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- PDB-6v1a: immune receptor complex -

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基本情報

登録情報
データベース: PDB / ID: 6v1a
タイトルimmune receptor complex
要素
  • (HLA class II histocompatibility antigen, ...) x 2
  • Fibrinogen beta 74cit69-81
  • M134 TCR alpha chain
  • M134 TCR beta chain
キーワードIMMUNE SYSTEM / Immune receptor
機能・相同性
機能・相同性情報


induction of bacterial agglutination / 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 / autolysosome membrane / fibrinogen complex / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity ...induction of bacterial agglutination / 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 / autolysosome membrane / fibrinogen complex / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / Regulation of TLR by endogenous ligand / positive regulation of CD4-positive, alpha-beta T cell activation / platelet alpha granule / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / blood coagulation, fibrin clot formation / positive regulation of kinase activity / positive regulation of memory T cell differentiation / cellular response to leptin stimulus / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / intermediate filament / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / T-helper 1 type immune response / plasminogen activation / transport vesicle membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Generation of second messenger molecules / cellular response to interleukin-1 / immunological synapse / protein polymerization / Co-inhibition by PD-1 / epidermis development / Integrin cell surface interactions / Common Pathway of Fibrin Clot Formation / negative regulation of endothelial cell apoptotic process / detection of bacterium / T cell receptor binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / positive regulation of vasoconstriction / negative regulation of T cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / Integrin signaling / MHC class II antigen presentation / platelet alpha granule lumen / cell-matrix adhesion / trans-Golgi network membrane / positive regulation of protein secretion / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / platelet aggregation / cognition / response to calcium ion / Interferon gamma signaling / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MHC class II protein complex binding / Signaling by BRAF and RAF1 fusions / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / Platelet degranulation / extracellular vesicle / T cell receptor signaling pathway / positive regulation of protein phosphorylation / protein-folding chaperone binding / ER-Phagosome pathway / cell cortex / protein-containing complex assembly
類似検索 - 分子機能
Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / 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
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Fibrinogen beta chain / HLA class II histocompatibility antigen, DRB1 beta chain
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.29 Å
データ登録者Lim, J.J. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号国
Australian Research Council (ARC)CE140100011 オーストラリア
引用ジャーナル: Sci Immunol / 年: 2021
タイトル: The shared susceptibility epitope of HLA-DR4 binds citrullinated self-antigens and the TCR.
著者: Lim, J.J. / Jones, C.M. / Loh, T.J. / Ting, Y.T. / Zareie, P. / Loh, K.L. / Felix, N.J. / Suri, A. / McKinnon, M. / Stevenaert, F. / Sharma, R.K. / Klareskog, L. / Malmstrom, V. / Baker, D.G. ...著者: Lim, J.J. / Jones, C.M. / Loh, T.J. / Ting, Y.T. / Zareie, P. / Loh, K.L. / Felix, N.J. / Suri, A. / McKinnon, M. / Stevenaert, F. / Sharma, R.K. / Klareskog, L. / Malmstrom, V. / Baker, D.G. / Purcell, A.W. / Reid, H.H. / La Gruta, N.L. / Rossjohn, J.
履歴
登録2019年11月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年11月25日Provider: repository / タイプ: Initial release
改定 1.12021年6月9日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.02023年11月15日Group: Atomic model / Data collection / Derived calculations
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
改定 2.12024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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, DRB1-4 beta chain
C: Fibrinogen beta 74cit69-81
D: M134 TCR alpha chain
E: M134 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)99,30229
ポリマ－96,7745
非ポリマー2,52824
水5,206289
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: surface plasmon resonance
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)149.344, 56.990, 131.184
Angle α, β, γ (deg.)90.000, 90.870, 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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HLA class II histocompatibility antigen, ... , 2種, 2分子 AB

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


分子量: 21919.594 Da / 分子数: 1 / 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 / 細胞株 (発現宿主): HEK 293S / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01903
#2: タンパク質 HLA class II histocompatibility antigen, DRB1-4 beta chain / MHC class II antigen DRB1*4 / DR4


分子量: 23080.488 Da / 分子数: 1 / 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: P13760, UniProt: P01911*PLUS

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タンパク質 , 2種, 2分子 DE

#4: タンパク質 M134 TCR alpha chain


分子量: 22871.131 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#5: タンパク質 M134 TCR beta chain


分子量: 27609.865 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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タンパク質・ペプチド / 糖 , 2種, 4分子 C

#3: タンパク質・ペプチド Fibrinogen beta 74cit69-81


分子量: 1292.445 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P02675*PLUS
#6: 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: 3 / 由来タイプ: 天然 / 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 , 3種, 310分子

#7: 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: 20 / 由来タイプ: 合成 / 式: C3H8O3
#8: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 天然 / 式: Na
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 289 / 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: 2.85 Å3/Da / 溶媒含有率: 56.89 %
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: 0.2 M trisodium citrate, 20% PEG 3350

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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: 2018年8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: 2.29→49.24 Å / Num. obs: 49925 / % possible obs: 99.1 % / 冗長度: 6.9 % / Biso Wilson estimate: 40.9864860328 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.7
反射 シェル解像度: 2.29→2.36 Å / Num. unique obs: 4179 / CC1/2: 0.812 / % possible all: 91.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155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: 6BIL

6bil


解像度: 2.29→43.72 Å / SU ML: 0.253021454426 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.5391670115
Rfactor反射数%反射
Rfree0.2137 2456 4.92529830542 %
Rwork0.1869 --
obs0.1882 49865 99.0328090245 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 53.6986682417 Å2
精密化ステップサイクル: LAST / 解像度: 2.29→43.72 Å
タンパク質核酸リガンド溶媒全体
原子数6444 0 163 289 6896
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00468249676116772
X-RAY DIFFRACTIONf_angle_d0.6387862115459195
X-RAY DIFFRACTIONf_chiral_restr0.0459969606028999
X-RAY DIFFRACTIONf_plane_restr0.005999336942671180
X-RAY DIFFRACTIONf_dihedral_angle_d21.44827548952427
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.33040.3151110.28672200X-RAY DIFFRACTION84.652014652
2.3304-2.3780.2788988288281480.2558789730392651X-RAY DIFFRACTION99.7149982187
2.378-2.42970.2735708821561160.248120785172628X-RAY DIFFRACTION99.9271667881
2.4297-2.48620.2783704454691240.2415023706092666X-RAY DIFFRACTION99.9641705482
2.4862-2.54830.2674223288161550.2380443337072583X-RAY DIFFRACTION99.8905508938
2.5483-2.61720.2468342783311380.2275014934452657X-RAY DIFFRACTION99.8570918185
2.6172-2.69420.2622643035691300.2265504556822649X-RAY DIFFRACTION99.6771879484
2.6942-2.78120.2821521794761360.2167680272532646X-RAY DIFFRACTION99.9281609195
2.7812-2.88060.2455094190621250.2054974109412650X-RAY DIFFRACTION99.8201438849
2.8806-2.99590.2032469230391290.2011407683052671X-RAY DIFFRACTION99.8573466476
2.9959-3.13220.2354589132161250.1944876839972666X-RAY DIFFRACTION99.9641833811
3.1322-3.29730.215738230841500.1963353829792620X-RAY DIFFRACTION99.8198198198
3.2973-3.50380.2129426880631490.181041255032637X-RAY DIFFRACTION99.7851002865
3.5038-3.77420.2066245969391360.1690883422862705X-RAY DIFFRACTION99.9296517763
3.7742-4.15370.2077598352531040.1642561998492675X-RAY DIFFRACTION99.856270212
4.1537-4.75410.1626384687041490.1419292377142682X-RAY DIFFRACTION99.9294034592
4.7541-5.98730.1886566861780.1629717931572652X-RAY DIFFRACTION99.9293785311
5.9873-43.720.2013204776651530.1915619161582771X-RAY DIFFRACTION99.795221843
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)
14.080742920321.10128339228-0.5526815208222.20960911334-0.07167784449012.27142342418-0.1516140250920.251389072249-0.0080482213847-0.3233289541330.1159431466630.2948330018470.576138146908-0.08414703600470.0308077658780.42453833038-0.107192837159-0.02734190539790.55979512562-0.1098759938090.364248972047-26.1317300428-13.166395889319.295624826
23.0323875659-0.1381248747060.2885831809682.282353404840.4211782529523.78734217501-0.1589520497810.389369578872-0.633367452520.004113186706540.157196395969-0.1800674117450.6296563003460.128873618416-0.01653394060450.416891698026-0.04064632443230.03495505413160.464880074749-0.1171390442930.460015682266-14.9714895358-17.771541259122.3964656918
30.8788341560860.115288030776-0.251043985291.27452039840.7688462187082.05869520733-0.02864221450750.527100653242-0.360869322312-0.211098182136-0.005294744455490.1876997862470.451544102621-0.385251872140.09110481193550.526896093476-0.144596332455-0.08034254150710.657107075997-0.1409535442550.506316819448-30.9654869674-20.780005464815.6323532799
40.956636736586-0.239544830198-0.4051174986891.9524391381.191510395161.67298633607-0.1099996371080.25986614947-0.413925814202-0.2630350642790.1621198576660.02933830846320.535668149095-0.1832866683810.04038363553280.699598500016-0.174310291637-0.0441003225040.793045948686-0.194272594780.614554929645-27.4856850417-28.606966284112.5452630798
54.61589547989-3.1058610891-1.782582831585.102939629642.285471446813.657677856940.1630359618060.421714206776-0.512869791508-0.269618524314-0.0508338975674-0.2158406095060.527976653035-0.05965878729820.02216013572610.648297609403-0.1336138914670.02082342760870.647956474559-0.2425878990370.625017132109-21.6337004382-28.55594728529.67404954426
61.57337414237-1.35580640977-0.6853122428262.172304614471.55461467011.92484903726-0.02435911399920.277148190534-0.472107534445-0.19448000205-0.1977826451160.2098514038180.910937520641-0.2336458741640.1114424063241.03134489527-0.2576703678380.00131434447370.840197040536-0.3007926926680.785117304943-28.3592744978-36.45999138243.86823685982
72.992447695320.872331562451-0.6043860644441.658665627210.2601209499992.00577100223-0.1675982302210.219370221234-0.334103963563-0.379842311020.1043736051720.1442876068370.565552873431-0.4184009020990.03423749904880.425390724909-0.131374952457-0.04250396045910.628262730289-0.06312324197260.429161607872-33.4851787569-12.7863503418.9332949116
82.424856875860.5383747524490.4210069590152.377467828690.7092902380612.16909510341-0.0003440502363710.428796980861-0.0197202240622-0.391861176004-0.04686717746180.0396383538387-0.174792163228-0.3718314036660.007104563115210.375103739008-0.0482143759953-0.07073081096130.526110319192-0.0001884924740790.286368350964-26.1147651142-0.36061003799816.0335969952
90.220200326557-0.488634903933-0.6255249327841.005513864921.433746265792.09659638415-0.01073263725610.135113033747-0.247428449044-0.749507539124-0.3209700829270.2339689620760.258835119959-0.8062907089220.3453298369830.444725375272-0.082772190254-0.1285961798090.781541840597-0.04458731685160.385652704367-37.0425814896-4.1591083647117.8663312987
101.322003240670.779495058781-0.1085198984041.951956277090.06189905244482.794961369160.08841730839530.3830506224250.199538387782-0.1891388731930.001445032732060.583653739885-0.161010261106-0.9002517303160.0996327253790.329399032360.023743592813-0.05799908531550.6722700348530.02302751290440.469037016349-38.49740058013.3791574299223.2766426607
112.88126517739-1.14053813022-2.485419088521.016744777520.2961229986213.57331847355-0.3619078126080.0227302146950.0703863459961-0.05556171119940.303919391856-0.007236827894-0.0798256948595-0.0165265378512-0.06857738145660.340070242187-0.043122685273-0.04307531606320.44758375440.0282217352550.366204516651-25.86266513246.2803034565827.9051639923
120.5831784677470.0589979110085-0.03591599859911.580617393721.11703461312.30165400974-0.02829698817470.205079891512-0.271882363234-0.4580906064460.16652051563-0.200087378912-0.08280482919480.513522848478-0.1944009524530.396356044432-0.06108129534030.05471432823170.624392539339-0.08622984993030.423099446576-10.3772329832-7.453828094413.9949226795
130.857790640823-0.279089870807-0.1185166975851.293837832071.347114023783.706386037740.1757662935111.46477237306-0.489049393887-0.497513520623-0.1480626142080.0935175922453-0.0388750009945-0.327916435947-0.09352536823280.633238982646-0.02012984345860.02841081127571.29213780665-0.337284750330.528348910758-11.1975449372-20.1007497533-7.75884384902
140.9487977992980.134390115477-1.09656713830.00527173386322-0.1525199420871.278626987530.1188069314510.8934901538690.428184011924-0.513486574731-0.153422484542-0.0610015328653-0.08119266314940.0300166961995-0.2174114009741.036738349210.0610531382859-0.09446967049311.54719231362-0.1806225871670.678359119-13.4150151637-15.9296435685-19.6069647305
151.20199835116-0.061801932122-0.79125523780.922207075947-0.07329805308973.561179956460.4002317184070.998057319581-0.513577261752-0.33069466797-0.1292305833150.1943588812840.268690859216-0.205534029719-0.01955849293790.619916919525-0.08358058932410.03606679091621.0445693993-0.2493424026980.500647322508-16.555031812-19.8416180644-0.266733669882
160.299550001369-0.495346249574-0.475771489930.988245044331.636467749095.67544790646-0.2569807302470.987256764031-0.649893654133-0.6261692330340.3595225248610.137939022842-0.13358575412-0.125513075948-0.1122332665190.732058391617-0.0967404768122-0.0248504143221.65650320511-0.3194472305190.557052403617-8.27636101839-18.1930120975-14.6580858351
170.114555606434-0.26734494166-0.2348513314160.6145712983850.8685638297371.315323642690.07242400736561.20881515841-0.678569862941-0.4748784694750.1783132618240.259035197857-0.1068555357370.116018847987-0.1352153565520.6617555566430.002741344181130.05407769941981.24548395903-0.227690665490.672815468881-2.90966652437-16.0059198047-8.1437642188
180.1891007817340.1943320397110.5735185592631.19781772310.3351028293351.484187305140.06472122144950.2573204583080.0698900241177-0.19971219664-0.0265406774630.15494028153-0.0884247581735-0.304628644159-0.03908900720960.26627174573-0.05229479037890.02711781111170.395923506809-0.0639486092340.338121851998-25.8025799142-4.9176446497128.3970320569
192.010971638550.7640421973360.4851682615851.636391082710.3283399124592.72432699541-0.07621149180410.298216105736-0.3227477050760.01879408685050.195176641404-0.2984898467450.1568612946740.217992897538-0.1688518590920.207354793147-0.02064429104290.02044268155310.313479992988-0.009659980797020.523560993803-5.6543137545610.0573996345.9000404898
200.7575134496010.5801399180590.5647641224221.880188158961.37870585531.93976584422-0.07969938129970.1942184067040.0599313897217-0.1070961227710.0958576973265-0.0619162426092-0.1724569073580.139847798703-0.09115849599690.251719853148-0.04467149464520.02164396896520.3475437439630.03302897275680.411336995544-12.395072590513.381254181944.847508193
212.499566336670.1234371451920.4089186915022.4116389838-0.2537057794932.179772158330.0105605691105-0.20717207580.1535317069870.1496691377410.0858246031673-0.0557837800302-0.0449986762906-0.00964587319076-0.1016516960810.2381397159880.01583196373410.001445735361240.265709679799-0.01532976699060.453077287543-12.178065516325.872501868775.9873888532
220.752572080338-0.16575399017-0.2945730518061.228042894820.408442163144.227247834330.05333007403940.0260704987690.01735699484890.0954155557179-0.00368110011323-0.00123449397960.103706890709-0.07808327109110.02204310694970.219415403796-0.0380359126292-0.00182590249570.3005697175580.007572185179110.430279744211-27.3518292202-2.0280201430952.9926781048
230.3490964304940.325740112789-0.4396998302540.852879204718-0.08182295051092.911612082970.04326297380290.115316854074-0.194671087555-0.0114810614422-0.0061836665550.1222857888490.383484022163-0.07236200542490.002625031930020.271107062881-0.0206480885985-0.02611652403670.3472439827640.000246987892160.442094026145-26.5892424154-6.1900891332548.659181936
241.77606161027-0.382964215056-0.001723994025122.525459539353.187174442444.42369741060.0531809497627-0.191621023418-0.1675341395520.46846895290.159374657817-0.1282263913980.5299797082150.20749578077-0.004692995572040.277175027959-0.04332956022690.004947586884470.2414448390020.06377505229680.355133764256-25.1886689692-1.2771077296172.6511028076
251.32885373940.511880346711-0.1011014761912.388670215910.1481753298691.388841102450.03018373937690.01041069999220.0810107173953-0.0536604459095-0.00116734469881-0.100320902106-0.0373537597434-0.0827449999818-0.006914311222790.2068437069490.02432316945490.0157503864780.2484918014140.0009440717787450.392992181467-24.76349033622.013172117773.4300498138
261.59820513283-0.952578733145-0.4013005358154.7029755379-0.1871598741122.238403767330.00661437326634-0.125387575315-0.1924769723930.438304727464-0.1012497271450.4656663368650.386496687613-0.3644680467050.08405457977120.286515065187-0.06640275220720.08049071062690.3720373192450.007550672145570.402961924957-33.8451075918.6896081851977.992892198
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 144 )
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 181 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 18 )
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 32 )
9X-RAY DIFFRACTION9chain 'B' and (resid 33 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 63 )
11X-RAY DIFFRACTION11chain 'B' and (resid 64 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 97 )
13X-RAY DIFFRACTION13chain 'B' and (resid 98 through 132 )
14X-RAY DIFFRACTION14chain 'B' and (resid 133 through 144 )
15X-RAY DIFFRACTION15chain 'B' and (resid 145 through 161 )
16X-RAY DIFFRACTION16chain 'B' and (resid 162 through 177 )
17X-RAY DIFFRACTION17chain 'B' and (resid 178 through 188 )
18X-RAY DIFFRACTION18chain 'C' and (resid 69 through 81 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 33 )
20X-RAY DIFFRACTION20chain 'D' and (resid 34 through 134 )
21X-RAY DIFFRACTION21chain 'D' and (resid 135 through 218 )
22X-RAY DIFFRACTION22chain 'E' and (resid 3 through 57 )
23X-RAY DIFFRACTION23chain 'E' and (resid 58 through 121 )
24X-RAY DIFFRACTION24chain 'E' and (resid 122 through 136 )
25X-RAY DIFFRACTION25chain 'E' and (resid 137 through 227 )
26X-RAY DIFFRACTION26chain 'E' and (resid 228 through 257 )

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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