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- PDB-7jij: ATP-bound AMP-activated protein kinase -

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基本情報

登録情報
データベース: PDB / ID: 7jij
タイトルATP-bound AMP-activated protein kinase
要素
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
  • Maltose/maltodextrin ABC transporter substrate-binding protein MalE
キーワードSIGNALING PROTEIN / AMPK / activation / ATP-binding
機能・相同性
機能・相同性情報


negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation / bile acid signaling pathway / lipid droplet disassembly / Lipophagy / regulation of bile acid secretion / positive regulation of skeletal muscle tissue development / import into nucleus / CAMKK-AMPK signaling cascade / cAMP-dependent protein kinase regulator activity / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / nucleotide-activated protein kinase complex / : / positive regulation of T cell mediated immune response to tumor cell / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle / tau-protein kinase / negative regulation of hepatocyte apoptotic process / protein kinase regulator activity / cellular response to ethanol / negative regulation of TOR signaling / protein localization to lipid droplet / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / regulation of glycolytic process / bile acid and bile salt transport / positive regulation of protein targeting to mitochondrion / cAMP-dependent protein kinase activity / lipid biosynthetic process / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / tau-protein kinase activity / Macroautophagy / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / carbohydrate transmembrane transporter activity / positive regulation of protein kinase activity / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to nutrient levels / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / response to UV / positive regulation of protein localization / energy homeostasis / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / positive regulation of glycolytic process / cellular response to calcium ion / response to gamma radiation / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / ADP binding / regulation of circadian rhythm / tau protein binding / Wnt signaling pathway / autophagy / fatty acid biosynthetic process / cellular response to hydrogen peroxide / response to estrogen / neuron cellular homeostasis / glucose metabolic process / cellular response to prostaglandin E stimulus / positive regulation of T cell activation / rhythmic process / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / glucose homeostasis / cellular response to oxidative stress / cellular response to hypoxia / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / periplasmic space / non-specific serine/threonine protein kinase / response to hypoxia / protein kinase activity / nuclear speck / protein phosphorylation / apical plasma membrane / axon / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body
類似検索 - 分子機能
PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain ...PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / KA1 domain/Ssp2, C-terminal / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulin E-set / 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
alpha-maltose / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Maltodextrin-binding protein / 5'-AMP-activated protein kinase subunit beta-2 / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-1
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 5.5 Å
データ登録者Yan, Y. / Zhou, X.E. / Powell, K. / Xu, T. / Brunzelle, J.S. / Xu, H.X. / Melcher, K.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM129436 米国
引用ジャーナル: Science / 年: 2021
タイトル: Structure of an AMPK complex in an inactive, ATP-bound state.
著者: Yan Yan / Somnath Mukherjee / Kaleeckal G Harikumar / Timothy S Strutzenberg / X Edward Zhou / Kelly Suino-Powell / Ting-Hai Xu / Ryan D Sheldon / Jared Lamp / Joseph S Brunzelle / Katarzyna ...著者: Yan Yan / Somnath Mukherjee / Kaleeckal G Harikumar / Timothy S Strutzenberg / X Edward Zhou / Kelly Suino-Powell / Ting-Hai Xu / Ryan D Sheldon / Jared Lamp / Joseph S Brunzelle / Katarzyna Radziwon / Abigail Ellis / Scott J Novick / Irving E Vega / Russell G Jones / Laurence J Miller / H Eric Xu / Patrick R Griffin / Anthony A Kossiakoff / Karsten Melcher /
要旨: Adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in ...Adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in which the kinase activation loop (AL) is protected from protein phosphatases, thus keeping the AL in its active, phosphorylated state. At low AMP:ATP (adenosine triphosphate) ratios, ATP inhibits AMPK by increasing AL dynamics and accessibility. We developed conformation-specific antibodies to trap ATP-bound AMPK in a fully inactive, dynamic state and determined its structure at 3.5-angstrom resolution using cryo-electron microscopy. A 180° rotation and 100-angstrom displacement of the kinase domain fully exposes the AL. On the basis of the structure and supporting biophysical data, we propose a multistep mechanism explaining how adenine nucleotides and pharmacological agonists modulate AMPK activity by altering AL phosphorylation and accessibility.
履歴
登録2020年7月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年7月28日Provider: repository / タイプ: Initial release
改定 1.12021年9月8日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.32024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
M: Maltose/maltodextrin ABC transporter substrate-binding protein MalE
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase subunit beta-2
G: 5'-AMP-activated protein kinase subunit gamma-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)155,8148
ポリマ－154,1904
非ポリマー1,6244
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-68 kcal/mol
Surface area60990 Å2
単位格子
Length a, b, c (Å)126.688, 126.688, 332.384
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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要素

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タンパク質 , 2種, 2分子 MA

#1: タンパク質 Maltose/maltodextrin ABC transporter substrate-binding protein MalE


分子量: 40827.125 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: malE, GRW33_05015
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: A0A6D0N546
#2: タンパク質 5'-AMP-activated protein kinase catalytic subunit alpha-1 / AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA ...AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase / Tau-protein kinase PRKAA1


分子量: 56084.375 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PRKAA1, AMPK1
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q13131, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase

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5'-AMP-activated protein kinase subunit ... , 2種, 2分子 BG

#3: タンパク質 5'-AMP-activated protein kinase subunit beta-2 / AMPK subunit beta-2


分子量: 22384.650 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PRKAB2
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: O43741
#4: タンパク質 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


分子量: 34893.453 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PRKAG1
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P54619

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糖 , 1種, 1分子

#5: 多糖 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


タイプ: oligosaccharide, Oligosaccharide / クラス: 栄養素 / 分子量: 342.297 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: oligosaccharide / 参照: alpha-maltose
記述子タイププログラム
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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非ポリマー , 3種, 3分子

#6: 化合物 ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP


分子量: 507.181 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / コメント: ATP, エネルギー貯蔵分子*YM
#7: 化合物 ChemComp-AMP / ADENOSINE MONOPHOSPHATE / AMP


分子量: 347.221 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H14N5O7P / コメント: AMP*YM
#8: 化合物 ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: 5 Å3/Da / 溶媒含有率: 75.39 %
結晶化温度: 293 K / 手法: 蒸気拡散法
詳細: 0.2 M tri-lithium citrate,10% w/v PEG3350, pH7.5,0.01 M barium chloride

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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: 21-ID-D / 波長: 1.07823 Å
検出器タイプ: DECTRIS EIGER2 X 9M / 検出器: PIXEL / 日付: 2017年7月5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: 1.07823 Å / 相対比: 1
反射解像度: 5.5→49 Å / Num. obs: 10563 / % possible obs: 99.5 % / 冗長度: 9.7 % / CC1/2: 0.979 / Rmerge(I) obs: 0.298 / Net I/σ(I): 4.7
反射 シェル解像度: 5.5→6.15 Å / Rmerge(I) obs: 3.1 / Num. unique obs: 2894 / CC1/2: 0.323

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13_2998精密化
PDB_EXTRACT3.25データ抽出
MOSFLMデータ削減
Aimless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: 4RER

4rer


解像度: 5.5→24.901 Å / SU ML: 1.02 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 43.94 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3227 537 5.18 %
Rwork0.2492 9824 -
obs0.2531 10361 99.04 %
溶媒の処理減衰半径: 0.8 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: 971.36 Å2 / Biso mean: 429.4287 Å2 / Biso min: 166.08 Å2
精密化ステップサイクル: final / 解像度: 5.5→24.901 Å
タンパク質核酸リガンド溶媒全体
原子数9268 0 104 0 9372
Biso mean--370.02 --
残基数----1161
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
5.5002-6.04660.44691170.36122390250798
6.0466-6.90520.43541580.31862378253699
6.9052-8.6390.32891400.28924672607100
8.639-24.9010.27161220.20172589271199
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)
1-0.0023-0.003-0.0078-0.00390.01020.0004-0.021-0.01070.1233-0.0772-0.1801-0.12590.0243-0.156203.49270.26440.4433.3572-0.06513.5578-18.8099-13.1693-47.1454
20.0076-0.005-0.0141-0.00920.00810.00470.090.04630.0750.02790.13250.06260.07320.0014-03.31280.12010.24463.3693-0.19623.4958-35.4282-12.3954-52.1218
30.00450.0081-0.03150.01830.00610.00980.1825-0.13560.02810.10830.13640.00750.0814-0.021501.7924-0.20440.00511.6326-0.21792.1308-30.416-25.2554-62.6097
40.0083-0.0090.0021-0.0282-0.0030.00130.0094-0.07270.23650.0751-0.06410.1080.01710.1349-03.3967-0.1904-0.22363.0784-0.08163.0607-34.8182-44.4993-39.6997
5-0.0274-0.0519-0.0377-0.01090.09390.02240.627-0.2767-0.46890.1776-0.0456-0.46350.12720.2956-01.9982-0.3773-0.27742.5004-0.48232.3839-36.9162-34.2637-45.3852
6-0.0062-0.05270.04550.0443-0.001-0.00550.26570.0949-0.3849-0.00240.11390.3682-0.02540.0818-01.7567-0.1740.1872.64110.13762.0251-23.4971-27.4078-60.0842
7-0.0114-0.0161-0.0053-0.0052-0.0001-0.0016-0.05760.0437-0.0496-0.01880.1105-0.1658-0.01460.0141-02.75950.2440.1262.3569-0.41152.5083-51.2186-27.7729-41.9547
80.0202-0.0115-0.00330.01580.03310.01860.01050.2347-0.0516-0.0997-0.00140.1203-0.01580.007903.6726-0.91380.03442.4231-0.89853.5191-59.2283-13.0951-40.6526
9-0.00840.0134-0.0148-0.0077-0.00210.00020.4038-0.0349-0.0829-0.05820.3835-0.2622-0.04480.052103.5591-0.73651.08693.2705-0.49242.3179-55.6334-6.7283-28.4458
100.05860.02350.04390.0150.047-0.02520.1192-0.1045-0.4174-0.17970.161-0.50540.0566-0.182302.3818-0.26920.27331.8984-0.28143.3339-70.42292.5578-32.5562
110.0135-0.0021-0.0062-0.0149-0.0033-0.003-0.1128-0.0304-0.0988-0.0856-0.0935-0.0160.10540.010902.639-0.45630.03072.06170.25032.5456-54.368711.8303-29.4119
120.0166-0.00320.0103-0.02560.01490.0068-0.00530.0256-0.4361-0.1409-0.0885-0.05390.0553-0.0116-03.1905-0.8453-0.54722.2730.26922.4296-68.19820.3995-36.423
130.00260.004-0.00030.001-0.00180.0101-0.01650.0717-0.04120.0665-0.0646-0.04650.0095-0.0498-02.8976-0.1776-0.08492.48130.42422.4383-69.084322.783-24.982
14-0.05430.1435-0.0322-0.03880.00810.0665-0.1289-0.1861-0.52330.3625-0.04680.5638-0.13530.068203.0007-0.53530.52592.753-0.25572.6839-73.355716.9081-5.1361
150.0372-0.0326-0.03690.03030.00490.04340.31030.1049-0.0187-0.23810.4598-0.192-0.3054-0.167903.396-1.09740.40783.2137-0.64243.4533-35.819218.3719-11.2068
160.0035-0.0056-0.00110.00710.0026-0.0009-0.01390.0235-0.11710.0455-0.08580.0933-0.0750.015305.3886-0.0233-0.04295.3695-0.0715.4188-23.783213.7733-26.1176
170.00110.0088-0.00080.0046-0.0018-0.0022-0.03410.0088-0.01480.0234-0.0624-0.11070.00890.0182-01.6415-0.1327-0.39531.81760.22862.0668-30.746123.4982-33.3104
18-0.02480.0526-0.0431-0.02540.0327-0.01620.0248-0.22210.01960.1840.11530.2188-0.0325-0.1878-03.2732-0.6396-0.0512.7199-0.68653.5702-56.6924.1433-10.2012
190.0159-0.0083-0.03750.01440.03210.0945-0.01070.00180.0126-0.00990.00720.0258-0.0016-0.0055-0.00013.98670.01830.14653.886-0.02494.0226-60.992719.29162.9439
200.0277-0.0119-0.0360.00610.0170.05250.0219-0.0134-0.00570.0540.00010.0203-0.01190.0055-0.00033.01-0.0502-0.10433.0690.01753.215-58.52714.723-10.686
210.00490.0082-0.0089-0.00120.0129-0.0039-0.0538-0.01570.2520.05260.064-0.1533-0.0517-0.020702.3625-0.06660.3832.7144-0.69032.6284-45.708723.7852-6.3373
220.0115-0.02850.00810.0120.0023-0.0083-0.2440.15360.04460.0448-0.2418-0.00520.0311-0.0247-02.5602-0.20720.41362.319-0.2463.0014-49.379713.5233-3.4428
230.0055-0.00280.00360.00920.00030.00480.08-0.0385-0.15530.00610.04910.2039-0.0568-0.0335-02.8431-0.1949-0.44092.64240.06383.2266-45.378819.62640.9941
24-0.0547-0.0985-0.04950.06490.0699-0.02830.14560.1714-0.71420.23180.26070.6646-0.18260.1433-02.76660.3546-0.0882.1792-0.582.6125-51.477112.876210.4305
25-0.00790.00870.00670.00290.0257-0.0103-0.1913-0.0659-0.15870.002-0.0723-0.29530.05380.0543-03.241-0.11610.12223.6156-0.53793.0392-43.807431.552324.0933
260.00420.0167-0.02130.0125-0.03830.0258-0.28860.0845-0.01330.0297-0.1441-0.10890.2068-0.051204.0229-0.8566-0.37074.12970.2843.6858-42.179512.355119.3739
270.0130.01430.0006-0.00570.00080.0285-0.0192-0.0709-0.14510.00520.0285-0.32790.0572-0.2557-03.8759-0.75260.14133.59350.21373.5864-57.226.21613.0322
28-0.18230.2491-0.0525-0.03570.08440.09620.4664-0.36260.5557-0.0291-0.05460.3138-0.1566-0.049303.7779-1.0540.17552.8028-0.30162.7052-68.133620.013425.9456
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'M' and (resid 7 through 44 )M7 - 44
2X-RAY DIFFRACTION2chain 'M' and (resid 45 through 84 )M45 - 84
3X-RAY DIFFRACTION3chain 'M' and (resid 85 through 120 )M85 - 120
4X-RAY DIFFRACTION4chain 'M' and (resid 121 through 166 )M121 - 166
5X-RAY DIFFRACTION5chain 'M' and (resid 167 through 275 )M167 - 275
6X-RAY DIFFRACTION6chain 'M' and (resid 276 through 335 )M276 - 335
7X-RAY DIFFRACTION7chain 'M' and (resid 336 through 373 )M336 - 373
8X-RAY DIFFRACTION8chain 'A' and (resid 13 through 56 )A13 - 56
9X-RAY DIFFRACTION9chain 'A' and (resid 57 through 89 )A57 - 89
10X-RAY DIFFRACTION10chain 'A' and (resid 90 through 156 )A90 - 156
11X-RAY DIFFRACTION11chain 'A' and (resid 157 through 193 )A157 - 193
12X-RAY DIFFRACTION12chain 'A' and (resid 194 through 240 )A194 - 240
13X-RAY DIFFRACTION13chain 'A' and (resid 241 through 260 )A241 - 260
14X-RAY DIFFRACTION14chain 'A' and (resid 261 through 371 )A261 - 371
15X-RAY DIFFRACTION15chain 'A' and (resid 372 through 550 )A372 - 550
16X-RAY DIFFRACTION16chain 'B' and (resid 186 through 195 )B186 - 195
17X-RAY DIFFRACTION17chain 'B' and (resid 196 through 205 )B196 - 205
18X-RAY DIFFRACTION18chain 'B' and (resid 206 through 225 )B206 - 225
19X-RAY DIFFRACTION19chain 'B' and (resid 226 through 230 )B226 - 230
20X-RAY DIFFRACTION20chain 'B' and (resid 231 through 235 )B231 - 235
21X-RAY DIFFRACTION21chain 'B' and (resid 236 through 249 )B236 - 249
22X-RAY DIFFRACTION22chain 'B' and (resid 250 through 262 )B250 - 262
23X-RAY DIFFRACTION23chain 'B' and (resid 263 through 272 )B263 - 272
24X-RAY DIFFRACTION24chain 'G' and (resid 25 through 87 )G25 - 87
25X-RAY DIFFRACTION25chain 'G' and (resid 88 through 113 )G88 - 113
26X-RAY DIFFRACTION26chain 'G' and (resid 114 through 137 )G114 - 137
27X-RAY DIFFRACTION27chain 'G' and (resid 138 through 179 )G138 - 179
28X-RAY DIFFRACTION28chain 'G' and (resid 180 through 324 )G180 - 324

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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