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- PDB-8fj0: Crystal Structure of the Tick Evasin EVA-AAM1001(Y44A) Complexed ... -

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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: 8fj0
タイトルCrystal Structure of the Tick Evasin EVA-AAM1001(Y44A) Complexed to Human Chemokine CCL2
要素
  • C-C motif chemokine 2
  • Evasin P1243
キーワードCYTOKINE / Tick / Evasin / Chemokine / Anti-inflammatory
機能・相同性
機能・相同性情報


helper T cell extravasation / chemokine (C-C motif) ligand 2 signaling pathway / negative regulation of chemokine activity / positive regulation of NMDA glutamate receptor activity / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / chemokine binding / astrocyte cell migration / negative regulation of glial cell apoptotic process / CCR chemokine receptor binding ...helper T cell extravasation / chemokine (C-C motif) ligand 2 signaling pathway / negative regulation of chemokine activity / positive regulation of NMDA glutamate receptor activity / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / chemokine binding / astrocyte cell migration / negative regulation of glial cell apoptotic process / CCR chemokine receptor binding / positive regulation of apoptotic cell clearance / ATF4 activates genes in response to endoplasmic reticulum stress / NFE2L2 regulating inflammation associated genes / chemokine-mediated signaling pathway / C-C chemokine binding / eosinophil chemotaxis / cellular homeostasis / negative regulation of vascular endothelial cell proliferation / chemokine activity / Chemokine receptors bind chemokines / negative regulation of G1/S transition of mitotic cell cycle / Interleukin-10 signaling / positive regulation of macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / humoral immune response / cellular response to interleukin-1 / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cellular response to fibroblast growth factor stimulus / positive regulation of endothelial cell apoptotic process / cell surface receptor signaling pathway via JAK-STAT / sensory perception of pain / cytoskeleton organization / positive regulation of synaptic transmission, glutamatergic / viral genome replication / animal organ morphogenesis / response to bacterium / cytokine-mediated signaling pathway / cellular response to type II interferon / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / cellular response to tumor necrosis factor / regulation of cell shape / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / angiogenesis / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / protein kinase activity / cell adhesion / positive regulation of cell migration / protein phosphorylation / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / positive regulation of gene expression / 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 P1243 / C-C motif chemokine 2
類似検索 - 構成要素
生物種Amblyomma americanum (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: 2.91 Å
データ登録者Devkota, S.R. / Bhusal, R.P. / 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)APP1140867 オーストラリア
引用ジャーナル: Nat Commun / 年: 2023
タイトル: Engineering broad-spectrum inhibitors of inflammatory chemokines from subclass A3 tick evasins.
著者: Devkota, S.R. / Aryal, P. / Pokhrel, R. / Jiao, W. / Perry, A. / Panjikar, S. / Payne, R.J. / Wilce, M.C.J. / Bhusal, R.P. / Stone, M.J.
履歴
登録2022年12月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年3月29日Provider: repository / タイプ: Initial release
改定 1.12023年7月26日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
改定 1.22024年10月16日Group: Data collection / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Evasin P1243
B: Evasin P1243
C: Evasin P1243
D: C-C motif chemokine 2
F: C-C motif chemokine 2
E: C-C motif chemokine 2


分子量 (理論値)分子数
合計 (水以外)59,6516
ポリマ－59,6516
非ポリマー00
水19811
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
単位格子
Length a, b, c (Å)82.446, 49.636, 88.319
Angle α, β, γ (deg.)90.000, 112.910, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
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 17 and (name N or name...
d_2ens_1(chain "B" and ((resid 17 and (name N or name...
d_3ens_1(chain "C" and (resid 17 through 19 or (resid 20...
d_1ens_2(chain "D" and (resid 9 through 18 or (resid 20...
d_2ens_2(chain "E" and ((resid 9 and (name N or name...
d_3ens_2(chain "F" and (resid 9 through 16 or (resid 17...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TYRTHRA1 - 58
d_12ens_1PROLYSA60 - 85
d_21ens_1TYRTHRB2 - 59
d_22ens_1PROLYSB61 - 86
d_31ens_1TYRLYSC1 - 84
d_11ens_2VALARGD3 - 22
d_12ens_2ILEGLND24 - 63
d_21ens_2VALARGF2 - 11
d_22ens_2ILEARGF13 - 22
d_23ens_2ILEGLNF24 - 63
d_31ens_2VALARGE1 - 10
d_32ens_2ILEGLNE12 - 61

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.68119978689, 0.0237659606257, 0.731711711985), (0.0198626216474, -0.999704989584, 0.0139789149455), (0.731828071751, 0.00501127900832, -0.681470880141)17.3036861291, 4.09915016384, -40.5143074711
2given(-0.0802613125716, -0.00236715573636, -0.996771046067), (-0.000116741321332, 0.999997195583, -0.00236541710907), (0.996773850016, -7.34871129695E-5, -0.0802613638303)-23.8173979239, 0.0106021174519, -40.7408991135
3given(0.672013229888, -0.0174057022627, 0.740334559766), (-0.00780464562844, -0.999834684043, -0.0164223046799), (0.740498012396, 0.00525795712465, -0.672037980716)16.6699067903, -45.4487952623, -40.6100409765
4given(-0.0707355656328, -0.00875107031474, -0.997456715112), (0.0157095032576, 0.999827725147, -0.00988592605045), (0.997371390838, -0.0163688360863, -0.070585904706)-23.8639644026, -0.0138606799122, -41.0687438238

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要素

#1: タンパク質 Evasin P1243


分子量: 11210.546 Da / 分子数: 3 / 変異: Y44A / 由来タイプ: 組換発現 / 由来: (組換発現) Amblyomma americanum (ダニ) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A0C9S461
#2: タンパク質 C-C motif chemokine 2 / HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / ...HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / Monocyte chemotactic protein 1 / MCP-1 / Monocyte secretory protein JE / Small-inducible cytokine A2


分子量: 8673.009 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CCL2, MCP1, SCYA2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P13500
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 11 / 由来タイプ: 天然 / 式: H2O
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: 2.79 Å3/Da / 溶媒含有率: 55.92 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 2 M NH4SO4, 0.1 M bis-tris, Ph 5.6

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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: 0.953 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年8月3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: 0.953 Å / 相対比: 1
反射解像度: 2.89→47.11 Å / Num. obs: 14772 / % possible obs: 98.5 % / 冗長度: 6.6 % / Biso Wilson estimate: 55.65 Å2 / CC1/2: 0.971 / Net I/σ(I): 5.4
反射 シェル解像度: 2.89→3.07 Å / Num. unique obs: 2250 / CC1/2: 0.475

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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
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 / 解像度: 2.91→43.61 Å / SU ML: 0.4718 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 34.28
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2842 814 5.56 %
Rwork0.2537 13825 -
obs0.2554 14639 99.07 %
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: 62.49 Å2
精密化ステップサイクル: LAST / 解像度: 2.91→43.61 Å
タンパク質核酸リガンド溶媒全体
原子数2875 0 0 11 2886
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00282924
X-RAY DIFFRACTIONf_angle_d0.69984021
X-RAY DIFFRACTIONf_chiral_restr0.0396493
X-RAY DIFFRACTIONf_plane_restr0.0034533
X-RAY DIFFRACTIONf_dihedral_angle_d12.1589861
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.606019189872
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.32098597296
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.954853320542
ens_2d_3DX-RAY DIFFRACTIONTorsion NCS0.64312428858
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.090.41051290.36632301X-RAY DIFFRACTION99.31
3.09-3.330.33691510.29652257X-RAY DIFFRACTION98.97
3.33-3.670.29081190.24882277X-RAY DIFFRACTION98.56
3.67-4.20.28891540.23152262X-RAY DIFFRACTION98.53
4.2-5.280.25491240.21432345X-RAY DIFFRACTION99.96
5.29-43.610.24211370.25422383X-RAY DIFFRACTION99.1
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)
14.94987287254-0.303891730096-0.641186202624.570789880942.802027554033.83219202731-0.343137664211-0.1603183546470.0512378822223-0.0370919078006-0.203605618120.183449486507-0.010768711076-0.2076089362090.3827711170611.153210938380.1430822627230.08887994156010.380470539211-0.1245180823870.5112072884217.202-26.0622.71
20.8015023707330.404764747022-0.2279744969120.3374222795470.007162075045020.5723531618070.1230992253690.154185562460.169032566312-0.2247917035370.0611255676232-0.0443752243239-0.049780226955-0.06863970590040.2210029468810.883976561730.06290814368550.1302956970930.009662843785470.229903839433-0.002985260246855.008-8.256-15.82
30.222015904693-0.08764858594130.8044720016980.0764458396056-0.3419760474273.752228540130.0764914353504-0.5474214475360.01520546241310.3547531224220.06287622631610.1679142329910.3472302146370.2972882746140.1341530896450.532618821184-0.00586397573590.1081355762640.4025187108880.02857637386060.3618365329631.61-10.237-2.895
43.206847395422.43670621761-1.581681851232.12963805623-1.201914421881.43279653351-0.337025441569-0.122833719893-0.288515961334-0.4641099272820.0543904491888-0.2852241662590.01049094499870.0387585456350.2077735068341.180554419060.03959653574160.2754744793330.3930475533490.007828948031460.377636832412.233-14.5642.325
50.177150084550.328914719415-0.2455098771351.35012174424-0.6605548175410.403281244662-0.00535108560191-0.0365768162170.1644932383320.160029751493-0.09188290863070.0341353322038-0.1891563934670.0830389560374-0.4740958319060.828046010755-0.2061302398180.02515558283090.1954393411270.03887930558910.1877521764010.93-3.516-8.254
61.399302806631.38896863309-0.4045230248681.41559698124-0.8660841242365.911058910880.212156502589-0.2599643308160.2834888104420.274379056562-0.195990802570.0999727014194-1.02698089486-0.743712919952-0.2058826829621.152283763150.2265945334370.1249094760920.6670115620690.07159564578320.274533104858-7.699-6.421-20.71
73.604195259960.960867147213-2.084526802032.28753385169-1.132220591543.724839627750.0991852260352-0.383649850796-0.0985215326936-0.1446878126730.08286634441510.02073976211880.536044690325-0.446638527942-0.1355552016280.577258310982-0.01009157842450.2053322584890.2109910742070.03625824174550.1159029991693.1990.298-10.415
80.989910974161-0.1702931293840.5661579794211.41846339395-1.582641247271.909184273460.0978283988699-0.447024264865-0.3252731888470.09874562583220.032260641112-0.0204500606450.60952923277-0.1317344770540.002807971017590.850275063823-0.0435085869030.1151370557410.3335795427690.05994217647420.1986951282844.1941.136-2.979
90.09780765006320.173476173897-0.06825938768670.289155810699-0.1191659506080.04973263357250.008982497909310.06991019760980.0926426954759-0.112302441996-0.0810582402888-0.246676957911-0.1445184646760.1501911267040.05951390140841.10029838797-0.1782329009250.1931799616010.05663825139670.1294567826630.3127429623411.769-0.253-17.189
103.539381325231.30444489502-0.7364570153460.5829138446520.4477813645585.353058401290.06459897313970.233391214104-0.340931748695-0.2105320374710.0143959087067-0.2634338178790.139686178025-0.0054398406707-0.02317885334821.0796449709-0.02123039898520.1531764276310.374109296715-0.05993343708430.3272166418123.99430.387-37.141
110.597669644963-0.0135780391236-0.4851253011281.19928347156-1.71440038223.127019703520.05596164161210.172259643908-0.03612748118410.08708885680510.1996085929140.0885038231031-0.2617278499770.0833494387034-0.120541960630.429307008762-0.02703860862590.06688736970280.3306209437770.04026373763650.1943175235179.09412.552-26.258
121.21968288883-0.204391119499-0.6775823864272.117301607382.64915446943.463098667290.12943849298-0.03417786474510.129105356494-0.2073880948020.200905045016-0.168883934915-0.2664534888750.293651521817-0.03097411262410.8533331750650.1367361302930.02525956301870.28249971634-0.1590593166050.10660894663515.3813.586-38.17
130.0187227843611-0.2052686527690.02732387588183.49121368535-1.019562308490.454579928646-0.1137364514430.2720385409710.0719431491790.5203735625510.0434834554739-0.1908728041530.1951078160030.3052995464590.1124004065250.422528007828-0.05494019916630.004080264594610.428870492977-0.100317140430.36425315239219.92120.036-40.137
140.09357610017190.10679404608-0.0257882765420.120068788998-0.0277924428780.0542840989950.05074270882240.0757766158552-0.0333916089456-0.03104160897820.0236786720473-0.0516073661499-0.03880637428660.001735178275560.1619477987240.7844720429850.0608558761085-0.09943704328650.04405758449930.7605868478540.27564480240815.37.973-32.125
159.233681166012.301215434855.255367320717.181784204964.122093312824.187925729170.139084150882-0.334790701015-0.02957935401590.758527681007-0.6683587368370.6272336989260.399292985027-1.070406378570.5394279140450.801530728347-0.2505334426190.1059166399210.460773303412-0.1671704368770.4258250333381.3967.309-39.775
163.18154681820.063211693453-1.084845620310.1593350865750.457323993091.818408688780.4218359371430.2471460389450.463317236448-0.1802635700120.0248452448199-0.220179212149-0.779298695072-0.762371458697-0.2400549643840.788750963209-0.007639549205740.2726801631630.802790246691-0.2782550530910.584570554093-3.139.113-30.475
170.207562388002-0.1487672253640.08055240377131.09237789448-0.2114275497450.4117965224830.108696446935-0.004834815204870.0140841979391-0.09578691600230.0821154033576-0.0314528427228-0.0484179822181-0.05671625803460.5639550339691.183422215580.02055801278530.1160922811940.1355407107730.0908217395010.20716856663715.1863.354-32.96
180.642709524712-0.254655299211-0.4003913393840.3576324329240.2535345374181.19963259041-0.0551849885018-0.021946419083-0.0372863053566-0.0929307907859-0.0306416946872-0.0448772770010.0352245644104-0.0606408813832-0.2605822895461.21561895961-0.08537484565090.380729781260.35716210879-0.05630150688450.3627192774895.7925.125-27.708
197.099441023025.14059832024-1.54414852895.06736200157-0.9927801093260.3400609306170.399033589681-0.0913260676303-0.4632535217020.231724911975-0.3032454061530.3067171554420.142747818550.02363196243060.02784744105390.906482362544-0.196219228881-0.2605741545380.414806848484-0.1042022100180.50018931653-22.218-21.367-34.832
200.365430750184-0.988067765254-0.08731616048813.576287478951.828897007273.16711422225-0.180231612288-0.09913896314580.0664706976138-0.6765497273350.3191010988120.015524860763-0.3919162051830.118684428884-0.1093099184020.9844382563380.06669204726710.01738908632460.481477905130.02320567168210.399933491831-16.69-8.777-35.073
215.57695251523-0.9243825708815.378506581928.41400153628-5.980750067749.20220291023-0.075151907010.80574282357-0.0202734394278-1.16947871711-0.151237235844-0.659589990760.489474260059-0.1073532748270.1918883586070.637486124250.0791482859245-0.1034060021570.564202139279-0.2146981845540.600819202189-13.146-2.401-43.476
226.968549086825.000113602263.47100638595.834672710780.2643920074393.934503050770.3692891326070.167152870580.293719343841-0.271299821334-0.1677673565190.58147135675-0.219445398178-0.243330559002-0.1459292409560.5272893442750.374324433580.1217820973041.27562829422-0.09950911086971.17816509975-2.759-5.427-45.3
231.72792702764-2.77510908849-0.3203691625045.995007242031.952209846883.223007816410.454242127821-0.06683565623950.312230093539-0.1391589147590.37636725692-0.818470972503-0.214959444128-0.00303796121131-0.6300150473631.22317467762-0.121168395340.1983442776080.420012025247-0.06143860059590.497431492923-13.6290.776-36.736
240.77810473397-1.567346877851.750546192456.02165087545-4.731842386535.11729353775-0.0556553823365-0.1658710186650.08167230357330.395751444993-0.387650034775-0.240116982554-0.7317020295120.5612990654250.1344620052550.924662642003-0.1150565707280.3110783177340.4616592060880.08524752580090.47064305907513.445-21.429-2.846
250.01096067731190.0785756251351-0.04674872750160.397247244515-0.2304706485490.1364692487630.1520505654020.09460001714330.0869229170136-0.207144844081-0.152415523744-0.0686337398850.07927288120640.0329791769606-0.03692332033411.166686719480.1193160915270.4378030823140.180159830704-0.08525244077050.42530236601612.774-21.415-12.651
260.1105563459470.07674692576760.07401500313740.1302010508930.03771693430690.0530982513064-0.01318737179060.0662108262773-0.1097835426260.01718016357070.1154065951-0.1209289388870.07471398709690.05726363505610.2593523203610.814054047457-0.01956090948620.2499760347890.164527632696-0.05918435106140.3180231380597.791-29.026-4.481
276.69623474720.638075848013-2.601398051523.37955057659-3.840601360024.90026344836-0.1845145681420.0368123278852-0.0246425097181-0.24533921151-0.478195213335-0.44474183570.05789447110290.6124573121410.4924275050861.31666997334-0.08814183896640.00858013950120.5446061391030.1515945295470.38528731055218.938-20.511-6.996
280.9173609095710.6029225021270.603738353822.392985785991.329398428011.279785289550.09381508668630.3552208900060.0877377646834-0.0628539508982-0.0548143581974-1.378026624150.4155921755160.434246030309-0.2002567436270.8636014834690.4380095046620.3456298000430.6886686113360.2939862013580.98887206108620.742-31.071-8.682
291.4965737830.1239494515451.438923587331.966102650053.290203751728.78251528867-0.632098734837-0.0724344784753-0.07471161030921.056922509740.441015886472-0.07952775169591.23303832060.7202520900270.1860243094531.519249458290.3369755168360.2908737548620.5327501589310.1017970748691.0545605704216.395-43.515-19.359
306.37445896525-0.359057212482-0.7375856849623.884911874021.094198852534.18462864409-0.528300021289-0.674953571587-0.01825772291750.7410960158460.2927581975810.1746678642580.511933781893-0.8240128716020.2740770066231.765204736430.03769344465180.02200637403360.725506636973-0.04664577624370.543565459822-19.383-16.286-28.929
318.01514913924-1.525553081483.518175323792.09129612371.377238748673.869295358250.0296678079199-0.952167793854-0.4751969684780.266612313204-0.121690566557-0.3422842920840.0660328362332-0.02639610581680.1610210438260.849302662136-0.140310931843-0.2892165618470.9378394796840.4709010321571.0746665341-19.043-30.108-26.476
321.883383233530.660258317353-0.03454817249032.68396161207-0.5173528131543.575321763310.528038437550.031545290821-0.9055576987820.3332898393470.419656333684-0.3751315003411.380784048360.51786592248-0.6898453678090.931700420137-0.121491696812-0.3309152540460.622715775082-0.07129587554330.388508917453-10.566-13.616-26.661
332.09886893529-0.93533039517-0.5522804625654.1316094872-2.216731472681.778908088140.122002658891-0.05539945657250.3555674455260.257878396789-0.152412404627-0.6486039966950.182841124199-0.03654208252830.145591324931.34221896312-0.0576579374658-0.1470805344650.2362276781230.03684075652110.690039091675-19.126-26.615-31.287
340.0165111791368-0.0947900277099-0.04977500531550.8142782924570.3863869417070.1853290470840.409514561398-0.104198522077-0.3841809902960.292879651797-0.284897722444-0.01305449356160.868297455624-0.271753962027-0.2532828513672.31969713074-0.157340660406-0.4559629541780.762154614545-0.04295160305170.728798014624-16.849-28.77-19.14
352.492623450712.990379464271.884520622763.809410669192.614639687773.064941953240.06100770414160.2573062740850.0260276545165-0.4524425470060.286098050549-0.483780447321-0.05633508601410.695017471525-0.5374598222841.117414808430.1695812315010.333992459190.498370125463-0.03716373417550.5186058866220.956-26.822-28.431
361.69714229316-0.2013189897080.7043428511875.53079335739-2.593730080443.21021612747-0.0495985225494-0.0810335508056-0.2659582060560.174917876698-0.288115282381-0.456562508198-0.1034193350550.1614142797680.2105375823730.8171892182080.112479568360.1642818037790.1728630834360.1930358051130.56260817759820.865-13.535-27.063
370.7197791314040.0780769391639-0.2398746518760.2856979858050.2843048533170.4265010639620.0529929299695-0.05021258077040.06931154692940.4309056495630.2312945087260.9354958439230.08104586623660.0313951382116-0.1752906081831.38337788663-0.1898906269910.1158528844420.6881654989790.3736127327350.94688727731311.758-28.183-19.941
380.3351826741690.1867784196010.2502802266160.6390112932190.5217752356310.4597080217990.108699922816-0.0342042110245-0.1104699944770.247205076555-0.07479408068530.09063289149290.346763340878-0.062689928002-0.005318800796751.047233290780.002264622509510.2649330911480.0813844561874-0.008280279408170.33325294948718.235-24.622-25.124
392.089833532421.35782832408-0.5581043595623.21449951252-0.8462551476760.254057265127-0.0224815552588-0.468131263552-0.4088968290621.15878362666-0.193429066175-0.3375239121070.128804728591-0.015628782597-0.04529401516241.23776554259-0.09804719825190.1815810948910.132758262082-0.01718473806610.49649362053621.197-20.489-28.436
400.05100884937480.0898267549152-0.1333891802530.159269850948-0.2296279754310.3264953798820.124235989411-0.07499034059330.2997109946220.2659227371070.0803183488625-0.252421915547-0.212913699619-0.0828930933234-0.07388077682511.09633052378-0.05737548097980.2186189534950.248232332979-0.1412299044830.74409203544123.629-12.968-19.618
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 17:26 )A17 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:41 )A27 - 41
3X-RAY DIFFRACTION3( CHAIN A AND RESID 42:48 )A42 - 48
4X-RAY DIFFRACTION4( CHAIN A AND RESID 49:54 )A49 - 54
5X-RAY DIFFRACTION5( CHAIN A AND RESID 55:70 )A55 - 70
6X-RAY DIFFRACTION6( CHAIN A AND RESID 71:77 )A71 - 77
7X-RAY DIFFRACTION7( CHAIN A AND RESID 78:86 )A78 - 86
8X-RAY DIFFRACTION8( CHAIN A AND RESID 87:92 )A87 - 92
9X-RAY DIFFRACTION9( CHAIN A AND RESID 93:101 )A93 - 101
10X-RAY DIFFRACTION10( CHAIN B AND RESID 17:26 )B17 - 26
11X-RAY DIFFRACTION11( CHAIN B AND RESID 27:41 )B27 - 41
12X-RAY DIFFRACTION12( CHAIN B AND RESID 42:47 )B42 - 47
13X-RAY DIFFRACTION13( CHAIN B AND RESID 48:54 )B48 - 54
14X-RAY DIFFRACTION14( CHAIN B AND RESID 55:65 )B55 - 65
15X-RAY DIFFRACTION15( CHAIN B AND RESID 66:71 )B66 - 71
16X-RAY DIFFRACTION16( CHAIN B AND RESID 72:78 )B72 - 78
17X-RAY DIFFRACTION17( CHAIN B AND RESID 79:92 )B79 - 92
18X-RAY DIFFRACTION18( CHAIN B AND RESID 93:102 )B93 - 102
19X-RAY DIFFRACTION19( CHAIN C AND RESID 17:31 )C17 - 31
20X-RAY DIFFRACTION20( CHAIN C AND RESID 32:59 )C32 - 59
21X-RAY DIFFRACTION21( CHAIN C AND RESID 60:71 )C60 - 71
22X-RAY DIFFRACTION22( CHAIN C AND RESID 72:78 )C72 - 78
23X-RAY DIFFRACTION23( CHAIN C AND RESID 79:101 )C79 - 101
24X-RAY DIFFRACTION24( CHAIN D AND RESID 11:24 )D11 - 24
25X-RAY DIFFRACTION25( CHAIN D AND RESID 25:42 )D25 - 42
26X-RAY DIFFRACTION26( CHAIN D AND RESID 43:51 )D43 - 51
27X-RAY DIFFRACTION27( CHAIN D AND RESID 52:57 )D52 - 57
28X-RAY DIFFRACTION28( CHAIN D AND RESID 58:69 )D58 - 69
29X-RAY DIFFRACTION29( CHAIN D AND RESID 70:75 )D70 - 75
30X-RAY DIFFRACTION30( CHAIN F AND RESID 9:18 )F9 - 18
31X-RAY DIFFRACTION31( CHAIN F AND RESID 19:31 )F19 - 31
32X-RAY DIFFRACTION32( CHAIN F AND RESID 32:40 )F32 - 40
33X-RAY DIFFRACTION33( CHAIN F AND RESID 41:53 )F41 - 53
34X-RAY DIFFRACTION34( CHAIN F AND RESID 54:70 )F54 - 70
35X-RAY DIFFRACTION35( CHAIN E AND RESID 8:21 )E8 - 21
36X-RAY DIFFRACTION36( CHAIN E AND RESID 22:29 )E22 - 29
37X-RAY DIFFRACTION37( CHAIN E AND RESID 30:35 )E30 - 35
38X-RAY DIFFRACTION38( CHAIN E AND RESID 36:45 )E36 - 45
39X-RAY DIFFRACTION39( CHAIN E AND RESID 46:57 )E46 - 57
40X-RAY DIFFRACTION40( CHAIN E AND RESID 58:72 )E58 - 72

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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