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- PDB-8bw8: Crystal structure of the dCNK-SAM-CRIC-PDZ/dHYP-SAM complex -

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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: 8bw8
タイトルCrystal structure of the dCNK-SAM-CRIC-PDZ/dHYP-SAM complex
要素
  • Connector enhancer of KSR protein CNK
  • Protein aveugle
キーワードSIGNALING PROTEIN / Scaffolding protein / Connector enhancer of KSR (CNK) / Protein Aveugle (AVE) / Hyphen protein (HYP) / COmplex protein / Sterile alpha motif (SAM) domain / conserved region in CNK (CRIC) domain / PSD-95 / Dlg / and Zo-1. (PDZ) domain.
機能・相同性
機能・相同性情報


terminal region determination / Phosphorylation of CI / compound eye cone cell differentiation / Phosphorylation of SMO / torso signaling pathway / tracheal outgrowth, open tracheal system / compound eye photoreceptor cell differentiation / sevenless signaling pathway / Phosphorylation of PER and TIM / MAP2K and MAPK activation ...terminal region determination / Phosphorylation of CI / compound eye cone cell differentiation / Phosphorylation of SMO / torso signaling pathway / tracheal outgrowth, open tracheal system / compound eye photoreceptor cell differentiation / sevenless signaling pathway / Phosphorylation of PER and TIM / MAP2K and MAPK activation / eye photoreceptor cell differentiation / epithelial cell migration, open tracheal system / imaginal disc-derived wing vein specification / MAP-kinase scaffold activity / mitogen-activated protein kinase kinase kinase binding / positive regulation of Ras protein signal transduction / fibroblast growth factor receptor signaling pathway / enzyme regulator activity / cell surface receptor protein tyrosine kinase signaling pathway / visual perception / epidermal growth factor receptor signaling pathway / cytoplasmic side of plasma membrane / receptor tyrosine kinase binding / apical part of cell / insulin receptor signaling pathway / cell cortex / scaffold protein binding / defense response to virus / positive regulation of ERK1 and ERK2 cascade / cytoplasm / cytosol
類似検索 - 分子機能
Aveugle-like, SAM domain / : / CRIC domain / Connector enhancer of kinase suppressor of ras / CRIC domain profile. / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Aveugle-like, SAM domain / : / CRIC domain / Connector enhancer of kinase suppressor of ras / CRIC domain profile. / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily
類似検索 - ドメイン・相同性
Connector enhancer of KSR protein CNK / Protein aveugle
類似検索 - 構成要素
生物種Drosophila melanogaster (キイロショウジョウバエ)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.1 Å
データ登録者Maisonneuve, P. / Kurinov, I. / Sicheri, F.
資金援助 カナダ, 2件
組織認可番号国
Canadian Institutes of Health Research (CIHR)FRN-414829 カナダ
Canadian Institutes of Health Research (CIHR)FDN-143277 カナダ
引用ジャーナル: Nat Struct Mol Biol / 年: 2024
タイトル: The CNK-HYP scaffolding complex promotes RAF activation by enhancing KSR-MEK interaction.
著者: Pierre Maisonneuve / Malha Sahmi / Fanny Bergeron-Labrecque / Xianjie Iris Ma / Juliette Queguiner / Geneviève Arseneault / Martin Lefrançois / Igor Kurinov / Rémi Fronzes / Frank Sicheri / Marc Therrien /
要旨: The RAS-MAPK pathway regulates cell proliferation, differentiation and survival, and its dysregulation is associated with cancer development. The pathway minimally comprises the small GTPase RAS and ...The RAS-MAPK pathway regulates cell proliferation, differentiation and survival, and its dysregulation is associated with cancer development. The pathway minimally comprises the small GTPase RAS and the kinases RAF, MEK and ERK. Activation of RAF by RAS is notoriously intricate and remains only partially understood. There are three RAF isoforms in mammals (ARAF, BRAF and CRAF) and two related pseudokinases (KSR1 and KSR2). RAS-mediated activation of RAF depends on an allosteric mechanism driven by the dimerization of its kinase domain. Recent work on human RAFs showed that MEK binding to KSR1 promotes KSR1-BRAF heterodimerization, which leads to the phosphorylation of free MEK molecules by BRAF. Similar findings were made with the single Drosophila RAF homolog. Here we show that the fly scaffold proteins CNK and HYP stabilize the KSR-MEK interaction, which in turn enhances RAF-KSR heterodimerization and RAF activation. The cryogenic electron microscopy structure of the minimal KSR-MEK-CNK-HYP complex reveals a ring-like arrangement of the CNK-HYP complex allowing CNK to simultaneously engage KSR and MEK, thus stabilizing the binary interaction. Together, these results illuminate how CNK contributes to RAF activation by stimulating the allosteric function of KSR and highlight the diversity of mechanisms impacting RAF dimerization as well as the regulatory potential of the KSR-MEK interaction.
履歴
登録2022年12月6日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年2月21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
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN
改定 1.22024年3月6日Group: Database references / カテゴリ: citation / citation_author / Item: _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: Protein aveugle
B: Connector enhancer of KSR protein CNK
C: Protein aveugle
D: Connector enhancer of KSR protein CNK
E: Protein aveugle
F: Connector enhancer of KSR protein CNK
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)155,86315
ポリマ－155,0346
非ポリマー8299
水5,098283
1
A: Protein aveugle
B: Connector enhancer of KSR protein CNK
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,9545
ポリマ－51,6782
非ポリマー2763
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-9 kcal/mol
Surface area17350 Å2
手法PISA
2
C: Protein aveugle
D: Connector enhancer of KSR protein CNK
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,8624
ポリマ－51,6782
非ポリマー1842
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-10 kcal/mol
Surface area17360 Å2
手法PISA
3
E: Protein aveugle
F: Connector enhancer of KSR protein CNK
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)52,0466
ポリマ－51,6782
非ポリマー3684
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-11 kcal/mol
Surface area16700 Å2
手法PISA
単位格子
Length a, b, c (Å)131.907, 131.907, 71.465
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and ((resid 20 through 21 and (name N...
d_2ens_1(chain "C" and (resid 21 through 75 or (resid 76...
d_3ens_1(chain "E" and ((resid 20 through 21 and (name N...
d_1ens_2(chain "B" and (resid 4 through 7 or (resid 8...
d_2ens_2(chain "D" and (resid 4 through 7 or (resid 8...
d_3ens_2(chain "F" and (resid 4 through 39 or (resid 40...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSTYRA2 - 87
d_21ens_1LYSTYRC1 - 86
d_31ens_1LYSTYRE2 - 87
d_11ens_2ILEALAB2 - 100
d_12ens_2LYSASPB103 - 158
d_13ens_2LEULYSB160 - 201
d_14ens_2PHEASPB205 - 219
d_15ens_2LYSPROB222 - 264
d_21ens_2ILEASPD2 - 156
d_22ens_2LEULYSD158 - 199
d_23ens_2PHEASPD207 - 221
d_24ens_2LYSPROD233 - 275
d_31ens_2ILEALAF1 - 99
d_32ens_2LYSASPF104 - 159
d_33ens_2LEUPROF163 - 262

NCSアンサンブル:
ID
ens_1
ens_2

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要素

#1: タンパク質 Protein aveugle


分子量: 13143.911 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ)
遺伝子: ave, CG30476 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8ML92
#2: タンパク質 Connector enhancer of KSR protein CNK / Connector enhancer of ksr / isoform A / isoform B / SD09985p


分子量: 38534.203 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ)
遺伝子: cnk, anon-WO0140519.129, anon-WO0257455.27, CNK, Cnk, Dmel\CG6556, EC2-3, EK2-3, l(2)k16314, sag, CG6556, Dmel_CG6556
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q7KNQ9
#3: 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: 9 / 由来タイプ: 天然 / 式: C3H8O3
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 283 / 由来タイプ: 天然 / 式: H2O
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: 2.9 Å3/Da / 溶媒含有率: 57.52 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 0.1M Bis-Tris Propane pH 7.0, and 1.0M Ammonium tartrate dibasic

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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 PILATUS 6M-F / 検出器: PIXEL / 日付: 2017年11月6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: 0.9792 Å / 相対比: 1
反射解像度: 2.1→114.23 Å / Num. obs: 81051 / % possible obs: 99.8 % / 冗長度: 5.2 % / Biso Wilson estimate: 49.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.069 / Net I/σ(I): 14
反射 シェル解像度: 2.1→2.14 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4475 / CC1/2: 0.397

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
HKL2Map位相決定
PHASER位相決定
SHELXDE位相決定
Aimlessデータスケーリング
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.1→65.95 Å / SU ML: 0.2885 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 25.9199
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2188 4137 5.11 %
Rwork0.1884 76864 -
obs0.1899 81001 99.8 %
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
原子変位パラメータBiso mean: 63.64 Å2
精密化ステップサイクル: LAST / 解像度: 2.1→65.95 Å
タンパク質核酸リガンド溶媒全体
原子数8397 0 54 283 8734
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00178588
X-RAY DIFFRACTIONf_angle_d0.470411635
X-RAY DIFFRACTIONf_chiral_restr0.03891340
X-RAY DIFFRACTIONf_plane_restr0.00381490
X-RAY DIFFRACTIONf_dihedral_angle_d15.4193153
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.88465150883
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.663617800744
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.561764748428
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.623205168215
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.35461140.30042547X-RAY DIFFRACTION99.92
2.12-2.150.32071480.28822573X-RAY DIFFRACTION99.93
2.15-2.180.28611920.27462539X-RAY DIFFRACTION100
2.18-2.20.32831450.26572564X-RAY DIFFRACTION99.89
2.2-2.230.29471140.28062559X-RAY DIFFRACTION99.96
2.23-2.260.36471520.30772572X-RAY DIFFRACTION100
2.26-2.290.36691340.28042529X-RAY DIFFRACTION99.81
2.29-2.330.29541480.25922575X-RAY DIFFRACTION99.89
2.33-2.370.29920.2472574X-RAY DIFFRACTION99.85
2.37-2.40.27821360.23752624X-RAY DIFFRACTION99.86
2.4-2.450.24651840.21972524X-RAY DIFFRACTION99.93
2.45-2.490.27061070.23262611X-RAY DIFFRACTION99.82
2.49-2.540.2521260.23322557X-RAY DIFFRACTION100
2.54-2.590.22671800.2142528X-RAY DIFFRACTION99.96
2.59-2.650.2809940.22332603X-RAY DIFFRACTION99.89
2.65-2.710.31111390.24412507X-RAY DIFFRACTION100
2.71-2.780.24761660.24292608X-RAY DIFFRACTION99.86
2.78-2.850.24921440.22532547X-RAY DIFFRACTION99.85
2.85-2.930.24191080.21332575X-RAY DIFFRACTION99.93
2.93-3.030.24771590.21132550X-RAY DIFFRACTION99.93
3.03-3.140.21061340.20292586X-RAY DIFFRACTION99.96
3.14-3.260.21321280.1882565X-RAY DIFFRACTION99.67
3.26-3.410.23611300.18842599X-RAY DIFFRACTION99.89
3.41-3.590.17861100.17752564X-RAY DIFFRACTION99.81
3.59-3.820.20431820.15652501X-RAY DIFFRACTION99.78
3.82-4.110.1871400.14822558X-RAY DIFFRACTION99.78
4.11-4.520.18591360.14542583X-RAY DIFFRACTION99.74
4.53-5.180.16281390.15832530X-RAY DIFFRACTION99.07
5.18-6.520.23071160.18982602X-RAY DIFFRACTION99.93
6.52-65.950.1831400.15492510X-RAY DIFFRACTION98.37
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)
14.444171991192.8880117605-1.454377808348.721534239871.052054414347.53494487268-0.1741507517390.485387029624-0.0718534873674-0.1354422514290.3627277646941.326905772970.345411450395-1.01857025316-0.1740069060550.30625992546-0.01416374938080.02362843550370.4746631703760.06811995580130.64653729569737.910267331347.960598929845.5890472007
25.334105757970.569749315107-0.7682767145044.595658459440.3975568831678.83416837533-0.02470235238330.1239458499820.4978037454210.2248289326810.1297744067540.307493248897-0.4991476523040.118590264942-0.1049198365990.2963960686430.0009422247824990.08181721078660.2849860336620.009959985263730.38805058317348.969870347152.662667032648.7603318136
32.989137985294.36019094963-1.268386062054.31978901162-1.828668526391.10873071303-0.2627161628340.3202500376470.0622757852379-0.3169624296780.779161293770.55608145799-0.117675947964-0.33834689759-0.4581878309750.3640678764260.001530354541240.02050819035290.5377480697180.1406477174920.58233201930438.734742856241.365333670357.0013857168
47.84850067616-4.58225689553-1.545750416737.84039157662-0.6442288429867.82658102449-0.03958706067110.295046323217-0.178806989096-0.353958507293-0.0962603970748-0.1171320235690.9742002814240.4573277412460.004945953588380.494448781360.005209355826870.04853038581460.325443422196-0.04572801534760.27429543186562.561186212829.083525402838.5078592585
58.80568818445-0.586504098893-2.498727202726.120014830110.1871275675667.417621613570.04672257844620.07816438026130.042183978304-0.1216224517280.0251491150544-0.3396915164080.1569068954950.370098687287-0.03991623001480.302399694701-0.002095077378110.04499565600150.309120161317-0.001498698876260.26600877189963.803508826540.805383444940.0684098907
66.0608163045-5.168642889382.201005181675.3287146475-3.434302945753.12923701458-0.226514723228-0.448393367575-0.5483115563650.7002708204870.4880569679610.9422915692350.222258705017-0.235648678336-0.2293776663230.420706317441-0.004812471197270.05826018361850.389651936993-0.0259530699460.33901509524356.939387813634.437866715747.4844275743
73.00205379661-3.85369934367-2.255144636475.522312108084.549548993374.930178837020.123302860212-0.364240429550.0875617005139-0.4560061820990.610959601286-0.642367922549-0.3952365028140.0285261195101-0.7943764570740.385314280578-0.00596404559830.02403258654020.4848270336720.03654406649380.43272942936852.12298179428.357815355665.0959394627
84.542280225880.4492891041310.5234163060448.740933259413.113405816663.64689626913-0.198781847906-0.2727653592910.393505989358-0.5304058178790.604577168398-0.698092522089-0.57176449675-0.0616751393233-0.3813058281980.3211620989510.04006959020320.001892729163060.4425337222790.05457650723260.36151860212644.175457847138.126958300163.418459211
96.097375086480.930125375994-0.9167220891782.786256399262.631207838364.85859789399-0.026712580171-0.0978553784121-0.170991411277-0.1600042786690.202071811576-0.1176387477110.0195956596826-0.440427970489-0.1773085556080.257009287556-0.02448735463030.00866224742880.5274923213890.09488601474270.38425256715737.225662758124.048160725762.4688291457
104.37616201204-3.43923563918-1.300341428848.355271848180.1708151367565.19134713874-0.165592921466-0.459829163656-0.2609721377420.6902476985990.3284328272940.59210359587-0.0713945302995-0.540110687463-0.163880671180.3015803021780.0204844408119-0.006993733860450.5741332621650.1170870039920.39200985899644.126280574726.645929632470.0758214142
117.23899015791-3.671061479380.7653932342258.532177550133.407811454966.3963341061-0.3298965104060.314707724844-1.42621582243-0.1299372777070.2725651202861.930897473951.2792553713-0.8250147714410.06968176267210.946576307402-0.2696974542680.04811400119690.655843588904-0.1053200134230.8361910785547.625459356118.118108014240.4571472321
127.592546175066.138443856681.106918682249.07328895621-0.3104388181833.632862438540.480265763022-0.879374210152-0.4086747164370.808904821508-0.6433482296871.668744156181.00405703647-0.8545274233880.123524280230.827758213667-0.349334153080.14910798110.933461314484-0.01513790745510.95664107893643.103575270315.946170750143.2758210122
139.392762980761.494495498770.2358791247364.949531718020.9155023308481.95228254535-0.07769669460.723590323102-0.271116713301-0.8793848874070.2474902860740.7893843665490.794917585745-0.290642540207-0.1590278504820.805439337543-0.169707834373-0.04294174271930.4514802279-0.0779740421640.45655079701451.336409011220.804180284937.2654021675
146.66273833432-2.639234626012.180592368857.326681697590.5658557494417.455072400040.374850831266-0.0315685360118-0.713973337705-0.117809938534-0.14182090144-0.06902283929681.108732196170.0109666850722-0.2617447649210.5759582954120.003938379567720.0307685369380.3505738826930.03532723185910.674592103251-0.96415986869749.051926698151.5220580199
157.223331225220.7462066059635.076195090212.10317957288-0.07277977473735.021821427910.4517885808130.23798118276-0.7950775916760.2988721341610.136673647470.031543600850.282200567147-0.106079010869-0.5696849592010.5828326867170.07381795386640.09173532753310.4365903747450.05416777955730.6124558032894.6877088587652.725519880361.6915279483
168.174293146512.246527092240.6988607050467.9531783505-0.2840386465334.344914406780.03628622254280.1862924841420.15820386502-0.111430956818-0.07485242264950.111444053539-0.257231360008-0.1740237342770.02531491875420.3550436730150.06690604263820.006879138366840.4177300101560.0368291132760.302228455132.5731011673374.264194219545.3382242277
170.648601948037-0.3927473030991.642607773871.350341974240.1421351272313.47384463886-0.1132327624510.0500578389849-0.04818956400860.3672085535560.19090954579-0.07801620218040.06099474100230.126429061318-0.07431667166530.5009782944750.1067568217510.02187670997990.4964293190190.05372135351450.51366027531610.872629139967.663661819564.091932322
187.051767897011.452558546040.4370232542315.824976331960.7197102859993.28565472762-0.0527671044593-0.188786705441-0.7104794804980.729098877169-0.0319915022356-0.4163478899690.6511015762860.3477958590320.1382981193120.6448114172550.187098537625-0.02296724168220.4141443560910.02902764389910.59831636584318.824622063957.269263889471.5468447642
191.79651654754-1.43446000989-0.7910140272232.420357607360.9718205830777.83494827810.2162989409570.1539376359940.210427008274-0.1088654744580.255048039505-0.555025975383-0.2572076692840.410731547449-0.5254650216290.390111283801-0.03206581371310.02685965741330.7222999444190.1421477132440.86454733029830.660294512571.935456635452.4700043793
208.75843888235-3.40720411659-0.2552138902475.434289104550.01301927745582.10072843811-0.05404425812410.148347278053-0.2046047846750.0432421351727-0.123948841223-0.240023805547-0.06154235124550.1457388275770.1758017152430.3644268698140.01172679043090.08740906016530.5918565904220.1044051525090.50902896123525.911670876868.221452008244.9992368552
211.5838894587-0.1012367700362.638234653622.01229067211-0.6786651299424.569786077280.1117320756420.4676804789182.36468389852-0.7548122610760.0453567488011-2.00941950899-1.19254101950.733132500841-0.06424034426410.670661103029-0.1031577655440.0919451354290.4892254630590.01698005561461.12649982335-1.0847683341528.519386286281.9880476555
226.84634407506-0.506459920013-0.9207041316827.65537098809-1.530252601267.877813016260.3204187212040.08916579760661.222117398750.475204861995-0.0468722645424-0.0405448012426-0.813217420675-0.395445410973-0.1864319653480.3941443381260.07897011998930.1023970004790.331615496281-0.007930165078090.573775313455-13.718597771823.685231392180.5702059679
235.234291015611.57617785734-3.24962102932.49585559224-1.598196633173.155984184320.3785621705230.06308502648280.6985566226710.0400626526390.03689115523640.0376671156532-0.410647452389-0.0533501741938-0.4090784647960.4078814444260.04202733826590.04278516200010.3424617832280.04403906353670.547448134107-5.0567489764122.938876368870.795557514
245.853099932160.190391170183-0.8116876610082.32063238676-1.046468809873.3736338589-0.0118777511394-0.326228200687-0.2238060408920.213039308907-0.04364595386560.02729737669380.4359092093870.489077860860.04945942933050.3626512683020.071575951777-0.03134074873570.431946290629-0.008397186381560.2829799127941.331291893862.3906472704786.9481920585
252.06778691361-0.426357776721-3.2575276870.0329276188836-0.3826076732942.178141020460.0669578306243-0.122120768910.403343158508-0.06295058767620.114813119133-0.006136681604080.0604041360548-0.0655873743903-0.1888941661420.361897140787-0.0496643023087-0.05466195372320.3862481679560.02611180114140.4621057163167.1330201476211.391325280768.5345272076
267.29362641033-0.718371493402-1.209274494564.22680330960.1950562135283.790044025610.407809115160.2635291845181.07989461684-0.111422517327-0.000978021626224-0.264715772845-0.610061891080.11314840994-0.3410325974650.456077790208-0.01949228181140.1063083274420.2416326508040.01266788517410.6220302934959.3856430395225.221054626263.2998782987
277.72340799877-2.163447829580.3559047746074.830651199960.6909816940982.854397183680.4766773019221.056996639411.65064716259-0.388313998613-0.1017334139950.081807706986-0.725932876289-0.656435432901-0.3425403802470.5407011903620.09314264418260.1210706397670.5839512370760.2931545809980.7040664179464.9616157218725.601374786254.9250512597
281.419886359220.694430831276-1.355773214881.05007735261-0.2922396438190.743277093490.0853218394884-0.9306488344160.559311501110.331843735769-0.0969492693307-0.367310947749-0.4125671419040.7878161006620.1149332350740.426799890233-0.00771875547145-0.0813811684720.89602454954-0.09162731410690.51745846421324.790523239815.112084536575.3185311282
296.284918198443.73385028247-1.256356815598.536045531141.526842058986.972199715640.369889796512-0.8283364100441.116000650440.385417186781-0.2966565708250.216943493422-0.8770812579340.831854023094-0.02275905282110.531410274118-0.125882683289-0.07938744618820.859783424672-0.1219354498590.66553042272116.157005939516.06035289587.3222088472
303.303489544182.303372780972.308632766912.165749933363.870063603142.211238590260.393768914113-1.14532570009-0.05664095693270.2308265385890.515267615871-1.73601376465-0.8909253511092.22545909533-0.5299013148920.492085752725-0.128663534765-0.2110475283121.54013990986-0.1922232814480.6409215968924.7949994512.219436918687.2084310594
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 38 )AA19 - 381 - 20
22chain 'A' and (resid 39 through 73 )AA39 - 7321 - 55
33chain 'A' and (resid 74 through 105 )AA74 - 10556 - 87
44chain 'B' and (resid 3 through 22 )BB3 - 221 - 20
55chain 'B' and (resid 23 through 57 )BB23 - 5721 - 55
66chain 'B' and (resid 58 through 76 )BB58 - 7656 - 74
77chain 'B' and (resid 77 through 101 )BB77 - 10175 - 99
88chain 'B' and (resid 102 through 133 )BB102 - 133100 - 126
99chain 'B' and (resid 134 through 163 )BB134 - 163127 - 156
1010chain 'B' and (resid 164 through 202 )BB164 - 202157 - 193
1111chain 'B' and (resid 203 through 227 )BB203 - 227194 - 214
1212chain 'B' and (resid 228 through 249 )BB228 - 249215 - 227
1313chain 'B' and (resid 250 through 286 )BB250 - 286228 - 264
1414chain 'C' and (resid 21 through 59 )CC21 - 591 - 39
1515chain 'C' and (resid 60 through 106 )CC60 - 10640 - 86
1616chain 'D' and (resid 3 through 57 )DD3 - 571 - 55
1717chain 'D' and (resid 58 through 112 )DD58 - 11256 - 103
1818chain 'D' and (resid 113 through 191 )DD113 - 191104 - 180
1919chain 'D' and (resid 192 through 218 )DD192 - 218181 - 207
2020chain 'D' and (resid 219 through 286 )DD219 - 286208 - 275
2121chain 'E' and (resid 19 through 26 )EE19 - 261 - 8
2222chain 'E' and (resid 27 through 58 )EE27 - 589 - 40
2323chain 'E' and (resid 59 through 105 )EE59 - 10541 - 87
2424chain 'F' and (resid 4 through 57 )FF4 - 571 - 54
2525chain 'F' and (resid 58 through 103 )FF58 - 10355 - 100
2626chain 'F' and (resid 104 through 162 )FF104 - 162101 - 156
2727chain 'F' and (resid 163 through 191 )FF163 - 191157 - 185
2828chain 'F' and (resid 192 through 222 )FF192 - 222186 - 209
2929chain 'F' and (resid 223 through 274 )FF223 - 274210 - 250
3030chain 'F' and (resid 275 through 286 )FF275 - 286251 - 262

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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://pdbjlvh1.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