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- PDB-8t75: Crystal Structure of KRAS4a (GMPPNP) in complex with RAF1 (RBD-CRD) -

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基本情報

登録情報
データベース: PDB / ID: 8t75
タイトルCrystal Structure of KRAS4a (GMPPNP) in complex with RAF1 (RBD-CRD)
要素
  • GTPase KRas
  • RAF proto-oncogene serine/threonine-protein kinase
キーワードONCOPROTEIN (がん遺伝子) / KRAS (KRAS) / RAS / RAF1 (RAF1) / CRAF
機能・相同性
機能・相同性情報


death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / forebrain astrocyte development ...death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / forebrain astrocyte development / Negative feedback regulation of MAPK pathway / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / ERBB2-ERBB3 signaling pathway / Rac protein signal transduction / regulation of cell differentiation / face development / skeletal muscle cell differentiation / 仮足 / positive regulation of Rac protein signal transduction / somatic stem cell population maintenance / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / neurotrophin TRK receptor signaling pathway / thyroid gland development / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of protein-containing complex assembly / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / type II interferon-mediated signaling pathway / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / homeostasis of number of cells within a tissue / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / activation of adenylate cyclase activity / EGFR Transactivation by Gastrin / response to muscle stretch / 髄鞘 / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / 低分子量GTPアーゼ / insulin-like growth factor receptor signaling pathway / G protein activity / thymus development / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII
類似検索 - 分子機能
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / 低分子量GTPアーゼ / 低分子量GTPアーゼ / Rab subfamily of small GTPases / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas / RAF proto-oncogene serine/threonine-protein kinase
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: 2.65 Å
データ登録者Whitley, M.J. / Simanshu, D.K.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E 米国
引用ジャーナル: Sci Adv / 年: 2024
タイトル: Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties.
著者: Whitley, M.J. / Tran, T.H. / Rigby, M. / Yi, M. / Dharmaiah, S. / Waybright, T.J. / Ramakrishnan, N. / Perkins, S. / Taylor, T. / Messing, S. / Esposito, D. / Nissley, D.V. / McCormick, F. / ...著者: Whitley, M.J. / Tran, T.H. / Rigby, M. / Yi, M. / Dharmaiah, S. / Waybright, T.J. / Ramakrishnan, N. / Perkins, S. / Taylor, T. / Messing, S. / Esposito, D. / Nissley, D.V. / McCormick, F. / Stephen, A.G. / Turbyville, T. / Cornilescu, G. / Simanshu, D.K.
履歴
登録2023年6月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年2月14日Provider: repository / タイプ: Initial release
改定 1.12024年2月28日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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: GTPase KRas
B: RAF proto-oncogene serine/threonine-protein kinase
C: GTPase KRas
D: RAF proto-oncogene serine/threonine-protein kinase
E: GTPase KRas
F: RAF proto-oncogene serine/threonine-protein kinase
G: GTPase KRas
H: RAF proto-oncogene serine/threonine-protein kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)147,96824
ポリマ－145,2588
非ポリマー2,70916
水1,38777
1
A: GTPase KRas
B: RAF proto-oncogene serine/threonine-protein kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,9926
ポリマ－36,3152
非ポリマー6774
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: GTPase KRas
D: RAF proto-oncogene serine/threonine-protein kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,9926
ポリマ－36,3152
非ポリマー6774
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: GTPase KRas
F: RAF proto-oncogene serine/threonine-protein kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,9926
ポリマ－36,3152
非ポリマー6774
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: GTPase KRas
H: RAF proto-oncogene serine/threonine-protein kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,9926
ポリマ－36,3152
非ポリマー6774
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)104.409, 199.509, 113.428
Angle α, β, γ (deg.)90.000, 112.280, 90.000
Int Tables number5
Space group name H-MC121

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要素

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タンパク質 , 2種, 8分子 ACEGBDFH

#1: タンパク質
GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


分子量: 20426.123 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KRAS, KRAS2, RASK2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01116, 低分子量GTPアーゼ
#2: タンパク質
RAF proto-oncogene serine/threonine-protein kinase / Proto-oncogene c-RAF / cRaf / Raf-1


分子量: 15888.440 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAF1, RAF / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P04049, non-specific serine/threonine protein kinase

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非ポリマー , 4種, 93分子

#3: 化合物
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Gpp(NH)p / 5'-Guanylyl imidodiphosphate


分子量: 522.196 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H17N6O13P3
コメント: GppNHp, GMPPNP, エネルギー貯蔵分子類似体*YM
#4: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mg
#5: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn
#6: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 77 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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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: 3.96 Å3/Da / 溶媒含有率: 68.93 %
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: 0.1 M sodium acetate (pH 4.6), 2 M sodium formate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2022年7月1日
放射モノクロメーター: Si(111) / 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: 0.9792 Å / 相対比: 1
反射解像度: 2.65→46.45 Å / Num. obs: 61031 / % possible obs: 98.3 % / 冗長度: 3.3 % / Biso Wilson estimate: 63.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.098 / Net I/σ(I): 10.73
反射 シェル
解像度 (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.65-2.810.83398140.6040.9881
2.81-3.010.50193070.8120.5931
3.01-3.250.25986500.9460.3081
3.25-3.550.14479820.9780.1721
3.55-3.970.09169930.9890.111
3.97-4.580.05564080.9960.0661
4.58-5.60.04954050.9960.0591
5.6-7.860.04540800.9970.0541
7.86-46.450.02923920.9990.0341

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
PHENIX1.20.1_4487精密化
PDB_EXTRACT3.28データ抽出
精密化構造決定の手法: 分子置換 / 解像度: 2.65→46.45 Å / SU ML: 0.37 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 25.82 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.219 2013 3.3 %
Rwork0.178 59001 -
obs0.179 61014 98.46 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 192.32 Å2 / Biso mean: 76.6592 Å2 / Biso min: 33.03 Å2
精密化ステップサイクル: final / 解像度: 2.65→46.45 Å
タンパク質核酸リガンド溶媒全体
原子数9643 0 140 77 9860
Biso mean--66.2 62.14 -
残基数----1196
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0029953
X-RAY DIFFRACTIONf_angle_d0.37813450
X-RAY DIFFRACTIONf_chiral_restr0.0391510
X-RAY DIFFRACTIONf_plane_restr0.0031756
X-RAY DIFFRACTIONf_dihedral_angle_d10.2593784
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.720.36951410.35334130427197
2.72-2.790.33061450.29034246439199
2.79-2.870.33741440.28124227437199
2.87-2.970.29491460.26434280442699
2.97-3.070.31371430.25724201434499
3.07-3.20.26171450.22734230437599
3.2-3.340.26011440.19714224436899
3.34-3.520.23481450.19314243438899
3.52-3.740.24661420.18284185432798
3.74-4.030.22231410.16374121426296
4.03-4.430.18131440.13874227437199
4.43-5.070.15991450.12784257440299
5.07-6.390.18951440.15364232437698
6.39-46.450.17481440.15194198434297
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)
15.4266-1.456-0.16473.70081.01032.6105-0.0771-0.1847-0.08150.091-0.0119-0.02330.0379-0.04290.08820.408-0.09560.09740.49210.12580.389535.247390.544324.0757
25.48845.2375.30345.41565.45715.8837-0.31680.193-0.63420.35320.30541.85110.7561-0.85320.22890.7522-0.2687-0.01031.0890.04211.192318.751887.331620.7708
35.2155-0.1441-0.41316.68711.55462.74470.0834-0.5445-0.61980.6031-0.06560.55580.1829-0.84230.05650.7256-0.12840.18250.83230.15860.547124.558784.917535.0152
42.197-1.2153-0.14163.01240.69463.55320.2055-0.7231-0.87581.0353-0.0297-0.29390.7378-0.16240.00120.6509-0.07750.04710.64140.18570.565834.240680.397434.5352
52.868-0.4253-0.31083.23330.47735.0118-0.0198-0.06380.14980.06280.0390.0958-0.2137-0.3761-0.01430.4283-0.04910.11450.5486-0.0250.467130.2195102.61588.5288
65.7581-3.49055.21734.0799-4.45816.09680.1973-0.2902-0.6833-0.17210.13210.09730.4993-0.3642-0.31820.5724-0.00070.05920.52480.04820.552654.760588.861217.7591
74.7552-0.17110.14851.40690.32996.3173-0.0162-0.2940.02340.3324-0.29070.0871-0.4062-0.15930.25240.3429-0.0150.00260.295-0.05140.4220.4842129.078336.7611
83.3777-2.06681.50121.9203-0.21112.8387-0.15610.26560.11390.20310.22190.2994-0.16450.1934-0.02760.7319-0.1130.04050.6953-0.08040.708916.6131126.698947.8726
98.6156-3.447-1.91238.64631.8036.9873-0.10130.325-0.3097-0.24950.0561-0.12180.42950.1807-0.00220.437-0.0411-0.00930.36-0.05730.360525.2711134.959934.022
105.0616-1.7713-1.57983.1436-1.26982.82040.38230.90480.1358-0.2246-0.54320.7407-0.6922-0.72910.10970.66640.0407-0.12870.84290.01180.85857.8246131.121630.5392
113.4274-0.49910.8835.3687-4.79825.41490.1981-0.1918-0.2440.25350.23761.22940.2028-1.0708-0.3630.5026-0.07760.12480.5746-0.14820.574413.0413115.550935.3025
127.8293-1.8313.34159.4061-5.13468.30810.01620.2074-0.538-0.16520.13040.77510.6996-0.5577-0.21180.3708-0.07350.08660.4272-0.1390.501613.8098118.296329.8787
134.0955-3.0436-1.29784.598-3.66559.8369-0.05960.8535-0.5198-0.4199-0.18450.98220.5727-0.42330.35060.803-0.09760.20730.6473-0.09230.589917.8086109.440925.9726
149.6876-0.04296.88351.84941.06075.5061-0.15470.5022-0.2932-0.0163-0.0376-0.04170.52671.41770.18930.4915-0.0620.08280.4348-0.05140.518625.3792117.2136.3375
153.80320.7522-1.56475.3416-4.33454.5379-0.10450.47450.1268-0.73750.0057-0.37750.86170.18070.07960.4788-0.01310.06920.49320.00530.470325.8825128.544122.0375
169.7194.1665-3.03148.62-0.67549.29950.45010.32940.03240.32550.0746-0.2407-0.3579-0.5288-0.56820.34570.00870.03990.3025-0.01010.321510.807140.389543.2329
173.76-2.09840.67632.7004-0.69434.8026-0.009-0.00670.27150.2389-0.1285-0.17880.18630.21030.14840.4714-0.07030.02250.37710.01960.547815.0208141.683552.6834
182.582-1.1670.47534.9499-4.57424.367-0.041-0.70540.10490.49050.48570.3492-1.0199-0.1085-0.41340.5891-0.0013-0.09830.4548-0.04350.54127.0478153.060348.6341
193.07951.114-1.16867.6180.72083.7378-0.32021.15461.2228-1.14230.33610.6765-0.3027-0.932-0.02280.5863-0.048-0.00330.54660.03830.63867.501146.427447.8908
207.7704-5.2105-4.76369.10745.80754.28920.185-0.06250.6008-0.5-0.1167-0.2859-0.62360.6314-0.04620.593-0.00420.01940.5620.03560.692928.2975150.479944.2945
217.7914-4.13560.95373.4830.25668.1102-0.01420.2110.1696-0.04150.20760.0015-0.01960.5049-0.21590.4649-0.00340.0580.39650.00980.492546.8428136.339838.1136
224.7116-4.2563-2.59524.51193.63523.95390.29930.26060.3859-0.87630.04960.0476-0.3665-0.1031-0.4920.65220.02420.03630.5198-0.02830.747540.5627138.363837.3554
231.66881.20551.62266.78585.38714.5266-0.22430.00430.21610.47520.516-0.1530.06060.0256-0.24270.44790.0030.11440.4286-0.04460.532733.3234142.98244.1202
245.95360.2332-1.33475.74971.29792.1098-0.21580.1662-0.0535-0.00670.36940.0066-0.2434-0.2371-0.1610.42070.07340.01290.4597-0.050.357259.1547115.702530.9049
252.79410.4286-0.35752.69112.1252.7177-0.80140.4182-1.5107-0.14690.433-0.06850.66170.28230.39040.74670.12590.15240.56770.07350.690560.3164104.013833.5543
263.623-4.6049-2.32218.82822.50633.2943-0.1431-0.24680.99820.24360.1858-0.4562-0.2478-0.0831-0.15770.430.01760.03440.5536-0.04680.467956.2236119.377524.2773
275.18551.619-3.84785.238-2.47478.9339-0.2855-0.3138-0.42910.5212-0.1308-0.87240.03551.16320.43030.51460.1043-0.08940.6038-0.09270.491667.4716117.587139.3845
287.85981.3493-0.04475.9626-1.84719.4193-0.019-0.19680.87050.74920.0334-1.0431-0.69441.39320.04880.50620.0395-0.05450.6558-0.1070.707968.785125.090939.9228
292.59940.88051.1619.11942.84123.24020.0284-0.6314-0.07931.1067-0.11490.53940.3682-0.10460.09780.59370.10310.13870.5606-0.02360.381755.3965117.994647.2845
304.05324.7613-3.92926.7284-5.25724.15320.3147-0.10240.44630.73960.00690.7114-0.47760.3024-0.36650.4396-0.00130.05810.47740.0420.456856.0783129.962431.3803
315.92140.7657-0.21485.9748-0.65416.50240.0355-0.0955-0.15-0.0499-0.08030.04260.203-0.04330.05050.39210.05320.03610.4128-0.01210.344768.2522102.360516.6727
328.262-3.86613.58434.9258-2.42552.5307-0.0262-0.03350.75630.29060.0224-0.342-0.13640.2178-0.01550.56230.00330.05220.595-0.05460.464364.7254106.113112.2813
332.9952-1.1431-0.26466.6544-0.14950.175-0.24-0.2910.07230.0225-0.02960.34460.3335-0.29130.22290.47360.02430.11060.5909-0.00560.430936.1293120.109718.0504
345.4529-0.2947-3.38924.0192.81748.01190.088-0.43270.1464-0.06980.1379-0.2541-0.11160.252-0.20370.4090.00070.06080.5197-0.0010.384545.0234114.446316.2237
356.71972.29750.11547.7239-0.03687.245-0.39780.29330.57050.14970.0495-0.8297-0.5540.8790.35760.5501-0.08850.03030.39310.14690.7028-7.290285.784139.6089
364.4213-5.86781.34217.8722-2.18062.6652-0.5595-0.30260.15311.25560.0115-0.3059-0.2771-0.65830.44820.8768-0.181-0.03580.8796-0.12861.1147-7.227489.105951.2373
379.8726-0.19387.44628.01961.33699.2214-0.13691.11260.1309-0.5803-0.0898-0.4077-0.65370.8210.19070.4503-0.02090.13540.57530.15080.5975-10.918379.625235.9018
385.0935-2.69920.26549.65921.60757.22410.54330.88140.88250.9707-0.5326-1.0408-0.24870.4462-0.33350.6602-0.25160.14330.78730.08521.06665.263783.609737.5219
392.85840.10822.80756.88231.08662.8864-0.26870.35661.0690.1154-0.0815-1.3898-1.36811.16230.26381.1169-0.2776-0.02390.73740.39241.34580.697397.283935.9416
403.22582.5392-2.06062.6172-3.3586.1717-0.0459-0.0891.50830.4715-0.20750.0814-1.72040.1730.05911.2537-0.0965-0.16840.68270.30831.3454-7.4466100.613633.1308
418.155-2.6788-5.93027.44315.85796.60770.00631.29240.7028-0.3314-0.65650.616-1.403-1.09040.42290.669-0.0054-0.08860.64780.24880.6404-9.113886.529926.8936
425.34631.21335.06192.15580.60615.35320.25111.2199-0.0141-0.72430.26120.5230.08950.8404-0.35180.6029-0.08270.04650.60360.03660.8377-1.032374.416948.3127
435.76553.3897-5.26546.8835-1.64165.22920.4037-0.8011.33190.6367-0.17210.5831-2.37660.8638-0.34041.1641-0.1377-0.03310.8433-0.24970.92110.840880.304463.4831
444.4478-6.40182.92549.2195-4.34965.9266-0.2403-0.66260.5560.25860.1464-0.4445-1.18-0.7935-0.05830.4983-0.0660.10350.5487-0.09570.8626-7.692576.744857.4126
459.3341-6.29340.58757.7968-3.44186.6223-0.38710.1479-0.6880.60560.37550.8577-0.1001-0.60870.02840.537-0.04140.03260.4428-0.05670.6326-8.924669.505753.5509
461.3148-1.8785-1.85623.73591.20564.5923-0.17781.1453-0.7749-0.29060.8053-1.9501-0.71231.7824-0.58770.63490.00020.24410.8456-0.14011.16127.181857.346551.0508
474.76-5.3044-4.66536.15255.05154.6758-0.7568-1.86250.39012.27810.47320.56910.51380.30870.22910.7787-0.1097-0.01830.7745-0.04370.7342-2.90467.043662.1177
485.66183.17994.41194.1493.9096.3718-0.37290.8388-1.4925-0.76710.8377-0.08230.41491.0533-0.68490.5063-0.06030.06150.5409-0.03580.73431.796269.510355.1295
497.7504-5.33327.01674.4775-5.09456.32620.46210.5981-0.188-0.7409-0.3346-0.06950.81970.2850.20490.54070.00910.03470.4896-0.0070.6175-20.013467.888639.4785
509.5679-0.02614.29212.33681.54693.27530.0949-0.47910.62810.2944-0.277-0.392-0.9818-0.62510.05760.72510.05370.11020.47160.11270.7613-34.706580.256934.357
516.9578-6.30345.90726.9672-6.08755.56760.02320.05740.1206-0.24850.11370.19090.5518-0.3396-0.06450.5141-0.058-0.01870.55460.08040.5634-26.935474.344734.7643
524.808-1.6872-0.98027.9942-4.88294.2545-0.04580.27610.4867-0.7179-0.2365-0.46730.24580.12660.21280.61970.0104-0.00130.50420.02780.7324-22.168274.882941.1848
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 57 )A1 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 74 )A58 - 74
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 126 )A75 - 126
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 170 )A127 - 170
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 130 )B57 - 130
6X-RAY DIFFRACTION6chain 'B' and (resid 131 through 188 )B131 - 188
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 25 )C1 - 25
8X-RAY DIFFRACTION8chain 'C' and (resid 26 through 37 )C26 - 37
9X-RAY DIFFRACTION9chain 'C' and (resid 38 through 57 )C38 - 57
10X-RAY DIFFRACTION10chain 'C' and (resid 58 through 76 )C58 - 76
11X-RAY DIFFRACTION11chain 'C' and (resid 77 through 92 )C77 - 92
12X-RAY DIFFRACTION12chain 'C' and (resid 93 through 126 )C93 - 126
13X-RAY DIFFRACTION13chain 'C' and (resid 127 through 137 )C127 - 137
14X-RAY DIFFRACTION14chain 'C' and (resid 138 through 151 )C138 - 151
15X-RAY DIFFRACTION15chain 'C' and (resid 152 through 174 )C152 - 174
16X-RAY DIFFRACTION16chain 'D' and (resid 56 through 71 )D56 - 71
17X-RAY DIFFRACTION17chain 'D' and (resid 72 through 100 )D72 - 100
18X-RAY DIFFRACTION18chain 'D' and (resid 101 through 117 )D101 - 117
19X-RAY DIFFRACTION19chain 'D' and (resid 118 through 130 )D118 - 130
20X-RAY DIFFRACTION20chain 'D' and (resid 131 through 140 )D131 - 140
21X-RAY DIFFRACTION21chain 'D' and (resid 141 through 160 )D141 - 160
22X-RAY DIFFRACTION22chain 'D' and (resid 161 through 176 )D161 - 176
23X-RAY DIFFRACTION23chain 'D' and (resid 177 through 188 )D177 - 188
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 25 )E1 - 25
25X-RAY DIFFRACTION25chain 'E' and (resid 26 through 37 )E26 - 37
26X-RAY DIFFRACTION26chain 'E' and (resid 38 through 57 )E38 - 57
27X-RAY DIFFRACTION27chain 'E' and (resid 58 through 92 )E58 - 92
28X-RAY DIFFRACTION28chain 'E' and (resid 93 through 116 )E93 - 116
29X-RAY DIFFRACTION29chain 'E' and (resid 117 through 151 )E117 - 151
30X-RAY DIFFRACTION30chain 'E' and (resid 152 through 172 )E152 - 172
31X-RAY DIFFRACTION31chain 'F' and (resid 57 through 117 )F57 - 117
32X-RAY DIFFRACTION32chain 'F' and (resid 118 through 140 )F118 - 140
33X-RAY DIFFRACTION33chain 'F' and (resid 141 through 165 )F141 - 165
34X-RAY DIFFRACTION34chain 'F' and (resid 166 through 188 )F166 - 188
35X-RAY DIFFRACTION35chain 'G' and (resid 1 through 25 )G1 - 25
36X-RAY DIFFRACTION36chain 'G' and (resid 26 through 37 )G26 - 37
37X-RAY DIFFRACTION37chain 'G' and (resid 38 through 57 )G38 - 57
38X-RAY DIFFRACTION38chain 'G' and (resid 58 through 76 )G58 - 76
39X-RAY DIFFRACTION39chain 'G' and (resid 77 through 126 )G77 - 126
40X-RAY DIFFRACTION40chain 'G' and (resid 127 through 151 )G127 - 151
41X-RAY DIFFRACTION41chain 'G' and (resid 152 through 169 )G152 - 169
42X-RAY DIFFRACTION42chain 'H' and (resid 57 through 70 )H57 - 70
43X-RAY DIFFRACTION43chain 'H' and (resid 71 through 77 )H71 - 77
44X-RAY DIFFRACTION44chain 'H' and (resid 78 through 87 )H78 - 87
45X-RAY DIFFRACTION45chain 'H' and (resid 88 through 101 )H88 - 101
46X-RAY DIFFRACTION46chain 'H' and (resid 102 through 109 )H102 - 109
47X-RAY DIFFRACTION47chain 'H' and (resid 110 through 117 )H110 - 117
48X-RAY DIFFRACTION48chain 'H' and (resid 118 through 130 )H118 - 130
49X-RAY DIFFRACTION49chain 'H' and (resid 131 through 145 )H131 - 145
50X-RAY DIFFRACTION50chain 'H' and (resid 146 through 160 )H146 - 160
51X-RAY DIFFRACTION51chain 'H' and (resid 161 through 173 )H161 - 173
52X-RAY DIFFRACTION52chain 'H' and (resid 174 through 188 )H174 - 188

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万見について

-
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