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- PDB-6bqt: Complex of 14-3-3 theta with an IRSp53 peptide doubly-phosphoryla... -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 6bqt
タイトルComplex of 14-3-3 theta with an IRSp53 peptide doubly-phosphorylated at T340 and T360
要素
  • 14-3-3 protein theta
  • Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
キーワードSIGNALING PROTEIN / phosphate binding protein / protein complex / cytoskeleton regulation / cell motility
機能・相同性
機能・相同性情報


neuron projection branch point / dendritic spine cytoplasm / negative regulation of monoatomic ion transmembrane transport / actin crosslink formation / plasma membrane organization / cadherin binding involved in cell-cell adhesion / cytoskeletal anchor activity / positive regulation of dendritic spine morphogenesis / regulation of modification of postsynaptic actin cytoskeleton / protein localization to synapse ...neuron projection branch point / dendritic spine cytoplasm / negative regulation of monoatomic ion transmembrane transport / actin crosslink formation / plasma membrane organization / cadherin binding involved in cell-cell adhesion / cytoskeletal anchor activity / positive regulation of dendritic spine morphogenesis / regulation of modification of postsynaptic actin cytoskeleton / protein localization to synapse / cellular response to L-glutamate / neuron projection terminus / proline-rich region binding / small GTPase-mediated signal transduction / positive regulation of actin filament polymerization / dendrite development / actin filament bundle assembly / CDC42 GTPase cycle / Regulation of localization of FOXO transcription factors / excitatory synapse / postsynaptic cytosol / positive regulation of excitatory postsynaptic potential / Activation of BAD and translocation to mitochondria / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / postsynaptic density, intracellular component / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / ruffle / 14-3-3 protein binding / RAC1 GTPase cycle / substantia nigra development / cellular response to epidermal growth factor stimulus / axonogenesis / secretory granule / transcription coregulator binding / dendritic shaft / Translocation of SLC2A4 (GLUT4) to the plasma membrane / PDZ domain binding / adherens junction / filopodium / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / synaptic membrane / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / intracellular protein localization / insulin receptor signaling pathway / lamellipodium / regulation of cell shape / scaffold protein binding / microtubule / transmembrane transporter binding / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / neuronal cell body / synapse / glutamatergic synapse / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
14-3-3 theta / I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / AH/BAR domain superfamily / Variant SH3 domain / 14-3-3 domain ...14-3-3 theta / I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / AH/BAR domain superfamily / Variant SH3 domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 14-3-3 protein theta / BAR/IMD domain-containing adapter protein 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 分子置換 / 解像度: 2.8 Å
データ登録者Kast, D.J. / Dominguez, R.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01 MH087950 米国
引用ジャーナル: Nat Commun / 年: 2019
タイトル: Mechanism of IRSp53 inhibition by 14-3-3.
著者: Kast, D.J. / Dominguez, R.
履歴
登録2017年11月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年12月5日Provider: repository / タイプ: Initial release
改定 1.12019年6月19日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22019年11月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32023年10月4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
改定 1.42024年10月30日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: 14-3-3 protein theta
B: 14-3-3 protein theta
C: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
D: 14-3-3 protein theta
E: 14-3-3 protein theta
F: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
G: 14-3-3 protein theta
H: 14-3-3 protein theta
I: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
J: 14-3-3 protein theta
K: 14-3-3 protein theta
L: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)240,31129
ポリマ－237,14112
非ポリマー3,17017
水1,67593
1
A: 14-3-3 protein theta
B: 14-3-3 protein theta
C: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
ヘテロ分子


  • 登録者・ソフトウェアが定義した集合体
  • 根拠: light scattering, The assembly has a determined mass of 60 kDa, consistent with the theoretical mass of a single 14-3-3 dimer bound to one doubly-phosphorylated IRSp53 peptides., isothermal ...根拠: light scattering, The assembly has a determined mass of 60 kDa, consistent with the theoretical mass of a single 14-3-3 dimer bound to one doubly-phosphorylated IRSp53 peptides., isothermal titration calorimetry, Stoichiometry determined from ITC is consistent with one 14-3-3 dimer binding to one doubly-phosphorylated IRSp53 peptide.
  • 60.7 kDa, 3 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)60,70310
ポリマ－59,2853
非ポリマー1,4187
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-28 kcal/mol
Surface area22700 Å2
手法PISA
2
D: 14-3-3 protein theta
E: 14-3-3 protein theta
F: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,9928
ポリマ－59,2853
非ポリマー7075
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-13 kcal/mol
Surface area23880 Å2
手法PISA
3
G: 14-3-3 protein theta
H: 14-3-3 protein theta
I: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,8546
ポリマ－59,2853
非ポリマー5693
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-28 kcal/mol
Surface area23090 Å2
手法PISA
4
J: 14-3-3 protein theta
K: 14-3-3 protein theta
L: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,7625
ポリマ－59,2853
非ポリマー4772
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-30 kcal/mol
Surface area23040 Å2
手法PISA
単位格子
Length a, b, c (Å)61.103, 69.572, 150.473
Angle α, β, γ (deg.)99.160, 92.980, 115.980
Int Tables number1
Space group name H-MP1

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要素

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タンパク質 / タンパク質・ペプチド , 2種, 12分子 ABDEGHJKCFIL

#1: タンパク質
14-3-3 protein theta / 14-3-3 protein T-cell / 14-3-3 protein tau / Protein HS1


分子量: 27795.234 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: YWHAQ / プラスミド: pTYB11 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P27348
#2: タンパク質・ペプチド
Insulin receptor substrate protein of 53 kDa, peptide (IRSp53) / Protein BAP2 / Fas ligand-associated factor 3 / FLAF3 / Insulin receptor substrate p53/p58 / ...Protein BAP2 / Fas ligand-associated factor 3 / FLAF3 / Insulin receptor substrate p53/p58 / IRSp53/58 / Insulin receptor substrate protein of 53 kDa / Insulin receptor substrate p53


分子量: 3694.822 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q9UQB8

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非ポリマー , 8種, 110分子

#3: 化合物 ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / ヘプタエチレングリコ-ルモノエチルエ-テル


分子量: 354.436 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C16H34O8 / コメント: 沈殿剤*YM
#4: 化合物
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / ペンタエチレングリコ-ル


分子量: 238.278 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C10H22O6 / コメント: 沈殿剤*YM
#5: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H6O2
#6: 化合物 ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル


分子量: 194.226 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C8H18O5 / コメント: 沈殿剤*YM
#7: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#8: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H14O4
#9: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H10O3
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 93 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.37 Å3/Da / 溶媒含有率: 48.13 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 / 詳細: 0.1 M CaCl2, 13% Peg 3350

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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: SEALED TUBE / タイプ: BRUKER IMUS MICROFOCUS / 波長: 1.54 Å
検出器タイプ: APEX II CCD / 検出器: CCD / 日付: 2015年7月29日 / 詳細: Quazar MX optics
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: 1.54 Å / 相対比: 1
反射解像度: 2.8→49 Å / Num. obs: 51911 / % possible obs: 96.7 % / 冗長度: 4.8 % / Biso Wilson estimate: 30.91 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.142 / Net I/σ(I): 20.5
反射 シェル解像度: 2.8→2.9 Å / 冗長度: 2.1 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5197 / CC1/2: 0.717 / % possible all: 95.7

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.12_2829精密化
PROTEUM2データ収集
PROTEUM2data processing
SAINTデータスケーリング
PHASER位相決定
PDB_EXTRACT3.22データ抽出
PROTEUM2データ削減
精密化構造決定の手法: 分子置換
開始モデル: 2BR9

2br9


解像度: 2.8→42.983 Å / SU ML: 0.41 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 29.42
Rfactor反射数%反射
Rfree0.2867 1997 3.88 %
Rwork0.234 --
obs0.236 51490 95.98 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 130.01 Å2 / Biso mean: 41.892 Å2 / Biso min: 1.15 Å2
精密化ステップサイクル: final / 解像度: 2.8→42.983 Å
タンパク質核酸リガンド溶媒全体
原子数15278 0 492 93 15863
Biso mean--51.91 18.45 -
残基数----1899
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00315766
X-RAY DIFFRACTIONf_angle_d0.54821193
X-RAY DIFFRACTIONf_chiral_restr0.0322393
X-RAY DIFFRACTIONf_plane_restr0.0032690
X-RAY DIFFRACTIONf_dihedral_angle_d17.1859806
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 (%)
2.8-2.870.31331400.25883516365696
2.87-2.94760.35871390.26063561370096
2.9476-3.03430.34461500.27913568371896
3.0343-3.13230.31931440.26813545368997
3.1323-3.24420.31981470.25873566371397
3.2442-3.3740.34851490.26623562371196
3.374-3.52750.30111310.27673406353793
3.5275-3.71340.30151370.27693352348991
3.7134-3.94590.30991440.25063442358694
3.9459-4.25030.27461360.21443573370997
4.2503-4.67760.24891440.2083536368095
4.6776-5.35330.24721450.18833631377699
5.3533-6.74040.2551490.2153634378399
6.7404-42.98770.21081420.16963601374398
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)
10.89210.50680.09670.76340.1640.9772-0.0876-0.0178-0.11770.15230.1003-0.0452-0.0721-0.00670.01330.1621-0.0403-0.08310.14380.02820.2275-9.714-6.78056.2378
20.86550.07360.03980.17630.05220.3886-0.0173-0.1468-0.1330.02530.03390.01240.0898-0.14470.10340.159-0.08260.06970.19930.03650.0597-16.2713-20.69231.7931
31.3537-0.1117-0.21981.78980.16981.4999-0.04560.34480.1534-0.38140.0529-0.2864-0.29610.00020.04730.161-0.0263-0.00720.15630.04240.1714-12.6235-20.0143-14.1108
42.8597-0.3495-0.11311.7159-0.49781.93790.075-0.1526-0.17760.22-0.0232-0.19420.10150.2362-0.08740.2373-0.0011-0.17730.26150.07710.529414.9953-4.99913.66
50.33860.0864-0.00140.8417-0.09120.50670.0104-0.01880.06690.0884-0.0378-0.0529-0.12740.06120.03730.1924-0.0291-0.07240.07530.07460.217912.50392.52513.4468
64.5662-0.90571.69071.5046-0.49282.19840.05290.23930.1269-0.1234-0.02-0.13190.0533-0.0217-0.02590.1807-0.01450.02830.1148-0.0220.24834.62510.24222.6127
71.92650.19260.72721.44120.22851.726-0.0547-0.01330.1647-0.1051-0.03740.3733-0.1034-0.251-0.02030.18-0.05640.0760.11450.02990.2789-4.489716.56517.4715
80.68470.7423-0.07080.99920.39871.1830.0877-0.0830.05980.03510.038-0.0185-0.00870.2368-0.00850.1381-0.0798-0.09580.18960.05410.243415.332417.28768.2661
93.8956-1.70460.21962.44750.03961.73430.0832-0.07790.37060.1196-0.00310.0135-0.11950.1198-0.05170.1194-0.0242-0.0220.0607-0.03320.163116.346526.0024.5549
100.70510.4425-0.01781.4964-0.15361.7083-0.14940.20660.0449-0.12910.16950.08080.19410.1803-0.01680.1346-0.0122-0.00810.13760.00660.184721.604419.6317-7.5672
116.846-3.01211.27563.6204-0.20861.89190.03570.0492-0.1284-0.1203-0.06210.01520.19210.08350.01280.19620.0244-0.02430.1934-0.04480.240519.783411.3979-11.6151
127.40430.90371.81523.4345-0.71446.6852-0.03720.03370.0727-0.05550.13060.415-0.0572-0.3772-0.12730.115-0.0947-0.01660.23530.06160.33089.907513.3333-5.5928
130.51560.86970.50672.36940.84850.5043-0.0445-0.0571-0.10080.3877-0.1573-0.16340.0424-0.02590.07050.5593-0.1094-0.07560.35730.08410.6134.2544-4.8197-3.7255
141.65370.1885-0.66912.2037-0.46490.33990.0204-0.03340.1394-0.12890.0233-0.0625-0.27180.1423-0.10180.4601-0.01760.00910.3891-0.17330.1672-7.2669-10.5517-6.6523
151.4592-0.1551-0.04431.07490.12711.2597-0.00510.1633-0.00630.05280.06070.1330.0960.0435-0.00130.11160.0467-0.02780.17620.03270.176425.80588.333528.8849
161.3944-0.3499-0.01930.995-0.12160.8729-0.01550.0923-0.1795-0.0385-0.0067-0.040.07180.1771-0.07440.0870.0945-0.01690.1747-0.05430.133537.8029-3.734330.3574
172.17440.42290.21371.5908-0.0571.5496-0.141-0.11020.0180.180.0923-0.0187-0.0110.2054-0.00330.13560.07240.02010.1687-0.01380.091341.8746-3.196344.0747
183.37161.5824-0.71833.1178-0.80421.71230.0705-0.15290.22230.09980.0119-0.2773-0.22040.2918-0.00930.23870.02940.05150.28720.03890.192645.03846.470548.1469
196.55720.89391.16811.62570.17811.8134-0.078-0.0701-0.29230.1492-0.01240.53540.0831-0.4480.05730.2898-0.04040.20050.2816-0.05750.4623.07710.18135.9322
202.43960.36480.33021.4385-0.271.37290.00750.04630.10310.04080.02120.1104-0.0002-0.12670.01640.1599-0.05910.01170.18940.020.43613.758517.602132.1685
212.33480.3804-0.46541.3664-0.16261.4396-0.10260.00570.2447-0.007-0.005-0.095-0.05840.1412-0.260.110.06970.08030.225-0.00470.240820.620428.388432.1067
223.6456-0.1949-1.46290.7944-0.04171.30290.15120.1249-0.0124-0.1225-0.00320.1257-0.036-0.072-0.08310.2612-0.0039-0.09460.154-0.02190.220117.17829.9223.8014
232.65650.0298-0.41761.80760.52471.9389-0.00770.11670.0245-0.0366-0.00010.09760.0876-0.26060.0340.1182-0.00110.08520.23830.08070.20953.829233.071534.4022
245.21340.8792-2.2022.6776-0.65663.14890.10130.26020.2024-0.15530.1040.1256-0.1713-0.1539-0.1270.22320.1144-0.01890.25070.06260.24134.584942.293235.4904
251.2878-0.783-0.58871.4738-0.04052.92050.11220.00470.00310.09420.0232-0.011-0.0652-0.0268-0.12590.1556-0.01060.00620.1571-0.0110.16248.942739.37144.6771
261.56480.5203-1.37091.8505-0.72323.0980.0561-0.08220.08570.07430.0721-0.0684-0.09220.0815-0.14130.30930.08430.05370.2633-0.07950.169710.453343.930952.3979
278.88412.82711.9741.01060.23334.08110.04040.29110.0229-0.3750.0935-0.2086-0.1725-0.0252-0.0970.975-0.01120.37790.99210.00270.9873-0.055932.282961.1068
285.49652.1604-1.46863.5615-0.96953.45310.0839-0.1411-0.40750.16120.0376-0.01290.2126-0.0903-0.07810.43740.089-0.04490.2783-0.00130.263913.443133.621153.5979
294.8499-1.6639-0.01896.0551-0.93572.5038-0.0654-0.13040.03020.10720.09980.482-0.1182-0.1885-0.09470.2640.1961-0.10750.3169-0.09950.264932.14584.477343.1288
302.2807-2.0084-0.72351.79990.64330.23050.19640.08770.0559-0.25880.00550.0412-0.0705-0.1122-0.05150.5564-0.0172-0.09560.54450.05790.503126.759822.270840.2397
310.0429-0.0234-0.19212.127-0.1680.896-0.0242-0.0875-0.32140.1480.011-0.23980.31890.2128-0.03220.4110.2417-0.04650.35180.05470.607815.338528.139543.2473
321.8799-1.33420.59312.1192-0.39470.2097-0.01390.0047-0.0271-0.15070.102-0.54410.11190.4688-0.07920.3061-0.1037-0.03730.4708-0.01880.629448.206611.7385-35.2423
330.70220.1115-0.39311.10560.7970.9195-0.06380.0504-0.0237-0.0506-0.0235-0.1030.04990.0815-0.08410.3358-0.12910.11540.28510.12710.35341.008411.858-40.4638
343.4233-3.5554-3.71643.78943.92294.0758-0.20880.2131-0.4113-0.2887-0.0182-0.00220.46990.04770.21820.280.06540.07440.4591-0.04380.370644.8732-1.5006-37.0566
351.8987-0.87350.10631.7896-0.27841.2527-0.1635-0.12170.1089-0.26710.150.1896-0.2389-0.13170.00330.2104-0.0681-0.11770.26420.07210.239126.478912.8079-40.2705
363.30871.742.41850.91641.27821.794-0.13230.2250.2704-0.29260.13720.1771-0.15790.07740.06050.6896-0.022-0.23590.51070.04020.61298.235325.5633-57.4744
371.1995-0.19480.02621.6848-0.41390.9053-0.13120.3528-0.0323-0.30810.01020.09240.12130.08160.01220.41010.00630.0180.2735-0.02020.117727.82234.2932-44.3789
381.6466-0.43230.94771.3112-0.08252.25510.06360.1015-0.0219-0.27810.00520.07840.1158-0.04960.01860.3995-0.0145-0.04590.2285-0.06910.107621.5609-6.312-38.1787
391.68480.7364-0.3661.35020.51051.3717-0.02370.0284-0.0306-0.1895-0.13840.1055-0.05720.03090.03850.2146-0.0595-0.05570.13640.03120.141920.2088-0.6631-29.4526
402.39250.09622.73650.12240.14073.65420.1687-0.078-0.1011-0.0360.04030.0150.2211-0.0663-0.24520.4276-0.172-0.07320.24840.04870.316215.5111-1.8832-21.8206
412.72870.97780.2851.7149-0.07462.24750.0581-0.12770.04380.03520.2593-0.04790.12650.1056-0.16160.3116-0.01440.0120.2342-0.08550.24423.37834.9936-18.7517
421.24690.1412-0.0281.2076-0.13581.04650.12080.0763-0.2677-0.55160.1507-0.0015-0.24180.082-0.12970.5096-0.05840.00430.1896-0.0140.274636.547831.9963-45.8935
431.5203-0.1903-0.63291.30940.35711.86750.07060.18650.08310.0157-0.2032-0.2472-0.0874-0.2505-0.01180.4115-0.15380.06840.18930.00450.305335.265348.879-35.1744
440.48480.48420.09932.6643-0.25650.07920.1655-0.23970.17810.01930.13930.1622-0.21150.05230.09060.5098-0.14870.12440.3309-0.00430.199128.048924.1563-32.4322
451.44310.04220.26191.95550.38320.7410.0114-0.0726-0.12980.16490.0774-0.3369-0.03150.17430.0180.3307-0.04620.0190.32320.10490.3565.666136.8626-71.3063
460.8780.184-0.64760.7132-0.27331.5380.0928-0.2018-0.05870.2878-0.22660.17170.0289-0.0266-0.04840.58690.05840.21450.366-0.02410.2443-8.353134.4854-58.2695
471.78060.13340.79652.15290.34881.4669-0.12530.10930.14790.0352-0.1275-0.1587-0.20550.18420.07330.2653-0.0508-0.00960.14660.04220.1961-0.802149.3828-71.7042
481.4460.5795-1.15951.1361-0.80681.992-0.0041-0.0592-0.04650.24240.01180.1494-0.0673-0.0001-0.1790.4470.04080.20440.2847-0.04720.1025-9.116954.3776-71.7724
490.3658-0.14320.11990.81130.43091.1332-0.02230.0011-0.02960.0128-0.09470.07010.05-0.0945-0.21780.35730.06730.14830.2112-0.05660.1107-9.909148.6514-80.8867
501.0655-0.9174-0.22091.95580.45812.2441-0.07810.3486-0.0514-0.32510.0693-0.11770.00420.04150.01370.20440.02330.06650.30620.0150.1279-11.040850.2207-91.1498
514.41530.2645-2.31041.8451-0.09283.14840.01460.3114-0.1164-0.2143-0.066-0.08910.06730.04210.01840.46540.0866-0.0250.2998-0.1090.1956-8.715641.2106-89.7025
521.1868-0.0362-0.32881.4815-0.12191.97280.0329-0.1395-0.16810.27330.08560.08860.2346-0.082-0.06990.56460.01050.09330.27330.09490.3759-0.014515.7397-63.1001
533.09622.7957-0.17792.5253-0.1540.0483-0.00650.3081-0.6418-0.431-0.0051.10790.1032-0.89410.00881.5674-0.0277-0.03631.5938-0.05741.681127.506227.1544-84.654
541.15570.19060.24180.97140.37771.019-0.1602-0.09910.13860.17810.083-0.46440.06430.28180.14170.50010.1339-0.13380.3817-0.00610.496513.886915.233-64.3407
551.2943-0.05620.03561.65750.07941.7676-0.0766-0.1129-0.07150.12910.0185-0.00390.1001-0.21230.01010.33990.1016-0.00240.2438-0.02420.24573.6523-0.9581-75.0467
560.3327-1.16740.12714.091-0.44740.0512-0.02180.04870.02110.14210.12730.03350.31020.111-0.01770.30870.0965-0.02410.40780.0060.4594-2.553123.8725-77.8761
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 111 )A1 - 111
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 159 )A112 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 230 )A160 - 230
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 15 )B1 - 15
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 37 )B16 - 37
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 67 )B38 - 67
7X-RAY DIFFRACTION7chain 'B' and (resid 68 through 103 )B68 - 103
8X-RAY DIFFRACTION8chain 'B' and (resid 104 through 135 )B104 - 135
9X-RAY DIFFRACTION9chain 'B' and (resid 136 through 159 )B136 - 159
10X-RAY DIFFRACTION10chain 'B' and (resid 160 through 207 )B160 - 207
11X-RAY DIFFRACTION11chain 'B' and (resid 208 through 230 )B208 - 230
12X-RAY DIFFRACTION12chain 'C' and (resid 337 through 342 )C337 - 342
13X-RAY DIFFRACTION13chain 'C' and (resid 343 through 358 )C343 - 358
14X-RAY DIFFRACTION14chain 'C' and (resid 359 through 365 )C359 - 365
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 103 )D1 - 103
16X-RAY DIFFRACTION16chain 'D' and (resid 104 through 159 )D104 - 159
17X-RAY DIFFRACTION17chain 'D' and (resid 160 through 201 )D160 - 201
18X-RAY DIFFRACTION18chain 'D' and (resid 202 through 230 )D202 - 230
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 16 )E1 - 16
20X-RAY DIFFRACTION20chain 'E' and (resid 17 through 37 )E17 - 37
21X-RAY DIFFRACTION21chain 'E' and (resid 38 through 75 )E38 - 75
22X-RAY DIFFRACTION22chain 'E' and (resid 76 through 103 )E76 - 103
23X-RAY DIFFRACTION23chain 'E' and (resid 104 through 135 )E104 - 135
24X-RAY DIFFRACTION24chain 'E' and (resid 136 through 159 )E136 - 159
25X-RAY DIFFRACTION25chain 'E' and (resid 160 through 184 )E160 - 184
26X-RAY DIFFRACTION26chain 'E' and (resid 185 through 201 )E185 - 201
27X-RAY DIFFRACTION27chain 'E' and (resid 202 through 207 )E202 - 207
28X-RAY DIFFRACTION28chain 'E' and (resid 208 through 230 )E208 - 230
29X-RAY DIFFRACTION29chain 'F' and (resid 337 through 342 )F337 - 342
30X-RAY DIFFRACTION30chain 'F' and (resid 343 through 358 )F343 - 358
31X-RAY DIFFRACTION31chain 'F' and (resid 359 through 365 )F359 - 365
32X-RAY DIFFRACTION32chain 'G' and (resid 1 through 15 )G1 - 15
33X-RAY DIFFRACTION33chain 'G' and (resid 16 through 31 )G16 - 31
34X-RAY DIFFRACTION34chain 'G' and (resid 32 through 37 )G32 - 37
35X-RAY DIFFRACTION35chain 'G' and (resid 38 through 68 )G38 - 68
36X-RAY DIFFRACTION36chain 'G' and (resid 69 through 75 )G69 - 75
37X-RAY DIFFRACTION37chain 'G' and (resid 76 through 135 )G76 - 135
38X-RAY DIFFRACTION38chain 'G' and (resid 136 through 159 )G136 - 159
39X-RAY DIFFRACTION39chain 'G' and (resid 160 through 184 )G160 - 184
40X-RAY DIFFRACTION40chain 'G' and (resid 185 through 201 )G185 - 201
41X-RAY DIFFRACTION41chain 'G' and (resid 202 through 230 )G202 - 230
42X-RAY DIFFRACTION42chain 'H' and (resid 1 through 111 )H1 - 111
43X-RAY DIFFRACTION43chain 'H' and (resid 112 through 230 )H112 - 230
44X-RAY DIFFRACTION44chain 'I' and (resid 337 through 364 )I337 - 364
45X-RAY DIFFRACTION45chain 'J' and (resid 1 through 68 )J1 - 68
46X-RAY DIFFRACTION46chain 'J' and (resid 69 through 103 )J69 - 103
47X-RAY DIFFRACTION47chain 'J' and (resid 104 through 134 )J104 - 134
48X-RAY DIFFRACTION48chain 'J' and (resid 135 through 159 )J135 - 159
49X-RAY DIFFRACTION49chain 'J' and (resid 160 through 184 )J160 - 184
50X-RAY DIFFRACTION50chain 'J' and (resid 185 through 207 )J185 - 207
51X-RAY DIFFRACTION51chain 'J' and (resid 208 through 230 )J208 - 230
52X-RAY DIFFRACTION52chain 'K' and (resid 2 through 67 )K2 - 67
53X-RAY DIFFRACTION53chain 'K' and (resid 68 through 73 )K68 - 73
54X-RAY DIFFRACTION54chain 'K' and (resid 74 through 111 )K74 - 111
55X-RAY DIFFRACTION55chain 'K' and (resid 112 through 230 )K112 - 230
56X-RAY DIFFRACTION56chain 'L' and (resid 337 through 364 )L337 - 364

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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