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- PDB-6sak: Structure of the OTULINcat C129A - SNX27 PDZ domain complex. -

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基本情報

登録情報
データベース: PDB / ID: 6sak
タイトルStructure of the OTULINcat C129A - SNX27 PDZ domain complex.
要素
  • Sorting nexin-27
  • Ubiquitin thioesterase otulin
キーワードHYDROLASE / MET1-SPECIFIC DEUBIQUITINASE
機能・相同性
機能・相同性情報


establishment of natural killer cell polarity / protein linear deubiquitination / LUBAC complex / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis ...establishment of natural killer cell polarity / protein linear deubiquitination / LUBAC complex / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / endosomal transport / negative regulation of NF-kappaB transcription factor activity / endosome to lysosome transport / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / cysteine-type peptidase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / phosphatidylinositol binding / Regulation of TNFR1 signaling / intracellular protein transport / Schaffer collateral - CA1 synapse / Wnt signaling pathway / negative regulation of inflammatory response / early endosome membrane / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / early endosome / endosome / protein ubiquitination / intracellular membrane-bounded organelle / innate immune response / glutamatergic synapse / signal transduction / proteolysis / cytosol / cytoplasm
類似検索 - 分子機能
Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain ...Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
類似検索 - ドメイン・相同性
Ubiquitin thioesterase otulin / Sorting nexin-27
類似検索 - 構成要素
生物種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 Å
データ登録者Elliott, P.R. / Komander, D.
資金援助 英国, 2件
組織認可番号国
Medical Research Council (United Kingdom)U105192732 英国
European Research Council724804 英国
引用ジャーナル: Nat Commun / 年: 2019
タイトル: Regulation of the endosomal SNX27-retromer by OTULIN.
著者: Stangl, A. / Elliott, P.R. / Pinto-Fernandez, A. / Bonham, S. / Harrison, L. / Schaub, A. / Kutzner, K. / Keusekotten, K. / Pfluger, P.T. / El Oualid, F. / Kessler, B.M. / Komander, D. / Krappmann, D.
履歴
登録2019年7月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年10月2日Provider: repository / タイプ: Initial release
改定 1.12024年1月24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

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集合体

登録構造単位
A: Ubiquitin thioesterase otulin
B: Ubiquitin thioesterase otulin
C: Sorting nexin-27
D: Sorting nexin-27
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)85,64419
ポリマ－84,2384
非ポリマー1,40515
水4,828268
1
A: Ubiquitin thioesterase otulin
C: Sorting nexin-27
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,86810
ポリマ－42,1192
非ポリマー7498
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Ubiquitin thioesterase otulin
D: Sorting nexin-27
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,7769
ポリマ－42,1192
非ポリマー6577
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)54.645, 62.912, 72.017
Angle α, β, γ (deg.)65.132, 85.976, 85.380
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

#1: タンパク質 Ubiquitin thioesterase otulin / Deubiquitinating enzyme otulin / OTU domain-containing deubiquitinase with linear linkage ...Deubiquitinating enzyme otulin / OTU domain-containing deubiquitinase with linear linkage specificity / Ubiquitin thioesterase Gumby


分子量: 31894.590 Da / 分子数: 2 / 変異: C129A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: OTULIN, FAM105B / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Rosetta / 参照: UniProt: Q96BN8, ubiquitinyl hydrolase 1
#2: タンパク質 Sorting nexin-27


分子量: 10224.640 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNX27, KIAA0488, My014 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q96L92
#3: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 6 / 由来タイプ: 合成 / 式: SO4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 268 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.7 Å3/Da / 溶媒含有率: 54.49 % / 解説: Large thin plates
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: 6.8
詳細: 19% (w/v) PEG 3,350, 200 mM Li2(SO4), 100 mM Bis-Tris pH 6.8

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データ収集

回折平均測定温度: 110 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I03 / 波長: 0.96861 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2017年12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: 0.96861 Å / 相対比: 1
反射解像度: 2→42.65 Å / Num. obs: 55998 / % possible obs: 95.6 % / 冗長度: 1.7 % / Biso Wilson estimate: 33.68 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.7
反射 シェル解像度: 2→2.05 Å / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7167 / CC1/2: 0.382

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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
PHENIX1.16_3549精密化
DIALS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: 3ZNZ, 4P2A

3znz

4p2a


解像度: 2→42.65 Å / SU ML: 0.2458 / 交差検証法: FREE R-VALUE / σ(F): 2.03 / 位相誤差: 30.9879
Rfactor反射数%反射
Rfree0.2529 2674 4.78 %
Rwork0.2152 --
obs0.2171 55971 95.53 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 53.45 Å2
精密化ステップサイクル: LAST / 解像度: 2→42.65 Å
タンパク質核酸リガンド溶媒全体
原子数5629 0 84 268 5981
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00315864
X-RAY DIFFRACTIONf_angle_d0.58087977
X-RAY DIFFRACTIONf_chiral_restr0.0412904
X-RAY DIFFRACTIONf_plane_restr0.00311024
X-RAY DIFFRACTIONf_dihedral_angle_d7.64664650
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.3291610.36142784X-RAY DIFFRACTION94
2.04-2.080.38981580.3362746X-RAY DIFFRACTION94.84
2.08-2.120.35751370.32162776X-RAY DIFFRACTION94.55
2.12-2.160.33141460.29222789X-RAY DIFFRACTION94.56
2.16-2.210.29151500.2662760X-RAY DIFFRACTION95.04
2.21-2.270.32371160.26172783X-RAY DIFFRACTION94.77
2.27-2.330.26391060.25752854X-RAY DIFFRACTION95.02
2.33-2.40.3141400.24592779X-RAY DIFFRACTION95.08
2.4-2.480.3311300.24742819X-RAY DIFFRACTION94.98
2.48-2.570.28791060.24322796X-RAY DIFFRACTION94.96
2.57-2.670.29141260.23032815X-RAY DIFFRACTION95.46
2.67-2.790.23431290.22712767X-RAY DIFFRACTION94.7
2.79-2.940.26011350.21652802X-RAY DIFFRACTION95.33
2.94-3.120.23071310.21482850X-RAY DIFFRACTION96.07
3.12-3.360.25831620.2132830X-RAY DIFFRACTION97.24
3.36-3.70.21891350.18562859X-RAY DIFFRACTION96.77
3.7-4.230.20921480.17362862X-RAY DIFFRACTION97.47
4.23-5.330.20082090.16682782X-RAY DIFFRACTION97.43
5.33-42.650.28311490.21462844X-RAY DIFFRACTION96.99
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)
14.276789344692.102433052830.9259269762621.922820960410.04450965354023.7192902406-0.08497592938390.4085297634340.375283319454-0.107150768812-0.04544826320710.254252805299-0.133985296706-0.8342789807880.1318431534810.4425757273890.2053213172640.08869709614560.7332719202430.09511928007190.457260693216-48.8476400912102.582870333-58.6402430439
25.7023901808-3.385645711382.338316448198.00357996332-4.449467801445.760549927520.3314060210661.027075897660.350187458599-1.27924981535-0.2656584109040.5337505445610.08713216632280.07692767976740.002110696943420.4053418182150.086702540349-0.04788223089360.8507671130590.1319888670920.397648991172-44.292840664102.88171243-69.9303663746
33.830735120381.148142473320.8213999681124.406784960091.74060811142.60111322264-0.03833074532170.2392784908290.419008701166-0.05754194693370.03788005060350.0717495372418-0.0993296423394-0.1953923397410.02723276245110.370195900880.1282209438760.04100908581020.4982097447730.1111783958560.302948671157-36.4821020024105.046781046-52.3429794806
43.802381273172.268353993440.2880530365872.992051362030.8313729241332.98596133137-0.1023288833180.376233442972-0.3492276786630.2099530512810.308587398159-0.54585777184-0.1884663255170.734537666998-0.2585596277310.3970973990970.0855436374329-0.05544504379560.5241942473130.0705785783660.355636601394-16.2632165073106.918715324-41.9543192239
52.189178460881.241887180490.4316509887811.75247353777-0.6003782297465.89537186499-0.806129678583-0.7871293494480.823370510728-0.1064350511230.1594196826070.490609783173-0.557916367158-0.70211940960.5419064531790.7128730709320.057023636052-0.00628210936540.459894187039-0.07712396734770.661094457871-23.8089064805123.373627617-41.0026128957
63.872665900243.558775962960.7377142752759.192565807032.059231251944.440954219750.04356904084350.01755930965890.2357158675191.015595794320.2185221538-0.0801826847966-0.228698727492-0.0716576987734-0.255312482370.4840860468040.142444368380.004949443868640.3735108334520.05252811320950.278437478733-23.9071420393108.091676462-37.2949378395
72.645813831650.5380245652430.3973713740952.178084532-0.6878684457341.17280065656-0.194764057012-0.106116120507-0.1626431553190.141384525320.4205228396670.317006164734-0.181971638606-0.354312280634-0.1156446891050.4146694200490.05268009837610.04226317888680.4894842592160.06207021677760.254770813269-36.526949954298.492623278-42.5641771706
87.378940250912.77267555466-1.97115871053.46057039674-1.756446944473.788896218460.2304468973040.3601620174590.4556738393010.2985593379190.05593605225180.171774905222-0.3294865314320.101092695875-0.1791613985450.4123332756770.0653338827096-0.01823038620770.3626841816080.03463085116310.328418106131-20.4244215266114.807818542-48.2875751622
92.241567750830.67064453931-0.1453107068182.66811553221.625479593873.52853069166-0.1148160831180.5031153871640.619080250303-0.2304272828850.2496815063260.196424442561-0.8745146190350.170457682256-0.1326484973010.5618714232010.03442139455580.02185951844370.5876016977130.1865840996520.470057609093-21.8396623442119.842133551-56.7945045923
101.219732384171.070939528031.45837665852.17968856445-1.089308976996.26323266537-0.09561212291141.107035420270.323286730307-0.2112445859040.4577907503310.208132587735-0.2897869940810.0295405602539-0.1348196214850.2735153220580.0360566211520.03117336842310.7884791187210.1672917740130.275425279568-30.5906262572105.850300586-65.045399139
114.778706558551.12311361256-0.822895357472.709960378740.646848881951.492525336120.0335956919890.605922250445-0.131737550697-0.1722408748310.0622895636983-0.03117263509990.0457551716954-0.0242570756424-0.06919271252990.3960461019460.1357902674820.01365609656760.6825963938680.04991285386790.245656754394-32.904692786599.4638857916-60.5459564413
124.57354522803-1.883851795050.632166152563.321032280450.5036049781124.474541040160.202890865058-0.124503474531-0.06498933888470.0284632324669-0.2449160511160.406710874552-0.264789530703-0.8067274789110.01701714485110.243881443177-0.00885937830506-0.02398052678230.3658988759520.03884849340150.312434681558-21.437334214287.6815615028-20.6818990352
132.95157167032-1.22603763135-0.7688585013164.101997305380.2401807877744.43724718127-0.103914872125-0.967884907611-0.486167069730.4651288112810.2024096908660.0652603560360.109491086765-0.44799093436-0.02397110437430.164294363501-0.0143806881973-0.002489109309240.4170733138870.09317691599510.30719526245-14.733657757886.454324156-17.5466669327
144.590614485610.394294795444-0.260215826290.78295678507-0.6393503386152.767500433840.1940697450940.1760534028610.198452167440.0391055798869-0.0600089901566-0.208319471096-0.09869346423890.0464736092298-0.1586135429680.3300455718970.0832281033643-0.0002598015351120.3422497593660.01205878043550.3162638506770.71697326645387.705008705-32.1776537789
151.861750481730.0593101362648-1.387092779827.61492601307-2.878424966424.505785952560.1031004205660.680678755909-0.200581228747-1.31313851577-0.169698820398-0.7881216158440.8513193062270.2938089776940.09589146788650.5470691410290.1853302035970.05797765394750.406056203266-0.02326944439050.49570002212911.516037008771.2422707656-39.2458429786
163.55366771639-0.887343436328-0.2660513464235.880695316190.44347429123.547689736230.1392692271690.145796840190.0706818301318-0.453250891833-0.140923389059-0.008812328331660.0926291069549-0.0850016854771-0.02178683920330.4288816601080.1377310547860.01362865201030.425488122110.02687194368920.227780404303-2.6338512563387.6999543091-39.7433402438
178.10745271558-1.980404354391.363649336584.86947113395-0.4699420124645.324934196210.195462960676-0.237269638635-0.299657201839-0.210403854375-0.176547312739-0.0994976771440.4650776437420.538557104285-0.08788781666470.3240265566420.1089596902050.01977229771480.2931332354230.002593797558050.2570999172216.9211041250975.3822910222-31.5776711825
183.37578145774-0.772130114135-0.0336549735051.82943552031.467477679563.93651770394-0.257041793315-0.677148381142-0.9161935463580.6422227853760.254102361843-0.2123601723760.8844263317870.5175553153420.06474094423140.50449469790.196753643469-0.01385899460810.537617771330.1161980886430.49469357533610.24386075268.4809407758-21.1753210428
194.104541480761.33652040074-1.438767672626.999160668530.1783027061992.53593020984-0.0511558573211-0.130956344802-0.84223461237-0.0203140233244-0.05302521803130.05402089915180.369551859417-0.06107653775670.08604317619080.3689315611080.08958175768830.007843699478750.3672407534540.07402405056430.4205170263071.0741814533973.7774330926-25.0594658763
205.68599647095-1.78612672708-1.949489788862.402167368040.03117203276434.88623288888-0.586882262951-1.77484714251-0.4392578989320.5299062326010.51789406921-0.09853835091890.1861569301980.3401112279260.2102986643980.292746693360.01636845588880.01738893897460.5250264152110.1172012274530.26015405467-3.6144570937284.4526433523-14.0652911106
214.61599524379-0.9394719095880.4976423504942.112386506360.8859879088512.100973061060.0872918606999-0.4612668539760.1268962642490.228970246406-0.0569872515063-0.017604162892-0.149232356797-0.154366289199-0.02433093338490.3268716489780.05462357049360.02825091306510.4436591189180.03500455265740.217375550262-5.9449328797290.5517987285-19.3692439877
224.37675015596-4.84861856138-2.38276617615.397742820952.374113623825.25078037932-0.2510687639380.6439508729360.0794202281828-1.113393244880.851990452186-0.428035131360.6205051222550.0334280786916-0.4561595898980.763473190247-0.2197791500190.2499724978140.990699945487-0.576840400321.09354154302-58.604460539178.4644761634-64.9558492432
234.478388711571.817910923774.011681147624.81182590643-0.3006517358584.50204727832-0.423592439181.81540385289-1.13219373055-0.578745482719-0.2385658373810.1584730499711.59784243853-0.2859813656220.2502781901910.752715095874-0.1663318091850.2204356022681.07537635194-0.4759762443030.571554826057-47.253275899578.2129584709-71.5238971786
248.50765206322-0.908849118643-3.472218725050.8315369678-0.1678185229917.08629042304-0.294956936265-1.496259489610.191309697461.461189270260.205643683191-0.6314595855221.44141399621.94871832244-0.1336439123330.789588794750.220704485937-0.05478526926590.887022855121-0.1067137955120.351965823536-41.32955357686.8964891331-52.10035172
251.10288410574-0.07747150757010.6731491802441.852902015180.517655942724.2016543310.5301210063790.855026151674-0.393059499949-0.250052224348-0.3023927154930.343967990196-0.762033755037-1.80731740021-0.02167577314050.4848130016560.1738623009340.06026525146410.783686802048-0.05463016047110.345229191017-51.003032554789.4293003246-57.2161440649
260.831329715335-0.347387723036-0.7782186781692.97624162257-1.177092642994.466382188360.8856993119020.86393928066-0.672168073742-0.5680583352250.351181784517-0.2737292511851.30118008679-0.0958421405515-0.8253699823561.07854502257-0.0838801677583-0.2921642350351.64150779082-0.6142683788581.01845996047-54.342542082280.9576293408-76.5352869679
275.27828435773-0.3965867748041.035248291217.442246593481.121508010295.82710687562-0.2002648191860.424211311277-0.369894937712-0.231597134418-0.01856905473720.9694708269460.361859683756-1.381338745680.2966198513330.427285750661-0.05301896662870.07622695211350.919182181105-0.1597460952410.562802675059-53.210792267584.2129520748-62.9712560662
284.38144760111.66867776971-0.5634626744061.35810641026-1.789575550063.39215627457-0.308228404906-0.179239830023-1.29433520840.4233196337820.03715713132680.1376911718870.8200354424250.01012346332040.2169118340450.7177994160130.1247090689590.1738374254330.470283272723-0.07106560284670.677160759047-45.678637980276.5323229482-58.3453325134
295.15741156391-0.9877865983380.6985181837516.206274320770.5461667809074.9934103796-0.1468598021340.431174533105-0.9784268741250.453865813258-0.0990426809876-0.2384071936080.747277279617-0.6569733712770.1073874810530.759308476474-0.2983467435680.2892202235981.07530416772-0.3819264915590.853888380301-54.616639136576.3045364362-63.8865339431
309.227900626785.271513980444.931401061599.089969347884.583890534023.16120739785-0.020620356746-1.344591870150.8611592504660.436687522539-1.493995178081.27469531673-0.155114431784-2.347641412131.565686016860.4924413693720.1374360664570.0590455221520.689355986526-0.1536770527140.540572437528-32.159236833110.591983353-14.0373675205
314.99409789745-1.046196345610.5234850256564.758027932290.2945674121744.17576315044-0.0309179185648-0.4092826071650.436456032293-0.19674627751-0.191025294895-0.15325048912-0.982716760892-0.0440095491725-0.1366437076860.3543880121440.0128666653282-0.007213526882880.357799242603-0.1157503647750.389806096023-17.9747046678108.015766902-16.2831941938
322.08677509116-0.1680466361711.463852538933.163788943332.061883935792.565675771270.199495673224-0.3112447906090.271116007154-0.101872485766-0.1216008826740.3762121174010.112120235638-0.947624552689-0.07925756674240.4181178481920.0842490427921-0.007397057392110.494923165773-0.01875655070170.344354225551-23.86154334100.383171764-22.6246905568
333.37995893842-1.80730893707-2.308561794933.394588447083.386214709873.450852125210.152450598764-0.611897472459-0.3861537587510.598925300924-0.1040004073520.347758658002-0.148306839329-1.278605588450.1826637486810.6126873443720.2430748682860.0613305176070.8431433704-0.1568917991190.345835721201-27.7297687094106.010381057-6.6871120964
345.91314140421-1.54810253214-1.52877430214.08177422698-1.108407540193.11145777960.09078046798470.1972460370710.616660587273-0.1208371124790.004009221504610.114615994123-0.861373960842-0.452852892741-0.1602317258770.6090400521730.1518700791980.01064349004870.441469193343-0.02066529047540.372063229919-22.7812194765112.034907467-19.4029623114
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 79 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 140 )
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 204 )
7X-RAY DIFFRACTION7chain 'A' and (resid 205 through 222 )
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 249 )
9X-RAY DIFFRACTION9chain 'A' and (resid 250 through 297 )
10X-RAY DIFFRACTION10chain 'A' and (resid 298 through 319 )
11X-RAY DIFFRACTION11chain 'A' and (resid 320 through 352 )
12X-RAY DIFFRACTION12chain 'B' and (resid 80 through 100 )
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 128 )
14X-RAY DIFFRACTION14chain 'B' and (resid 129 through 151 )
15X-RAY DIFFRACTION15chain 'B' and (resid 152 through 184 )
16X-RAY DIFFRACTION16chain 'B' and (resid 185 through 222 )
17X-RAY DIFFRACTION17chain 'B' and (resid 223 through 248 )
18X-RAY DIFFRACTION18chain 'B' and (resid 249 through 275 )
19X-RAY DIFFRACTION19chain 'B' and (resid 276 through 298 )
20X-RAY DIFFRACTION20chain 'B' and (resid 299 through 319 )
21X-RAY DIFFRACTION21chain 'B' and (resid 320 through 352 )
22X-RAY DIFFRACTION22chain 'C' and (resid 40 through 47 )
23X-RAY DIFFRACTION23chain 'C' and (resid 48 through 58 )
24X-RAY DIFFRACTION24chain 'C' and (resid 59 through 67 )
25X-RAY DIFFRACTION25chain 'C' and (resid 68 through 84 )
26X-RAY DIFFRACTION26chain 'C' and (resid 85 through 93 )
27X-RAY DIFFRACTION27chain 'C' and (resid 94 through 104 )
28X-RAY DIFFRACTION28chain 'C' and (resid 105 through 123 )
29X-RAY DIFFRACTION29chain 'C' and (resid 124 through 134 )
30X-RAY DIFFRACTION30chain 'D' and (resid 40 through 47 )
31X-RAY DIFFRACTION31chain 'D' and (resid 48 through 67 )
32X-RAY DIFFRACTION32chain 'D' and (resid 68 through 84 )
33X-RAY DIFFRACTION33chain 'D' and (resid 85 through 99 )
34X-RAY DIFFRACTION34chain 'D' and (resid 100 through 135 )

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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://pdbjlc1.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