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- PDB-6aj4: Crystal structure of the DHR-2 domain of DOCK7 in complex with Cdc42 -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6aj4
タイトルCrystal structure of the DHR-2 domain of DOCK7 in complex with Cdc42
要素
  • Cell division control protein 42 homolog
  • Dedicator of cytokinesis protein 7
キーワードSIGNALING PROTEIN / DOCK / GEF / DHR-2 / GTPase / Rho / Rac / Cdc42
機能・相同性
機能・相同性情報


establishment of neuroblast polarity / interkinetic nuclear migration / GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process ...establishment of neuroblast polarity / interkinetic nuclear migration / GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / organelle transport along microtubule / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / GTP-dependent protein binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / basal part of cell / regulation of Rho protein signal transduction / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / regulation of modification of postsynaptic structure / regulation of lamellipodium assembly / regulation of stress fiber assembly / positive regulation of vascular associated smooth muscle cell migration / adherens junction organization / embryonic heart tube development / RHO GTPases activate KTN1 / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / sprouting angiogenesis / negative regulation of cold-induced thermogenesis / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / nuclear migration / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / RHOJ GTPase cycle / Rac protein signal transduction / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / macrophage differentiation / CDC42 GTPase cycle / regulation of neurogenesis / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / axonogenesis / guanyl-nucleotide exchange factor activity / secretory granule / actin filament organization / small monomeric GTPase / positive regulation of DNA replication / integrin-mediated signaling pathway / filopodium / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / RHO GTPases Activate Formins / EGFR downregulation / MAPK6/MAPK4 signaling
類似検索 - 分子機能
Dedicator of cytokinesis C, C2 domain / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A ...Dedicator of cytokinesis C, C2 domain / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / DHR-2, Lobe C / DHR-2, Lobe B / C2 DOCK-type domain profile. / DOCKER domain profile. / Cdc42 / Small GTPase Rho / Small GTPase Rho domain profile. / C2 domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Cell division control protein 42 homolog / Dedicator of cytokinesis protein 7
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: 3.256 Å
データ登録者Kukimoto-Niino, M. / Shirouzu, M.
資金援助 日本, 1件
組織認可番号国
Japan Society for the Promotion of Science15K06987 日本
引用ジャーナル: Structure / 年: 2019
タイトル: Structural Basis for the Dual Substrate Specificity of DOCK7 Guanine Nucleotide Exchange Factor.
著者: Kukimoto-Niino, M. / Tsuda, K. / Ihara, K. / Mishima-Tsumagari, C. / Honda, K. / Ohsawa, N. / Shirouzu, M.
履歴
登録2018年8月27日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02019年3月20日Provider: repository / タイプ: Initial release
改定 1.12019年4月3日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
改定 1.22019年5月22日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
改定 1.32023年11月22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: Dedicator of cytokinesis protein 7
B: Cell division control protein 42 homolog
C: Dedicator of cytokinesis protein 7
D: Cell division control protein 42 homolog
E: Dedicator of cytokinesis protein 7
F: Cell division control protein 42 homolog
G: Dedicator of cytokinesis protein 7
H: Cell division control protein 42 homolog


分子量 (理論値)分子数
合計 (水以外)221,3568
ポリマ－221,3568
非ポリマー00
水00
1
A: Dedicator of cytokinesis protein 7
B: Cell division control protein 42 homolog


分子量 (理論値)分子数
合計 (水以外)55,3392
ポリマ－55,3392
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-25 kcal/mol
Surface area22530 Å2
手法PISA
2
C: Dedicator of cytokinesis protein 7
D: Cell division control protein 42 homolog


分子量 (理論値)分子数
合計 (水以外)55,3392
ポリマ－55,3392
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-25 kcal/mol
Surface area22510 Å2
手法PISA
3
E: Dedicator of cytokinesis protein 7
F: Cell division control protein 42 homolog


分子量 (理論値)分子数
合計 (水以外)55,3392
ポリマ－55,3392
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-22 kcal/mol
Surface area22810 Å2
手法PISA
4
G: Dedicator of cytokinesis protein 7
H: Cell division control protein 42 homolog


分子量 (理論値)分子数
合計 (水以外)55,3392
ポリマ－55,3392
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-24 kcal/mol
Surface area22600 Å2
手法PISA
単位格子
Length a, b, c (Å)196.460, 105.560, 118.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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要素

#1: タンパク質
Dedicator of cytokinesis protein 7


分子量: 33877.574 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: SF file contains Friedel pairs. / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DOCK7, KIAA1771 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: Q96N67
#2: タンパク質
Cell division control protein 42 homolog / G25K GTP-binding protein


分子量: 21461.537 Da / 分子数: 4 / Mutation: C188S / 由来タイプ: 組換発現 / 詳細: SF file contains Friedel pairs. / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CDC42 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P60953

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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: 2.77 Å3/Da / 溶媒含有率: 55.55 %
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 / 詳細: PEG3350 and tri-potassium citrate monohydrate

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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: SPring-8 / ビームライン: BL32XU / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2016年7月16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: 3.256→50 Å / Num. obs: 73997 / % possible obs: 99.4 % / 冗長度: 3.9 % / CC1/2: 0.996 / Rrim(I) all: 0.12 / Net I/σ(I): 11.9
反射 シェル解像度: 3.26→3.45 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 11796 / CC1/2: 0.639 / Rrim(I) all: 0.96 / % possible all: 97.8

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.13_2998: ???)精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3VHL

3vhl


解像度: 3.256→46.802 Å / SU ML: 0.5 / 交差検証法: FREE R-VALUE / σ(F): 0.95 / 位相誤差: 27.6 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2588 3777 5.11 %
Rwork0.1837 --
obs0.1876 73981 99.47 %
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
精密化ステップサイクル: LAST / 解像度: 3.256→46.802 Å
タンパク質核酸リガンド溶媒全体
原子数14684 0 0 0 14684
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01115020
X-RAY DIFFRACTIONf_angle_d1.28920320
X-RAY DIFFRACTIONf_dihedral_angle_d5.1559152
X-RAY DIFFRACTIONf_chiral_restr0.0612248
X-RAY DIFFRACTIONf_plane_restr0.0082624
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.256-3.29720.3531270.32122446X-RAY DIFFRACTION91
3.2972-3.34060.37761380.30252556X-RAY DIFFRACTION100
3.3406-3.38630.32241450.29062653X-RAY DIFFRACTION100
3.3863-3.43470.36511400.28092596X-RAY DIFFRACTION100
3.4347-3.48590.43611410.2762589X-RAY DIFFRACTION99
3.4859-3.54040.32941370.26032582X-RAY DIFFRACTION99
3.5404-3.59840.31181400.23452629X-RAY DIFFRACTION99
3.5984-3.66040.31081340.22422576X-RAY DIFFRACTION99
3.6604-3.7270.30871420.22152575X-RAY DIFFRACTION100
3.727-3.79860.31071410.19952630X-RAY DIFFRACTION100
3.7986-3.87610.27531430.20292615X-RAY DIFFRACTION100
3.8761-3.96040.27531410.20272581X-RAY DIFFRACTION100
3.9604-4.05240.28551440.19222632X-RAY DIFFRACTION100
4.0524-4.15370.28911410.18882596X-RAY DIFFRACTION100
4.1537-4.2660.31071390.17312607X-RAY DIFFRACTION100
4.266-4.39140.23641410.15772667X-RAY DIFFRACTION100
4.3914-4.5330.20451380.15352564X-RAY DIFFRACTION100
4.533-4.69490.19081440.14842586X-RAY DIFFRACTION100
4.6949-4.88270.24251410.14992627X-RAY DIFFRACTION100
4.8827-5.10460.23121380.15072614X-RAY DIFFRACTION100
5.1046-5.37340.23891390.14992625X-RAY DIFFRACTION100
5.3734-5.70950.26211370.16032599X-RAY DIFFRACTION100
5.7095-6.14950.21791430.16542623X-RAY DIFFRACTION100
6.1495-6.76670.28261430.18732603X-RAY DIFFRACTION100
6.7667-7.7420.24681400.18022606X-RAY DIFFRACTION100
7.742-9.73960.18341400.12882617X-RAY DIFFRACTION100
9.7396-46.80690.21941400.17942610X-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)
14.05021.871-3.24376.08532.36446.4901-0.14010.9221-0.4635-0.9380.2168-0.0840.10720.9605-0.02470.58120.02470.00330.9096-0.06760.45687.83467.5708-0.506
27.1338-0.8232-4.56576.45925.71167.7471-0.1161.2326-0.1912-2.26790.85080.0343-1.46212.0557-0.57251.2056-0.48210.1231.4763-0.27210.68618.275414.8679-7.318
34.91910.97161.2334.63612.3063.5741-0.32920.75230.1622-0.82950.2720.1004-1.2063-0.2680.03880.80740.10.05030.67940.08050.4043-0.08719.57755.7498
43.432-0.7420.36245.6559-0.34884.8686-0.0826-0.67120.51940.13490.3365-0.0224-0.69190.0819-0.20450.5759-0.07010.05560.5992-0.15360.49317.089828.442530.4674
56.00161.0604-0.48617.5691-1.26279.5628-0.01040.4709-0.3418-0.0142-0.1135-0.2502-0.7211.16450.15790.55760.01930.02140.8211-0.15580.475719.198112.922122.8827
63.3104-1.39810.78757.51192.04544.16190.31720.4409-0.2923-0.1879-0.2182-0.108-0.32940.4403-0.11390.5733-0.12690.01360.8324-0.12490.61212.428114.643517.0521
73.28870.03510.69336.04610.78974.86850.1607-0.51980.30270.4274-0.0236-0.8998-0.07670.7889-0.11760.4418-0.0258-0.05810.9643-0.20530.667227.241912.283629.2014
83.38513.404-0.43537.0701-1.37830.3055-0.69692.50660.4858-3.68230.2087-1.3168-0.81822.58170.46431.5317-0.20790.59241.57140.19791.051637.342214.95366.7446
96.28933.0651-2.04156.32232.47526.4821-1.09960.4672-0.7969-1.62170.6351-0.68641.08310.97150.55080.5465-0.09120.21291.2469-0.06041.064939.38844.777317.5538
103.5156-1.1775-4.05719.8933-1.03665.35960.5724-0.2820.7177-1.246-0.4433-0.97320.70410.7014-0.01630.5950.01710.16940.5922-0.12640.572426.69365.252916.339
115.16131.9229-5.16075.3442-1.77385.2025-1.14880.7391-0.98-0.3229-0.4368-0.61421.0204-0.80961.17910.6230.0138-0.0060.6936-0.09820.578618.50581.251921.7495
124.30440.39571.76073.62831.55324.0119-0.2038-0.64980.51070.91450.331-0.5454-0.11320.76850.00350.65820.0397-0.00410.9789-0.24180.680413.689-6.024291.0116
135.2136-0.6616-0.05023.9358-0.08792.5119-0.103-0.41970.06630.38540.22590.03920.682-0.0292-0.11310.654-0.0628-0.03740.48220.00220.39825.9904-18.610982.5451
146.8595-4.63535.14425.0461-6.56468.7143-0.4316-0.47130.2490.17450.8820.2467-0.1983-1.1804-0.30610.5015-0.0369-0.00270.5089-0.010.482311.3129-23.407565.366
152.7589-0.18540.14537.2951-2.09044.7003-0.08070.4965-0.2877-0.86570.1769-0.5380.80250.3946-0.07220.696-0.0110.10150.6751-0.12680.5116.2962-25.024556.3559
160.7349-1.02392.35037.60420.8169.69380.0603-0.0349-0.18310.4203-0.0049-0.15710.630.679-0.13180.4387-0.1430.09990.4806-0.10580.699822.0783-6.503665.8099
170.5747-0.6539-1.74766.19760.21827.3290.1842-0.42610.51070.26420.0299-0.38650.15760.8602-0.34060.3463-0.00480.04360.6043-0.06670.693420.4569-9.669465.7152
181.2069-0.3861-1.57973.7311-1.13612.7531-0.09590.47890.0703-0.33390.2883-1.0676-0.36220.9877-0.22290.5676-0.11810.15180.859-0.13320.924532.3896-2.142959.3
198.4661-0.2266-4.87225.63670.81073.1664-0.6312-1.6341-0.271.22220.3645-1.8712-0.16320.54080.02550.65260.0367-0.16750.663-0.14210.985737.0884-0.120474.0241
208.4448-2.07429.89312.6723-0.74482.0015-2.2450.68872.595-0.31210.1408-1.5187-2.74820.39491.46720.994-0.27130.14030.7715-0.2521.633535.931910.684567.3508
214.10950.3091-0.73733.8994.87966.39760.6384-0.0451-0.34540.3677-0.4353-0.08570.36250.0877-0.25460.5472-0.0109-0.12070.3740.04350.769822.50243.663569.8451
227.2246-1.85212.26927.8139-3.90616.5430.7854-0.8351-1.01140.9626-0.11-0.79451.50680.7485-0.43551.50270.2297-0.42770.7634-0.09640.78427.317-34.06535.1834
236.7833-1.40671.9733.6133-2.60197.0480.1018-0.7304-1.04010.98410.38580.28210.5486-0.3731-0.45040.9160.0405-0.12030.6070.02390.648316.9625-31.230826.888
245.2081-1.01171.01025.1994.54196.31230.6635-0.0811-1.02490.67440.32350.04061.88840.4484-0.32051.31720.1882-0.25120.4618-0.02910.714317.0329-36.389722.1552
255.50483.12710.91256.58691.33721.35040.05841.6551-0.0496-0.60780.1572-0.08680.41410.6136-0.18640.78210.3844-0.05671.4169-0.02470.558222.8059-22.0079-0.7305
264.35450.65880.37923.15081.11411.76370.0530.8387-0.30830.22540.102-0.52740.05820.074-0.10990.76570.3601-0.09131.2442-0.17020.662541.7779-23.022111.298
278.591-5.7997-0.04434.01380.72534.33561.64980.0899-3.3777-0.3121-0.11020.85052.7522-0.1858-1.06251.50340.2638-0.74661.1663-0.46172.024850.831-43.658519.6308
283.0259-1.7508-0.13984.857-1.55190.81650.40130.1991-0.29410.3062-0.0476-0.83520.3506-0.1308-0.320.87550.3518-0.34581.1529-0.20130.865149.5683-25.528421.2529
295.31641.2282-0.67747.6628-2.83937.1574-0.11220.92870.2085-0.8832-0.265-0.8528-0.48630.09740.33160.8253-0.01920.10510.4433-0.01320.485315.078439.065953.4551
306.89136.1915-6.15745.7814-5.34515.73541.2771.47510.1953-0.5289-0.0540.4984-2.6042-1.0628-1.38051.45290.03740.0950.82370.13150.926415.168253.237756.5184
313.39630.7766-0.84293.75310.55276.47020.1690.05270.139-0.21190.1073-0.0463-0.5244-0.7441-0.17090.64060.1160.01360.4251-0.01540.47164.704734.547264.6148
327.1309-2.2759-1.26573.4264-1.41085.91210.0362-1.245-0.330.7983-0.1563-0.4052-0.56720.15820.12650.7987-0.2788-0.17560.6240.10580.61413.973128.043389.3303
333.588-1.49410.22311.5281-0.10062.36640.2007-0.35820.41240.3284-0.4444-1.0903-0.47770.54050.15540.7195-0.2819-0.22580.69410.21650.980532.108235.150378.0632
343.5301-1.93761.13387.96123.78783.669-0.00141.36521.3488-3.6879-1.77360.6528-2.80321.04441.85791.28130.0776-0.04181.19110.29441.501232.619254.011267.2465
352.40052.97851.76973.83792.91624.9658-0.74220.36411.4321-0.77880.07491.4542-3.08820.49440.21411.9193-0.4915-0.25931.09140.69721.860539.332859.385772.8604
364.86353.11140.46192.5910.85680.61620.00831.08820.4056-0.0801-0.7165-1.4275-0.46161.03580.33670.7103-0.217-0.08831.09050.50441.037538.761437.406167.5884
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1805 through 1853 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1854 through 1877 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1878 through 1960 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1961 through 2079 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 49 )
7X-RAY DIFFRACTION7chain 'B' and (resid 50 through 115 )
8X-RAY DIFFRACTION8chain 'B' and (resid 116 through 132 )
9X-RAY DIFFRACTION9chain 'B' and (resid 133 through 148 )
10X-RAY DIFFRACTION10chain 'B' and (resid 149 through 164 )
11X-RAY DIFFRACTION11chain 'B' and (resid 165 through 178 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1805 through 1877 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1878 through 1960 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1961 through 1980 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1981 through 2079 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 25 )
17X-RAY DIFFRACTION17chain 'D' and (resid 26 through 67 )
18X-RAY DIFFRACTION18chain 'D' and (resid 68 through 104 )
19X-RAY DIFFRACTION19chain 'D' and (resid 105 through 138 )
20X-RAY DIFFRACTION20chain 'D' and (resid 139 through 149 )
21X-RAY DIFFRACTION21chain 'D' and (resid 150 through 178 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1805 through 1862 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1863 through 1908 )
24X-RAY DIFFRACTION24chain 'E' and (resid 1909 through 1960 )
25X-RAY DIFFRACTION25chain 'E' and (resid 1961 through 2079 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 115 )
27X-RAY DIFFRACTION27chain 'F' and (resid 116 through 132 )
28X-RAY DIFFRACTION28chain 'F' and (resid 133 through 178 )
29X-RAY DIFFRACTION29chain 'G' and (resid 1805 through 1854 )
30X-RAY DIFFRACTION30chain 'G' and (resid 1855 through 1877 )
31X-RAY DIFFRACTION31chain 'G' and (resid 1878 through 1960 )
32X-RAY DIFFRACTION32chain 'G' and (resid 1961 through 2079 )
33X-RAY DIFFRACTION33chain 'H' and (resid 1 through 115 )
34X-RAY DIFFRACTION34chain 'H' and (resid 116 through 125 )
35X-RAY DIFFRACTION35chain 'H' and (resid 126 through 138 )
36X-RAY DIFFRACTION36chain 'H' and (resid 139 through 178 )

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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