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- PDB-9cgr: Structure of human MAIT A-F7 TCR in complex with human MR1-Pyridoxal -

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基本情報

登録情報
データベース: PDB / ID: 9cgr
タイトルStructure of human MAIT A-F7 TCR in complex with human MR1-Pyridoxal
要素
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR TRAV1-2
  • TCR TRBV 6-1
キーワードIMMUNE SYSTEM / immune receptors
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 / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : / : / 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 / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / 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
ACETIC ACID / Chem-PXL / Beta-2-microglobulin / Major histocompatibility complex class I-related gene 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: 2.4 Å
データ登録者Awad, W. / Rossjohn, R.
資金援助 オーストラリア, 1件
組織認可番号国
Australian Research Council (ARC) オーストラリア
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2024
タイトル: MR1 presents vitamin B6-related compounds for recognition by MR1-reactive T cells.
著者: McInerney, M.P. / Awad, W. / Souter, M.N.T. / Kang, Y. / Wang, C.J.H. / Chan Yew Poa, K. / Abdelaal, M.R. / Le, N.H. / Shepherd, C.M. / McNeice, C. / Meehan, L.J. / Nelson, A.G. / Raynes, J.M. ...著者: McInerney, M.P. / Awad, W. / Souter, M.N.T. / Kang, Y. / Wang, C.J.H. / Chan Yew Poa, K. / Abdelaal, M.R. / Le, N.H. / Shepherd, C.M. / McNeice, C. / Meehan, L.J. / Nelson, A.G. / Raynes, J.M. / Mak, J.Y.W. / McCluskey, J. / Chen, Z. / Ang, C.S. / Fairlie, D.P. / Le Nours, J. / Illing, P.T. / Rossjohn, J. / Purcell, A.W.
履歴
登録2024年6月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年11月27日Provider: repository / タイプ: Initial release
改定 2.02024年12月11日Group: Atomic model / Data collection / Database references
カテゴリ: atom_site / citation ...atom_site / citation / citation_author / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nonpoly_scheme.auth_seq_num

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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: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: TCR TRAV1-2
E: TCR TRBV 6-1
F: Beta-2-microglobulin
G: TCR TRAV1-2
H: TCR TRBV 6-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)189,76728
ポリマ－188,1008
非ポリマー1,66720
水5,945330
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TCR TRAV1-2
H: TCR TRBV 6-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,68912
ポリマ－94,0504
非ポリマー6398
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: TCR TRAV1-2
E: TCR TRBV 6-1
F: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,07716
ポリマ－94,0504
非ポリマー1,02712
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)216.075, 69.897, 142.444
Angle α, β, γ (deg.)90.000, 103.833, 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

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要素

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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 TRAV1-2


分子量: 22781.268 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)
#4: タンパク質 TCR TRBV 6-1


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)

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非ポリマー , 6種, 350分子

#5: 化合物 ChemComp-PXL / 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE / PYRIDOXAL / ピリドキサ-ル


分子量: 167.162 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H9NO3 / タイプ: SUBJECT OF INVESTIGATION
#6: 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: 10 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物
ChemComp-ACY / ACETIC ACID / 酢酸


分子量: 60.052 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C2H4O2
#8: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#9: 化合物 ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Ca
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 330 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
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: 2.82 Å3/Da / 溶媒含有率: 56.43 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG 3350, BTP, Ca 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: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2024年4月9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: 0.9537 Å / 相対比: 1
反射解像度: 2.4→46.15 Å / Num. obs: 79691 / % possible obs: 98.08 % / 冗長度: 3.5 % / Biso Wilson estimate: 58.65 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.63
反射 シェル解像度: 2.4→2.49 Å / Num. unique obs: 7875 / CC1/2: 0.635

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21.1_5286精密化
XDSデータ削減
Aimlessデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.4→46.15 Å / SU ML: 0.3499 / 交差検証法: FREE R-VALUE / σ(F): 1.45 / 位相誤差: 26.3933
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2159 2000 2.51 %
Rwork0.1732 77604 -
obs0.1745 79604 98.07 %
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: 66.19 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→46.15 Å
タンパク質核酸リガンド溶媒全体
原子数12751 0 105 330 13186
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00213313
X-RAY DIFFRACTIONf_angle_d0.505218120
X-RAY DIFFRACTIONf_chiral_restr0.04181930
X-RAY DIFFRACTIONf_plane_restr0.00362355
X-RAY DIFFRACTIONf_dihedral_angle_d14.00424772
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.39211420.31845472X-RAY DIFFRACTION97.52
2.46-2.530.32511410.28685502X-RAY DIFFRACTION97.95
2.53-2.60.31441420.27265509X-RAY DIFFRACTION98.04
2.6-2.680.37051420.2715513X-RAY DIFFRACTION98.26
2.68-2.780.31631420.26745510X-RAY DIFFRACTION98.35
2.78-2.890.24771420.23845525X-RAY DIFFRACTION98.33
2.89-3.020.26191430.21665532X-RAY DIFFRACTION98.27
3.02-3.180.22511430.20235530X-RAY DIFFRACTION98.3
3.18-3.380.291420.20155522X-RAY DIFFRACTION97.96
3.38-3.640.19191420.16325523X-RAY DIFFRACTION98.06
3.64-4.010.20421430.15465571X-RAY DIFFRACTION98.35
4.01-4.590.15851450.12655605X-RAY DIFFRACTION98.34
4.59-5.780.16921440.13235576X-RAY DIFFRACTION97.89
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)
12.04626720278-0.842910966939-0.2665385934641.678247644681.034741865871.620774312520.05001965158120.1487546028250.256588681112-0.3229800775350.0670113033267-0.278957007294-0.02611218568530.131453151258-0.1240902573150.478256240247-0.06854570921950.0293606137580.5091098938810.01664348582140.51082063745752.777477967476.898213479223.264401148
21.75047896158-0.5464376710430.327242794132.112336287010.2435871716521.11209152778-0.00735698047549-0.1225092766950.0482281837847-0.0165016369842-0.0334006722420.130875405274-0.00915398379154-0.05090211941970.03868260267290.430867540806-0.03066473490940.02496515950060.4887797434880.003791453497230.46387249615840.194451852380.6260489903233.995542511
32.62735445322-0.3452004579641.134697865281.515341224970.975809196291.971960041470.05106408447050.0153435348918-0.04091853525760.1030681345530.218957189421-0.3142958027860.1346029438120.231364877373-0.2380370101540.4646208216320.002523887503870.01346931229540.4951186310150.01400250162130.52273885190865.537016709270.6488269097243.069951095
41.366603241970.0524843299690.4749384083571.59838560337-0.7222634106471.81940057509-0.0703422676466-0.2749271292450.3704881842580.2927460489750.095729892789-0.0469190810513-0.481151997474-0.115851679477-0.01047471326580.5374582383080.113095493769-0.04122154072790.673424452417-0.1567713632840.68137884006769.527905535379.9512756355256.410144932
51.878212059262.9661036579-2.091353848086.18576294947-0.5119931946277.482651225850.05587457735120.8957221264671.152487481730.2304167485880.585397739760.289450720627-0.576455549028-0.846091481765-0.7461679482830.651544557214-0.0298933449340.01177466615740.6674683298870.04972115387860.85529889213755.693074960896.6891811119234.94689765
64.0044838097-0.02290154868360.9216727152961.80491561652-0.6867321989251.79058895324-0.06825006613050.08721382514220.5541580380760.0964478703507-0.0443789222964-0.636673586033-0.07178832780690.4201434039430.2240561476120.48053228563-0.0362849220981-0.01012437112770.692185038991-0.008818813502520.79378923146776.450219852284.2413308546238.275658087
77.48477091116-0.157758171763-0.05401535951420.6823501103360.2272193871361.310716439460.01080727911521.411416970320.469603765222-0.397029021117-0.0287793702101-0.524358561853-0.2614636341630.523914524371-0.07961104216550.537093573501-0.1925850345010.06435908457380.8941207311820.09891987021880.97647206144773.549692517191.2828647097227.673362796
89.61809773692-2.09002244002-2.459416360793.343673985720.9990886824123.028386357140.008983588611890.379769643961-0.1769863550020.426153901487-0.121083709302-0.06754799785940.4237068534960.09463733215580.1260829458610.457273745844-0.008879625878360.03827187485590.508086297342-0.005061048144850.53252168672557.25761429783.5423194023233.044344761
97.97701550123-0.3202092575681.004942787730.597771678356-0.3468840219180.687586198574-0.5838906556140.891050103094-0.526053501007-0.6321024512270.456152067208-0.498342641592-0.09084664908930.4372790375450.1012542743990.462487415241-0.1059093344050.1472092883810.717353309351-0.05182271022740.74629675021773.164540267783.9140621062231.796474861
102.31901802413-0.3689137307771.175327745120.0809956888979-0.1894197161360.589992207267-0.444909741912-0.365338183316-0.4890876342530.0613783412180.0313185957682-0.181135627257-0.4566676721340.1582133801220.6297987568960.805597882866-0.07401051520680.0117512691881.12130783884-0.05464956870341.3591757704889.026578510590.9004219134237.619673975
110.9275130306210.049631467779-0.4992861104723.584553652371.282174243810.7491910835330.09715049403090.2539973713090.909009771925-0.0173964353212-0.0535839572531-0.351559046289-0.3449875279980.566196168792-0.05741826073320.672486877831-0.1338062410270.033866071230.6724795930470.02481814433530.9663772206873.057306826496.2605504771235.024427826
122.196123260930.369985264402-0.1411811950511.19993595887-0.6286770405352.42472413960.07921178908260.254654238027-0.0427079180258-0.089483323513-0.04225244070220.126830688114-0.107489528255-0.0755455709188-0.02506483888340.417180486190.0153621659348-0.01145832268970.446827671386-0.01782173806670.446006684306-3.1897362380863.0023491089159.91999258
132.41810344188-0.8066047470280.07795137048051.65597243799-0.9932620131681.37659802480.0291734192761-0.014786347142-0.1777717594660.263966811685-0.1006069295-0.2084596338570.03221670297490.1633863423820.07203408127810.452320018166-0.0261511271247-4.91155059564E-60.512438506681-0.01167597445190.427530758394.8658392377255.8592848934170.092143351
141.57012794351-0.263693638635-0.2457984352191.079233679910.6923495518491.522617934040.0486747124714-0.142863230093-0.00530172573689-0.0259903512775-0.08156387004450.126810697893-0.0863989670088-0.06790506313660.01835072167160.5353832211960.00842716593780.005138886233690.432577892546-0.02501871562460.523553025865-18.741107648472.0416525123188.779180366
151.61371451393-0.410053973870.09731799713931.840955740150.5933004491812.923992855230.146044990933-0.1134999524-0.2554619683030.184539356874-0.0273585249359-0.02573706158910.161107420953-0.193061134784-0.00107849177560.5578688713160.0115768533759-0.01121666705060.440742529798-0.01149734478750.529725367076-18.622967536472.7445311573194.72853733
161.081165675550.53192731311-0.08210279081440.786830132054-0.6632372899721.33828246648-0.03165079574950.1270002354460.0610217298779-0.0486379761618-0.0231831767632-0.00207791991182-0.1069603359260.1714394854010.04525204475990.427472827604-0.0572360849834-0.008907438211160.5677833135190.06015003266190.46069541710530.094519381863.3725011846157.62532434
173.111409664260.115202739298-0.8300921081050.7646638630860.3934154689372.01280877876-0.01645974792840.108549800320.06917178196830.02862492069330.02388530823860.04358875031140.05624495381690.170421145878-0.009510112884570.478424805221-0.0610436007824-0.02415286692490.5904507662290.08635214850860.50534926202929.855764901660.9967852477160.109973694
185.57657136782-0.215145077247-2.23255106373-0.008514882563320.07228265613790.862011112455-0.114838883385-0.300104529076-0.17087957344-0.09498989878170.206132734385-0.164428353240.1630641110470.596080042023-0.06718937309840.434475698186-0.0005186810484630.007389911090210.8656051474980.0260098505310.53764967564552.477608282558.9703172489150.791718056
193.18033788076-1.01456859631.388998787541.211714982280.1878311820533.785922161030.1473753022240.05675106669160.150386332596-0.2328669138660.0805442932598-0.497920308561-0.170694078920.357420979504-0.1448394530170.651672277501-0.02767049055030.09159123608170.774451953607-0.009478271249240.71833340254457.880999924862.6643620176136.628379485
202.35371028281-0.695634134908-1.272130080321.75374173303-0.4112621660832.63151189120.06284038406520.132392513017-0.00848445473453-0.2926613933230.06829662428880.3304521401540.203655753071-0.522360612175-0.1191198565180.596061733348-0.103560127501-0.08789791523980.7504432261130.08721058297270.57036338703716.140470772261.7975167505138.657145766
211.119607506031.051129095130.4327927969091.9848255591-1.167342553372.668067849870.376781861502-0.396605239824-0.6365156917120.338634839031-0.3376087211780.133195826261-0.517787628121-0.968290884689-0.02613986037770.597161561681-0.1041246485140.007188994444890.8368328256180.04061028137510.60701923734816.682242889555.4263838851152.028941517
221.295221748160.418529525408-0.5942654978760.852373351659-0.02706240462040.9968249861650.5101915803410.277960873363-0.181316979397-0.295791886417-0.0412105369683-0.1688680424250.3190963026190.198415452967-0.4111611920840.7652270870470.0879011519120.06215237512490.711296649577-0.08121426173490.52162658097145.043233463459.6968870612127.928437758
234.221020132660.2319580934721.483784394561.82410726422-0.08957616810292.050372261280.5773102472360.4445446084-0.956355880376-0.42052680366-0.05519427194990.2512826742540.4923601547640.267011372042-0.427832940120.7352173055940.082586783005-0.05860205551870.557665106124-0.1129828247310.5716489104543.890555070255.0517097392127.60244913
241.86159513360.1728474803250.411718297662.25073472636-0.46000363741.763606855230.009024909543030.144533937103-0.0538120102753-0.266533053172-0.0355578093036-0.162184959585-0.1430180517670.01741245474780.09639143179460.433990337284-0.0353457571418-0.0004114852190420.459476272519-0.06941870118280.588033774088-21.528824595957.4816871755173.269044859
252.44323483063-0.510439943231.248529122630.142670671135-0.2446081600270.631893853974-0.1926454091750.1257267635350.690192460441-0.0754177399268-0.4167527448310.375906738499-0.455259453369-0.6023174233430.0828505181890.7351954332270.1912491761050.021664812750.672328972527-0.1794817038080.915041159468-30.888722861180.3399225678178.28015934
262.54456937794-1.73381158931-0.9047026859932.028434608780.7271204993321.32043841841-0.2184221317430.2041497376170.0651463254380.0863493984638-0.1071017752560.220781694135-0.508785123513-0.1084296854170.2634742760430.5697464282350.0492504211706-0.09795130165180.547766705233-0.07218164540740.562441218872-23.844535902368.8579197947172.061486626
277.57117790507-6.40922104897-1.19102092666.215826191591.186530542250.8838454805870.5404652600310.566644469124-0.223711019766-0.535948248513-0.4899839805130.0540219582356-0.0700774168072-0.481940888608-0.07687800164040.5339922476030.0347047525114-0.02481364037510.748079421212-0.04987008163680.585256781633-25.202020073460.8405379845164.379388795
284.42275278876-0.573303108149-0.009552607282120.7987981428420.2728076205981.15798878497-0.4202015565950.4614636172250.744582417485-0.2091217069850.06561361810110.264213635228-0.0050997724266-0.237310948470.1221973714710.7773121833670.111982282262-0.08983957780590.843234293283-0.09482243096890.716816192621-30.733722439770.7002393934162.222020903
291.42233043286-0.9832721875471.673234113221.43044836947-1.550361254372.176038180510.161121570455-0.2181593630660.104124642923-0.3364444581010.1337405801680.004443181328510.133771614732-0.01211377118690.09075305236570.596301883022-0.01021246303630.02722647980020.551806836788-0.05424338915620.58577280734-11.104755311860.4961135919168.843446353
304.02108590307-2.6220050682-0.6957362965462.549074077070.652415052151.110041419770.1842275669140.2938497062910.467739401343-0.541032735610.00394483534848-0.169220336789-0.549190127087-0.166888042006-0.09234637908990.6568933374340.0138562600316-0.0256418342680.5877005626360.0001432382058970.551294450878-23.431690741170.5188575143168.516020952
313.2597123963-1.91914626549-0.5983814310951.948298995391.866615446893.00287178014-0.05094532828660.0479578846436-0.111227731588-0.342871900524-0.1916994516560.2693073434820.228212986331-0.6964313175370.347417575830.9040895640730.2030649539250.01491764921690.852454739215-0.03674995502490.993588741839-40.490132576374.0939655025173.940711223
322.53842760153-2.11410756895-0.8057970780916.2902199721-0.1043902594841.228719049420.2206385745990.100133902657-0.1171312986260.00855772850163-0.3081094256170.4417930028480.0543894436303-0.4624670067830.1463174934370.487471745913-0.0378253845293-0.08181734034330.564070314188-0.07228815021980.561964764533-31.380435812161.3461345753171.515834029
332.325525326021.899842060851.284978549582.076492782260.6755342795541.743860500770.002520443431760.0962673534370.03148881286010.03746848915110.07579431488230.1034365539230.08195591182230.04684907921-0.07478676507420.503334782418-0.04681936673550.004105080176170.433670665220.02304540015590.47028946452125.538185038258.1566905308222.098860303
343.648718260291.540481738171.938927943971.720076741560.4386106929481.134085225850.0950800753393-0.714566343256-0.0653218745379-0.0429935566608-0.1172068155930.2240606629260.109086900042-0.259192034653-0.006624167570890.530016787552-0.0564504350183-0.02709464711240.5571312770740.04096573993990.5622436307351.7956701584947.1613860875210.115729678
352.870947457850.452850927313-1.052431784972.76997836257-0.4550222977233.75705428924-0.0273230566553-0.103557877755-0.243452724662-0.2662070405810.06937844624040.1237598611350.400107239170.186234988569-0.06707112893330.6099523967590.00534538270909-0.03547282621010.405940101320.02498241874050.57097517043.5928433904544.0344139093198.57862121
365.58171189887-0.8248683704311.754195658483.77666993685-1.14464830784.70711809754-0.158678254341-0.143088638128-0.43327867425-0.146581757860.07643381460840.4932499924470.113543219089-0.4867405638230.06098621204990.762648221706-0.0934421598178-0.1357554948770.604557458750.07915909318160.758691188369-5.4642628402236.3925894634202.44818754
372.244607795980.253630622090.2304263327681.111876174111.556145786732.263337492450.01940402760270.37752067520.166910136114-0.351231290488-0.0236116382172-0.161756003914-0.2576068755210.3570938252490.008979104004660.627702882603-0.0704536291781-0.006545127997190.6370389870240.05091514671370.46327338757836.222514584766.7224227809202.047334596
381.208231426510.4136862628630.7320761966840.6875951551250.2576151521721.627414010580.05986621024160.205429815418-0.1298449378140.02519841259210.0740559793957-0.02188993648340.0490059821980.424586803047-0.1800995942750.5780250334990.0277078781192-0.04581041293550.4020289663590.02234437953370.41989828303318.173583018957.7985112483198.05527477
393.838469526880.601952693612-2.186595358870.938564927669-0.7135147462562.708728138150.14382364052-0.1421525492930.1913172751460.0166043308385-0.1043221284450.0332871146534-0.09097393903920.296668758579-0.02128418015410.511874988244-0.032819550212-0.05486118681930.4059232657160.005273527924650.38729979786710.397843905856.4333061338190.63590877
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 83 )AA0 - 831 - 84
22chain 'A' and (resid 84 through 158 )AA84 - 15885 - 159
33chain 'A' and (resid 159 through 205 )AA159 - 205160 - 201
44chain 'A' and (resid 206 through 270 )AA206 - 270202 - 266
55chain 'B' and (resid 0 through 5 )BG0 - 51 - 6
66chain 'B' and (resid 6 through 30 )BG6 - 307 - 31
77chain 'B' and (resid 31 through 51 )BG31 - 5132 - 52
88chain 'B' and (resid 52 through 61 )BG52 - 6153 - 62
99chain 'B' and (resid 62 through 71 )BG62 - 7163 - 72
1010chain 'B' and (resid 72 through 77 )BG72 - 7773 - 78
1111chain 'B' and (resid 78 through 97 )BG78 - 9779 - 98
1212chain 'C' and (resid 0 through 84 )CH0 - 841 - 85
1313chain 'C' and (resid 85 through 171 )CH85 - 17186 - 172
1414chain 'C' and (resid 172 through 237 )CH172 - 237173 - 238
1515chain 'C' and (resid 238 through 270 )CH238 - 270239 - 266
1616chain 'D' and (resid 1 through 52 )DP1 - 521 - 52
1717chain 'D' and (resid 53 through 102 )DP53 - 10253 - 102
1818chain 'D' and (resid 103 through 116 )DP103 - 116103 - 116
1919chain 'D' and (resid 117 through 199 )DP117 - 199117 - 197
2020chain 'E' and (resid 3 through 94 )EQ3 - 941 - 92
2121chain 'E' and (resid 95 through 109 )EQ95 - 10993 - 107
2222chain 'E' and (resid 110 through 140 )EQ110 - 140108 - 138
2323chain 'E' and (resid 141 through 244 )EQ141 - 244139 - 242
2424chain 'F' and (resid 0 through 11 )FR0 - 111 - 12
2525chain 'F' and (resid 12 through 19 )FR12 - 1913 - 20
2626chain 'F' and (resid 20 through 30 )FR20 - 3021 - 31
2727chain 'F' and (resid 31 through 41 )FR31 - 4132 - 42
2828chain 'F' and (resid 42 through 51 )FR42 - 5143 - 52
2929chain 'F' and (resid 52 through 61 )FR52 - 6153 - 62
3030chain 'F' and (resid 62 through 71 )FR62 - 7163 - 72
3131chain 'F' and (resid 72 through 77 )FR72 - 7773 - 78
3232chain 'F' and (resid 78 through 99 )FR78 - 9979 - 100
3333chain 'G' and (resid 2 through 103 )GV2 - 1031 - 102
3434chain 'G' and (resid 104 through 120 )GV104 - 120103 - 119
3535chain 'G' and (resid 121 through 189 )GV121 - 189120 - 188
3636chain 'G' and (resid 190 through 201 )GV190 - 201189 - 200
3737chain 'H' and (resid 1 through 94 )HW1 - 941 - 94
3838chain 'H' and (resid 95 through 140 )HW95 - 14095 - 140
3939chain 'H' and (resid 141 through 244 )HW141 - 244141 - 244

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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