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- PDB-7s58: Crystal Structure of the tick evasin EVA-P974 complexed to human ... -

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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: 7s58
タイトルCrystal Structure of the tick evasin EVA-P974 complexed to human chemokine CCL7
要素
  • C-C motif chemokine 7
  • Evasin P974
キーワードIMMUNE SYSTEM / Inflammation / Chemokine / Evasin / Evasin-chemokine complex
機能・相同性
機能・相同性情報


CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines ...CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / cytoskeleton organization / neutrophil chemotaxis / response to gamma radiation / cellular response to type II interferon / intracellular calcium ion homeostasis / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / heparin binding / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region
類似検索 - 分子機能
Evasins Class A / Evasins Class A / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like
類似検索 - ドメイン・相同性
Evasin P974 / C-C motif chemokine 7
類似検索 - 構成要素
生物種Amblyomma cajennense (ダニ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.82 Å
データ登録者Bhusal, R.P. / Devkota, S.R. / Aryal, P. / Wilce, M.C.J. / Stone, M.J.
資金援助 オーストラリア, 1件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia) オーストラリア
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2022
タイトル: Structure-guided engineering of tick evasins for targeting chemokines in inflammatory diseases.
著者: Bhusal, R.P. / Aryal, P. / Devkota, S.R. / Pokhrel, R. / Gunzburg, M.J. / Foster, S.R. / Lim, H.D. / Payne, R.J. / Wilce, M.C.J. / Stone, M.J.
履歴
登録2021年9月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年3月16日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Evasin P974
B: Evasin P974
C: Evasin P974
D: Evasin P974
E: C-C motif chemokine 7
F: C-C motif chemokine 7
J: C-C motif chemokine 7
H: C-C motif chemokine 7


分子量 (理論値)分子数
合計 (水以外)74,7068
ポリマ－74,7068
非ポリマー00
水3,909217
1
A: Evasin P974
H: C-C motif chemokine 7


分子量 (理論値)分子数
合計 (水以外)18,6772
ポリマ－18,6772
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Evasin P974
E: C-C motif chemokine 7


分子量 (理論値)分子数
合計 (水以外)18,6772
ポリマ－18,6772
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Evasin P974
J: C-C motif chemokine 7


分子量 (理論値)分子数
合計 (水以外)18,6772
ポリマ－18,6772
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Evasin P974
F: C-C motif chemokine 7


分子量 (理論値)分子数
合計 (水以外)18,6772
ポリマ－18,6772
非ポリマー00
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)58.025, 64.415, 181.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
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 2 through 3 and (name N...
d_2ens_1(chain "B" and ((resid 2 through 3 and (name N...
d_3ens_1(chain "C" and ((resid 2 through 3 and (name N...
d_4ens_1(chain "D" and ((resid 2 through 3 and (name N...
d_1ens_2(chain "E" and (resid 8 through 15 or (resid 16...
d_2ens_2(chain "F" and (resid 8 through 16 or (resid 17...
d_3ens_2(chain "H" and ((resid 8 and (name N or name...
d_4ens_2(chain "J" and (resid 8 through 15 or (resid 16...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TYRGLYA1 - 83
d_21ens_1TYRGLYB1 - 83
d_31ens_1TYRGLYC2 - 84
d_41ens_1TYRGLYD2 - 84
d_11ens_2SERTHRE2 - 25
d_12ens_2HISLYSE29 - 69
d_21ens_2SERLYSF1 - 65
d_31ens_2SERTHRH2 - 25
d_32ens_2HISLYSH27 - 67
d_41ens_2SERTHRG1 - 24
d_42ens_2HISLYSG28 - 68

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.234394217857, 0.227674206836, 0.9451051826), (0.219989313265, -0.959391724254, 0.176556567371), (0.946923467174, 0.166529201567, -0.274961765234)32.7190746737, 10.8363914317, -43.8173741102
2given(-0.233552461725, -0.205465436191, -0.950387921931), (-0.109583437012, -0.965630160954, 0.235690183481), (-0.966149428378, 0.159192797536, 0.203009692522)-3.70948136896, 17.1867259689, -4.58976688846
3given(-0.999136663447, -0.00778136609618, 0.0408090443148), (-0.0165941708214, 0.975288021804, -0.22031320437), (-0.0380862344025, -0.22080019218, -0.974575145324)31.0927156234, -5.04842864839, -42.1804496035
4given(-0.228039641342, -0.2365468617, -0.944480547283), (-0.0607261894982, -0.964695363161, 0.256271703871), (-0.971756271853, 0.115794812129, 0.205624195071)-0.75811138682, 16.0822956698, -2.98452060056
5given(0.243112142659, 0.194454003719, 0.950307385286), (0.191646188139, -0.970017353902, 0.149459264351), (0.950877607615, 0.145787425954, -0.273089365905)31.9151683091, 10.027131568, -44.2877042394
6given(-0.999715448893, -0.0234234831921, 0.00451239175435), (-0.0234755183454, 0.932512443894, -0.360374030726), (0.00423335358893, -0.360377416633, -0.932796974855)29.4248352253, -7.32649653824, -41.473607414

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要素

#1: タンパク質
Evasin P974


分子量: 9702.080 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Amblyomma cajennense (ダニ) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A023FDY8
#2: タンパク質
C-C motif chemokine 7 / Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small- ...Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small-inducible cytokine A7


分子量: 8974.482 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: CCL7, MCP3, SCYA6, SCYA7 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P80098
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 217 / 由来タイプ: 天然 / 式: H2O

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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: 2.27 Å3/Da / 溶媒含有率: 45.8 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 0.1 M BIS-TRIS 6.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年3月10日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 1.82→48.88 Å / Num. obs: 61992 / % possible obs: 99.4 % / 冗長度: 13.4 % / Biso Wilson estimate: 40.65 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.5
反射 シェル解像度: 1.82→1.85 Å / Num. unique obs: 3397 / CC1/2: 0.678

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874精密化
XDS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: 7S4N

7s4n


解像度: 1.82→30.77 Å / SU ML: 0.2626 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 30.3065
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.244 3048 4.93 %
Rwork0.2236 58716 -
obs0.2246 61764 99.06 %
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: 55.96 Å2
精密化ステップサイクル: LAST / 解像度: 1.82→30.77 Å
タンパク質核酸リガンド溶媒全体
原子数4499 0 0 217 4716
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0074600
X-RAY DIFFRACTIONf_angle_d1.00456234
X-RAY DIFFRACTIONf_chiral_restr0.0756678
X-RAY DIFFRACTIONf_plane_restr0.0062809
X-RAY DIFFRACTIONf_dihedral_angle_d11.3625651
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.52201649749
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.440630027833
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.790296131393
ens_2d_2EX-RAY DIFFRACTIONTorsion NCS1.04176568618
ens_2d_3EX-RAY DIFFRACTIONTorsion NCS0.699051727234
ens_2d_4EX-RAY DIFFRACTIONTorsion NCS0.575997870306
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.40031210.34462443X-RAY DIFFRACTION91.25
1.84-1.870.32861190.31642608X-RAY DIFFRACTION98.52
1.87-1.910.34011310.32252627X-RAY DIFFRACTION99.32
1.91-1.940.41431450.35212550X-RAY DIFFRACTION96.08
1.94-1.980.36491430.29762644X-RAY DIFFRACTION99.93
1.98-2.020.35751380.28992660X-RAY DIFFRACTION99.26
2.02-2.060.30781340.27652665X-RAY DIFFRACTION99.86
2.06-2.110.31751500.26252629X-RAY DIFFRACTION99.39
2.11-2.160.33581480.26862655X-RAY DIFFRACTION99.5
2.16-2.220.29551200.2552695X-RAY DIFFRACTION99.89
2.22-2.290.28371230.26992624X-RAY DIFFRACTION98.99
2.29-2.360.30791390.25092657X-RAY DIFFRACTION99.75
2.36-2.450.28581540.25842669X-RAY DIFFRACTION99.75
2.45-2.540.31791480.26622670X-RAY DIFFRACTION99.61
2.54-2.660.30831460.26532671X-RAY DIFFRACTION99.93
2.66-2.80.27561180.25292736X-RAY DIFFRACTION100
2.8-2.970.29131430.25422686X-RAY DIFFRACTION100
2.97-3.20.23631270.23242744X-RAY DIFFRACTION100
3.2-3.530.2471460.2142703X-RAY DIFFRACTION99.96
3.53-4.040.20191480.18932745X-RAY DIFFRACTION99.97
4.04-5.080.16831530.1632763X-RAY DIFFRACTION100
5.08-30.770.22161540.21792872X-RAY DIFFRACTION98.5
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)
17.933763284240.550428083899-3.096838952620.771179119599-0.07070231683667.92730643269-0.395021683228-0.6484213067570.2700314216320.2885819070070.684691419534-0.3287614658660.7992412007190.501629491568-0.29090509790.265136965628-0.0264000937907-0.04118406959480.265314461510.01528163472270.373862354584.24328445746-11.8552893023-24.1417626725
28.60904797515-1.05253925866-7.18606113661.054423490780.8416729589956.00569071671-2.06096107174-1.21601511347-1.742507948920.2600872687840.6554931869420.002017202083673.335811516791.494250922170.7615723972980.7656789541160.1390231922640.2312156801150.4617843254710.07168737670070.5691685273262.15034271521-19.4446844157-21.1150446044
38.20659720227-0.862300450794-4.360710957373.468793383411.50101993245.482083552790.121655252645-0.3435777740481.069880497170.1736215794920.221451971153-0.0668836217978-0.002919959270460.35388294013-0.252295057080.2634318341610.01277816001930.005798176848530.3369092570810.01208482709110.503925176583-5.54429900263-5.95190512604-18.4069507821
47.043098657740.936293163696-1.377529520845.98562661880.5701804779767.926762657980.6292853886190.001282132748641.388307995570.058722174566-0.5309798580830.33668104014-1.03146878321-0.949807064902-0.1369767541150.5234590990540.02382589447970.07627642848930.3892387562680.006745260655210.6510289529062.3317056187226.1774621436-32.9480864419
54.84473528186-0.519627819922-1.072937052644.1949315520.7859309067953.719546580430.3188580056140.3153835253520.155278546546-0.380797385139-0.1649442965890.1923773613620.231607755196-0.122641122039-0.199616841050.5028322837120.0465960146289-0.08581065249630.2875894613580.01300521952120.32073708271511.523761369318.5954989382-39.8170483497
69.538794253723.905186447982.234593601943.17675982749-2.012303740735.749192752530.8164006562830.630679054642-0.1186095921891.08615367894-0.5866132005291.986766067390.226992447619-0.94134607961-0.2889261519580.558749086580.163646179217-0.117325692960.423576776545-0.09212148515850.5998328092442.9794958873412.7621849013-46.5707463428
76.476018996422.610565015550.3242369284066.701530506270.8200309374025.043008946540.1468460270240.520565719859-0.372392133153-0.2479547908740.160411731174-0.184006833540.6948405702460.360467364081-0.2301413194450.5915791371090.133772885477-0.103696473070.38322770604-0.04842522960810.40088021102813.324069649510.9215158369-44.3339232624
85.990236491380.42228807785-0.940433210285.44702033091.127397958583.696044534350.2105566205920.229930654348-0.702861184778-0.495112753496-0.0472710797377-0.2793956146470.609240419025-0.0247732591358-0.07554821309430.5939149852270.0676702975943-0.05659717018180.347917842848-0.02469581188850.34626198824115.843040481411.3546292828-44.2340801241
94.535669351570.446911659184-0.9055126809293.604273518341.151299567665.064254788110.165158566573-0.3663806740620.837152206436-0.1975039242060.163604253690.275759504447-1.526792885931.56840094529-0.1856892307390.642395905005-0.26408904124-0.09823363223760.717211131799-0.09051936655760.56058724913627.867444224529.576704449-20.9520061298
105.877084436320.639599743623-1.014286266756.40538907834-1.286362986485.63631791093-0.207850384356-0.547937239395-0.412993243719-0.231338399472-0.06088752830251.046634713450.893857990806-0.2097026896570.194425716570.636373375408-0.1448905747440.06091364367920.4578342803280.02999633492480.46737390688315.022033038316.7159082979-10.896887384
115.43846237606-1.09143428297-1.335360677832.304761257810.4071327935324.37474375554-0.262366097535-0.4530739217540.69417785025-0.07882453340390.1325662028720.0363327003431-0.4165292673590.5958775925240.1212895479140.552977528364-0.256937414861-0.001345123779910.545800959958-0.0254395667630.48487397091320.451227751531.1297351372-13.9140160264
124.436103284590.5716010573650.2057041808953.681120358150.07378873991055.601940369970.403882161351-0.327275758231-0.5519575990910.199065470993-0.714811460885-0.6814712246091.118887475771.135698353680.3403445725060.731302199582-0.00481486486981-0.01302676175950.6230212648530.1242380144460.4040660195120.535131193216.8040448389-4.02810419277
133.02575094699-0.555236384741-0.4005542324112.88579414036-0.05072539818354.61062406590.0758250320666-0.748311088329-0.1516059741660.4196782427680.04558235442740.5084610102740.4644935875780.0482753252702-0.1461011634940.723634773502-0.1727874619050.07383332047640.642698142861-0.01858056530390.44988010917912.397508254420.6136529075-4.35270523789
148.28540872751.16659359831-2.866648081527.565955463922.096634025365.83783928911-0.448155350568-0.034741314677-0.9149670112710.9800668563290.8655040027840.9486364468131.38781962028-0.599770701665-0.4897048863370.501061178058-0.04794615065830.01354314421580.5698690307230.1845404601460.5318504193723.0380378392-18.9049205917-9.22137599749
154.439051719910.341408560516-2.680664937010.52454193739-0.8406168690482.712734073770.6035484427631.816789092330.911388895041-0.589279371115-0.02943725083931.03403035844-0.195792997067-0.763162453366-0.4759437632970.240950575757-0.02345261761270.04889049433660.8749758343110.3324692577320.60855440575628.6838726891-4.76898585857-22.7292837259
169.05505853628-2.31070139059-0.7876831898472.304762824460.1689602448359.17289372686-1.272783382710.195248275222-0.548160970162-0.1350683775911.23999650647-0.4853504184081.1648815829-0.3538172622380.1863102766390.459703506718-0.1099146832240.01779759955990.5352499360980.1008616133250.48125188119729.4073121707-20.152353302-12.4766226313
176.59564847651.59225573111-0.5900566025976.096193337721.90190221973.664922048330.2659395640881.107510417270.1748568207570.145494089065-0.711977789598-0.2806222903680.651836912465-1.334181503580.2717487583280.324782572977-0.1943593058140.007391899317840.935311736851-0.007580536228660.39505687439131.8938044327-13.3466104463-24.2164418505
188.78603996653-4.95790268439-1.941563186469.020858989851.177223851619.593764451630.227157380369-1.50392664480.8041875205960.1222239633030.26317536504-0.5553816205810.1638422025040.188306778008-0.554256346890.333960296595-0.0753041748622-0.02258570218970.3848304215820.04801100023420.49445247414939.0617826809-7.60124982037-13.749135922
197.245148428161.21928001256-2.276174478024.939511797940.06667940847474.722684923270.2377768100681.012302667351.14830067506-0.179230230992-0.05956407532090.276091915752-0.111936526572-0.955342571579-0.1926532654430.257322208136-0.01855599442130.02612203769660.5714669069410.1821709777860.51138168311935.0907573658-5.53220405077-24.0523346127
205.87334525277-0.512517964829-3.237340536542.831442376950.04922395093135.158576561260.338411225119-0.1879752041730.4432393881540.06254122709730.0242701342842-0.165686978633-0.2860810765360.366342997886-0.29252928170.427231593564-0.0234019007797-0.01699275236610.3149995414790.004198089017330.4389076759015.0558660040322.4965668091-28.1858711618
218.82153340953-0.844024803459-3.019407985058.15226657331-0.301867707356.1874507841-0.1646092666510.928756471671-0.4511372779220.1519980945650.224301950812-0.1464514866720.493832581475-0.451032185565-0.04417045595420.396412792319-0.06972944372270.01094427856230.45044296622-0.03232030968470.629449781707-4.3941147939818.3929341912-22.7058930442
227.917712125440.691610572589-2.044597081372.84712384627-0.8426855904346.86591274240.05451970272350.390601183206-0.7136571734340.191243639564-0.07624358989290.0009995267302910.331531628911-0.122555386781-0.04099311597590.435575071982-0.04742924038-0.004700311614490.257717046085-0.04998666918220.4969882366973.3587023657718.7023188359-26.001516122
234.705859388565.12913369313-0.04359985337517.769929693-1.34162134274-0.04618773209270.416209710947-0.872155239609-0.1945368676460.323846319457-0.5073912528370.933369914546-0.211588619289-0.07962447133480.03201750223570.457202854923-0.01554379762060.1028251557710.355729501829-0.01308923131260.593262538776-5.7105291836415.2893557247-15.6133243573
246.3223140422-0.733188860826-2.118318643942.86523889978-0.9193458492535.30645866746-0.1708268875481.384970239230.03871232182980.125610643660.522313529441-0.1639587467020.531912871494-1.15320061179-0.3557941741910.360871179048-0.109246310438-0.05999763948740.6949867618370.1596681585550.45989645091218.9964286196-13.6686888087-11.3279913089
257.352216854440.35176144588-2.565948187997.753648935-3.391825596889.282119382530.503936076301-0.7501117904420.934923618688-0.1232814735070.6031938038240.500261350251-0.09124594223760.451773358018-0.9604059508910.331447166736-0.07194542256640.01897669835920.685858177489-0.0005294867900660.55526758731217.6258359228-8.73763729211-0.606824222153
265.82043285006-0.64627130136-2.985621573653.160947928461.061678575274.768635012430.3734698919950.8344508924381.23579729204-0.52287625850.6628046739780.4485511350960.152310715015-0.95136461333-0.4540763501360.261427256171-0.0272559617478-0.004532709539860.7648132297070.3559523809730.5382895983218.5818018999-9.85428573383-8.69102128621
274.312059744962.586779337730.8734156296482.925580930461.838869551915.635496937950.297009429758-0.2865830136391.006173227061.65871105759-0.517153860332.06594510051-0.537441421751-0.644301120683-0.101690967140.6236356977830.04281971548510.2125262318850.5630801799620.1342396292920.68776402804511.0437755039-3.603128505210.363278457648
284.28481300308-0.200783874166-2.115172368014.390546089570.2021230858424.71632879824-0.0006421970366690.0708430526004-0.163993689470.0290895237411-0.00085162093606-0.00268341147282-0.01770587433470.199166827418-0.07096131144790.41465345824-0.0279845026795-0.02347148886290.432770198891-0.02882344537390.39207229563723.827052663823.9896795163-23.7683213813
297.53541333123-1.82515523654-4.275680980235.851772626853.189548548147.96791628054-0.516672148163-1.896910532550.1623835744490.8080884735451.889347873990.4174375216140.3450321399521.03764249308-0.8533508843670.5032193015950.149179409170.03173114778240.9502876105180.1522493218790.5266546319433.559455133419.1976968803-27.2836899469
306.32047764718-1.12843688523-1.978891919325.809066960530.6127781214755.767685644890.133374834137-0.850878378504-0.3526448438440.331111583799-0.1457565747660.128610752740.4262126575490.903916774192-0.05841047219070.4512638550180.0041950614621-0.05165073990310.5201694292640.03274720725410.45362574162825.541821635819.3981628472-23.7909075239
317.96868618485-5.14365654463-1.279640130389.8953360733-0.1897726754273.205033561490.1341565576750.5555050376460.0719120484403-0.167943758878-0.677884416169-0.8494684151030.6322716999080.9182119694950.4512196313450.5733321481840.1254339081810.02189441328560.5704777880750.05597365389010.46316792504531.354461592816.8602559867-34.5040430903
323.67831087518-4.36201653964-1.005662088052.00091082675-0.8195219312634.64171877544-0.01604712434121.355330889331.934567738370.335526086387-0.5359139162990.13923373424-0.9501974392510.2220612821630.2751154882460.4675347015580.07297119284620.01791342193470.5855574298520.4498937289171.1673678540242.28646779113.1064321074-26.7563026076
337.55964469859-0.98330087309-7.392318768425.357494938272.900268539387.8296698063-0.177871387912-0.9249188148030.511263805304-0.111761397380.828111540592-0.05916505210890.7085894624151.0037823779-0.5746003068880.4242079839310.119247728647-0.1177928219820.415730384066-0.08139767190460.35047996128110.6904365089-14.6461722393-28.7112914641
347.79365520293-1.51042259207-3.185077739248.853366403652.284668188119.795308467450.05008141433290.8806147439640.6449690611320.2067410126860.2648593509460.005103612424670.429283108639-0.817126072101-0.339769908490.413874287747-0.00267367128388-0.05417651915790.4511405176350.156968065330.41731479449112.7452039544-13.2415322378-39.7417036655
358.21581458356-0.977935891008-4.294508041257.130753288290.6894266794367.955570362720.264400950319-0.5708192536451.019630959270.06032243550810.461822584223-0.3418084275010.2917777991660.245608604313-0.6231032688710.2603914970430.010392553736-0.05451297336920.355792263991-0.1191936061010.45427357277811.3635663741-12.1591192548-31.6898041202
363.89956546448-1.622672660891.708737507493.72894031599-2.723866196273.204634230250.08469012959240.2559494198191.02498593584-0.806466744347-0.789316546729-1.05077894459-0.1265602951961.376551296270.5063405925830.5766373787760.04440572550310.0004000553753860.451336797058-0.08125849554890.54464118270518.7582527686-9.12782754837-42.6716399329
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 2 through 26 )AA2 - 261 - 25
22chain 'A' and (resid 27 through 41 )AA27 - 4126 - 40
33chain 'A' and (resid 42 through 85 )AA42 - 8541 - 84
44chain 'B' and (resid 2 through 12 )BB2 - 121 - 11
55chain 'B' and (resid 13 through 47 )BB13 - 4712 - 46
66chain 'B' and (resid 48 through 53 )BB48 - 5347 - 52
77chain 'B' and (resid 54 through 70 )BB54 - 7053 - 69
88chain 'B' and (resid 71 through 85 )BB71 - 8570 - 84
99chain 'C' and (resid 1 through 12 )CC1 - 121 - 12
1010chain 'C' and (resid 13 through 26 )CC13 - 2613 - 26
1111chain 'C' and (resid 27 through 41 )CC27 - 4127 - 41
1212chain 'C' and (resid 42 through 59 )CC42 - 5942 - 59
1313chain 'C' and (resid 60 through 84 )CC60 - 8460 - 84
1414chain 'D' and (resid 1 through 12 )DD1 - 121 - 12
1515chain 'D' and (resid 13 through 26 )DD13 - 2613 - 26
1616chain 'D' and (resid 27 through 36 )DD27 - 3627 - 36
1717chain 'D' and (resid 37 through 47 )DD37 - 4737 - 47
1818chain 'D' and (resid 48 through 53 )DD48 - 5348 - 53
1919chain 'D' and (resid 54 through 85 )DD54 - 8554 - 85
2020chain 'E' and (resid 7 through 21 )EE7 - 211 - 15
2121chain 'E' and (resid 22 through 30 )EE22 - 3016 - 24
2222chain 'E' and (resid 31 through 57 )EE31 - 5725 - 51
2323chain 'E' and (resid 58 through 76 )EE58 - 7652 - 70
2424chain 'F' and (resid 8 through 21 )FF8 - 211 - 14
2525chain 'F' and (resid 22 through 30 )FF22 - 3015 - 23
2626chain 'F' and (resid 31 through 57 )FF31 - 5724 - 47
2727chain 'F' and (resid 58 through 75 )FF58 - 7548 - 65
2828chain 'J' and (resid 8 through 21 )JG8 - 211 - 14
2929chain 'J' and (resid 22 through 30 )JG22 - 3015 - 23
3030chain 'J' and (resid 31 through 57 )JG31 - 5724 - 50
3131chain 'J' and (resid 58 through 70 )JG58 - 7051 - 63
3232chain 'J' and (resid 71 through 76 )JG71 - 7664 - 69
3333chain 'H' and (resid 7 through 21 )HH7 - 211 - 15
3434chain 'H' and (resid 22 through 30 )HH22 - 3016 - 24
3535chain 'H' and (resid 31 through 57 )HH31 - 5725 - 49
3636chain 'H' and (resid 58 through 75 )HH58 - 7550 - 67

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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