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- PDB-8trl: T cell recognition of citrullinated alpha-enolase peptide present... -

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基本情報

登録情報
データベース: PDB / ID: 8trl
タイトルT cell recognition of citrullinated alpha-enolase peptide presented by HLA-DR4
要素
  • (HLA class II histocompatibility antigen, ...) x 2
  • Alpha-enolase
  • RA2.7 TCR alpha chain
  • RA2.7 TCR beta chain
キーワードIMMUNE SYSTEM / immune receptor complex
機能・相同性
機能・相同性情報


regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of protein phosphorylation / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
類似検索 - 分子機能
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
ACETATE ION / FORMIC ACID / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain
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Lim, J.J. / Loh, T.J. / Reid, H.H. / Rossjohn, J.
資金援助 オーストラリア, 米国, 2件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)2008981 オーストラリア
Janssen Pharmaceuticals 米国
引用ジャーナル: Nat Commun / 年: 2024
タイトル: T cell recognition of citrullinated alpha-enolase peptide presented by HLA-DR4
著者: Lim, J.J. / Loh, T.J. / Rossjohn, J.
履歴
登録2023年8月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年7月31日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: Alpha-enolase
I: RA2.7 TCR alpha chain
J: RA2.7 TCR beta chain
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1 beta chain
F: Alpha-enolase
G: RA2.7 TCR alpha chain
H: RA2.7 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)195,60534
ポリマ－191,80810
非ポリマー3,79824
水6,179343
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: Alpha-enolase
I: RA2.7 TCR alpha chain
J: RA2.7 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,21115
ポリマ－95,9045
非ポリマー1,30710
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1 beta chain
F: Alpha-enolase
G: RA2.7 TCR alpha chain
H: RA2.7 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,39419
ポリマ－95,9045
非ポリマー2,49014
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)185.857, 58.546, 216.479
Angle α, β, γ (deg.)90.000, 113.600, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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要素

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HLA class II histocompatibility antigen, ... , 2種, 4分子 ADBE

#1: タンパク質 HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


分子量: 21084.826 Da / 分子数: 2 / 断片: UNP residues 26-206 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DRA, HLA-DRA1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01903
#2: タンパク質 HLA class II histocompatibility antigen, DRB1 beta chain / Human leukocyte antigen DRB1 / HLA-DRB1


分子量: 22275.748 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: HLA-DRB1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01911

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タンパク質・ペプチド , 1種, 2分子 CF

#3: タンパク質・ペプチド Alpha-enolase


分子量: 1421.467 Da / 分子数: 2
断片: UNP residues 10-22 with modified residue citrulline (CIR) at position 15
由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)

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タンパク質 , 2種, 4分子 IGJH

#4: タンパク質 RA2.7 TCR alpha chain


分子量: 22717.113 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 BL21(DE3) (大腸菌)
#5: タンパク質 RA2.7 TCR beta chain


分子量: 28404.611 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 BL21(DE3) (大腸菌)

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糖 , 3種, 6分子

#6: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1114.016 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-1/a4-b1_b4-c1_c3-d1_c6-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#8: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 4 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 4種, 361分子

#9: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H3O2
#10: 化合物
ChemComp-FMT / FORMIC ACID / ギ酸


分子量: 46.025 Da / 分子数: 4 / 由来タイプ: 合成 / 式: CH2O2
#11: 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: 11 / 由来タイプ: 合成 / 式: C3H8O3
#12: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 343 / 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

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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: 2.87 Å3/Da / 溶媒含有率: 57.12 % / 解説: rod-like
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 4-10% Tacsimate, 18-23% w/v PEG3350

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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: 2021年2月22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→45.87 Å / Num. obs: 84275 / % possible obs: 100 % / 冗長度: 6.2 % / Biso Wilson estimate: 53.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.5
反射 シェル解像度: 2.4→2.44 Å / Rmerge(I) obs: 0.875 / Num. unique obs: 4524 / CC1/2: 0.721

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
PHENIX1.20.1_4487精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 6V1A

6v1a


解像度: 2.4→45.87 Å / SU ML: 0.3095 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 24.1698
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2344 4121 4.89 %
Rwork0.2096 80142 -
obs0.2108 84263 99.96 %
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: 62.89 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→45.87 Å
タンパク質核酸リガンド溶媒全体
原子数12325 0 249 343 12917
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003112890
X-RAY DIFFRACTIONf_angle_d0.594817600
X-RAY DIFFRACTIONf_chiral_restr0.04451994
X-RAY DIFFRACTIONf_plane_restr0.00432272
X-RAY DIFFRACTIONf_dihedral_angle_d13.87374401
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.30171500.27312776X-RAY DIFFRACTION100
2.43-2.460.27561480.27532711X-RAY DIFFRACTION99.97
2.46-2.490.30791410.28092738X-RAY DIFFRACTION100
2.49-2.520.28041340.27882752X-RAY DIFFRACTION99.93
2.52-2.560.3041540.29962749X-RAY DIFFRACTION100
2.56-2.590.32421160.27592707X-RAY DIFFRACTION100
2.59-2.630.2991380.28192767X-RAY DIFFRACTION100
2.63-2.670.30831400.27152794X-RAY DIFFRACTION99.97
2.67-2.720.26591390.25022703X-RAY DIFFRACTION100
2.72-2.760.30491500.24162734X-RAY DIFFRACTION99.93
2.76-2.810.2721310.23982733X-RAY DIFFRACTION99.9
2.81-2.870.26311570.22722749X-RAY DIFFRACTION100
2.87-2.930.22941520.23182751X-RAY DIFFRACTION100
2.93-2.990.29231330.24262736X-RAY DIFFRACTION100
2.99-3.060.2571230.23742783X-RAY DIFFRACTION100
3.06-3.140.26511280.24532768X-RAY DIFFRACTION99.86
3.14-3.220.29071280.23912754X-RAY DIFFRACTION100
3.22-3.320.24331700.22712706X-RAY DIFFRACTION100
3.32-3.420.25371400.20572769X-RAY DIFFRACTION100
3.42-3.540.25551610.19422739X-RAY DIFFRACTION100
3.54-3.690.22331570.19312758X-RAY DIFFRACTION100
3.69-3.850.22841350.19842781X-RAY DIFFRACTION100
3.85-4.060.22711470.20182759X-RAY DIFFRACTION100
4.06-4.310.19071540.17982760X-RAY DIFFRACTION99.97
4.31-4.640.17651520.16372779X-RAY DIFFRACTION100
4.64-5.110.17171400.16652804X-RAY DIFFRACTION100
5.11-5.850.23321240.19792831X-RAY DIFFRACTION99.97
5.85-7.360.2581570.2282809X-RAY DIFFRACTION99.97
7.36-45.870.22051220.19742942X-RAY DIFFRACTION99.38
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)
11.93110989757-0.449244209432-1.681461631493.920481752760.1221461783792.626839732710.132822601113-0.063920343488-0.193649737872-0.112612172848-0.07866368318030.01078049650230.178717771616-0.0788262338227-0.08406710100460.2603459411520.01741098430080.02065285663180.290948770320.004596131162820.48876168396419.243-23.10941.758
23.293866725-0.133331492695-0.827109223613.699273077330.9037121407185.128538456280.196286111914-0.14630395337-0.0279303792548-0.116280678624-0.292919884249-0.549975902787-0.2746917656360.7083680669740.1048055213740.309908825473-0.001152575030890.01451127678480.3725070459160.0925702875530.44265653541127.814-14.80538.086
31.81433464575-0.605015688354-0.7888769027371.114002123770.0524356382033.58312178337-0.1719896846030.0457761915454-0.4638485874350.0545764024156-0.0436703009858-0.02219110148650.646207607530.1778197309520.2480082917530.3699602988780.0494149593332-0.003630633284490.2826914794540.02322415579820.5402334992824.249-32.12436.863
41.124216016360.756435543953-1.964140877012.84230663321-0.4025262222432.98276539739-0.03535787667960.0533276711725-0.359937434714-0.0128658537141-0.0598908108017-0.1043276535950.5599536334830.3595536612940.09872058964570.4237062438510.0640010129179-0.07098240985670.4202417776990.02426408169690.39657307241827.916-30.85332.16
53.005245699121.1138071888-2.759095746811.31590539224-1.051225062255.33694607254-0.349642032846-0.00450959246178-1.06636642628-0.181386425807-0.216337326433-0.2845045663730.9712453226330.7235594242570.6509302227460.4919295585310.1599229198290.03248059773380.4734852074350.03921669114490.67669260246733.114-33.67524.545
60.9921414354920.47843926103-0.05221071765991.27952038537-1.558052936822.50331323906-0.4717422113330.198116899895-1.07275770791-0.121751166383-0.105405444003-0.0377409649531.053877923810.2800715185340.6456837073390.9834039816830.2271199427290.1702638135440.488029909446-0.07992396742590.8113247261129.128-41.84526.024
72.751959862680.606402539532-1.423720625792.425208349910.223675539223.590160008080.00756849841102-0.0881921267514-0.2298040002330.0409510590117-0.1673067696720.1408532054830.0640756722587-0.2600006239590.1374943545690.2143282410330.01628809225840.004871124241170.2557757424940.02050890811090.3289738287888.464-19.84145.748
81.138166864110.858450307435-0.5419994608184.121575859671.219101880346.781091556810.01590199985450.404794839657-0.149682487293-0.439151016275-0.04807619984730.264908009510.0889405292047-0.2277960381580.05791366631470.4180713583690.0907924749198-0.07282229528620.497221446960.009401563446230.41482372614219.916-19.20612.284
92.052079658190.250319414018-1.517160797943.67357531090.2262348868123.239473098540.06487668989060.629856799657-0.110182235529-0.830337803519-0.04883295483690.4315669751350.0738456585396-0.7525195460230.01035225519150.4487903129710.0652435216404-0.1073931272910.561176770349-0.005651603597390.46470901635717.886-21.6778.18
102.105186796427.6606083-5.320250139357.043499795690.7141922131638.15793034845-0.01675288134970.4020402556590.826942072773-1.215222000330.6139117490751.78803071748-0.390461568174-0.378485008095-0.5699684565660.4409587232180.0843373749997-0.04625824821770.3448949123540.126880187010.45380283900520.042-7.88843.095
118.141656021260.802382525040.986251747012.05515889663-1.40693356314.60819694323-0.088849324546-1.07690584538-0.5489622530210.623037359718-0.08345109172480.1052964790810.532485720318-0.3857542168530.2507052632930.4630728571540.09503118569320.0865568828740.4069201255630.08395592227550.3949671287811.41-23.56857.736
121.80351954651-0.1833157111160.7272617803523.440300260542.930891386937.230566706730.0615362234305-0.2992438413120.417227061211-0.381505865398-0.0155348275395-0.132963442412-1.46532619555-0.2005100999810.02042795393240.6533021479050.02241819929690.01142536276110.3681655588380.006966679078530.46817458579313.8568.55867.823
134.302118078390.1963071302130.4485339996911.922367981960.2158690723812.029346774470.5729388921040.279261948511-0.9624521453720.143230533336-0.581469845317-0.1000258343870.47289145043-0.215832282953-0.08005842146681.45635728854-0.1278298390840.07859503017131.09572092824-0.09354981642391.1440924765129.28823.46585.441
141.882835245560.5595725493381.161176665531.24085296253-1.539952933164.839583032820.0856691932997-0.2862817200250.5532449920851.413473530.222092670628-0.626977084446-0.874254228548-0.601921810146-0.2528555579511.176798626460.201612816427-0.2785576994930.820739873426-0.2433542491171.0051341546713.24216.38888.193
153.627614058440.3048934079850.6701109055740.595653920911-0.7583334725741.22283162241-0.519431333222-0.4222172453080.4704184062920.6728478239770.762951144452-1.07690302314-0.561892105330.606088655526-0.3588399767621.44906029610.0903015032891-0.3929553541710.820942503402-0.3729493814271.0062161145315.43319.40589.15
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281.752050077930.1720898020411.120570106084.772282994321.527921933583.562066533750.099164788549-0.0649035746240.36074101647-0.0574564064525-0.114645465364-0.03125627412060.0249161689024-0.1110759654050.03667732038790.2809882718150.0435015822362-0.0623473721390.255063792627-0.05617704239850.432336465038-25.544-1.53529.726
293.82185982250.4606613552290.04504829248842.88151166912-2.313961870034.09736039998-0.00408514182727-0.0647116980186-0.18231354592-0.391064390346-0.003542362285880.4069453618390.347671432856-0.5695573674950.004751417921310.407890207524-0.00874994545148-0.06394187382960.367199734651-0.07657228475060.410396937818-34.574-9.4526.81
304.708350069773.600507720020.9977025348656.254636033260.3049969515591.921676492990.0229822713856-0.4340764286410.5740393003080.783539783062-0.0387736807353-0.0307340438167-0.07406070756490.0763537705701-0.00179139730050.407679779030.0795030295424-0.0534151929330.36200386177-0.1409919615040.543574606956-22.6621.64242.264
313.21358796469-0.0259921279161.944872798481.45134253731-0.2254619414733.66803623261-0.3567156524020.5135430867780.57119227813-0.289792616560.0637335255894-0.163929030378-0.6585653681050.1943102569430.3208131403240.3717075245850.06961744925710.02868200779340.279437904510.05090589075780.491315845941-32.0089.58517.451
321.933507499480.423339780170.4473801404731.97250927010.5775581219562.741125683990.07451481754870.136922971880.559656186878-0.104287064568-0.0753136738505-0.0719919680829-0.452203319138-0.3130184936350.01248250889630.3767605484650.07651978298530.002678233777550.333538386673-0.02020673826150.45935499925-35.9518.70421.781
334.231795861230.09280249921751.912620134192.37754034271-0.04164928659992.90503076722-0.2997044328730.2606414217540.933134166068-0.2274719859060.07283129086140.151319253242-0.957052535334-0.3726839660190.2354757426840.5768492549560.15065516815-0.03884912435750.4172940962450.08031341154630.624330132391-39.20612.60514.679
343.417204506690.8718123261181.437256674781.4051743635-0.8074492587713.842944415040.02244172270080.1284956965550.2079942086750.00298542988808-0.0517296786565-0.2687332040110.3453014386930.5309932133840.03653275307160.2575299391610.0795165451513-0.01774168017970.31195540182-0.04932284482750.396251855041-13.875-4.44732.865
353.02560928887-1.271877327631.120584644325.10950063401-1.360008097268.072970472260.5816635352780.2508361132630.200388469151-1.0540654101-0.307541948916-0.03403105616990.403434354366-0.320586148967-0.2089709345920.6203068937780.07653060806020.02919770581370.483439781378-0.09270754428060.402054620663-32.039-6.9563.197
362.62789637267-0.178753953742-0.9983634589562.218654605932.370184103984.124990969180.3153112870060.3978483964840.525972508921-0.9620038910540.00971334258654-0.232640075544-0.86522424538-0.050149900872-0.3072679381550.645933134670.08503657213450.08277648170640.4137377601650.02908700411390.406427034549-27.637-4.088-4.415
372.062810149614.889529813732.407977343237.80481922652-2.148927739447.58738608748-0.3133522431450.268838766407-1.03709326573-1.254408654190.548969713508-0.7889678796711.436773684350.41145224929-0.2504054133860.5552279007970.01247487820670.04732783256820.292848727835-0.06428259577060.441116447305-26.796-16.71731.036
387.520710921661.5211348767-0.2769355901337.265031223290.5181489089423.669669520250.236493169276-0.6954513831240.9758194267880.0624132249926-0.0356698859525-0.532775683585-0.4258306918860.353082673578-0.2040462941010.3457010032320.121974170679-0.0237095958180.432058370237-0.1467234019320.47626160795-15.566-1.59344.419
392.487219271721.43284369844-0.7231043029792.1991874562-0.8719123554662.97716882246-0.179708115509-0.40103496117-0.455148581534-0.4352524863790.2417243629840.3901230682710.545242163018-0.363792800286-0.04852804190270.590708000695-0.09755034392430.04750086444560.380286776527-0.02332030458470.536319518946-21.005-38.11951.785
402.13681910489-0.6106494878270.2522576582186.29303963793-2.523116867823.383412673720.153015753382-0.000852541379723-0.279506719828-1.01126002606-0.3137418447290.002262567860320.7214224324960.3405223568330.2007428077870.4773751983320.06653515120260.04600126949250.3098534397260.003785176952750.359771295514-16.314-29.85247.553
412.628383998320.762070450998-1.071135872313.61572959576-0.6777638442074.67589477806-0.0240643446901-0.279939607874-0.0298385565439-0.3342551155330.06372148934180.1316255046590.360468735752-0.322903305726-0.06837327850480.37911354424-0.03832807143290.03839322752190.431129661951-0.09043907409810.363117058201-21.446-32.30454.722
429.60051000647-1.90476494951-4.824418941799.282835464023.459245605378.83960189641-0.21471111867-1.730060627580.1853364682390.1251410708540.402515277014-0.350880612217-1.36697920618-0.0482078486997-0.1644578637611.5172910414-0.168769325614-0.1222517236971.112833447660.1638013535270.732654994941-24.026-45.53689.485
431.2343034738-0.6997908139691.321939205893.647215915940.7133967698362.802366507580.246589339396-0.284342409679-0.3012399530570.269605585824-0.2622199515950.3484172520230.810254575455-0.75253011785-0.03071152171790.850343454337-0.2500013626530.02739618305031.037747332280.189561260480.656743549387-24.289-47.79276.567
441.33611630639-0.650620227257-0.1482567375935.23894408566-2.282601009723.956085184980.0241072415305-1.039374043080.2658141396590.6008820735950.04915039776020.740892933691-0.2808917638080.0838015520833-0.04743829865820.42931263927-0.01079349990680.06098904067990.66407051658-0.1344751154430.459620552804-26.997-13.36363.597
452.45462936671.70521883447-1.915187692644.50527137387-1.691660482162.462851216850.1908553266440.1465836600570.571431666375-0.3836977706450.3197868517121.65386269471-0.0357322524916-0.527547553395-0.4176794750130.4171268170490.0219928091594-0.1159223545210.602767801575-0.08880441694780.640057938959-31.39-9.26552.055
463.95200615649-2.499219990550.7335613544064.98963849019-1.03301513378.09196936227-0.002056896938520.0597090866979-0.2307836088120.1398585777930.6425819682410.213529338819-0.876077773642-0.507982286278-0.5838618794980.5894304916450.1025160792410.1538730678630.689466038264-0.0748893761630.649396660622-31.864-5.92561.117
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481.25908553735-0.1840806717980.7096986589624.22409832517-1.958540161012.951452777880.149659342753-0.474523007599-0.09223234775260.5071440586590.04711224438080.530883200891-0.301225597252-0.808593081387-0.1894158043610.341670392071-0.002962898274570.07588016174230.64077135607-0.09790665585110.396350310971-26.806-17.53564.49
491.80166958809-0.395730684821-1.385069597382.65241744485-0.02943288587972.707014696540.252335777414-0.225476991866-0.2832249681850.337449148158-0.2400334491980.2656458629950.13851734541-0.239264012078-0.0262683912780.587629887723-0.1835025229810.05582511314831.095758059430.157771054470.531318536944-23.283-35.3281.191
502.677000017370.0203504461613-0.5152180691962.2400024130.03929941880561.599952699510.230608481228-0.906440848805-0.2823244944710.464614836248-0.384908191726-0.5039713331190.2716388970030.6102869662670.2227625112580.749246571413-0.12290708369-0.001318391790531.267748661520.2480723996710.531377929041-14.654-35.91786.239
511.980624282020.811250710419-0.794871473972.24218124236-0.7905216403831.57756953317-0.01119385363-0.951308815452-0.04512659800121.28961495980.2174801448220.553078223766-0.668374624493-0.14763872146-0.1316869860631.10239056291-0.130347838860.1981846915151.27809391988-0.05700629976170.499846785861-28.273-22.6388.391
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:26 )A3 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:55 )A27 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:123 )A56 - 123
4X-RAY DIFFRACTION4( CHAIN A AND RESID 124:144 )A124 - 144
5X-RAY DIFFRACTION5( CHAIN A AND RESID 145:166 )A145 - 166
6X-RAY DIFFRACTION6( CHAIN A AND RESID 167:181 )A167 - 181
7X-RAY DIFFRACTION7( CHAIN B AND RESID 3:89 )B3 - 89
8X-RAY DIFFRACTION8( CHAIN B AND RESID 90:133 )B90 - 133
9X-RAY DIFFRACTION9( CHAIN B AND RESID 134:190 )B134 - 190
10X-RAY DIFFRACTION10( CHAIN C AND RESID 10:14 )C10 - 14
11X-RAY DIFFRACTION11( CHAIN C AND RESID 16:22 )C16 - 22
12X-RAY DIFFRACTION12( CHAIN I AND RESID 2:158 )I2 - 158
13X-RAY DIFFRACTION13( CHAIN I AND RESID 159:168 )I159 - 168
14X-RAY DIFFRACTION14( CHAIN I AND RESID 169:183 )I169 - 183
15X-RAY DIFFRACTION15( CHAIN I AND RESID 184:192 )I184 - 192
16X-RAY DIFFRACTION16( CHAIN I AND RESID 193:215 )I193 - 215
17X-RAY DIFFRACTION17( CHAIN J AND RESID 1:18 )J1 - 18
18X-RAY DIFFRACTION18( CHAIN J AND RESID 19:57 )J19 - 57
19X-RAY DIFFRACTION19( CHAIN J AND RESID 58:79 )J58 - 79
20X-RAY DIFFRACTION20( CHAIN J AND RESID 80:107 )J80 - 107
21X-RAY DIFFRACTION21( CHAIN J AND RESID 108:135 )J108 - 135
22X-RAY DIFFRACTION22( CHAIN J AND RESID 136:151 )J136 - 151
23X-RAY DIFFRACTION23( CHAIN J AND RESID 152:173 )J152 - 173
24X-RAY DIFFRACTION24( CHAIN J AND RESID 174:199 )J174 - 199
25X-RAY DIFFRACTION25( CHAIN J AND RESID 200:226 )J200 - 226
26X-RAY DIFFRACTION26( CHAIN J AND RESID 227:244 )J227 - 244
27X-RAY DIFFRACTION27( CHAIN J AND RESID 245:256 )J245 - 256
28X-RAY DIFFRACTION28( CHAIN D AND RESID 3:26 )D3 - 26
29X-RAY DIFFRACTION29( CHAIN D AND RESID 27:55 )D27 - 55
30X-RAY DIFFRACTION30( CHAIN D AND RESID 56:76 )D56 - 76
31X-RAY DIFFRACTION31( CHAIN D AND RESID 77:112 )D77 - 112
32X-RAY DIFFRACTION32( CHAIN D AND RESID 113:144 )D113 - 144
33X-RAY DIFFRACTION33( CHAIN D AND RESID 145:181 )D145 - 181
34X-RAY DIFFRACTION34( CHAIN E AND RESID 2:86 )E2 - 86
35X-RAY DIFFRACTION35( CHAIN E AND RESID 87:122 )E87 - 122
36X-RAY DIFFRACTION36( CHAIN E AND RESID 123:188 )E123 - 188
37X-RAY DIFFRACTION37( CHAIN F AND RESID 10:14 )F10 - 14
38X-RAY DIFFRACTION38( CHAIN F AND RESID 16:22 )F16 - 22
39X-RAY DIFFRACTION39( CHAIN G AND RESID 2:18 )G2 - 18
40X-RAY DIFFRACTION40( CHAIN G AND RESID 19:99 )G19 - 99
41X-RAY DIFFRACTION41( CHAIN G AND RESID 100:134 )G100 - 134
42X-RAY DIFFRACTION42( CHAIN G AND RESID 135:147 )G135 - 147
43X-RAY DIFFRACTION43( CHAIN G AND RESID 148:216 )G148 - 216
44X-RAY DIFFRACTION44( CHAIN H AND RESID 1:49 )H1 - 49
45X-RAY DIFFRACTION45( CHAIN H AND RESID 50:71 )H50 - 71
46X-RAY DIFFRACTION46( CHAIN H AND RESID 72:91 )H72 - 91
47X-RAY DIFFRACTION47( CHAIN H AND RESID 92:107 )H92 - 107
48X-RAY DIFFRACTION48( CHAIN H AND RESID 108:135 )H108 - 135
49X-RAY DIFFRACTION49( CHAIN H AND RESID 136:201 )H136 - 201
50X-RAY DIFFRACTION50( CHAIN H AND RESID 202:226 )H202 - 226
51X-RAY DIFFRACTION51( CHAIN H AND RESID 227:256 )H227 - 256

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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://pdbjlvh1.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