[日本語] English
- PDB-9o08: Structure of human MAIT A-F7 TCR in complex with human MR1-lumichrome -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 9o08
タイトルStructure of human MAIT A-F7 TCR in complex with human MR1-lumichrome
要素
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR-alpha
  • TCR-beta
キーワードIMMUNE SYSTEM / receptor
機能・相同性
機能・相同性情報


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / innate immune response / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / 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
LUMICHROME / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
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: 2.2 Å
データ登録者Abdelaal, M. / Rossjohn, J. / Awad, W.
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: Major histocompatibility complex class I-related gene protein / TCR alpha /TCR beta / Beta-2-microglobulin complex
著者: Abdelaal, M. / Rossjohn, J. / Awad, W.
履歴
登録2025年4月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年11月19日Provider: repository / タイプ: Initial release

-
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

-
集合体

登録構造単位
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: TCR-alpha
E: TCR-beta
F: Beta-2-microglobulin
G: TCR-alpha
H: TCR-beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)189,08016
ポリマ-188,1008
非ポリマー9808
18,5191028
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TCR-alpha
H: TCR-beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,5128
ポリマ-94,0504
非ポリマー4624
724
タイプ名称対称操作
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: TCR-alpha
E: TCR-beta
F: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,5698
ポリマ-94,0504
非ポリマー5194
724
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)216.427, 69.733, 143.128
Angle α, β, γ (deg.)90.000, 104.383, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
要素

-
タンパク質 , 4種, 8分子 ACBFDGEH

#1: タンパク質 Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


分子量: 31711.670 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: MR1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q95460
#2: タンパク質 Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 2 / 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 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769
#3: タンパク質 TCR-alpha


分子量: 22781.268 Da / 分子数: 2 / Fragment: UNP residues 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)
#4: タンパク質 TCR-beta


分子量: 27677.760 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)

-
非ポリマー , 4種, 1036分子

#5: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 5 / 由来タイプ: 合成 / : C3H8O3
#6: 化合物 ChemComp-LUM / LUMICHROME / 7,8-DIMETHYLALLOXAZINE / 6,7-DIMETHYLALLOXAZINE


分子量: 242.233 Da / 分子数: 2 / 由来タイプ: 合成 / : C12H10N4O2 / タイプ: SUBJECT OF INVESTIGATION
#7: 化合物 ChemComp-CL / CHLORIDE ION


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / : Cl
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1028 / 由来タイプ: 天然 / : H2O

-
詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.78 Å3/Da / 溶媒含有率: 55.77 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.3 / 詳細: Bis-Tris-propane, PEG3350 and sodium acetate

-
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: 0.953651189804 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2023年3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: 0.953651189804 Å / 相対比: 1
反射解像度: 2.2→45.43 Å / Num. obs: 104865 / % possible obs: 99.45 % / 冗長度: 2 % / Biso Wilson estimate: 41.26 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.6
反射 シェル解像度: 2.2→2.22 Å / Num. unique obs: 3501 / CC1/2: 0.802

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.21_5207精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.2→45.43 Å / SU ML: 0.2851 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 24.7417
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2199 5230 4.99 %
Rwork0.1663 99537 -
obs0.1689 104767 99.45 %
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: 48.87 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→45.43 Å
タンパク質核酸リガンド溶媒全体
原子数12625 0 67 1028 13720
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.006813540
X-RAY DIFFRACTIONf_angle_d0.855418571
X-RAY DIFFRACTIONf_chiral_restr0.05382003
X-RAY DIFFRACTIONf_plane_restr0.00742457
X-RAY DIFFRACTIONf_dihedral_angle_d13.75764939
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.32261900.26743300X-RAY DIFFRACTION99.37
2.23-2.250.34561840.26453291X-RAY DIFFRACTION99.12
2.25-2.280.29171700.26063302X-RAY DIFFRACTION99.68
2.28-2.310.3391590.24533299X-RAY DIFFRACTION99.31
2.31-2.340.26571660.24153280X-RAY DIFFRACTION99.65
2.34-2.370.28271640.23283328X-RAY DIFFRACTION99.63
2.37-2.40.28251620.22543309X-RAY DIFFRACTION99.48
2.4-2.440.25551700.21923297X-RAY DIFFRACTION99.66
2.44-2.480.28111880.21883322X-RAY DIFFRACTION99.6
2.48-2.520.28031810.20913278X-RAY DIFFRACTION99.54
2.52-2.560.28751810.2143298X-RAY DIFFRACTION99.74
2.56-2.610.25571720.20783290X-RAY DIFFRACTION99.68
2.61-2.660.30141900.21023306X-RAY DIFFRACTION99.71
2.66-2.710.24631810.20213297X-RAY DIFFRACTION99.83
2.71-2.770.31691580.20973367X-RAY DIFFRACTION99.66
2.77-2.840.2451670.19973290X-RAY DIFFRACTION99.83
2.84-2.910.28331820.1993343X-RAY DIFFRACTION99.75
2.91-2.990.29031710.19343307X-RAY DIFFRACTION99.86
2.99-3.070.24261690.18323336X-RAY DIFFRACTION99.6
3.07-3.170.20991850.1753305X-RAY DIFFRACTION99.37
3.17-3.290.23181740.17413270X-RAY DIFFRACTION99.57
3.29-3.420.21831930.16043293X-RAY DIFFRACTION98.95
3.42-3.570.2011700.14873345X-RAY DIFFRACTION99.77
3.57-3.760.19151750.14543330X-RAY DIFFRACTION99.52
3.76-40.20971730.14133327X-RAY DIFFRACTION99.57
4-4.310.16631720.12483352X-RAY DIFFRACTION99.35
4.31-4.740.15221680.10953322X-RAY DIFFRACTION98.67
4.74-5.420.18471690.12343351X-RAY DIFFRACTION98.96
5.42-6.830.19311670.15743355X-RAY DIFFRACTION98.43
6.83-45.430.18441790.16133447X-RAY DIFFRACTION98.69
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)
11.92898426233-0.05197822980890.1257694225492.012403818160.3086254709822.03338777097-0.04677804302770.1013190660730.252475605463-0.08277989737950.116623273565-0.067418502068-0.02796986453210.135033108275-0.06170464188420.234728227888-0.0428042653522-0.01407029117960.321579974713-0.006336526927050.31443362070646.858093361879.1979781953228.226944513
20.6302076664811.281166415990.5552984462313.068945110761.071200766221.748517050130.2524332463190.0232025497242-0.29745480429-0.154930378029-0.04616383323240.3892326663040.1966405426070.0684073774628-0.1976437942110.276381020635-0.01341237254510.04800481298980.3502568202320.01008540521230.22433052671242.501214244271.6224066136234.090601764
32.442552890130.9619511337040.3264211496422.404364531720.1285057433094.19978951857-0.0695180240762-0.4535548213660.5985369653260.4085373665630.015942326675-0.118994145391-0.561451938608-0.08120758397590.06515851379080.4643643694950.171553484573-0.1241410516140.688943715789-0.2339931971060.59775707313168.553257028879.9898889056255.854232762
40.581100744464-0.0715899355375-0.7346426155183.512200449160.2862110773751.68125320052-0.292498850615-0.4702996332130.9675453797160.1501374591630.280604670655-0.251970812901-0.2726229023870.159925367490.05271147599790.466540106355-0.0416606971638-0.06146705069060.505140251432-0.1547711720170.72491716528362.724321991391.8135120055238.498254405
55.884554614232.166648721860.03093259024342.958687424621.35318305850.834483329688-0.62945928626-0.279241817751-0.6929191764920.2366667882140.0342557477243-1.67857593511-0.205941441751.684809693780.4678570983620.3607647968540.0447762853246-0.1601595470741.09158857048-0.03306869495291.0535216791782.51909026379.7781836894241.142967074
60.5160836963530.509891022204-0.9798831555431.21173229742-0.1754324310572.83090414021-0.0349471603755-0.0734834886581-0.0367676427336-0.1507130225830.549911070318-0.8632588272930.1134168419190.65880247004-0.4504023615640.338545991925-0.0873153096805-0.07735466047240.788205882973-0.1032974394310.82994845673570.467581799884.9909222976235.842266079
73.30014067805-0.4884344205922.458702530651.26467303367-0.3244301396391.833157893550.07111199294611.207478486171.28418439237-0.4838235773780.0188149558653-0.715115541459-0.8410685379270.805043458436-0.001622394373040.530035674966-0.2087385697810.0212928418050.6651313788250.06602631204970.69913613240765.358860517793.077048492229.182177372
85.449156682652.636564552152.091333881494.021789413090.5716549241572.20717959889-0.2238311178610.754031614259-0.0899449081108-0.3931484172960.272644585827-0.571916127336-0.1126422500360.960181747629-0.04567615202680.385407881715-0.0600937441290.004568468792570.6142304850340.006819251827970.52672034072864.985552091586.4788144647230.185926986
91.99635866227-0.5755641326430.8855782168933.02513542825-0.2844186592664.28076388369-0.02027406786631.747330921-0.539844593117-0.363307730399-0.0941286351362-0.6690471896610.06656007856140.9217237206340.1170042095710.36347260486-0.01209997572980.05348767716380.615108499473-0.0270950276310.49418773891270.560061455983.9710530255232.174317141
100.3089383107690.0220426401838-0.1151803228940.74900076645-0.3481989440620.196307022025-0.04296247935260.1937848902590.3688955367070.02152389449820.4234212914870.004739134593190.0568004833178-0.189308852694-0.2346233012710.401150508886-0.0402948416106-0.2007850172931.53519842083-0.2135017061361.2994535938387.085541211990.0204261903238.058173474
117.99949895349-1.059855409161.076180308051.736621885540.8710530326351.57924653171-0.1156744679140.2862137296331.598030191630.253694302764-0.113546648836-1.30659077234-0.4059321492090.6649478104270.2444883120230.499007825306-0.175937451805-0.1005492476730.6216911855340.05317845191591.078297161570.285558289696.2832749193235.19924539
121.01482185240.03109551919990.1286613321392.97748253499-0.3238351211491.785932199320.01395576241870.1417880763080.01100952172230.0105008593433-0.1344330546710.113468737059-0.05002715633650.1166259391630.1203093706280.235981688834-0.0489221509210.02657857460290.328966953432-0.02268418109120.26142137138-0.92215498235159.4745634267165.595397526
132.709287754070.176632319151-0.02150317885671.490338929590.283889669191.98055689023-0.0723983257476-0.224248091928-0.1236730300450.0807470465616-0.04674121861290.1513625208810.0747411314366-0.257676718860.128426786840.4013707798690.01591955756920.01213442737080.285138323058-0.01410768691690.38753931459-20.305205906872.5373460609191.328910993
143.613872008440.29065162694-0.8720132179110.6788127588430.36029965042.43148848736-0.06531083441990.128697120660.07098468356160.00977138213345-0.0353236599024-0.1201655015940.0118533142280.3000215062380.09595307921440.352560580697-0.081144298653-0.0258017719140.4556585598720.1193307036210.32672177190229.743947605761.5308330461159.977041685
157.95897233706-0.288557237942-3.958410276350.6301363021130.1866948466572.7410470720.13083276414-0.167730586828-0.430694859483-0.167435133963-0.0473835257289-0.1352400076030.07138501113760.198547878616-0.08959347826230.415022235692-0.0682787978359-0.05104356736070.496688680880.03056901526580.37280559899144.342654624861.2153011703144.838910919
167.7532678558-0.1534220700311.250914479861.321431199972.256540247066.852655116850.130319954526-0.9652296890530.09046482424330.5185472904130.223424129818-0.210071082043-0.178143230882-0.143759376136-0.3237975949250.392372458764-0.03545915508440.01328915023540.6032455884240.02545134296120.49352124455251.827800188361.6524092176141.690857719
175.034402960060.1242253215221.196604229883.253119213371.862058327221.45971933949-0.1006026636030.3310771128230.704973578636-0.2440166747970.292978220516-0.326718465795-0.2710346888720.831833116238-0.2374620507740.566345961192-0.1487106795470.09119950170.6981617546310.08689127076030.64050398231959.051735912665.7445435251136.37581085
183.68315494815-0.41225441068-0.6288643437472.08606692757-0.2271897472362.838648247180.1311151124070.308799653254-0.140986161515-0.210741323331-0.2285520335690.08007781690870.114549130497-0.2512994574150.0745244972560.400928112104-0.069828034438-0.04371663552910.4871954217710.03029095263490.27450867862613.68711657161.1233338966140.128949703
195.962200461462.80025338573-3.207273146285.93056679659-2.950617685323.855908890810.2719103110360.5240036099440.3851648531390.009357348297830.1357504476060.364569578397-0.368967693867-0.265059251701-0.4185845271690.397192783655-0.07554897692060.00352191430670.4771175129670.05522078399190.31527013755216.696901865264.2492071594136.6776036
205.192099556471.620371966671.477613402574.48932298913-1.773328891551.719283071850.243713950071-1.17578908371-0.09116252062270.495843495274-0.2451011198660.5080238575420.00127320039749-0.451115543293-0.001903297244070.342495754893-0.09440292206940.01036587612660.500600340350.02095715221490.38489990042314.777549582156.1117168289152.796056032
218.224822988390.423664843766-5.340703437940.8413976979571.253245989726.323508513530.4276035518960.8791294422950.715962818552-0.515668371892-0.01101316366530.1233150646510.0449624285745-0.0758058631712-0.3971579074560.54723606487-0.009066956469240.04014681419050.5774440155190.08670026078110.3679815625829.045487280666.721058612124.010983972
226.530769911870.3785329898221.268625443811.47464430216-0.7448628146862.887748106640.327762321869-0.0645218034905-1.27468484238-0.07414905541490.08985999851640.05768674453960.3754389999430.242835497274-0.4292898413790.5088966044427.57055842017E-6-0.02412068691780.465753810444-0.002153256796770.42462618496747.265167782655.7840376551132.138030269
234.779171630950.412475647142-0.2995767073923.4950003405-0.001190770502064.270359389880.65637990441.07595691912-1.50586202992-0.462497472537-0.01496941560360.1400531899730.534105620604-0.0512136926054-0.610943146710.753945421052-0.0274632696714-0.162229774310.570733417028-0.2010282790210.64423040498936.53956040152.6240151567123.129001413
248.52543124075-0.002877343120253.423554891920.471231900269-0.5488260793082.779291594530.8465859196311.44541650169-1.24504695652-0.770168419593-0.233639474057-0.05943794601230.4322426010810.830956894751-0.6702968189350.8242068642540.0515675871907-0.06353643710.699726356751-0.2466997875640.51782629317639.214492950654.4263146982119.336889766
252.71390719072-1.91027382699-0.8108908393988.594658965732.417585367534.232718062340.03457590712220.300672459916-0.2069278238410.978979800969-0.0832224197119-0.6250827770630.295617722158-0.1377784060960.06108231959920.329368480743-0.0574717227389-0.07933776112780.3081592913510.002259198120190.393000425084-24.002933685259.1515369172174.279707529
264.225032243960.1085042947342.314562488835.85293101954-1.000813731523.51143305306-0.0600441806478-0.3753850872851.878974476880.359352558372-0.04068374286770.437802260688-0.948953497359-0.8351900591850.134107353570.5024606268270.12591382034-0.0405848633620.397333817421-0.1069525637140.75920322748-32.416395104480.8317969998178.470135051
274.90910056715-3.58417520209-0.9830468304122.914083613961.591034416392.74778278755-0.05761234901510.1777487239980.0261294041925-0.1575995268530.02130848067650.330202047778-0.327563486187-0.129382896430.1309452620340.377263059872-0.0128275801346-0.01858534305120.323622840589-0.04609895591020.346063741023-25.410900775269.0916821935172.367886478
288.9372297743-5.77120135737-1.794149983125.767400467251.62273023671.231883545790.1896442783580.839874850225-0.370712881051-0.307257211515-0.4170420282960.150958698155-0.173072879759-0.2181508972280.1930661734330.509955075255-0.0411096360267-0.08512948886280.474399755714-0.02208089385210.463582783725-26.822970071161.1138993983164.823916891
298.021494949072.04235465928-3.923625349949.273516397530.08477964483835.02612406717-0.126968248410.7617524699480.884689072109-0.588970403008-0.1357906891830.4263312037980.355313158801-0.03303022335660.2273712424590.5166950265460.0582308078731-0.1724142628570.6067591183270.01555368658140.557172922258-37.776283712269.0106088358163.600767599
302.920198161170.8198684963643.265412844141.134044037041.195728488913.76043564296-0.3622395492110.7492378990960.498339281304-0.4042576962180.306204448652-0.268227264677-0.262890449703-0.2603910257770.02166268514720.690327562732-0.0788820173222-0.1552916440990.800847789610.03701640403240.663740091325-26.312910519572.6377270735162.205846534
314.36245571563-4.014669439322.920336833734.81335626038-2.651849752592.934582085750.09312834315790.3185768014510.0339497541571-0.0584236672303-0.117799166732-0.0316945317415-0.08357177466590.2006053104150.03137343364390.4311683970520.01232341234890.02952394531270.370790717504-0.09602570816740.413278950877-12.73372138660.4839108273169.489285748
328.92752171588-5.89437472083-1.02825128034.037198800441.619173014436.00906893302-0.04004170486760.698864835090.751379537253-0.461160096803-0.135169553545-0.339299741625-0.623759627051-0.2618645728040.1757226336820.442731082722-0.069999712252-0.02056724383340.3073825784310.01163506197240.407354138353-24.735006701270.441835706168.781413775
338.25897436414-4.38078932677-0.378275532715.924367379435.60559700318.157926362170.00921401019624-0.2301002815540.2883560952040.449339190884-0.1620248177971.158806948990.13887790121-1.125587288560.2050041436310.3879174096340.01342289582550.006574017594880.4658356176010.05176830625170.899041830183-42.098812341474.7169752193174.077977551
345.60530488528-3.920545021440.169478194354.08688733071-1.770725959672.10441328644-0.06396972979670.2764181754670.378095213412-0.6752152750570.261673238633-0.154770578819-0.3121647562090.18976618978-0.2000500929790.368838419309-0.0378489572616-0.1136407235440.278662009592-0.0473140839120.47670736589-33.086408615663.7388212555168.005390536
351.684082769390.758344837860.7995769040175.74783884812-1.920593743243.96351886808-0.0794827667019-0.148772468565-0.0776018068261-1.0330210139-0.2556718591070.7918714340170.0498501877274-0.7422362729080.309520486030.368197232384-0.0100174256868-0.03643393678980.476182305089-0.2102317533270.582570829859-30.399059820651.61688273166.5882773
364.56022829110.8663159474960.7104543051463.799845340313.947980128554.12531512904-0.0489890248641-0.4918472600740.8663687280160.273277523398-0.3034769776190.9462760244220.134397602733-0.6325717593280.3444234686190.323315853354-0.02152496220230.06993526887270.490829637255-0.1106152422840.606250845235-35.322605947866.5357524842176.429528347
373.218750684960.659806648104-0.6991537605113.12452522237-0.2070299468631.51439974356-0.0869101137632-0.0250342973101-0.348782956740.1545873160570.0634547561951-0.1304576404470.1498618476950.06413002809450.01169897059370.383362994571-0.0492949330724-0.04443547319360.2772009214470.0600213019190.32117121219218.71688215450.7538262537220.40196163
381.940071674741.431839708711.559669536233.516032206160.7130886533483.260060161960.127538280210.0611176723438-0.5040703488020.1449830001090.189189614504-0.2376306100540.3297132143050.0778155077789-0.3149118488940.365069538866-0.00831451489853-0.04464330788080.2972350342410.01298553562780.3628056602927.171948163557.6957442796223.42159587
391.891113787150.3493832899180.4756800554322.043378215680.4144382406616.038287282810.0661232765389-0.01866731230730.0407646264289-0.2395361793340.3136410246350.237906371522-0.358506090806-0.500726383596-0.3640665777070.356538595002-0.07405392158671.95461203731E-50.2798295989960.06059593510720.3963243690422.47841286664.1607477446219.995465993
407.422920934540.7068839237325.151926333091.321646906261.306381580036.377340999030.0199974529094-0.500512572376-0.2958608573780.04308508024890.01163396289850.261665442637-0.024009397204-0.455453563014-0.06749929282620.35392098134-0.02355871470950.02762255518020.2609027955640.009852330986150.35130418863121.023385289358.7418248567229.694734021
412.532532117281.833343727261.316233757481.963471938470.09464812036361.8573585563-0.0841947754408-0.02847094760970.3808179132010.005053525673680.07165714893390.274120856965-0.0121528073611-0.2330614526740.02267164650250.381539076667-0.0258482716412-0.006043882026720.3189579018440.0186778631790.32613661108915.850636924558.4623401878218.944795427
425.564621772893.054529517522.355712818232.363793813171.139304712461.573667957470.0194887814476-0.28738994232-0.130108844535-0.0576673795236-0.0151589025410.0195583526146-0.0895779712863-0.0452556679140.01206274608270.330341869847-0.00129209015534-0.0147786941170.2364889785140.02665499519190.27361598951214.949948860252.9797235258214.207640281
431.572101728540.422069110934-1.367357508360.901438755828-0.4935685518238.582796137820.02127858953940.3511243212880.00401975973074-0.5827870176950.1538969222940.1911905039180.160898194784-0.265343650002-0.181947514740.521004001635-0.0384003208591-0.04934430309250.2708136047160.01944039353330.383668184097-1.4797813632345.547278323192.737065142
444.15452752002-0.913039386862-1.504753163884.114121979880.1056565886224.90899233108-0.0536275763814-0.556494996324-0.003562370123670.1250632483590.0253288648501-0.2751770709690.2178166445930.3685896756490.03319489439390.40870560372-0.0812240852141-0.06273778418290.4030725242610.07388137121960.3974366012013.9552081119245.8605666503203.746001033
454.84051391331-0.221871879295-1.807260584750.207957487227-0.8585601613595.04106800399-0.1500774351780.0721203413264-0.513674413459-0.322998580876-0.0167060820490.1362916514830.780898817371-0.4806438337960.160402167890.549709678244-0.0312332233576-0.02197927181120.2750956110810.02125945583330.405714472180.77256735197541.7918056447196.768656153
462.60970686283-2.245530488482.9692046413.0087972423-1.327864004224.847445986330.483439468968-0.157119113847-0.948888236877-0.68892556976-0.1083180518110.2823970285891.10435946777-0.361770726971-0.3939971761860.553439811662-0.0339047429681-0.03001544746890.3628440092710.09179196301690.545043700626-4.0123387205835.8313944254203.056445868
473.214882609551.078745069720.6954557604692.545944416291.464873373282.4788505129-0.1042390098590.4122964342510.192837461218-0.2678995641850.0370907632322-0.149735432553-0.3373735601370.4061259096160.06793659919530.351580593867-0.0843670250042-0.007896827573140.4290304926460.06340353995830.27570176152233.788095384166.9889138018202.683413517
482.29190260178-0.22568887464-3.17701086647.512683470051.055115467054.493265530090.243751983258-0.541935891935-0.08606486899380.8912467885330.119854910126-0.588430063562-0.01946958685160.625913381272-0.4257582585170.474686856222-0.0822736071183-0.1244423948240.454170187260.01758793555750.47185442442829.717799527871.6276636816215.758245332
496.463855496142.37608565874.483174978753.532918466061.315396789573.57882622930.375855327985-0.115130660182-0.49462838260.259373433663-0.0344524783728-0.06191392709830.4774706388520.719646557059-0.3542322351730.393920222806-0.0121604645115-0.02650370902070.4819152006290.01880062388830.31697224579725.516954359754.1646945215188.202891949
506.26401349964-0.273382088649-1.773353780151.00130273529-0.2867002456422.806777174160.00489797539149-0.297875056093-0.165707980174-0.105949084454-0.01843923202080.0230167133534-0.1369371246440.259300343040.009449417532390.381325246768-0.0484000413777-0.0268929700730.2174111557990.01759442467270.2519076193473.9827372666753.7612625886195.392288469
512.859130150930.4876000537671.497912767480.687356639904-0.3857362786211.59115229718-0.08398147868850.5109649089090.665716689733-0.3081251974430.2937815146370.334515426201-0.2258556147950.057047431419-0.2094573204710.507546460532-0.0602351915942-0.05550809283820.2899054973950.08941755389490.427966388835-2.2380095118961.9383361222189.890784049
523.95333843777-1.24397316895-1.650199690241.81348465224-0.2737826031233.304885683220.134975274288-0.02326884527250.003784377907330.00223540860396-0.0729912443951-0.0302697904211-0.08135239146890.166869600707-0.03771035778020.448784013394-0.0489682116924-0.04484204662930.3588982538770.06766488017570.30865437238914.900436893858.845598203182.096961956
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 'A' and (resid 0 through 133 )AA0 - 1331 - 134
22chain 'A' and (resid 134 through 182 )AA134 - 182135 - 183
33chain 'A' and (resid 183 through 270 )AA183 - 270184 - 265
44chain 'B' and (resid 1 through 11 )BD1 - 111 - 11
55chain 'B' and (resid 12 through 19 )BD12 - 1912 - 19
66chain 'B' and (resid 20 through 30 )BD20 - 3020 - 30
77chain 'B' and (resid 31 through 41 )BD31 - 4131 - 41
88chain 'B' and (resid 42 through 61 )BD42 - 6142 - 61
99chain 'B' and (resid 62 through 71 )BD62 - 7162 - 71
1010chain 'B' and (resid 72 through 77 )BD72 - 7772 - 77
1111chain 'B' and (resid 78 through 97 )BD78 - 9778 - 97
1212chain 'C' and (resid 0 through 171 )CE0 - 1711 - 172
1313chain 'C' and (resid 172 through 270 )CE172 - 270173 - 266
1414chain 'D' and (resid 2 through 91 )DG2 - 911 - 90
1515chain 'D' and (resid 92 through 135 )DG92 - 13591 - 132
1616chain 'D' and (resid 136 through 166 )DG136 - 166133 - 163
1717chain 'D' and (resid 167 through 199 )DG167 - 199164 - 196
1818chain 'E' and (resid 3 through 73 )EH3 - 731 - 71
1919chain 'E' and (resid 74 through 94 )EH74 - 9472 - 92
2020chain 'E' and (resid 95 through 109 )EH95 - 10993 - 107
2121chain 'E' and (resid 110 through 124 )EH110 - 124108 - 122
2222chain 'E' and (resid 125 through 203 )EH125 - 203123 - 201
2323chain 'E' and (resid 204 through 225 )EH204 - 225202 - 223
2424chain 'E' and (resid 226 through 243 )EH226 - 243224 - 241
2525chain 'F' and (resid 1 through 11 )FJ1 - 111 - 11
2626chain 'F' and (resid 12 through 19 )FJ12 - 1912 - 19
2727chain 'F' and (resid 20 through 30 )FJ20 - 3020 - 30
2828chain 'F' and (resid 31 through 41 )FJ31 - 4131 - 41
2929chain 'F' and (resid 42 through 46 )FJ42 - 4642 - 46
3030chain 'F' and (resid 47 through 51 )FJ47 - 5147 - 51
3131chain 'F' and (resid 52 through 61 )FJ52 - 6152 - 61
3232chain 'F' and (resid 62 through 71 )FJ62 - 7162 - 71
3333chain 'F' and (resid 72 through 77 )FJ72 - 7772 - 77
3434chain 'F' and (resid 78 through 83 )FJ78 - 8378 - 83
3535chain 'F' and (resid 84 through 90 )FJ84 - 9084 - 90
3636chain 'F' and (resid 91 through 98 )FJ91 - 9891 - 98
3737chain 'G' and (resid 2 through 17 )GL2 - 171 - 16
3838chain 'G' and (resid 18 through 37 )GL18 - 3717 - 36
3939chain 'G' and (resid 38 through 52 )GL38 - 5237 - 51
4040chain 'G' and (resid 53 through 75 )GL53 - 7552 - 74
4141chain 'G' and (resid 76 through 91 )GL76 - 9175 - 90
4242chain 'G' and (resid 92 through 120 )GL92 - 12091 - 119
4343chain 'G' and (resid 121 through 137 )GL121 - 137120 - 136
4444chain 'G' and (resid 138 through 165 )GL138 - 165137 - 164
4545chain 'G' and (resid 166 through 185 )GL166 - 185165 - 184
4646chain 'G' and (resid 186 through 200 )GL186 - 200185 - 199
4747chain 'H' and (resid 1 through 94 )HN1 - 941 - 94
4848chain 'H' and (resid 95 through 109 )HN95 - 10995 - 109
4949chain 'H' and (resid 110 through 124 )HN110 - 124110 - 124
5050chain 'H' and (resid 125 through 202 )HN125 - 202125 - 202
5151chain 'H' and (resid 203 through 215 )HN203 - 215203 - 215
5252chain 'H' and (resid 216 through 244 )HN216 - 244216 - 244

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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