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- PDB-8xwx: Crystal structure of FIS1-BAP31 complex from human -

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基本情報

登録情報
データベース: PDB / ID: 8xwx
タイトルCrystal structure of FIS1-BAP31 complex from human
要素
  • B-cell receptor-associated protein 31
  • Mitochondrial fission 1 protein
キーワードAPOPTOSIS / MAM complex / mitochondria / ER.
機能・相同性
機能・相同性情報


positive regulation of retrograde protein transport, ER to cytosol / negative regulation of fatty acid transport / negative regulation of ATP metabolic process / Class I peroxisomal membrane protein import / protein localization to endoplasmic reticulum exit site / positive regulation of ERAD pathway / Apoptotic execution phase / perinuclear endoplasmic reticulum / mitochondria-associated endoplasmic reticulum membrane contact site / peroxisome fission ...positive regulation of retrograde protein transport, ER to cytosol / negative regulation of fatty acid transport / negative regulation of ATP metabolic process / Class I peroxisomal membrane protein import / protein localization to endoplasmic reticulum exit site / positive regulation of ERAD pathway / Apoptotic execution phase / perinuclear endoplasmic reticulum / mitochondria-associated endoplasmic reticulum membrane contact site / peroxisome fission / mitochondrial fission / positive regulation of ubiquitin-dependent protein catabolic process / peroxisomal membrane / clathrin-coated vesicle / protein targeting to mitochondrion / Golgi cisterna membrane / Apoptotic cleavage of cellular proteins / RSV-host interactions / MHC class I protein binding / RHOA GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of intrinsic apoptotic signaling pathway / lipid droplet / endoplasmic reticulum-Golgi intermediate compartment membrane / response to endoplasmic reticulum stress / lumenal side of endoplasmic reticulum membrane / mitochondrion organization / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / peroxisome / spermatogenesis / molecular adaptor activity / mitochondrial outer membrane / Golgi membrane / apoptotic process / lipid binding / endoplasmic reticulum membrane / protein-containing complex binding / endoplasmic reticulum / protein-containing complex / mitochondrion / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
B-cell receptor-associated protein 29/31 / BAP29/BAP31, transmembrane domain / Bap31/Bap29 cytoplasmic coiled-coil domain / Bap31/Bap29 transmembrane region / Bap31/Bap29 cytoplasmic coiled-coil domain / Mitochondria fission 1 protein / Fis1, N-terminal tetratricopeptide repeat / Fis1, C-terminal tetratricopeptide repeat / Mitochondria fission protein Fis1, cytosolic domain / Fis1 N-terminal tetratricopeptide repeat ...B-cell receptor-associated protein 29/31 / BAP29/BAP31, transmembrane domain / Bap31/Bap29 cytoplasmic coiled-coil domain / Bap31/Bap29 transmembrane region / Bap31/Bap29 cytoplasmic coiled-coil domain / Mitochondria fission 1 protein / Fis1, N-terminal tetratricopeptide repeat / Fis1, C-terminal tetratricopeptide repeat / Mitochondria fission protein Fis1, cytosolic domain / Fis1 N-terminal tetratricopeptide repeat / Fis1 C-terminal tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
類似検索 - ドメイン・相同性
BETA-MERCAPTOETHANOL / B-cell receptor-associated protein 31 / Mitochondrial fission 1 protein
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: 2.69 Å
データ登録者Nguyen, M.D. / Bong, S.M. / Lee, B.I.
資金援助 韓国, 2件
組織認可番号国
National Research Foundation (NRF, Korea)2018R1A5A2023127 韓国
National Research Foundation (NRF, Korea)2019R1A2C1002545 韓国
引用
ジャーナル: To Be Published
タイトル: A crystal structure containing FIS1 and BAP31 suggests the clue for FIS1-BAP31 interaction
著者: Nguyen, M.D. / Bong, S.M. / Lee, B.I.
#1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2024年1月17日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年5月15日Provider: repository / タイプ: Initial release

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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
E: B-cell receptor-associated protein 31
A: Mitochondrial fission 1 protein
G: B-cell receptor-associated protein 31
D: B-cell receptor-associated protein 31
F: B-cell receptor-associated protein 31
C: Mitochondrial fission 1 protein
B: Mitochondrial fission 1 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,8679
ポリマ－75,6937
非ポリマー1742
水45025
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)104.632, 237.267, 90.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-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 3 through 18 or resid 21...
d_2ens_1(chain "B" and (resid 3 through 18 or resid 21...
d_3ens_1(chain "C" and (resid 3 through 18 or resid 21...
d_1ens_2(chain "D" and (resid 170 or resid 172 through 203...
d_2ens_2(chain "F" and (resid 170 or resid 172 through 203...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAGLUGLUAB3 - 185 - 20
d_12ens_1PHEPHEALAALAAB21 - 3923 - 41
d_13ens_1CYSCYSGLUGLUAB41 - 5943 - 61
d_14ens_1LEULEUPROPROAB61 - 6363 - 65
d_15ens_1GLYGLYSERSERAB65 - 6667 - 68
d_16ens_1GLUGLUGLUGLUAB6870
d_17ens_1GLNGLNVALVALAB70 - 9472 - 96
d_18ens_1GLYGLYLEULEUAB96 - 9898 - 100
d_19ens_1THRTHRPROPROAB100 - 102102 - 104
d_110ens_1ALAALAGLUGLUAB107 - 111109 - 113
d_111ens_1LEULEULYSLYSAB113 - 119115 - 121
d_21ens_1ALAALAGLUGLUBG3 - 185 - 20
d_22ens_1PHEPHEALAALABG21 - 3923 - 41
d_23ens_1CYSCYSGLUGLUBG41 - 5943 - 61
d_24ens_1LEULEUPROPROBG61 - 6363 - 65
d_25ens_1GLYGLYSERSERBG65 - 6667 - 68
d_26ens_1GLUGLUGLUGLUBG6870
d_27ens_1GLNGLNVALVALBG70 - 9472 - 96
d_28ens_1GLYGLYLEULEUBG96 - 9898 - 100
d_29ens_1THRTHRPROPROBG100 - 102102 - 104
d_210ens_1ALAALAGLUGLUBG107 - 111109 - 113
d_211ens_1LEULEULYSLYSBG113 - 119115 - 121
d_31ens_1ALAALAGLUGLUCF3 - 185 - 20
d_32ens_1PHEPHEALAALACF21 - 3923 - 41
d_33ens_1CYSCYSGLUGLUCF41 - 5943 - 61
d_34ens_1LEULEUPROPROCF61 - 6363 - 65
d_35ens_1GLYGLYSERSERCF65 - 6667 - 68
d_36ens_1GLUGLUVALVALCF69 - 9471 - 96
d_37ens_1GLYGLYLEULEUCF96 - 9898 - 100
d_38ens_1THRTHRPROPROCF100 - 102102 - 104
d_39ens_1ALAALAGLUGLUCF107 - 111109 - 113
d_310ens_1LEULEULYSLYSCF113 - 119115 - 121
d_11ens_2VALVALVALVALDD1705
d_12ens_2ASNASNGLUGLUDD172 - 2037 - 38
d_13ens_2ALAALAARGARGDD205 - 21340 - 48
d_14ens_2GLNGLNLEULEUDD215 - 23350 - 68
d_21ens_2VALVALVALVALFE1705
d_22ens_2ASNASNGLUGLUFE172 - 2037 - 38
d_23ens_2ALAALAARGARGFE205 - 21340 - 48
d_24ens_2GLNGLNLEULEUFE215 - 23350 - 68

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.86279582209, -0.500522724544, 0.0711362889023), (-0.504405130336, 0.842798232493, -0.187794046228), (0.0340416491179, -0.197909427574, -0.979629023969)76.1972068975, 28.2095241993, 72.0043077603
2given(0.905874670702, -0.410457491195, -0.104478365715), (0.423324970345, 0.869458311883, 0.254633488331), (-0.013676639312, -0.274894328459, 0.961377167254)-9.94365442973, -40.1918791561, -11.5554189336
3given(-0.849129247239, -0.528180085996, -0.00230613112325), (-0.528184191425, 0.849127849217, 0.00183183319154), (0.000990662348064, 0.00277352514165, -0.999995663064)79.8839306777, 22.618648922, 70.1826806363

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要素

#1: タンパク質
B-cell receptor-associated protein 31 / BCR-associated protein 31 / Bap31


分子量: 8053.073 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BCAP31, BAP31 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P51572
#2: タンパク質 Mitochondrial fission 1 protein / FIS1 homolog / hFis1


分子量: 14493.609 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: FIS1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): DE3 / Variant (発現宿主): pLysS / 参照: UniProt: Q9Y3D6
#3: 化合物 ChemComp-BME / BETA-MERCAPTOETHANOL / 2-メルカプトエタノ-ル


分子量: 78.133 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6OS
#4: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 1 / 由来タイプ: 合成 / 式: SO4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 25 / 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: 3.72 Å3/Da / 溶媒含有率: 66.9 %
結晶化温度: 287 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.4 / 詳細: 100 mM sodium acetate pH 4.6, 1.5 M lithium sulfate

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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: PAL/PLS / ビームライン: 5C (4A) / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2019年12月2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: 2.69→40.96 Å / Num. obs: 27276 / % possible obs: 85.8 % / Observed criterion σ(F): 1.35 / 冗長度: 8.2 % / Biso Wilson estimate: 36.52 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rpim(I) all: 0.018 / Rrim(I) all: 0.05 / Net I/σ(I): 99.8
反射 シェル解像度: 2.69→2.76 Å / Num. unique obs: 946 / CC1/2: 0.57 / CC star: 0.852 / Rpim(I) all: 0.587 / % possible all: 42.16

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21rc1_5156精密化
HKL-2000データ削減
HKL-2000データスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.69→40.96 Å / SU ML: 0.3878 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 30.1803
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2868 2000 7.33 %
Rwork0.2536 25276 -
obs0.256 27276 85.8 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 54.22 Å2
精密化ステップサイクル: LAST / 解像度: 2.69→40.96 Å
タンパク質核酸リガンド溶媒全体
原子数4730 0 9 25 4764
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00544779
X-RAY DIFFRACTIONf_angle_d0.78176391
X-RAY DIFFRACTIONf_chiral_restr0.0404724
X-RAY DIFFRACTIONf_plane_restr0.0051816
X-RAY DIFFRACTIONf_dihedral_angle_d21.88131850
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2BAX-RAY DIFFRACTIONTorsion NCS1.08336378198
ens_1d_3BAX-RAY DIFFRACTIONTorsion NCS1.03313440872
ens_2d_2DDX-RAY DIFFRACTIONTorsion NCS0.781961312362
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.760.4621700.3237876X-RAY DIFFRACTION42.16
2.76-2.830.3151870.28851110X-RAY DIFFRACTION53.44
2.83-2.920.35791040.27831305X-RAY DIFFRACTION63.41
2.92-3.010.32051200.28551528X-RAY DIFFRACTION73.34
3.01-3.120.37021360.31031715X-RAY DIFFRACTION82.78
3.12-3.240.34441510.2761914X-RAY DIFFRACTION91.21
3.24-3.390.34211580.29091986X-RAY DIFFRACTION95.2
3.39-3.570.31061620.26762056X-RAY DIFFRACTION98.75
3.57-3.790.28471660.24492087X-RAY DIFFRACTION99.91
3.79-4.080.29431660.24052099X-RAY DIFFRACTION100
4.08-4.490.23391660.21722105X-RAY DIFFRACTION99.96
4.49-5.140.22411680.21812113X-RAY DIFFRACTION99.91
5.14-6.470.32691700.29552156X-RAY DIFFRACTION99.83
6.48-40.960.23091760.22442226X-RAY DIFFRACTION99.05
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)
10.950889428884-1.803123227650.3218093026576.43909966396-1.035967711030.2435116663270.0177872834309-0.00254945614953-0.2408926910240.0691162201937-0.001106486701390.0001553102613750.138834282330.00787634299908-0.02744386739730.6689847168560.374569233435-0.03514361768990.35931065916-0.002979782267450.45555389508623.724153415453.1216430965.4844519986
26.13029406061-2.52855591464-1.426740370278.585382015982.597588197354.46012319320.0420494377941-0.2660702938670.3685377426920.204770491010.0817642752161-0.162450715924-0.6828442532030.0540398135063-0.1255268322420.237037908870.00962555014885-0.08140790558440.151935456587-0.007508591691550.12004255709658.548631147323.961427130452.013672157
31.1309624672-0.773634888972-0.5306496343551.641088182521.19265983911.715120088570.08928630033020.120667682810.0797555090474-0.171228586053-0.07000366215560.00705505704748-0.370513064439-0.1332299635140.07860258166080.2445040793040.166810156097-0.0394527985540.186732768222-0.02104099863570.031449749749748.751906749323.387678505655.2703778431
40.712442768831-0.09827281303070.3560467583280.5922842380540.445515349330.598341971814-0.0334377983903-0.01871670259430.0347812624381-0.1072603390990.03413650410960.17859912138-0.114630999684-0.167306375954-0.05430708186150.2111806640760.116392624263-0.08987512297090.2171796520860.2285952659680.17361926474835.610993043218.059684768550.0724781911
52.13516058773-2.90524090188-1.049304428216.110916938732.225816903490.812367899238-0.129081268878-0.285685721612-0.292452327550.4570387823450.07515937478780.2170874650860.3303648651370.2185143159880.0326486862580.9402610964510.3114931802610.01476477004380.456628029703-0.04221554879680.25239355229831.053725023955.64364368074.91139303251
61.2838660711-2.53781453974-0.4720229528137.181184412520.977130984630.629970408589-0.0553393389972-0.05914943149190.04989178604790.0622906674975-0.0003754807677110.0264562506761-0.128821671639-0.0575182803696-0.009353925191550.7401576621070.41219282263-0.05945428674910.409938899038-0.05628189983260.193615195828.304292213661.387150264772.7374647003
70.2759267958740.05526152673090.04087126245661.86854816945-0.4722669363150.3903877020110.210982061109-0.0531516627395-0.07351134607210.117616008158-0.163358802347-0.017198757158-0.1185034240380.02938112623740.1075104383170.8901729060770.298787131282-0.04693818214020.396787430203-0.0239687362360.17521326182823.486007560558.4642666648-2.18772605735
82.23245766356-1.17569573713-0.2965087406742.59490247290.8801020830721.52279250336-0.002440009906530.01619958922740.0852086808808-0.1148993266030.05952258364990.212617698196-0.267926073082-0.4839440703330.01674546482190.4383337663420.0663814897537-0.2639942539120.4798378527550.230304853040.44927848148627.506759091919.538092520230.9951417477
92.7103778555-2.867729479552.540699163923.71645763297-2.071822323022.939937966260.4463131211370.413736626532-0.123137373899-0.644154638918-0.4982034406640.225651122241-0.00307100014979-0.02336473489460.08728456104040.4480762653830.0431830670603-0.2092744278490.6841457536550.3463915282430.7399693926721.195358549314.978571744931.53449559
106.36652306689-2.58219479951.816628322584.160627560830.01042367037783.45854195959-0.136021902696-0.2224461686030.206737756921-0.144644583124-0.2085399211660.259569492607-0.387197535663-0.6371263630520.3641823349990.3341216657060.0872177184458-0.0718361929930.822499962840.3728358513590.90197643844716.513543646914.421231210638.4984667005
116.39698742497-0.8552255040795.326154365471.48948739997-1.594727063456.1934252965-0.4269835742391.022273697330.348155691859-0.4392398499440.05878267159850.58007874057-0.757461682944-0.1970582071540.3756719859280.691553786627-0.0924750243777-0.4383146035271.338808798850.3482840003041.345155604015.4671420606917.811581206826.9467757919
128.05280145303-2.59982035511.085331854682.872995603240.2331127784551.61876113284-0.1261552449460.9065704523960.460331683189-0.316059383575-0.07426351534670.428854655761-0.227900397844-0.07041416354840.1484544337160.405286248875-0.177070531486-0.208374976370.9373428571510.3931170094351.125208073812.52249556188.0658496011831.0930058865
135.475823002351.23549972605-0.299558160442.040222778150.5894298576660.261421263676-0.09029520105460.0578540532021-0.660970309215-0.0439801048136-0.05165599571730.4221268422770.126757224884-0.3825013317490.1472495125770.355929702983-0.115433600208-0.1054353076631.101876417380.2850251157241.211557286017.877534544152.8523991973135.0313394938
145.523390153071.011435596737.06148686652.696233944940.5550811435079.24480371731-0.55029146644-0.1265236187130.528396704641-0.8748285813340.3417382077450.9057199855120.293720201182-1.644964097220.2113066505340.877707679836-0.287788123372-0.2118615401191.143605574410.2738708332641.284236128817.271115708371.0358142576321.5736095022
156.111757572523.16862597439-0.8212521771793.429671898550.4005969227713.16241297738-0.463149314420.102385268038-0.748588985308-0.146092953506-0.00232665864513-0.1466833665090.384185059476-0.2741192276740.4553157839180.615667229314-0.300491420985-0.1636837734821.058995285340.4879462556861.5071279491212.1824944263-6.9011376794734.0880651838
162.710177505860.47117417970.926788785770.4719195487960.6842788401472.710102918870.226632125348-0.0881558463846-0.340516378685-0.0999669405594-0.1358329866550.238159845470.170308689628-0.755947937728-0.143921126420.913824687737-0.229086788844-0.555169512720.8584299952680.2590873477850.89813926239119.68828306710.552085530218.0774010203
171.39901709921-0.5411006843381.118032672580.868215069464-0.5547464472132.323211516110.147789456440.155966983124-0.178838037327-0.402381157923-0.002972381381210.2360999346070.2374664670560.01694191728730.001898534990260.532629315541-0.0224443629887-0.2443450903020.3121440133770.1347319684730.16721702120937.774309294215.534932475918.761879979
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 179 through 236 )EA179 - 2361 - 58
22chain 'A' and (resid 1 through 31 )AB1 - 311 - 31
33chain 'A' and (resid 32 through 62 )AB32 - 6232 - 62
44chain 'A' and (resid 63 through 120 )AB63 - 12063 - 120
55chain 'G' and (resid 179 through 235 )GC179 - 2351 - 57
66chain 'D' and (resid 169 through 233 )DD169 - 2331 - 65
77chain 'F' and (resid 170 through 235 )FE170 - 2351 - 66
88chain 'C' and (resid 2 through 31 )CF2 - 311 - 30
99chain 'C' and (resid 32 through 47 )CF32 - 4731 - 46
1010chain 'C' and (resid 48 through 61 )CF48 - 6147 - 60
1111chain 'C' and (resid 62 through 69 )CF62 - 6961 - 67
1212chain 'C' and (resid 70 through 83 )CF70 - 8368 - 81
1313chain 'C' and (resid 84 through 100 )CF84 - 10082 - 98
1414chain 'C' and (resid 101 through 107 )CF101 - 10799 - 103
1515chain 'C' and (resid 108 through 121 )CF108 - 121104 - 117
1616chain 'B' and (resid 2 through 47 )BG2 - 471 - 46
1717chain 'B' and (resid 48 through 120 )BG48 - 12047 - 119

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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