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- PDB-8eo8: Cross-reactive 3180 TCR recognition of HLA-B*35:01-NP8 epitope fr... -

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基本情報

登録情報
データベース: PDB / ID: 8eo8
タイトルCross-reactive 3180 TCR recognition of HLA-B*35:01-NP8 epitope from 2005 H1N1 influenza strain
要素
  • 3180 alpha chain
  • 3180 beta chain
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein NP8 epitope
キーワードIMMUNE SYSTEM / HLA B*3501 / NP418 EPITOPE / T CELL IMMUNITY / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE
機能・相同性
機能・相同性情報


: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
MHC class I antigen / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Influenza A virus (A型インフルエンザウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.30000092477 Å
データ登録者Littler, D.R. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号
Australian Research Council (ARC) オーストラリア
引用ジャーナル: To Be Published
タイトル: Molecular determinants of cross-strain influenza A virus recognition by T-cell receptors
著者: Quinones-Parra, S.M. / Littler, D.R. / Rossjohn, J. / Kedzierska, K.
履歴
登録2022年10月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年3月27日Provider: repository / タイプ: Initial release
改定 1.12024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein NP8 epitope
D: 3180 alpha chain
E: 3180 beta chain
F: MHC class I antigen
G: Beta-2-microglobulin
H: Nucleoprotein NP8 epitope
I: 3180 alpha chain
J: 3180 beta chain
K: MHC class I antigen
L: Beta-2-microglobulin
M: Nucleoprotein NP8 epitope
N: 3180 alpha chain
O: 3180 beta chain
P: MHC class I antigen
Q: Beta-2-microglobulin
R: Nucleoprotein NP8 epitope
S: 3180 alpha chain
T: 3180 beta chain


分子量 (理論値)分子数
合計 (水以外)380,71520
ポリマ-380,71520
非ポリマー00
31,8871770
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein NP8 epitope
D: 3180 alpha chain
E: 3180 beta chain


分子量 (理論値)分子数
合計 (水以外)95,1795
ポリマ-95,1795
非ポリマー00
905
タイプ名称対称操作
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: Nucleoprotein NP8 epitope
I: 3180 alpha chain
J: 3180 beta chain


分子量 (理論値)分子数
合計 (水以外)95,1795
ポリマ-95,1795
非ポリマー00
905
タイプ名称対称操作
identity operation1_555x,y,z1
3
K: MHC class I antigen
L: Beta-2-microglobulin
M: Nucleoprotein NP8 epitope
N: 3180 alpha chain
O: 3180 beta chain


分子量 (理論値)分子数
合計 (水以外)95,1795
ポリマ-95,1795
非ポリマー00
905
タイプ名称対称操作
identity operation1_555x,y,z1
4
P: MHC class I antigen
Q: Beta-2-microglobulin
R: Nucleoprotein NP8 epitope
S: 3180 alpha chain
T: 3180 beta chain


分子量 (理論値)分子数
合計 (水以外)95,1795
ポリマ-95,1795
非ポリマー00
905
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)168.088, 79.468, 172.173
Angle α, β, γ (deg.)90.000, 95.530, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

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タンパク質 , 4種, 16分子 AFKPBGLQDINSEJOT

#1: タンパク質
MHC class I antigen


分子量: 31940.246 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: HLA-B / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: F4NBT2
#2: タンパク質
Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 4 / Fragment: UNP residues 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61769
#4: タンパク質
3180 alpha chain


分子量: 22731.090 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: TRAV13-1 / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#5: タンパク質
3180 beta chain


分子量: 27591.828 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: TRBV20-1 / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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タンパク質・ペプチド / 非ポリマー , 2種, 1774分子 CHMR

#3: タンパク質・ペプチド
Nucleoprotein NP8 epitope


分子量: 1036.265 Da / 分子数: 4 / 由来タイプ: 合成
由来: (合成) Influenza A virus (A型インフルエンザウイルス)
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1770 / 由来タイプ: 天然 / : H2O

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詳細

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: 3.01 Å3/Da / 溶媒含有率: 59.09 %
結晶化温度: 297 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG, 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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.95365 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2017年10月24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: 0.95365 Å / 相対比: 1
反射解像度: 2.3→49 Å / Num. obs: 201262 / % possible obs: 100 % / 冗長度: 2 % / Biso Wilson estimate: 33.6600188899 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.057 / Net I/σ(I): 13.1
反射 シェル解像度: 2.3→2.38 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 20019 / CC1/2: 0.817 / Rrim(I) all: 0.396 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
BUSTER精密化
PHENIX1.10.1_2155精密化
XDSデータ削減
XSCALE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: 3LKS
解像度: 2.30000092477→48.9468431936 Å / SU ML: 0.238391782281 / 交差検証法: FREE R-VALUE / σ(F): 1.96797016213 / 位相誤差: 22.1938559884
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.21858751782 10121 5.03096821657 %
Rwork0.180808352844 191053 -
obs0.182718374785 201174 99.934428184 %
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: 49.1252454965 Å2
精密化ステップサイクル: LAST / 解像度: 2.30000092477→48.9468431936 Å
タンパク質核酸リガンド溶媒全体
原子数26464 0 0 1770 28234
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.013634794375227232
X-RAY DIFFRACTIONf_angle_d1.6617323667537022
X-RAY DIFFRACTIONf_chiral_restr0.1149943547873936
X-RAY DIFFRACTIONf_plane_restr0.008970595627274856
X-RAY DIFFRACTIONf_dihedral_angle_d19.584381594110086
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.32610.2635445056553260.234341167436375X-RAY DIFFRACTION99.8212423656
2.3261-2.35350.2737456209913540.2295782937266302X-RAY DIFFRACTION99.9849782184
2.3535-2.38220.2753133200653490.2213789231066313X-RAY DIFFRACTION100
2.3822-2.41240.2372877462093350.2147892588286358X-RAY DIFFRACTION100
2.4124-2.44410.283989766242980.2168177567466316X-RAY DIFFRACTION99.984882842
2.4441-2.47760.2708077493813500.2077164837036346X-RAY DIFFRACTION99.9552171966
2.4776-2.5130.2346830902143340.2049134250376319X-RAY DIFFRACTION100
2.513-2.55050.2731447060923250.205606172166375X-RAY DIFFRACTION100
2.5505-2.59030.2487671430823300.2076550453116298X-RAY DIFFRACTION100
2.5903-2.63280.2724100058983240.2018301677326384X-RAY DIFFRACTION100
2.6328-2.67820.234811315163510.1930992605516286X-RAY DIFFRACTION99.9849352215
2.6782-2.72690.2645096743833380.1992857929436388X-RAY DIFFRACTION99.9851345325
2.7269-2.77930.2578342877073310.1962186665236323X-RAY DIFFRACTION99.984973704
2.7793-2.83610.2454058298073410.1875157235736377X-RAY DIFFRACTION99.9851168329
2.8361-2.89770.2474759827773390.1854264529876315X-RAY DIFFRACTION99.984973704
2.8977-2.96510.2246933168573370.1869542652016361X-RAY DIFFRACTION99.9850723989
2.9651-3.03930.2240027625613300.1874512449176389X-RAY DIFFRACTION99.9851190476
3.0393-3.12140.2284548460743150.1878072230086315X-RAY DIFFRACTION100
3.1214-3.21330.220782177983070.1827116333986411X-RAY DIFFRACTION100
3.2133-3.31690.2292596406183650.1783833406716377X-RAY DIFFRACTION100
3.3169-3.43550.2193404187793370.1769364176586345X-RAY DIFFRACTION99.9850366602
3.4355-3.5730.1995350973723420.1714340670556367X-RAY DIFFRACTION99.9701981821
3.573-3.73550.2112123685343210.1728466431556373X-RAY DIFFRACTION99.9850634802
3.7355-3.93240.1900959513133270.1627143660186402X-RAY DIFFRACTION99.970286733
3.9324-4.17870.1937155737034090.1546093024676344X-RAY DIFFRACTION99.970392302
4.1787-4.50110.1684232406523520.1461420073126373X-RAY DIFFRACTION99.9851323223
4.5011-4.95370.18065623260.1477906774376446X-RAY DIFFRACTION100
4.9537-5.66950.1976963958353140.1658474868056457X-RAY DIFFRACTION99.8525291255
5.6695-7.13950.2209157553833840.2020868733146439X-RAY DIFFRACTION99.9121394055
7.1395-48.90.2153675137593300.1954147184656579X-RAY DIFFRACTION98.8412017167
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)
12.448712646530.389795808472-0.03722578915654.368868753281.249857307951.06803661183-0.0356854937070.1252910795560.0167881874432-0.3010119605860.06897180598750.43941168923-0.09191271501720.0663564265481-0.004727282695920.1968353933620.0102811142461-0.03736028876680.1468578050290.04981178403820.333066934388466.31784009610.1911036221216.110344875
23.14505422610.9415306079490.4243277336814.97589935551.656546040543.02070918938-0.1001979084460.1552949447990.436519153389-0.6130590071470.1995221095930.443509886817-0.761608608053-0.0378411738649-0.1310166062030.43057457495-0.02280060243030.01107004971270.208659448450.06883457282740.400256753043469.6359645921.4337358049213.453847334
31.027336091910.772322959569-0.6827264049998.323285894050.3372710684031.208588021590.05948132196650.03272332417830.0348260276076-0.216299913838-0.1195525627320.131578706885-0.03270931736980.1045744605160.03170713184620.1772995620990.0142413058703-0.02774268384740.1974041360450.03669082016570.228179876141475.4806980876.30108745486211.370648147
41.605482988310.8609837599260.9757297317333.35167229825-0.0508482693682.76824294121-0.0474040833894-0.0857593401554-0.02612725336910.411612140866-0.01383839370790.320155334296-0.0549333762436-0.03215052925910.0557468141830.2060645686580.03066262243750.06603632992390.1898624208580.0446721630620.306980755254469.933073096-0.48596507565224.446005206
51.996190624090.5185506817090.1437973922142.080686864280.9897132283321.25903982571-0.0500222755994-0.2645287377470.1868035551790.1921544667140.1118591041510.0425908745494-0.1487471712090.100372886221-0.0798182628690.228818180955-0.02270824665850.02629460947580.202851731750.04551277370750.153928880459475.03217449710.0417358751227.539999611
64.643209949680.537287118806-0.2650740353281.771538504960.1196166469531.680145307790.142286679968-1.21521471129-0.230446609610.5353956339520.04462573091790.5782528387250.0619176877405-0.421050623442-0.1566611169450.4912500793520.01678089723990.157125847850.7410425417280.1536118215870.717616651649441.33475653214.5779568259238.134867695
72.53174460189-2.68097271353-1.611441135133.150124018282.390510525982.59631877195-0.1133623022760.09512098962180.03367682202940.07694262157060.01962978460210.2156847798430.268585824875-0.07498384008510.0430990028550.270162439066-0.0310364393470.01485075607980.256525281756-0.01241263725080.587782528359447.6424845695.9720450166219.650236287
88.15718274098-0.4641511329554.863409511080.940380930855-1.431748032964.389753771740.00129306480439-0.4068049238810.6208854568390.3023789248560.131455497097-0.167855204659-0.63755583215-0.281970279869-0.09704231146360.3983160786520.0898140927528-0.05418924172680.3691432449880.02259263796380.867483006531440.32186478328.2988012641222.706026268
90.944234358466-1.70595411911-0.7582734477132.957397995241.216696459810.485792007146-0.108808681797-0.05038223349630.235030515517-0.145792935457-0.0006252603809880.44735497522-0.207954883767-0.1625107949680.141449864790.2610906631090.0390685124086-0.02780622763130.313871536890.02268231822660.674597017568449.95641292311.7899808829216.492158112
108.58337947512-2.047929622460.4118213435383.21004861802-1.264492066373.261840804810.1622168190211.14050630879-0.217493859962-0.586969305009-0.312901812922-0.256992177495-0.1080858541980.3166668196750.1635925216130.3561784818210.0364635247737-0.04279929960830.4817714969830.006299963587060.590641437565444.1585193217.5001134244207.614586127
114.98089634053-2.581720503310.4012192816229.55402211125-1.427203021910.849769718442-0.313424328956-0.1686050775550.2825726705060.6505440999360.5009333723130.142179059975-0.206440290304-0.0486097602271-0.150808808350.2852311622970.01206339821390.05485137323230.2367188007-0.03531048602870.508758465759459.0277224466.54817895297220.519159598
124.50174870679-5.90897500067-1.980606735527.74402562992.553427562151.60475922890.05496606167671.036161406930.123787633566-0.171421868028-0.3861211356780.183286016528-0.42341450689-0.231218324530.2555948723290.3730488207090.0250983131350.02452728703960.3556696351090.09786509236260.688418975064447.59380798320.6313708925214.522470942
132.94522875148-1.4115749369-2.916658137073.71998577949-1.928833020636.55591842890.05171284593670.786820087322-0.377907874498-0.194834568605-0.4994613876150.4085709569210.399705017305-0.4392333118120.3027084234330.3412942242620.07930846665290.007834143055730.4125381397270.01255719420520.7429656417431.1837120823.6192990659215.570428293
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611.997187406371.713039739521.768406204782.024489306761.146174852232.01638537343-0.0992727819367-0.644822619352-0.1980091195780.7625287700270.246038650413-0.00407857816880.7189564158580.0711521264549-0.1195954923080.63518204524-0.01580460773420.002271598242290.5667226100990.04001914403450.318601640593572.603224748-6.61730575134270.699101981
621.29369166454-1.424266572681.139554963165.48221419288-4.708426057354.04873873212-0.132817180516-0.0462561591106-0.03618431031690.4219850710930.1313572104180.0313632887239-0.479047402540.200341529880.01400258531840.609932272303-0.009665196748810.01541475213920.445187344975-0.03232698974460.225505908773573.36762923411.3820314148257.45492525
634.555711217613.57465817494-1.517595978088.99869772125-2.380424489823.325503135640.0309901782428-0.8519964412770.1359663030181.072916704910.09046792750740.550523440609-0.226876749094-0.60467127674-0.06771887322080.6077050278740.03247929419060.08631414932840.654261632220.02577500899110.276095877448565.6727064761.32693525246264.40789478
640.6332273881950.223784751519-0.1545492710350.771103186097-0.8854871432131.15203135458-0.1101737367450.0293624919413-0.08737325222370.03442927002810.15986291378-0.08139279082440.0620362324379-0.263139610888-0.04223847960820.226258560662-0.00800346558744-0.02449011077830.215491607612-0.01987091129470.212357617238568.4408541666.50571084724221.68476603
651.986490869140.5069477163740.6397932871271.616127403720.1999206801894.293775002870.0205440170030.247213977827-0.036631260314-0.3247313827840.01800357992620.2193223273780.325732321642-0.412174758405-0.04628832982830.269532833834-0.0250822438161-0.03118620151710.259440091557-0.005402014019830.231933340919564.4897158491.93337675792198.770227835
661.01615446235-1.968216814472.081423275463.90857437661-4.123483653964.30676337924-0.06941891980870.1090585194780.146439149523-0.2738286109620.2353423661080.4219569262580.0457567081402-0.628265577994-0.1909730870940.591871171813-0.0721172458644-0.1342634397240.6166187211430.09253839448290.401593315207561.3261312288.89085904537175.361392715
675.38767801517-0.0494828020944-0.0691334267443.496096480260.2463541647263.97146106375-0.03034107612070.0518204340837-0.362225611583-0.2880063843550.0688344372837-0.04658143858330.2642165961930.0323477668884-0.02991044375070.618585361267-0.0278120533436-0.08191117305660.300050947985-0.0002510453871960.23944080189572.76460080216.1306828566167.613308221
680.3601555572550.453959698447-0.2723395137413.99335626226-2.037850082872.03150529195-0.109472831979-0.196536978926-0.330567204226-0.7174044212570.0568046816134-0.8853587975160.5816384694280.5280128412780.01245090999250.8528015318720.0368735657024-0.09084987912830.7539275224090.02205758196480.601883380029580.4844271247.77230225112160.125122979
691.905516274290.78115654128-0.60881738641.65871925909-0.6123977964592.14247728719-0.07101280381610.113917717252-0.126396079941-0.1183129233550.0221690866078-0.2327341608120.1804119669760.2244940587750.04863405306140.2062267274360.02293451886970.0165428585830.200673946164-0.02128648454080.262107221082586.00083495411.4228127459202.145507045
702.878187050110.00122653081071.331692895591.458190691850.2684615331623.4080365628-0.2383870527740.06353857074410.288108803352-0.2017295796680.106786890278-0.0563872150195-0.3546819628540.1529520125170.1181996043740.54780667991-0.0377852047235-0.07713469730280.27930459374-0.005239533595680.26824380687579.89691692825.512178188175.344081844
711.58023938364-0.1079510222850.1074040626091.826307955-0.1209459188381.130111687460.01738663815120.138524314912-0.092723225035-0.104158886980.02467544700670.06155681140380.09214126084680.0478527103108-0.04683092593620.1937174512510.008237002681890.003353979629270.242202521702-0.002489704611530.180402812928489.049372366-33.0185884254199.708410681
721.55167884553-0.697471750974-0.8460514972361.1886588727-0.3125195832443.661937195940.1439341844820.5079939692060.0716559492906-0.392986443997-0.175300907515-0.4214863045430.0597146137780.8016934551910.03549733231430.4197785687820.05689470197690.1079002295750.76348319242-0.06022291737370.487480398757508.87790619-44.7979511834176.736203406
731.895827368470.7273320283640.08855952024243.52454261439-0.2752423168011.977238037610.3188109673530.177401230446-0.0324064644567-0.0774676601448-0.511148171492-0.344394786058-0.0287430465829-0.2273243219620.1079985638960.32495393460.0489173106014-0.0004614975906540.613687457756-0.01127830911720.257991257116494.114247682-40.1679862701172.519026751
740.0853584825969-0.299501202978-0.6074486773221.853428494062.320571143213.388916995060.1084446736960.387125878513-0.213462800364-0.357387879917-0.2511506057990.217400069067-0.083933644087-0.5301969254060.1526299365660.4515137255780.0658569090311-0.02374893333330.688088327224-0.09362896051520.335653996533485.184509692-38.4158171075173.308558123
750.148547260849-0.739019773787-0.1985099461623.095249762083.239223639866.045506708280.1364196489070.431515131784-0.226501271977-0.0972910689374-0.0989961617280.172499739740.429852490869-0.313632881423-0.1317961125630.330872910120.03124139534010.01618301452720.501689137834-0.08916166561130.303881627923490.09402116-40.0293372683176.383840688
761.30862934689-0.00741838685175-0.7839523888233.215130822461.253471644392.232503599140.3964783398680.970065267353-0.122556811536-1.14832612339-0.269130983862-0.0756369312934-0.72342215974-0.490466254666-0.1748128145540.6420570986040.1539155460360.04357152074430.820888986359-0.06203191836320.326664046472489.952223597-33.509899202167.616862764
771.028362181490.187726392284-0.2523053586080.1054985101580.303099743351.69721890412-0.1205904813640.1626674524480.05950413984550.2089202565230.0473801502802-0.0326695819479-0.09700232212340.1082039511590.03170370637640.192188857402-0.00219986446173-0.03838036472190.2340324768540.01804838269130.20393224921486.998848218-33.4077845156206.490586855
781.94549473858-0.4442178520090.2733257519731.651246099160.07425166525844.22175616232-0.0898378553441-0.269090660652-0.05736691667620.4235530071750.111141577405-0.1745783447390.3055396066980.360113938077-0.02147231000260.288732593760.0446296273232-0.03321401580680.2405913626760.04107972849490.205371232348489.247509064-37.6979619601229.818952756
790.03992006672860.1115412825370.08866414042323.278454100843.376414145193.50829219916-0.138678446383-0.2950266733210.3522965341920.518471768390.37832669417-0.522013316548-0.3066476096130.251688681525-0.1935616294640.8872173642120.102434058699-0.08498304089140.597968338182-0.1070849970470.340729635569490.425888096-30.6359306841253.434523702
804.189052827720.2150109487580.7250076985142.341026067780.4838816823084.00046115011-0.228134925095-0.11851165682-0.2340891717990.5633854439950.1372899483910.07559498934720.290262342083-0.01054332877330.07572996711631.110967588640.05444823192660.02128053544080.366658365031-0.005528430906510.270407849228478.232639881-23.6074943187260.331032742
810.276754897823-0.3539683626720.06513694718370.8923052798050.03995353902410.544583760931-0.123320686804-0.140729452226-0.2966254686260.745305562875-0.09240714023780.6985720584940.368145129206-0.5209945577720.07036737079581.429404920630.04441439042180.05831545261430.822053365567-0.1283574337580.625388166182469.861165328-32.0459981904267.050409158
822.14542032857-0.563363245248-0.7803452261891.277156855760.6379025018822.30036454959-0.138123613088-0.0697042544376-0.1132216385290.1887018914180.01103064574790.3617339471790.174510317518-0.2715441548370.1362760217440.24306298403-0.02331791164510.04588960496560.2144406314310.01855393619510.318670882691468.014952038-28.3848747276224.637840779
832.398319097280.3542864954881.42925567321.866330959070.2369941545663.3997017698-0.178366848311-0.06975683415710.3090571650880.42048144128-0.02815656177970.193956053792-0.290399530202-0.1169497885220.2014836126080.7818960848220.06155347351750.03049530142110.301690859749-0.02998632418510.326670925882471.317960166-14.4149426392252.003741947
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 185 )
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 11 )
8X-RAY DIFFRACTION8chain 'B' and (resid 12 through 19 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 35 )
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 51 )
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 63 )
12X-RAY DIFFRACTION12chain 'B' and (resid 64 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 77 )
14X-RAY DIFFRACTION14chain 'B' and (resid 78 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 9 )
17X-RAY DIFFRACTION17chain 'D' and (resid -1 through 120 )
18X-RAY DIFFRACTION18chain 'D' and (resid 121 through 134 )
19X-RAY DIFFRACTION19chain 'D' and (resid 135 through 153 )
20X-RAY DIFFRACTION20chain 'D' and (resid 154 through 218 )
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 136 )
22X-RAY DIFFRACTION22chain 'E' and (resid 137 through 257 )
23X-RAY DIFFRACTION23chain 'F' and (resid 2 through 84 )
24X-RAY DIFFRACTION24chain 'F' and (resid 85 through 118 )
25X-RAY DIFFRACTION25chain 'F' and (resid 119 through 174 )
26X-RAY DIFFRACTION26chain 'F' and (resid 175 through 276 )
27X-RAY DIFFRACTION27chain 'G' and (resid 1 through 11 )
28X-RAY DIFFRACTION28chain 'G' and (resid 12 through 19 )
29X-RAY DIFFRACTION29chain 'G' and (resid 20 through 30 )
30X-RAY DIFFRACTION30chain 'G' and (resid 31 through 41 )
31X-RAY DIFFRACTION31chain 'G' and (resid 42 through 61 )
32X-RAY DIFFRACTION32chain 'G' and (resid 62 through 71 )
33X-RAY DIFFRACTION33chain 'G' and (resid 72 through 77 )
34X-RAY DIFFRACTION34chain 'G' and (resid 78 through 90 )
35X-RAY DIFFRACTION35chain 'G' and (resid 91 through 99 )
36X-RAY DIFFRACTION36chain 'H' and (resid 1 through 9 )
37X-RAY DIFFRACTION37chain 'I' and (resid -1 through 18 )
38X-RAY DIFFRACTION38chain 'I' and (resid 19 through 57 )
39X-RAY DIFFRACTION39chain 'I' and (resid 58 through 91 )
40X-RAY DIFFRACTION40chain 'I' and (resid 92 through 120 )
41X-RAY DIFFRACTION41chain 'I' and (resid 121 through 134 )
42X-RAY DIFFRACTION42chain 'I' and (resid 135 through 153 )
43X-RAY DIFFRACTION43chain 'I' and (resid 154 through 193 )
44X-RAY DIFFRACTION44chain 'I' and (resid 194 through 218 )
45X-RAY DIFFRACTION45chain 'J' and (resid 2 through 136 )
46X-RAY DIFFRACTION46chain 'J' and (resid 137 through 257 )
47X-RAY DIFFRACTION47chain 'K' and (resid 2 through 56 )
48X-RAY DIFFRACTION48chain 'K' and (resid 57 through 84 )
49X-RAY DIFFRACTION49chain 'K' and (resid 85 through 103 )
50X-RAY DIFFRACTION50chain 'K' and (resid 104 through 118 )
51X-RAY DIFFRACTION51chain 'K' and (resid 119 through 137 )
52X-RAY DIFFRACTION52chain 'K' and (resid 138 through 162 )
53X-RAY DIFFRACTION53chain 'K' and (resid 163 through 185 )
54X-RAY DIFFRACTION54chain 'K' and (resid 186 through 276 )
55X-RAY DIFFRACTION55chain 'L' and (resid 0 through 11 )
56X-RAY DIFFRACTION56chain 'L' and (resid 12 through 19 )
57X-RAY DIFFRACTION57chain 'L' and (resid 20 through 30 )
58X-RAY DIFFRACTION58chain 'L' and (resid 31 through 41 )
59X-RAY DIFFRACTION59chain 'L' and (resid 42 through 51 )
60X-RAY DIFFRACTION60chain 'L' and (resid 52 through 71 )
61X-RAY DIFFRACTION61chain 'L' and (resid 72 through 77 )
62X-RAY DIFFRACTION62chain 'L' and (resid 78 through 90 )
63X-RAY DIFFRACTION63chain 'L' and (resid 91 through 99 )
64X-RAY DIFFRACTION64chain 'M' and (resid 1 through 9 )
65X-RAY DIFFRACTION65chain 'N' and (resid -1 through 120 )
66X-RAY DIFFRACTION66chain 'N' and (resid 121 through 134 )
67X-RAY DIFFRACTION67chain 'N' and (resid 135 through 193 )
68X-RAY DIFFRACTION68chain 'N' and (resid 194 through 211 )
69X-RAY DIFFRACTION69chain 'O' and (resid 2 through 136 )
70X-RAY DIFFRACTION70chain 'O' and (resid 137 through 257 )
71X-RAY DIFFRACTION71chain 'P' and (resid 2 through 162 )
72X-RAY DIFFRACTION72chain 'P' and (resid 163 through 276 )
73X-RAY DIFFRACTION73chain 'Q' and (resid 1 through 19 )
74X-RAY DIFFRACTION74chain 'Q' and (resid 20 through 51 )
75X-RAY DIFFRACTION75chain 'Q' and (resid 52 through 77 )
76X-RAY DIFFRACTION76chain 'Q' and (resid 78 through 99 )
77X-RAY DIFFRACTION77chain 'R' and (resid 1 through 9 )
78X-RAY DIFFRACTION78chain 'S' and (resid -1 through 120 )
79X-RAY DIFFRACTION79chain 'S' and (resid 121 through 134 )
80X-RAY DIFFRACTION80chain 'S' and (resid 135 through 193 )
81X-RAY DIFFRACTION81chain 'S' and (resid 194 through 211 )
82X-RAY DIFFRACTION82chain 'T' and (resid 2 through 136 )
83X-RAY DIFFRACTION83chain 'T' and (resid 137 through 255 )

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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