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- PDB-6tbl: Crystal structure of MMS19(CTD)-CIAO1-CIAO2B CIA targeting complex -

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基本情報

登録情報
データベース: PDB / ID: 6tbl
タイトルCrystal structure of MMS19(CTD)-CIAO1-CIAO2B CIA targeting complex
要素
  • MIP18 family protein galla-2
  • MMS19 nucleotide excision repair protein homolog
  • Probable cytosolic iron-sulfur protein assembly protein Ciao1
キーワードBIOSYNTHETIC PROTEIN / Fe-S cluster / Fe-S / CIA / CIA targeting complex
機能・相同性
機能・相同性情報


cytosolic [4Fe-4S] assembly targeting complex / : / MMXD complex / iron-sulfur cluster assembly / protein maturation / nuclear estrogen receptor binding / chromosome segregation / spindle / transcription coactivator activity / cell division ...cytosolic [4Fe-4S] assembly targeting complex / : / MMXD complex / iron-sulfur cluster assembly / protein maturation / nuclear estrogen receptor binding / chromosome segregation / spindle / transcription coactivator activity / cell division / DNA repair / enzyme binding / nucleoplasm / nucleus / cytoplasm
類似検索 - 分子機能
Probable cytosolic iron-sulfur protein assembly protein, CIAO1/Cia1 / MMS19, C-terminal / MMS19, N-terminal / MIP18 family / DNA repair/transcription protein MET18/MMS19 / RNAPII transcription regulator C-terminal / Dos2-interacting transcription regulator of RNA-Pol-II / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily ...Probable cytosolic iron-sulfur protein assembly protein, CIAO1/Cia1 / MMS19, C-terminal / MMS19, N-terminal / MIP18 family / DNA repair/transcription protein MET18/MMS19 / RNAPII transcription regulator C-terminal / Dos2-interacting transcription regulator of RNA-Pol-II / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Alpha
類似検索 - ドメイン・相同性
: / Probable cytosolic iron-sulfur protein assembly protein Ciao1 / MMS19 nucleotide excision repair protein homolog / MIP18 family protein galla-2
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
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 / 分子置換 / 解像度: 2.65 Å
データ登録者Kassube, S.A. / Thoma, N.H.
資金援助 スイス, 3件
組織認可番号国
European Molecular Biology OrganizationALTF 871-2014 スイス
Swiss National Science FoundationCRSII3_160734 スイス
European Research Council666068 スイス
引用ジャーナル: Nat Struct Mol Biol / 年: 2020
タイトル: Structural insights into Fe-S protein biogenesis by the CIA targeting complex.
著者: Susanne A Kassube / Nicolas H Thomä /
要旨: The cytosolic iron-sulfur (Fe-S) assembly (CIA) pathway is required for the insertion of Fe-S clusters into cytosolic and nuclear client proteins, including many DNA replication and repair factors. ...The cytosolic iron-sulfur (Fe-S) assembly (CIA) pathway is required for the insertion of Fe-S clusters into cytosolic and nuclear client proteins, including many DNA replication and repair factors. The molecular mechanisms of client protein recognition and Fe-S cluster transfer remain unknown. Here, we report crystal structures of the CIA targeting complex (CTC), revealing that its CIAO2B subunit is centrally located and bridges CIAO1 and the client adaptor protein MMS19. Cryo-EM reconstructions of human CTC bound either to the DNA replication factor primase or to the DNA helicase DNA2, combined with biochemical, biophysical and yeast complementation assays, reveal an evolutionarily conserved, bipartite client recognition mode facilitated by CIAO1 and the structural flexibility of the MMS19 subunit. Unexpectedly, the primase Fe-S cluster is located ~70 Å away from the CTC reactive cysteine, implicating conformational dynamics of the CTC or additional maturation factors in the mechanism of Fe-S cluster transfer.
履歴
登録2019年11月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年7月29日Provider: repository / タイプ: Initial release
改定 1.12021年2月10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 / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年5月1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

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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: MMS19 nucleotide excision repair protein homolog
B: MMS19 nucleotide excision repair protein homolog
C: MIP18 family protein galla-2
D: MIP18 family protein galla-2
E: Probable cytosolic iron-sulfur protein assembly protein Ciao1
F: Probable cytosolic iron-sulfur protein assembly protein Ciao1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)137,58311
ポリマ－137,3196
非ポリマー2645
水18010
1
A: MMS19 nucleotide excision repair protein homolog
C: MIP18 family protein galla-2
E: Probable cytosolic iron-sulfur protein assembly protein Ciao1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,8236
ポリマ－68,6593
非ポリマー1633
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: MMS19 nucleotide excision repair protein homolog
D: MIP18 family protein galla-2
F: Probable cytosolic iron-sulfur protein assembly protein Ciao1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,7615
ポリマ－68,6593
非ポリマー1012
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)144.070, 144.070, 166.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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要素

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タンパク質 , 3種, 6分子 ABCDEF

#1: タンパク質 MMS19 nucleotide excision repair protein homolog / MET18 homolog / MMS19-like protein


分子量: 13570.036 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Mms19, Mms19l / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9D071
#2: タンパク質 MIP18 family protein galla-2


分子量: 17806.127 Da / 分子数: 2 / 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: galla-2, CG7949 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9VTC4
#3: タンパク質 Probable cytosolic iron-sulfur protein assembly protein Ciao1


分子量: 37283.277 Da / 分子数: 2 / 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: Ciao1, CG12797 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q7K1Y4

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非ポリマー , 3種, 15分子

#4: 化合物 ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 2 / 由来タイプ: 合成 / 式: K
#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: 3 / 由来タイプ: 合成 / 式: C2H6O2
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 10 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 3.22 Å3/Da / 溶媒含有率: 61.76 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.2 M KSCN, 20% PEG 3350

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データ収集

回折平均測定温度: 292 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06DA / 波長: 0.999995 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2018年4月15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: 0.999995 Å / 相対比: 1
反射解像度: 2.65→19.99 Å / Num. obs: 51309 / % possible obs: 99.64 % / 冗長度: 53.1 % / Biso Wilson estimate: 81.78 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.2125 / Rpim(I) all: 0.02927 / Rrim(I) all: 0.2146 / Net I/σ(I): 23.53
反射 シェル解像度: 2.65→2.744 Å / 冗長度: 50.4 % / Mean I/σ(I) obs: 0.83 / Num. unique obs: 5018 / CC1/2: 0.363 / % possible all: 99.98

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
XDSデータ削減
XDS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: CIAO1-CIAO2B structure, to be deposited

解像度: 2.65→19.99 Å / SU ML: 0.4329 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 28.9381
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2422 2566 5 %
Rwork0.1977 48721 -
obs0.1999 51287 99.96 %
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: 102.97 Å2
精密化ステップサイクル: LAST / 解像度: 2.65→19.99 Å
タンパク質核酸リガンド溶媒全体
原子数9425 0 14 10 9449
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00239668
X-RAY DIFFRACTIONf_angle_d0.497613164
X-RAY DIFFRACTIONf_chiral_restr0.0441522
X-RAY DIFFRACTIONf_plane_restr0.00341684
X-RAY DIFFRACTIONf_dihedral_angle_d13.07555826
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.70.41021390.36822630X-RAY DIFFRACTION99.96
2.7-2.760.3481410.33272678X-RAY DIFFRACTION100
2.76-2.820.33821400.32252668X-RAY DIFFRACTION99.96
2.82-2.880.38681400.30542655X-RAY DIFFRACTION99.89
2.88-2.950.33321410.3032687X-RAY DIFFRACTION99.96
2.95-3.030.37671400.28412662X-RAY DIFFRACTION99.96
3.03-3.120.32171410.2872673X-RAY DIFFRACTION99.93
3.12-3.220.31241400.27762654X-RAY DIFFRACTION99.89
3.22-3.340.31121430.26112713X-RAY DIFFRACTION99.96
3.34-3.470.31581410.24442674X-RAY DIFFRACTION99.96
3.47-3.630.29391420.23012700X-RAY DIFFRACTION99.93
3.63-3.820.23921420.20712700X-RAY DIFFRACTION100
3.82-4.050.23161420.18122706X-RAY DIFFRACTION100
4.05-4.360.20621440.16732732X-RAY DIFFRACTION100
4.36-4.80.17911440.15082719X-RAY DIFFRACTION100
4.8-5.480.2381450.15982762X-RAY DIFFRACTION100
5.48-6.860.2061470.18692794X-RAY DIFFRACTION100
6.86-19.990.19321540.15112914X-RAY DIFFRACTION99.77
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)
13.29359385702-1.758785482120.5095978989384.74323852302-0.01202218508852.280441009950.075107984799-0.295162712875-0.487199320612-0.124082963216-0.4279252976150.4472067324760.221068071189-0.699864951263-0.1867342338280.72365512177-0.108511593555-0.004571600621241.28729207424-0.1399146150960.727640029162454.860826552140.12422305514.2417040286
24.65357455877-1.824520028160.6124644223482.597103269460.6409648010873.248808946080.0186037874427-0.03109088142910.0381127036620.01075431588-0.04120489964960.09353461818640.406361813578-0.955465153625-0.1252233390010.645569674599-0.06404968331460.002610189328431.12697319429-0.06478431038370.726821042772458.582805075142.0975389822.7014525775
35.13145282484-3.31559954058-0.2225425954244.979949518381.17148019060.723055718273-0.176553458633-1.18576397328-0.2172659646310.7972412038740.1147214729020.5645833295480.211258199681-1.23130029325-0.1179917242350.654858390178-0.1077468164190.01107074585191.27296949782-0.04658925496910.728900833267459.812347608143.86059350333.5513458242
43.81923601708-1.451665922940.1768354602172.182496581630.3833517786093.295729737630.1909556721560.2006990540840.2694716925380.00226992588464-0.174970512698-0.1939517276070.146347956613-0.824845447892-0.08324632436960.614442028574-0.0239531985750.01589372269230.942195083025-0.04140635006360.740246313899469.292152803144.09499336729.3450248018
53.51898365343-1.12654377224-0.2657102778781.33967887334-0.9663511899111.58071016295-0.7751822394040.1009966896-1.47684479714-0.3070835609920.766919788214-0.8923905051451.325054345791.36787427649-0.1982103791941.42486414210.2616459534770.1890407832770.920298668480.03824052627860.939953700978445.172152379162.357036271-6.83091776612
60.503705160979-0.4333510498770.3036086800272.4819832782-0.03055743302862.31791196707-0.3406159215250.3283458828960.874691682903-0.2430947084440.3296925463730.186613916720.7852733118970.381360146543-0.03001786844691.149416670610.2367463212730.1269640348810.738399209753-0.005815013319850.637417585754439.222548748171.314795472-6.0953433063
72.285892731260.04821344037550.02003436080574.77175776798-0.5663825568093.6448511491-0.2270176799050.213888154083-0.171452246943-0.07393083247280.1990633961580.1867754153870.8181632686630.676589709446-0.01165765006651.016044230860.1887338311660.1377934552670.777113737620.01349125180460.681659858885439.594488848171.0212139742.40262702176
83.997416408173.00550359776-0.8847489989536.24968744564-0.5293188560580.995848953898-0.27210571805-0.443729635355-0.2122968401391.151460581640.124676658658-0.2944632595880.6355843890360.332547744821-0.01630801909691.066799516710.1485512067820.1645140612510.743127429120.09679545840840.761569397116437.732480289171.88110319113.199832395
93.458614361961.79729768805-0.3239915731854.48296571546-1.428562290152.44622196884-0.134490364209-0.31966892655-0.03679831421380.2300669244140.2143895581260.215373613570.3031443421720.641216175090.08185022943930.8360263719620.1600870577390.04904636330650.7846540675798.02221987991E-50.711604703996439.94655086183.2317124077.60834731487
105.090402222823.31642844793-3.226160902983.79150498618-2.442352593912.107807299010.346827258788-0.305307956203-1.10935713229-0.1113968114160.3733491093892.954028999241.01137696626-1.96244998334-0.01051251025121.07741305128-0.0001907084635460.01073302088640.9060379227670.1626680623541.37364195818423.785957784174.20775872314.2754763064
110.5666008078841.614270201271.308141857765.713278626194.854428931744.09900848758-0.237689355457-1.457915645440.2361542296261.0917078208-0.3116165807540.604696898714-0.333730480294-0.5536505161250.4169889439961.13133230420.03787737861630.1575318681161.06016182564-0.1257848971331.16645548715487.887906519119.16339827652.3633225114
127.54954968864-0.3196660168183.450972542354.63607563847-1.58873897242.02222592513-0.4188678617050.8185564780470.259831750887-0.758775208917-0.183353040995-0.0411342788802-0.755715504305-0.3050472381970.05812476999131.23058927065-0.161629722750.09180156436421.33780817911-0.1581306382041.39314645252478.740213429116.26040527939.0480421387
131.88835684084-0.683373828154-2.081330559640.6520513018420.6349239550792.84764843850.465958134980.760722287082-0.751584594411-1.709944612260.0234624414969-0.999413916021-0.826593921072-0.6238029977220.02478830611740.7588305377110.0927168036456-0.1003347469281.02795911577-0.1802266107340.897304659152477.914230683127.33430163227.1034990076
141.658303474880.5373964746080.3854970796582.743111393970.6334319912592.20102911598-0.1431039380810.3162328286640.101191932088-0.2362670769090.0838414529326-0.07456539947760.1274848533180.023338704757-0.003600261365610.6121772047370.01214582856150.02749738842570.7404781467270.03392394772150.751034529567486.355715339148.44556685536.3343532493
150.462868482950.0846917917778-0.1753498678441.719636633740.2817039951331.298386715830.112186075478-0.413137580028-0.145209949440.361988510664-0.216922273317-0.0349386308453-0.0196271893744-0.373948224469-0.02761635421630.585459486958-0.04293405392550.02717368654120.739949683737-0.02806591147570.681246536379479.562953984148.39621590445.8093172148
162.03976509255-0.07762612901462.510386589221.6996289647-1.667301062114.400388240480.2735473377491.289290854160.370845014276-0.823764829386-0.5802564032350.420173387488-0.598604850003-1.25878332775-0.04199091165140.7734231958250.0791139284391-0.101040188140.93903851955-0.04452825852281.0144246373472.692395779158.55482742836.6898931643
172.627163602930.8945396483750.651211680252.50975750398-0.758398222690.561067931702-0.1348960928850.698637495907-0.858664092476-0.0906712083829-0.0886299106925-0.207079715051.47474972966-0.2037863680370.1929960762021.20065685787-0.04939039461630.1614285547840.97519834063-0.06422413357670.940246367943460.673415944198.30050436325.2411929652
181.10483485967-0.2996696004381.220800386333.187680792520.09206024372421.897750291850.08499368385521.051158979730.271739847042-0.419375523516-0.0870216644435-0.1631274678550.0347152151980.06164268882170.03668183313450.7147727331750.03886941938360.04230371576650.7942078088910.02878463638370.739308316103434.277756422196.33421627511.5104071734
191.86928561599-0.7600942736190.5683546905630.742679045449-0.5260858257552.49130218673-0.105719908077-0.3991321314470.09586816754580.2656895474650.1164182605650.0624216711482-0.0599681159795-0.05430320989360.08860053985070.649836599160.00532218663120.03097945933740.665666820701-0.03020807071990.786718050816431.0461706193.11581573224.6053517554
203.054687908-0.7339302333051.918041771462.694877882622.053390238693.64269562316-0.8089870566090.485342718524-1.08069411387-0.5452180206390.4266937209030.05750279240371.0865693484-0.597771975887-0.03483230942930.708156519341-0.06681484225340.08244959891030.822366176101-0.117209158910.975080158216421.818794532182.94151595416.6689950226
211.549899937160.06454163680150.2213131203391.87969867217-0.0807349577250.8356137808330.0265948617277-0.1622021943130.06072888791750.953909276765-0.1831805679440.7945634907680.122699486442-1.01414543578-0.06490678838141.04384813324-0.2794051276620.3219330054161.40961001124-0.2900618029791.17128864672457.823472371133.57987899956.7936416125
221.573444732910.8612709299330.5584370662392.63717144993-0.4194551722611.225522484240.198473613428-0.06797116528210.3588761034320.344317788159-0.2822791762981.27997693692-0.0256464928933-1.07188752507-0.1981803957050.907036624361-0.1643114346490.3330341653341.47766258784-0.3602853598121.31314162676452.954944374143.08665111357.9337276928
230.6941400240670.4713800668120.8238521808470.750150876570.4441831302581.073973317130.225471479904-1.171339137370.09094215140780.2241996133530.1708992210820.427735299310.328714396189-1.67652329147-0.2114485271651.14783143364-0.2214249072230.3335274382922.09668465175-0.2725187207591.58550539023451.967515705151.52674208461.3913188592
241.5587433269-1.170693466810.0633305360612.8606725177-0.8173728739141.382794878380.109144616442-0.252732480176-0.1519797530150.715594974724-0.1445842716241.16633820196-1.20404326163-0.430774716677-0.09400492718141.205493284290.08777561216580.2963771600011.58671380393-0.2806439959561.29074200624459.891364336155.55016483363.3018881192
251.09725694557-1.137693055451.078685514711.48446534084-1.282889429391.057508886240.0580122433685-1.031086359860.660149891970.891549339819-0.3503996651730.527527276140.397943244718-0.481947879077-0.3024548255271.28137108984-0.2843829859070.5278269946921.35808521789-0.5748178702571.16922263113463.901087796154.16902573870.7093249444
261.85924481184-0.751060987077-0.456994869262.484049454890.6138756627841.772102075520.207325111749-0.8412589545860.4606673936771.18274681566-0.3814086831630.604368938429-0.0546766138882-0.404639097361-0.04841282782981.42726343247-0.388101861630.2499389254341.47260086879-0.2757948545011.03462004988470.605996656151.42602405773.5224651184
270.670750164889-0.4838526507821.151837454222.25859955366-2.387143652083.260514035730.34861794146-0.9740331399940.1742190067441.35879427628-0.5516341441610.6423570645880.718087779576-0.126376765281-0.09813703290451.62943632356-0.3911156700510.1568728011941.39264285943-0.09890331911970.859515457427475.303563732137.5881267271.1614549494
282.03097180891-0.5318301863270.2374432301331.86996044133-0.3858564708331.052488514140.21798304596-0.933122455896-0.09369818568111.18514444692-0.2341744253530.170702703571.166853224920.0853760402149-0.165250926061.41623496385-0.351712631130.1130460876761.277516992070.03825956232810.961330904463475.858738339134.88142214170.763844461
291.88930972209-0.6474309474880.2518654254981.58772336833-0.229256137791.271416889110.0586732551253-0.308173363636-0.8411184454131.15010758232-0.3182431690230.2909503252730.739322917173-0.447898926868-0.2088827294631.36970497906-0.368944935210.2163510528931.2615707464-0.05052404468271.1274919796467.611204084128.66224731862.2899534074
302.07028226758-1.492452726810.2190431412962.05045687635-0.818755448492.151133151490.284136236427-0.0268563121826-0.780676105346-0.1495402482490.0463675103774-0.05477254822160.4398767992230.4269811052110.08876829650050.7763946980630.1357838189380.09577163790210.913942865960.1131162194450.996903286353449.861408312172.93654008237.4270549615
311.72446574749-0.3124340696170.5528162223221.122723889770.5650477023221.417858020080.173592869662-0.357430782837-0.4806084963160.2524006429970.2150009654510.2796853781980.6051330267510.0438882280416-0.07397205954250.899717851940.107658341449-0.02228036789270.8204817688080.1358901056891.02902683274437.915618832166.25117739239.0254053766
320.6409534572190.4266609001620.2770249708961.358788882130.6100048549921.93690323220.0880312949346-0.720076755816-1.262882681550.3436760994850.2998611257880.642148441320.906926645464-0.302350384027-0.1962361422521.1014536099-0.04682669010490.04303724880831.028092584980.2798416102491.19184101126429.829659921168.82623465346.3897080144
331.701519362840.2637021349090.0538719999782.61962481689-0.7132986006391.610967761450.0100001830846-0.842893122449-0.2293116600890.7505838665960.1464034142240.259925209771-0.254718951157-0.03277734209620.06802816201390.8724093221960.07962704624040.108465189351.132527503910.02201047454280.818040778645434.35477024186.00604210453.2270544837
342.42977008949-0.6673600962660.2738313368832.92854290587-1.01815211691.106023496560.0109279566708-0.4547501005090.2167048058250.2477915181770.011991132914-0.525216928626-0.08613757989750.6691150553920.1282096473230.733913942501-0.0726489120655-0.0204251978821.13802456677-0.04886158916580.951554301519451.699094997187.0457975244.4330666853
351.98832389921-1.638211734450.5851909785062.07518394222-1.326895543511.87723914860.106861239785-0.746726849014-0.141829513536-0.04517458122520.0446695738035-0.367004905331-0.06451677884970.3776284388230.02575552109940.6975429082830.0517970238982-0.004019230647481.045340832140.1029375686090.863609095951451.188199502175.94968110739.9139605361
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 913 through 945 )
2X-RAY DIFFRACTION2chain 'A' and (resid 946 through 986 )
3X-RAY DIFFRACTION3chain 'A' and (resid 987 through 1006 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1007 through 1031 )
5X-RAY DIFFRACTION5chain 'B' and (resid 912 through 927 )
6X-RAY DIFFRACTION6chain 'B' and (resid 928 through 945 )
7X-RAY DIFFRACTION7chain 'B' and (resid 946 through 986 )
8X-RAY DIFFRACTION8chain 'B' and (resid 987 through 1006 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1007 through 1024 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1025 through 1031 )
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 9 )
12X-RAY DIFFRACTION12chain 'C' and (resid 10 through 20 )
13X-RAY DIFFRACTION13chain 'C' and (resid 21 through 35 )
14X-RAY DIFFRACTION14chain 'C' and (resid 36 through 88 )
15X-RAY DIFFRACTION15chain 'C' and (resid 89 through 141 )
16X-RAY DIFFRACTION16chain 'C' and (resid 142 through 155 )
17X-RAY DIFFRACTION17chain 'D' and (resid -1 through 20 )
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 69 )
19X-RAY DIFFRACTION19chain 'D' and (resid 70 through 141 )
20X-RAY DIFFRACTION20chain 'D' and (resid 142 through 155 )
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 27 )
22X-RAY DIFFRACTION22chain 'E' and (resid 28 through 73 )
23X-RAY DIFFRACTION23chain 'E' and (resid 74 through 93 )
24X-RAY DIFFRACTION24chain 'E' and (resid 94 through 111 )
25X-RAY DIFFRACTION25chain 'E' and (resid 112 through 132 )
26X-RAY DIFFRACTION26chain 'E' and (resid 133 through 196 )
27X-RAY DIFFRACTION27chain 'E' and (resid 197 through 224 )
28X-RAY DIFFRACTION28chain 'E' and (resid 225 through 281 )
29X-RAY DIFFRACTION29chain 'E' and (resid 282 through 335 )
30X-RAY DIFFRACTION30chain 'F' and (resid 0 through 27 )
31X-RAY DIFFRACTION31chain 'F' and (resid 28 through 87 )
32X-RAY DIFFRACTION32chain 'F' and (resid 88 through 122 )
33X-RAY DIFFRACTION33chain 'F' and (resid 123 through 254 )
34X-RAY DIFFRACTION34chain 'F' and (resid 255 through 305 )
35X-RAY DIFFRACTION35chain 'F' and (resid 306 through 335 )

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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