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- PDB-6krz: Crystal structure of the human adiponectin receptor 1 D208A mutant -

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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: 6krz
タイトルCrystal structure of the human adiponectin receptor 1 D208A mutant
要素
  • Adiponectin receptor protein 1
  • The heavy chain variable domain (Antibody)
  • The light chain variable domain (Antibody)
キーワードMEMBRANE PROTEIN/IMMUNE SYSTEM / membrane protein / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / leptin-mediated signaling pathway / negative regulation of epithelial cell migration / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of non-canonical NF-kappaB signal transduction / negative regulation of epithelial to mesenchymal transition / fatty acid oxidation ...adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / leptin-mediated signaling pathway / negative regulation of epithelial cell migration / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of non-canonical NF-kappaB signal transduction / negative regulation of epithelial to mesenchymal transition / fatty acid oxidation / regulation of lipid metabolic process / regulation of glucose metabolic process / positive regulation of insulin receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / negative regulation of cell growth / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis / protein kinase binding / metal ion binding / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
AdipoR/Haemolysin-III-related / Haemolysin-III related
類似検索 - ドメイン・相同性
OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Adiponectin receptor protein 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.05 Å
データ登録者Tanabe, H. / Fujii, Y. / Okada-Iwabu, M. / Iwabu, M. / Yamauchi, T. / Kadowaki, T. / Yokoyama, S.
資金援助 日本, 2件
組織認可番号
Japan Agency for Medical Research and Development (AMED)JP17am010108 日本
Ministry of Education, Culture, Sports, Science and Technology (Japan)16K18509 日本
引用ジャーナル: Commun Biol / : 2020
タイトル: Human adiponectin receptor AdipoR1 assumes closed and open structures.
著者: Tanabe, H. / Fujii, Y. / Okada-Iwabu, M. / Iwabu, M. / Kano, K. / Kawana, H. / Hato, M. / Nakamura, Y. / Terada, T. / Kimura-Someya, T. / Shirouzu, M. / Kawano, Y. / Yamamoto, M. / Aoki, J. / ...著者: Tanabe, H. / Fujii, Y. / Okada-Iwabu, M. / Iwabu, M. / Kano, K. / Kawana, H. / Hato, M. / Nakamura, Y. / Terada, T. / Kimura-Someya, T. / Shirouzu, M. / Kawano, Y. / Yamamoto, M. / Aoki, J. / Yamauchi, T. / Kadowaki, T. / Yokoyama, S.
履歴
登録2019年8月22日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年8月19日Provider: repository / タイプ: Initial release
改定 1.12020年9月16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_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 1.22023年11月22日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Adiponectin receptor protein 1
B: Adiponectin receptor protein 1
C: Adiponectin receptor protein 1
D: The heavy chain variable domain (Antibody)
E: The light chain variable domain (Antibody)
F: The heavy chain variable domain (Antibody)
G: The light chain variable domain (Antibody)
H: The heavy chain variable domain (Antibody)
I: The light chain variable domain (Antibody)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)181,17519
ポリマ-179,4169
非ポリマー1,75910
1,60389
1
A: Adiponectin receptor protein 1
D: The heavy chain variable domain (Antibody)
E: The light chain variable domain (Antibody)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)60,5317
ポリマ-59,8053
非ポリマー7254
543
タイプ名称対称操作
identity operation1_555x,y,z1
2
B: Adiponectin receptor protein 1
F: The heavy chain variable domain (Antibody)
G: The light chain variable domain (Antibody)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,9665
ポリマ-59,8053
非ポリマー1602
543
タイプ名称対称操作
identity operation1_555x,y,z1
3
C: Adiponectin receptor protein 1
H: The heavy chain variable domain (Antibody)
I: The light chain variable domain (Antibody)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)60,6797
ポリマ-59,8053
非ポリマー8734
543
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)104.589, 119.350, 197.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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要素

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タンパク質 , 1種, 3分子 ABC

#1: タンパク質 Adiponectin receptor protein 1 / Progestin and adipoQ receptor family member 1 / Progestin and adipoQ receptor family member I


分子量: 34996.789 Da / 分子数: 3 / 変異: D208A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ADIPOR1, PAQR1, TESBP1A, CGI-45 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q96A54

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抗体 , 2種, 6分子 DFHEGI

#2: 抗体 The heavy chain variable domain (Antibody)


分子量: 13160.635 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Escherichia coli (大腸菌)
#3: 抗体 The light chain variable domain (Antibody)


分子量: 11647.850 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Escherichia coli (大腸菌)

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非ポリマー , 5種, 99分子

#4: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 3 / 由来タイプ: 合成 / : PO4
#5: 化合物 ChemComp-OLA / OLEIC ACID / オレイン酸


分子量: 282.461 Da / 分子数: 2 / 由来タイプ: 合成 / : C18H34O2
#6: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 3 / 由来タイプ: 合成 / : Zn
#7: 化合物 ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-O-オレオイル-L-グリセロ-ル


分子量: 356.540 Da / 分子数: 2 / 由来タイプ: 合成 / : C21H40O4
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 89 / 由来タイプ: 天然 / : H2O

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詳細

研究の焦点であるリガンドがあるかN
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: 3.44 Å3/Da / 溶媒含有率: 64.25 %
結晶化温度: 293 K / 手法: 脂質キュービック相法 / pH: 7.5 / 詳細: PEG 400, tris, lithium acetate

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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: SPring-8 / ビームライン: BL32XU / 波長: 1 Å
検出器タイプ: RAYONIX MX-225 / 検出器: CCD / 日付: 2015年2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: 1 Å / 相対比: 1
反射解像度: 3.048→47.9 Å / Num. obs: 47972 / % possible obs: 99.8 % / 冗長度: 6.1 % / Biso Wilson estimate: 70.01 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.114 / Rrim(I) all: 0.284 / Net I/σ(I): 7
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.048-3.236.21.49475730.5150.6511.63199
9.14-47.95.50.04219430.9980.020.04799.2

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549+SVN精密化
Aimless0.5.32データスケーリング
PHASER位相決定
PDB_EXTRACT3.24データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 3WXV

3wxv
PDB 未公開エントリ


解像度: 3.05→47.9 Å / SU ML: 0.428 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.0443
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2731 1999 4.17 %
Rwork0.2158 45886 -
obs0.2182 47885 99.76 %
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: 74.8 Å2
精密化ステップサイクル: LAST / 解像度: 3.05→47.9 Å
タンパク質核酸リガンド溶媒全体
原子数12111 0 101 89 12301
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.001912580
X-RAY DIFFRACTIONf_angle_d0.430517061
X-RAY DIFFRACTIONf_chiral_restr0.03821814
X-RAY DIFFRACTIONf_plane_restr0.00322132
X-RAY DIFFRACTIONf_dihedral_angle_d3.16367162
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.120.37771370.3273148X-RAY DIFFRACTION97.36
3.12-3.210.39411400.29993224X-RAY DIFFRACTION99.97
3.21-3.30.35331420.28543269X-RAY DIFFRACTION100
3.3-3.410.29511410.27383228X-RAY DIFFRACTION100
3.41-3.530.31291420.26473257X-RAY DIFFRACTION100
3.53-3.670.30481420.24233247X-RAY DIFFRACTION99.97
3.67-3.840.2721410.22523255X-RAY DIFFRACTION99.91
3.84-4.040.30021420.20983243X-RAY DIFFRACTION99.97
4.04-4.30.24481430.19843296X-RAY DIFFRACTION99.97
4.3-4.630.24151420.1873267X-RAY DIFFRACTION100
4.63-5.090.2251430.17723288X-RAY DIFFRACTION99.94
5.09-5.830.26021460.19593320X-RAY DIFFRACTION99.88
5.83-7.340.27991450.20733348X-RAY DIFFRACTION99.97
7.34-47.90.24011530.18843496X-RAY DIFFRACTION99.73
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.90059714276-1.200383601656.553790686743.83779719514-0.9615430650368.774496701510.482494989416-0.370005063773-0.1595466647850.13396548169-0.5364920789620.8201954024930.277188924346-0.191864541793-0.06066657104860.9489733005310.130237060670.05456635797530.5072972047910.02194184610860.364737107911-38.5652808455-25.04871357454.9305212422
28.59627977951-1.515875017893.147221989614.45803663359-5.524972648047.11195059268-0.0574159908891-1.631662174660.5173207125430.2777407716890.685216069545-0.3445408688750.3585721152350.2821690360010.08744155597890.5030030804630.08139875230720.004456571399790.725879587049-0.1525582080460.694181897465-43.6908829197-23.578073542841.2988111834
36.279955725370.0317522468743-0.7745675509162.972693125242.435705741312.236500389590.04814986446820.0447281370472-0.2923887001480.3748810514240.2119468054850.907489209597-1.473082891-0.372141537227-0.01474348141770.9345655852140.04708354720620.0322650095660.4393621585180.0439918433220.304686351003-29.4108728769-20.538613680849.612934249
47.472509936694.11978411631.334950449228.246881160411.2603171074.454371233440.100693826930.252291157971-0.999498376197-0.4053610285510.413712900486-1.33777979599-0.9469849397420.377012654476-0.3385308432120.7649524892660.009757693598130.04020380845330.477181594401-0.01880919628020.370997761129-25.6082696863-20.5642936548.784595971
50.0232765267888-0.03595140796660.03806834861730.0250499193671-0.03575696072760.0149102235680.3590657878290.753869509216-0.7229917424370.328799174762-0.2134800672470.5756670231870.8784531080650.579429359851-0.3562843296081.032778623180.124808560779-0.04514933932730.483437745636-0.1515457765860.630000294544-32.3811325362-31.425209107842.4414986819
66.60918474652-2.13560525674-3.800109919088.05926962468-0.3785297682068.20581879498-1.444186158480.772777562005-0.6472789018951.019706621961.01004690905-0.6185492268690.494368113080.3459891402530.4734906833890.772492520889-0.0261318498395-0.02842668269980.487641186586-0.10028048330.36100837772-25.9915003472-30.020743523850.2886378641
78.22774563344-2.569152156685.660060767918.609202324772.04437403175.93579948855-0.515671207523-0.232885784804-0.01313738859450.63049976491-0.1281813388440.759932856105-0.771310912444-0.7713776060610.1609929923790.482838216612-0.08186283591190.1535574985750.595979646236-0.04080985530880.525371023765-38.3264225039-29.303661235552.2854928696
89.71745279461-2.715817284013.868291933791.555373632570.1153041660574.69941299466-0.9205340168510.891608728187-0.08728665309222.046093751042.11150572877-3.22939934064-0.1299973003560.934742815405-0.2092562190320.936351554412-0.118905445193-0.2067613428820.621056872326-0.1119101713020.83798032691-20.8147488307-26.386412883561.6163844841
97.832185798040.3053983320972.172366665191.492303638150.3479764130474.228891849630.176681242078-0.3547164759130.9215882169160.821058786146-0.2369103959060.23766400897-0.069494052411-0.141783510854-0.05359334273850.642174317635-0.0003178111227120.002491112190630.382354359061-0.04930667000930.492507249972-33.6790418232-16.903377651246.5872001234
104.681693676352.03493277753-1.370506499736.10865717069-3.046982232566.1723301589-0.2498031844831.43939503328-0.1985066384141.728678483570.1698179640061.81800976143-0.275725784322.167445322140.2038498056331.156673472250.0167420768717-0.05287483942290.568204165093-0.1905770074690.560334572585-26.3323749428-21.625572869866.473051188
111.00245384672-1.7727294650.8919809148396.84541353323-7.593109446232.000212373630.509095189426-1.40921451923-0.464778892719-0.363497329619-1.048237918750.5147203708591.969264952361.78014089158-0.568631696690.626159476211-0.107855531947-0.1773468866520.707037804637-0.01649712799910.865783927607-15.5940637479-13.539073066641.5007847547
126.09713490468-6.907992336465.317740834457.81173684218-6.029695275174.61162091242-0.7887943815290.798848134992.273609795130.3383059540040.442253822187-2.74357339407-1.73287748516-0.0896442699294-0.06444602062950.7880281528610.02382194264240.1500820735770.3957780913840.1870870166881.29351738611-18.70450101674.0370340399847.8027243409
135.18400054911-6.54110880086-3.945767716538.643946485985.099414534493.98867557234-0.8517957792210.1495471668291.401652536130.1468145764631.55833257463-0.710992885596-0.7878875283621.34663868907-0.4576725251120.5255978398540.00578427044642-0.1471953426150.4435048545080.1494014593470.852743446329-20.90271617412.0904028561140.8061863574
144.064918791971.48527554232-0.6877555909762.458504700791.101203063292.65889403201-0.6373625672250.0767057951025-0.2713528755670.2372515848050.341402449303-0.32066918149-0.494070540130.4907239980560.05666982312090.672642176976-0.0006207355448480.03853493973690.4276292496930.04237608929680.445415168055-23.9318267611-10.953436353737.5872006465
152.308374421640.4650509335251.207416677922.14211682733-0.7152045554373.92555099352-0.2795827432090.04178791576870.3713067967120.254325584615-0.473766138695-0.202591584656-0.392683485761-0.6806193272450.2154195509150.7011566827310.1307589001930.0302648387120.3436436906570.04786153816660.657207201641-33.2972202635-5.0426074018842.1933229149
163.33853486521-2.46989226273-2.34065390046.11026147957-3.28350904117.81059398640.188485030788-0.2368198025280.803865517618-0.986964726534-0.1109902947650.162829820284-0.932873708621-0.00777632220974-0.2148049294360.908527391227-0.0315675017833-0.1407007659310.373369713691-0.06014668115430.759439181419-23.0760275667-2.6178252150435.0410903139
176.57135028633-4.211541510682.071556138054.13693104746-1.130988598442.24861172623-1.22397513179-2.372373907461.667382397911.281044210420.6492735787240.275513231513-0.329770258781-0.5492104413380.2649041168870.7979193315440.1307315879390.06067386837150.663280555387-0.1056755020271.09100117233-31.06370929386.5819036070647.3546539214
184.34088390984-4.842919214932.184897888196.09766683057-2.512341853731.167716986910.09756754344570.627210694220.6722742992030.4644649115210.1121470891950.281613342715-0.4781563873450.136208706147-0.1461816246790.6440244901620.005227560015620.1910535848730.443108755216-0.0047009757180.703367116284-24.2513433187-8.2742264051345.100320125
195.96876449202-1.761489986514.051215152911.12907998278-0.3491423581344.63840975233-0.0322469759937-0.325937352765-0.0390519224858-0.300597418260.105870047648-0.0708324952975-1.46601603638-1.18614719547-0.3199208538920.5072595389350.0101353645674-0.07873200311850.3308580093420.07603619690220.558839714064-22.0221771623-17.764752884439.8994614807
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67-0.0763576817162-0.631175431393-0.5588937002384.72873771438-5.586669645779.829969180450.079908746427-0.2335033945380.03825899591050.7554570394720.0584908138893-0.0721162002596-1.02221263379-0.475256286229-0.1866826275990.713713714893-0.2115677180470.1445217822670.933297879447-0.1066199893780.636653970936-15.6383091129-41.3599238683105.972923649
683.98162492287-0.07845130851761.485514194448.10075470553-5.132860050843.53820077516-0.11015961313-0.5772797926730.2133319567931.10946097463-0.209361328972-0.467490224025-1.279636283011.085528108370.2635504131550.94279552747-0.1214203478230.1247102988290.729636276117-0.15406158090.642150652179-6.54439374148-40.0044869619114.527818916
694.700780457822.0472185708-4.81137854078.35041433679-3.791337163217.328606808260.0339112519819-0.2966310682360.1159372794230.383432703612-0.2775760838140.368935906343-0.8850471906260.01344702837530.2294635526780.929607668514-0.01817095829920.06225129634780.638644747622-0.05962500105050.353855730003-34.0799064149-47.314111277365.4936526547
705.238321283541.58069207244-0.3513313810228.67906950628-2.241480766620.603532474139-0.698099533065-0.9924461791810.3811887277440.01594063186370.268800448089-0.2471279367260.896946467144-0.8260918058480.3678720010150.684748730971-0.09267477743740.1196768307090.7486854452580.02031223020750.441437877168-30.9088666789-43.304355363847.8388250079
713.97843059993-6.111809745362.396365794379.62695280819-3.891144865357.901510972040.2519632877860.181269751077-0.402294709838-0.888525429620.2484214885450.6711308798911.43406533350.250414146185-0.3707583966430.472366166323-0.118596624820.02357041977930.574116138997-0.03234099367030.469791723746-33.0690746488-58.614680166758.8379802874
724.16733693413-4.590105009810.4626401716558.197302184012.76888130663.461780869-0.09219774009530.5069525296320.208640093783-1.6966573193-1.718886240320.09907857820290.424012955511-0.1856722049171.75028771670.636348982662-0.08960982777930.03711977451870.82954212940.03478267006350.466230438117-41.0044558607-50.331649273748.4144332584
738.85504187856-0.891305253204-0.7056105393079.63210389805-6.910554246515.10849013194-0.4030979100460.049168384192-0.309530391395-0.1188353644550.756977086720.3731267557250.170247790496-0.983756343769-0.3524797717670.755102562227-0.07508816663440.1361137735320.527012401002-0.0354779459840.466564115718-42.9272490836-56.025731020257.6802710511
746.38368314322.03193360112-1.696770743462.44287859942-3.389455455916.683850172510.30095467668-0.395102731032-0.1984282541280.8097601437060.4686484375061.78033900615-0.359111772001-0.293688924455-0.7832884327850.5744828838960.092388577740.08067580311910.5214342196670.04080739694120.510399732892-40.2012899206-51.814638225263.6963985401
755.319621785460.566984234707-2.286307910426.04245465121-2.815520290859.202026985640.243645527809-0.2756038291110.3779686888920.662986427752-0.19933265927-0.203671969724-1.359745472560.3233644647180.05814137779910.4952970917270.0534711208968-0.02345188868070.29127458361-0.01706852258770.325988933965-27.5649750735-52.864698645754.9870135158
768.11293052085-1.599291012042.444140240771.32509451859-2.471688423374.765825825260.9965204431271.156350283140.04011111835642.23313968866-0.3294934107490.2040932500261.552138776780.0597035475683-0.344600294781.2289527541-0.3124895027890.09766711294940.264053773819-0.0270195752290.56933988352-35.749767938-55.976782978875.0466071513
779.26436131292-2.541241544894.35179780725.203382867464.038545684258.05017702316-0.508803074417-1.3334779948-1.587352674661.6404190003-0.5782230789521.266355065130.580196809575-1.108047648570.02960398131160.969012249259-0.2511309959080.07264282085010.4369834015890.2114959520530.870967664978-29.6212471555-71.663694888551.948469292
783.96079942284-0.197013506855-5.061268472516.41811177049-2.715668680877.95351426910.186608874519-2.085170833480.267754440474-0.692888427607-0.19483566439-1.034648623190.908771706014-0.3904463780250.2764041424930.626713151350.0074538084387-0.2144867575020.5011715784590.01591232232270.483695973029-13.0700339015-73.114878701661.045248203
793.489139006520.155988564253-1.360252269324.977409364052.056342666921.43877018316-0.2826382768310.365788780332-0.704805814962-0.5746121770250.278536111842-0.294747467788-0.1766711244630.140409843781-0.0195253294930.75696979184-0.08092910848270.004457587986730.2790463860490.03310632067520.543098041152-18.9709305272-70.194207711348.8413362518
806.26974683064-1.78068160643-2.339592009669.00144086909-0.8781000002093.992590674830.148768230699-0.1601655687790.09674914081570.222843664506-0.0792465667248-0.337193858043-0.2673884106330.0193292362048-0.1042693750680.4422381260140.0207956179742-0.04970648265030.346010922699-0.01013479655560.346984734809-16.8533452179-58.529956702753.1175460753
812.044054244428.750719836645.019346359458.325591692934.134941214864.85932962714-0.2690737099950.113647733156-2.62129088876-0.792982195690.270536578701-1.483116687552.385790624780.0884485094339-0.5339179697170.668338277248-0.0346093236099-0.1714795138260.439058124001-0.03029662408040.603548193487-16.0032329683-68.700420355746.9804709919
829.69568328705-2.238464496554.87734187316.035996013311.880824962394.492153156520.132228217536-0.532148736466-0.450178830580.03506190670630.303985128553-0.703597747311-0.3837106335360.0507156100337-0.4108455295880.741194683183-0.07487053903810.1074348898490.36013914061-0.00221022918740.469745656059-13.8235744038-63.511577316157.9096602428
834.21672298120.356475537115-2.842846703734.11983920207-3.194432545183.94652997192-0.1883297526950.566634020989-0.839818231018-0.5684887794820.6814041036490.724422099353-0.00848316135564-1.29590702232-0.2915349562340.510918712961-0.108167580992-0.1417775985210.45049873571-0.08398815798260.524339821131-31.1877767732-64.429032993649.3380747038
849.04668963777-7.30932963104-5.109582368587.363956851573.122629591493.79078806265-0.163433131917-2.363360412131.067067567432.705829223390.38217190494-2.010161732741.57164509320.469770452646-0.4763791969551.14976544214-0.113798308442-0.4111973979260.275525681460.01522557833130.65217861161-11.8527207642-68.77350487464.7651263954
856.948767700341.759335676183.276225019672.055965521772.945685265845.845161312550.304530491029-1.415548481680.2209580158250.77505880606-0.002829878607960.03741076066650.561947275063-1.015953302850.06563779378410.744679570584-0.02016037692050.09228381099620.5241634641140.08514415021450.471156021318-34.8567530298-22.090370806959.9565283047
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 18 through 25 )
2X-RAY DIFFRACTION2chain 'F' and (resid 26 through 32 )
3X-RAY DIFFRACTION3chain 'F' and (resid 33 through 40 )
4X-RAY DIFFRACTION4chain 'F' and (resid 41 through 52 )
5X-RAY DIFFRACTION5chain 'F' and (resid 53 through 60 )
6X-RAY DIFFRACTION6chain 'F' and (resid 61 through 73 )
7X-RAY DIFFRACTION7chain 'F' and (resid 74 through 83 )
8X-RAY DIFFRACTION8chain 'F' and (resid 84 through 91 )
9X-RAY DIFFRACTION9chain 'F' and (resid 92 through 111 )
10X-RAY DIFFRACTION10chain 'F' and (resid 112 through 119 )
11X-RAY DIFFRACTION11chain 'G' and (resid 1 through 6 )
12X-RAY DIFFRACTION12chain 'G' and (resid 7 through 14 )
13X-RAY DIFFRACTION13chain 'G' and (resid 15 through 25 )
14X-RAY DIFFRACTION14chain 'G' and (resid 26 through 38 )
15X-RAY DIFFRACTION15chain 'G' and (resid 39 through 61 )
16X-RAY DIFFRACTION16chain 'G' and (resid 62 through 75 )
17X-RAY DIFFRACTION17chain 'G' and (resid 76 through 83 )
18X-RAY DIFFRACTION18chain 'G' and (resid 84 through 90 )
19X-RAY DIFFRACTION19chain 'G' and (resid 91 through 101 )
20X-RAY DIFFRACTION20chain 'G' and (resid 102 through 107 )
21X-RAY DIFFRACTION21chain 'H' and (resid 1 through 17 )
22X-RAY DIFFRACTION22chain 'H' and (resid 18 through 25 )
23X-RAY DIFFRACTION23chain 'H' and (resid 26 through 33 )
24X-RAY DIFFRACTION24chain 'H' and (resid 34 through 40 )
25X-RAY DIFFRACTION25chain 'H' and (resid 41 through 51 )
26X-RAY DIFFRACTION26chain 'H' and (resid 52 through 60 )
27X-RAY DIFFRACTION27chain 'H' and (resid 61 through 73 )
28X-RAY DIFFRACTION28chain 'H' and (resid 74 through 83 )
29X-RAY DIFFRACTION29chain 'H' and (resid 84 through 91 )
30X-RAY DIFFRACTION30chain 'H' and (resid 92 through 98 )
31X-RAY DIFFRACTION31chain 'H' and (resid 99 through 111 )
32X-RAY DIFFRACTION32chain 'H' and (resid 112 through 119 )
33X-RAY DIFFRACTION33chain 'I' and (resid 1 through 6 )
34X-RAY DIFFRACTION34chain 'I' and (resid 7 through 14 )
35X-RAY DIFFRACTION35chain 'I' and (resid 15 through 25 )
36X-RAY DIFFRACTION36chain 'I' and (resid 26 through 38 )
37X-RAY DIFFRACTION37chain 'I' and (resid 39 through 48 )
38X-RAY DIFFRACTION38chain 'I' and (resid 49 through 61 )
39X-RAY DIFFRACTION39chain 'I' and (resid 62 through 75 )
40X-RAY DIFFRACTION40chain 'I' and (resid 76 through 90 )
41X-RAY DIFFRACTION41chain 'I' and (resid 91 through 101 )
42X-RAY DIFFRACTION42chain 'I' and (resid 102 through 107 )
43X-RAY DIFFRACTION43chain 'A' and (resid 0 through 104 )
44X-RAY DIFFRACTION44chain 'A' and (resid 105 through 120 )
45X-RAY DIFFRACTION45chain 'A' and (resid 121 through 134 )
46X-RAY DIFFRACTION46chain 'A' and (resid 135 through 165 )
47X-RAY DIFFRACTION47chain 'A' and (resid 166 through 227 )
48X-RAY DIFFRACTION48chain 'A' and (resid 228 through 260 )
49X-RAY DIFFRACTION49chain 'A' and (resid 261 through 288 )
50X-RAY DIFFRACTION50chain 'A' and (resid 289 through 300 )
51X-RAY DIFFRACTION51chain 'A' and (resid 301 through 319 )
52X-RAY DIFFRACTION52chain 'A' and (resid 320 through 335 )
53X-RAY DIFFRACTION53chain 'A' and (resid 336 through 360 )
54X-RAY DIFFRACTION54chain 'A' and (resid 361 through 371 )
55X-RAY DIFFRACTION55chain 'B' and (resid 0 through 104 )
56X-RAY DIFFRACTION56chain 'B' and (resid 105 through 165 )
57X-RAY DIFFRACTION57chain 'B' and (resid 166 through 227 )
58X-RAY DIFFRACTION58chain 'B' and (resid 228 through 260 )
59X-RAY DIFFRACTION59chain 'B' and (resid 261 through 299 )
60X-RAY DIFFRACTION60chain 'B' and (resid 300 through 319 )
61X-RAY DIFFRACTION61chain 'B' and (resid 320 through 335 )
62X-RAY DIFFRACTION62chain 'B' and (resid 336 through 369 )
63X-RAY DIFFRACTION63chain 'C' and (resid 0 through 132 )
64X-RAY DIFFRACTION64chain 'C' and (resid 133 through 227 )
65X-RAY DIFFRACTION65chain 'C' and (resid 228 through 254 )
66X-RAY DIFFRACTION66chain 'C' and (resid 255 through 277 )
67X-RAY DIFFRACTION67chain 'C' and (resid 278 through 335 )
68X-RAY DIFFRACTION68chain 'C' and (resid 336 through 369 )
69X-RAY DIFFRACTION69chain 'D' and (resid 1 through 25 )
70X-RAY DIFFRACTION70chain 'D' and (resid 26 through 33 )
71X-RAY DIFFRACTION71chain 'D' and (resid 34 through 51 )
72X-RAY DIFFRACTION72chain 'D' and (resid 52 through 60 )
73X-RAY DIFFRACTION73chain 'D' and (resid 61 through 73 )
74X-RAY DIFFRACTION74chain 'D' and (resid 74 through 91 )
75X-RAY DIFFRACTION75chain 'D' and (resid 92 through 111 )
76X-RAY DIFFRACTION76chain 'D' and (resid 112 through 119 )
77X-RAY DIFFRACTION77chain 'E' and (resid 1 through 6 )
78X-RAY DIFFRACTION78chain 'E' and (resid 7 through 14 )
79X-RAY DIFFRACTION79chain 'E' and (resid 15 through 32 )
80X-RAY DIFFRACTION80chain 'E' and (resid 33 through 61 )
81X-RAY DIFFRACTION81chain 'E' and (resid 62 through 75 )
82X-RAY DIFFRACTION82chain 'E' and (resid 76 through 90 )
83X-RAY DIFFRACTION83chain 'E' and (resid 91 through 101 )
84X-RAY DIFFRACTION84chain 'E' and (resid 102 through 107 )
85X-RAY DIFFRACTION85chain 'F' and (resid 1 through 17 )

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万見について

-
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