / insulin receptor signaling pathway / cell migration / nervous system development / lamellipodium / T cell receptor signaling pathway / positive regulation of cold-induced thermogenesis / protein-containing complex assembly / microtubule binding / regulation of apoptotic process / spermatogenesis / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of cell cycle / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / mRNA binding / centrosome / ubiquitin protein ligase binding / DNA damage response / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein-containing complex / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane
類似検索 - 分子機能
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family ...Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / Type-1 KH domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / K Homology domain, type 1 superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / K Homology domain / K homology RNA-binding domain / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
類似検索 - ドメイン・相同性
Adenomatous polyposis coli protein / KH domain-containing, RNA-binding, signal transduction-associated protein 1
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: 2.4 Å
データ登録者Morishita, E.C.J. / Murayama, K. / Kato-Murayama, M. / Ishizuku-Katsura, Y. / Tomabechi, Y. / Terada, T. / Handa, N. / Shirouzu, M. / Akiyama, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
引用ジャーナル: Structure / 年: 2011
タイトル: Crystal structures of the armadillo repeat domain of adenomatous polyposis coli and its complex with the tyrosine-rich domain of sam68
著者: Morishita, E.C. / Murayama, K. / Kato-Murayama, M. / Ishizuka-Katsura, Y. / Tomabechi, Y. / Hayashi, T. / Terada, T. / Handa, N. / Shirouzu, M. / Akiyama, T. / Yokoyama, S.
履歴
登録2011年1月25日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02011年11月2日Provider: repository / タイプ: Initial release
改定 1.12023年11月1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: Adenomatous polyposis coli protein
B: KH domain-containing, RNA-binding, signal transduction-associated protein 1
C: Adenomatous polyposis coli protein
D: KH domain-containing, RNA-binding, signal transduction-associated protein 1


分子量 (理論値)分子数
合計 (水以外)87,9914
ポリマ－87,9914
非ポリマー00
水4,720262
1
A: Adenomatous polyposis coli protein
B: KH domain-containing, RNA-binding, signal transduction-associated protein 1


分子量 (理論値)分子数
合計 (水以外)43,9962
ポリマ－43,9962
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-7 kcal/mol
Surface area15200 Å2
手法PISA
2
C: Adenomatous polyposis coli protein
D: KH domain-containing, RNA-binding, signal transduction-associated protein 1


分子量 (理論値)分子数
合計 (水以外)43,9962
ポリマ－43,9962
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-7 kcal/mol
Surface area15310 Å2
手法PISA
単位格子
Length a, b, c (Å)148.223, 148.223, 63.379
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
要素

#1: タンパク質 Adenomatous polyposis coli protein / APC / Protein APC / Deleted in polyposis 2.5


分子量: 37502.219 Da / 分子数: 2 / 断片: Armadillo repeat domain, residues 396-732 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 解説: E. coli cell-free system / プラスミド: pCR2.1 / 発現宿主: cell free synthsis (unknown) / 参照: UniProt: P25054
#2: タンパク質 KH domain-containing, RNA-binding, signal transduction-associated protein 1 / Src-associated in mitosis 68 kDa protein / Sam68 / GAP-associated tyrosine phosphoprotein p62 / p21 ...Src-associated in mitosis 68 kDa protein / Sam68 / GAP-associated tyrosine phosphoprotein p62 / p21 Ras GTPase-activating protein-associated p62 / p68


分子量: 6493.303 Da / 分子数: 2 / 断片: Tyrosine-rich domain, residues 365-419 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 解説: E. coli cell-free system / プラスミド: pCR2.1 / 発現宿主: cell free synthsis (unknown) / 参照: UniProt: Q07666
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 262 / 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: 2.28 Å3/Da / 溶媒含有率: 46.15 %
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: 5.5
詳細: 100mM BIS-TRIS (pH 5.5), 150mM NaCl, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
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: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2010年3月30日
放射モノクロメーター: GRAPHITE / 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: 2.4→64.18 Å / Num. all: 31344 / Num. obs: 31344 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 11.2 % / Rmerge(I) obs: 0.095 / Rsym value: 0.091 / Net I/σ(I): 7.1
反射 シェル解像度: 2.4→2.53 Å / 冗長度: 10.8 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2 / Num. unique all: 4539 / Rsym value: 0.37 / % possible all: 100

-
解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
PHASER位相決定
REFMAC5.5.0102精密化
MOSFLMデータ削減
SCALAデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 3AU3

3au3


解像度: 2.4→64.18 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.657 / SU ML: 0.157 / 交差検証法: THROUGHOUT / ESU R Free: 0.239 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; ASN709-LEU710 and LEU710-ILE711 C-N bonds in chain C, 0.91A and 1.05A, respectively, lie outside of the accepted range for the peptide bond ...詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; ASN709-LEU710 and LEU710-ILE711 C-N bonds in chain C, 0.91A and 1.05A, respectively, lie outside of the accepted range for the peptide bond (1.30-1.45). depositors said that it was hard to build them suitably because these residues are in a region of poor density.
Rfactor反射数%反射Selection details
Rfree0.23046 1578 5 %RANDOM
Rwork0.18695 ---
all0.18915 31322 --
obs0.18915 29744 100 %-
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: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 32.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→64.18 Å
タンパク質核酸リガンド溶媒全体
原子数5100 0 0 262 5362
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9577007
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3255654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66524.591220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13815942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9081530
X-RAY DIFFRACTIONr_chiral_restr0.0720.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023786
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4051.53282
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.825235
X-RAY DIFFRACTIONr_scbond_it1.50831903
X-RAY DIFFRACTIONr_scangle_it2.5244.51772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 2.4→2.462 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.259 118 -
Rwork0.196 2180 -
obs--100 %
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)
112.92195.0391-0.44836.05910.42923.4143-0.19310.56110.1772-0.5990.2430.0215-0.28730.1637-0.04990.31530.046-0.08080.20090.08880.129934.2271123.2103-17.8859
216.3804-9.468121.200127.565111.039852.0089-0.44910.0111-0.2392-0.51550.76660.2194-1.32620.8229-0.31750.5640.2592-0.08930.5180.32160.620330.5282132.8954-15.2446
33.4802-0.6402-0.74364.4473-0.29683.4360.12030.0643-0.2075-0.2176-0.0440.34580.2932-0.1936-0.07630.1686-0.0133-0.1250.21390.05340.230325.3739115.1394-8.7447
41.48280.56840.35783.18470.24511.61890.05250.080.0129-0.17110.02330.18020.0111-0.0619-0.07580.15490.0081-0.02180.16180.04010.16737.2305120.9559-4.1588
51.3087-0.3219-0.29288.94690.21762.60580.0917-0.072-0.04420.0778-0.05650.0633-0.041-0.1071-0.03520.13840.0076-0.01760.1820.03670.182436.6392120.08235.5129
62.9416-0.4619-0.55037.293.94336.35240.07370.0527-0.0423-0.21780.1273-0.038-0.03370.213-0.2010.1330.0218-0.03570.15310.08360.177346.0904114.28986.6286
70.4509-0.51710.06772.3280.03971.77710.0607-0.04070.07330.0727-0.01510.1812-0.127-0.1396-0.04560.1463-0.0132-0.00260.1620.02610.21442.6437116.645516.6754
833.4326-18.0476-4.54459.74912.04434.9194-1.3343-1.5974-1.52280.74420.92450.8252-0.93070.29690.40980.5899-0.08180.2320.54670.00390.660926.9979122.499125.0302
94.0014-0.5928-0.39932.71990.18883.95880.0097-0.20960.18290.1693-0.0056-0.0638-0.04540.0632-0.00410.2151-0.0258-0.00840.15840.03840.217545.944112.843726.4079
1021.74455.86485.6277.0891-3.80697.4779-0.0398-1.59951.64040.8182-0.09930.6912-0.5857-1.25140.13910.2909-0.02480.04360.4897-0.14780.382433.4733108.499932.9297
115.2778-1.07540.37642.9731-1.32122.7209-0.0492-0.0967-0.13240.00580.0175-0.08350.06950.05280.03170.1809-0.03060.01680.1620.01880.193544.4838104.61428.9115
1211.93753.0921-9.49055.4837-2.31219.78970.1061-1.06480.02340.83230.0854-0.2674-0.29410.7265-0.19150.2484-0.0329-0.06630.24710.03090.138446.4535104.565240.6974
1313.43091.69514.18433.68820.6575.12340.07890.1236-0.2638-0.04570.0077-0.2262-0.04220.0706-0.08660.197-0.03260.03040.13610.05720.215239.318696.596731.6382
1412.9335-5.82591.0979.10893.899313.39950.5994-0.05590.1737-0.8319-0.1382-0.180.1969-0.5571-0.46120.3788-0.0309-0.02220.2430.06940.428732.5679109.63819.2276
152.22962.8946-5.371611.8863-5.849513.26660.3355-0.07340.3054-0.03130.08890.5553-0.88870.2977-0.42440.31630.0724-0.07230.3190.08560.53837.2743108.49821.7159
166.78172.72-4.25245.8743-3.50017.4581-0.06690.120.4620.06930.09480.1201-0.2586-0.4732-0.0280.1880.0501-0.02110.2585-0.01930.106-4.261194.524128.0151
1724.713310.24592.43734.24851.020.4998-0.8612.1471-0.2461-0.33750.8314-0.09380.2687-0.3490.02961.337-0.35110.2711.6767-0.15610.2562-11.376985.915528.1442
1810.95585.33510.34725.23111.37531.6999-0.23490.37320.5224-0.29160.0670.1878-0.1441-0.12750.16790.2533-0.0115-0.01360.19520.0530.10357.604795.906718.8843
198.415-5.56831.097417.6408-7.078517.5995-0.0294-0.21241.478-0.3976-0.0986-1.4383-0.5861.2530.1280.2941-0.0564-0.06130.22890.01170.392618.6731107.558625.7926
2031.0818-1.43471.17754.1212-9.653522.7775-0.5229-1.14361.58820.84080.2106-0.1954-1.9299-0.37780.31230.42520.0815-0.15590.14-0.09960.401710.9877107.162930.2959
211.81580.39280.3850.8617-0.04582.1106-0.0566-0.06650.10130.00930.0111-0.0516-0.015-0.14030.04550.16620.0095-0.01660.18470.01340.13059.659491.373329.4775
223.8204-0.0478-0.21382.34140.59685.2905-0.0005-0.0172-0.09230.0847-0.0062-0.01320.0944-0.1450.00670.1530.0213-0.00780.15940.0370.139216.78986.275533.8381
235.9668-2.4678-3.54747.45254.82558.6085-0.11660.037-0.46060.1971-0.04310.1930.4493-0.30890.15970.1459-0.0211-0.04890.20340.06330.189917.951179.311337.8503
243.4331-1.06260.46932.22050.4922.28450.0434-0.0238-0.25790.03810.058-0.08880.11780.0307-0.10140.1648-0.0258-0.02520.17390.01130.18526.660878.182138.288
254.798-0.80720.66675.6338-1.48864.50710.06550.2877-0.141-0.11510.0336-0.11480.20560.1983-0.09910.1509-0.0115-0.0650.2542-0.03370.294534.178573.950439.957
265.58770.23721.26676.3566-2.20994.52070.1971-0.0833-0.5261-0.062-0.0291-0.40680.52020.3974-0.16810.12250.013-0.08150.22-0.05420.236244.736174.989244.2651
277.37570.58162.093617.7048-6.9699.4762-0.0066-0.100400.48030.0346-0.158-0.27710.2244-0.0280.1406-0.0278-0.10650.232-0.07110.196148.29883.810448.9938
288.6985-1.48235.08896.5828-3.458917.2530.17640.0309-0.27840.21390.0356-0.07810.42490.4009-0.2120.089-0.04220.01960.1238-0.01070.231626.962490.788734.9721
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A401 - 440
2X-RAY DIFFRACTION2A441 - 445
3X-RAY DIFFRACTION3A446 - 473
4X-RAY DIFFRACTION4A474 - 533
5X-RAY DIFFRACTION5A534 - 553
6X-RAY DIFFRACTION6A554 - 579
7X-RAY DIFFRACTION7A580 - 622
8X-RAY DIFFRACTION8A623 - 627
9X-RAY DIFFRACTION9A628 - 665
10X-RAY DIFFRACTION10A666 - 672
11X-RAY DIFFRACTION11A673 - 694
12X-RAY DIFFRACTION12A695 - 704
13X-RAY DIFFRACTION13A705 - 731
14X-RAY DIFFRACTION14B379 - 388
15X-RAY DIFFRACTION15C402 - 411
16X-RAY DIFFRACTION16C412 - 425
17X-RAY DIFFRACTION17C426 - 439
18X-RAY DIFFRACTION18C440 - 458
19X-RAY DIFFRACTION19C459 - 464
20X-RAY DIFFRACTION20C465 - 470
21X-RAY DIFFRACTION21C471 - 526
22X-RAY DIFFRACTION22C527 - 559
23X-RAY DIFFRACTION23C560 - 581
24X-RAY DIFFRACTION24C582 - 622
25X-RAY DIFFRACTION25C623 - 661
26X-RAY DIFFRACTION26C662 - 706
27X-RAY DIFFRACTION27C707 - 731
28X-RAY DIFFRACTION28D379 - 389

+
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