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- PDB-6v13: immune receptor complex -

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基本情報

登録情報
データベース: PDB / ID: 6v13
タイトルimmune receptor complex
要素
  • (HLA class II histocompatibility antigen, ...) x 2
  • Fibrinogen beta 74cit69-81
  • G08 TCR alpha chain
  • G08 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 / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of exocytosis / 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 / lumenal side of endoplasmic reticulum membrane / positive regulation of protein secretion / 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: 2.75 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19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11月6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: G08 TCR alpha chain
E: G08 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,63913
ポリマ－96,5155
非ポリマー1,1248
水1,27971
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)150.457, 56.766, 136.253
Angle α, β, γ (deg.)90.000, 92.425, 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 / 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 G08 TCR alpha chain


分子量: 22742.938 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 G08 TCR beta chain


分子量: 27479.766 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: 合成 / 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 , 2種, 76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: 5 / 由来タイプ: 天然 / 式: C3H8O3
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 71 / 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: 3.09 Å3/Da / 溶媒含有率: 60.25 %
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7月7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: 2.75→45.38 Å / Num. obs: 30349 / % possible obs: 99.9 % / 冗長度: 7 % / Biso Wilson estimate: 50.2095536074 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.4
反射 シェル解像度: 2.75→2.9 Å / Rmerge(I) obs: 1.342 / Num. unique obs: 4424 / CC1/2: 0.587

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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: 2.75→45.38 Å / SU ML: 0.372829549175 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.5694403907
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2466 1528 5.03608977951 %
Rwork0.2096 28813 -
obs0.2115 30341 99.8946432687 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 49.2252702644 Å2
精密化ステップサイクル: LAST / 解像度: 2.75→45.38 Å
タンパク質核酸リガンド溶媒全体
原子数6497 0 72 71 6640
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01168794484996749
X-RAY DIFFRACTIONf_angle_d0.9426890902579191
X-RAY DIFFRACTIONf_chiral_restr0.05706214516321001
X-RAY DIFFRACTIONf_plane_restr0.006492460068531192
X-RAY DIFFRACTIONf_dihedral_angle_d20.29247468922436
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.751-2.83880.3741450.31372654X-RAY DIFFRACTION99.8572957545
2.8388-2.94020.3183646957191400.2948606022422528X-RAY DIFFRACTION99.925093633
2.9402-3.05790.2673633938241480.2642022727862584X-RAY DIFFRACTION99.9268471105
3.0579-3.19710.2977668292951220.2558252181342630X-RAY DIFFRACTION99.9273783588
3.1971-3.36560.3029465025951460.2385403890712605X-RAY DIFFRACTION99.9273519797
3.3656-3.57640.2447962181411250.2269069800222610X-RAY DIFFRACTION99.9634502924
3.5764-3.85240.2672898225171360.2051132471532591X-RAY DIFFRACTION99.7804610318
3.8524-4.23980.2322377855341440.1906141557572622X-RAY DIFFRACTION99.9638597759
4.2398-4.85270.1950277788111380.1605541249542624X-RAY DIFFRACTION99.9638074557
4.8527-6.11150.1928939463681230.1784150308192655X-RAY DIFFRACTION99.964015833
6.1115-45.370.2283953216711610.1955005729762710X-RAY DIFFRACTION99.6875
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)
13.53885907424-0.1269152033960.2950908342273.01076391928-0.985024277752.81786754881-0.1149539651480.06405736636510.390912332186-0.03144924406170.05690943359310.03573600548-0.242380078859-0.039523361918-0.085033577740.476707763802-0.08791725814030.01214312184590.443724402567-0.01411821324220.35552260943518.6486695048-11.4433516822.6895715253
20.2582776320740.167007556173-0.05118534001782.10785879931-1.211761507832.583508395510.003454604559860.1833413657480.134479475061-0.2341560602950.0394760747157-0.122043520702-0.5030822458490.2944931554160.09135653206720.666659188861-0.1509310217650.07954245431880.602939732352-0.0432896993250.47494312668928.2964948283-2.1755501316.6916422243
34.1174617394-1.80060610728-0.7971934698623.16820343654-1.833512976423.225001810840.2286057952380.05263984140060.169802274832-0.183950315903-0.079152002838-0.9245283856330.01934070239830.07897895101680.09854537844590.640472067252-0.13303819974-0.03178631312420.62670044427-0.0431176818280.37752287749827.7980703061-9.7332569115815.0397039926
42.00553914242-0.3855351822770.1830612607732.83760500661-0.7854991954982.810197992320.03757292998880.1372267540320.284609574547-0.0641126947671-0.116727223824-0.265366878998-0.9850029810330.3578069277350.06778652268991.04254332554-0.2495611772410.08555274074280.6697356369540.02100484787810.54647850010926.32271882086.950732191268.04048446086
52.220631145170.5361834220570.237515273161.76830131255-0.1883895282542.990379808050.3309451491910.1503438367150.3188565272810.0203695759229-0.0875085169823-0.00354274529948-0.1526972123170.4711254866520.1478612074790.530611626971-0.0228025787330.1182368600360.544881750502-0.04357663954750.50457769095631.8871297449-14.500486047521.4454564824
60.998782827751-1.64535323801-0.147853888612.94675796837-0.3611324914382.572945025240.02897414989550.204708567774-0.206474267536-0.436433775030.117620936769-0.4353519682510.1815981553660.5171495734490.1534098145070.54053476947-0.0244020804180.09251448876640.581151528958-0.05386373295080.48556526449830.0948500956-27.215868522219.7153353228
71.687505403521.69794562145-0.5270500049433.17177469397-2.40700773023.11509780076-0.4590183877530.534952677317-0.675394130514-0.4916731638860.12276683071-1.173517903510.7726019221960.8201188831340.3884881426330.410503408212-0.002670914877130.07661093107290.740085648061-0.0450717230360.65605250564638.6918894394-29.551539528429.5314822854
80.775774806565-1.07108301439-0.6525687161732.062309686110.1079534862892.571292195290.1316459767720.0995312445214-0.204566283376-0.4667335548430.2556514056480.2195424895440.514323062638-0.0725823750921-0.1177115407160.437345433847-0.0887909319627-0.005295360284580.44950608537-0.01793963050180.48038673477917.7472764199-28.629106807325.0370618926
92.95004391418-0.9219703977390.4939115547723.07244283169-0.5911056121764.447520158290.03508940482440.7904706983120.293195503835-0.773935331561-0.118397033539-0.298872449448-0.1370935619320.108141920403-0.2191270179180.831516669321-0.03909973235210.008906980332220.8519491899580.04385049752760.54632095935510.7060161419-8.25735137203-4.37699549069
100.544061601308-0.184195499953-0.09868269411421.39878716587-0.913204262840.6339762460720.7517400097071.52601636564-0.499855598258-0.598525883498-0.7525487952550.64472010242-0.76865389226-0.442063146261-0.1409817449191.15446445931-0.0387886651515-0.01885291697421.08695387746-0.1816058732350.59584327332617.4798841218-9.91666595503-11.3191536029
112.412560098540.435085987822-0.09918075611831.96713667064-0.5629825673332.71392208287-0.00459727014471.246381666570.593196800428-0.935048217269-0.00152470512368-0.0560085190539-0.1899592794640.0112720764706-0.2587088862350.994161206641-0.0350363973432-0.0005539131125211.095780389790.0718734824480.5668275693829.84834324017-7.61523646139-8.56482585691
120.1007988832250.0923569709883-0.6114183352542.26603517385-0.7755902528862.458374981510.457219830108-0.8371700165980.633121392305-0.273197853083-0.240668836509-0.1942283805210.4311206560660.008520019347770.003292317836280.378102563977-0.0156752598275-0.0116711047430.522859595359-0.06767539458080.32665020868723.4439603789-22.369621688330.3249682041
132.847205901790.116486106838-0.3393245385092.55871227934-1.304953687374.66900677912-0.07562179573510.1589357149750.1890370030780.1892098284870.2968640417360.418930808388-0.322921642064-0.649283548831-0.3957951660730.313393680520.00785987686102-0.003760491751130.455362549642-0.02779786324510.4690050330232.36452883692-35.753201043447.3845351848
140.8487845163280.609663147478-0.7559587033132.08394935202-0.6842175970822.16225243279-0.1117503703650.372155968768-0.3166332727630.0536602352193-0.00605804583024-0.2011347365010.01618611938720.206319716792-0.1307743902980.339476340522-0.0114248921584-0.01646396844480.381203198451-0.08177014955150.36323442435214.2313618556-37.211817086946.1943180032
151.172100716320.5748567461530.1590169214752.57591316217-1.494276705552.852775914220.1405977766710.341936908549-0.126171773902-0.5158668570210.294991478140.4460451669260.584413216561-0.310698031562-0.3064145649250.480177929466-0.100180763038-0.143417106390.541438613079-0.03344023849460.521839107065.36807477437-39.102257398737.3734487706
161.781670498491.563227676280.2023687169142.12588540276-2.350464514173.314480023570.0892645320458-0.0245101447484-0.1881565270950.162351816128-0.15194281984-0.0542439314185-0.1460279677990.0120007814901-0.2245849199890.2581445010010.01419303636940.03071573699750.387332270353-0.08278462562730.3750200472429.46185334105-38.010087561848.9707139199
172.77213302858-0.698196304157-1.765536943284.49272467921-3.348195562853.524265127110.12612157976-0.404883972127-0.04608434179930.4352665926130.111902243853-0.2169689973150.3320596164930.163303201822-0.2230685751990.3059081581670.05406780807710.04490420406750.337196263278-0.0337960769930.57079308290211.504758516-55.44127434378.7463526352
183.564628782691.26458012211.098654393142.831627137030.3405348611413.698838299190.1333703576640.0235169408073-0.031685309196-0.115101539862-0.0695811993340.287573361053-0.154810098665-0.379992217015-0.1938601252580.332131797781-0.0300792118462-0.002400165970460.2654007842420.04051288898670.4383953631449.2088780589-50.546605954272.8159420094
192.589951569772.125211740690.598154911173.533815912681.005067223114.822266001610.467538274033-1.038293804850.2460615673590.288672010635-0.2905855777060.370872550781-0.808278184322-0.0824568178632-0.1693280675290.677123289704-0.04727567385710.1173690520670.567220975057-0.02057029684110.4785286141434.03611214066-48.538946174186.500045821
204.24258868063-1.682025806471.058715827195.43356375305-1.965633828413.78677135299-0.109570564976-0.232116132927-0.098028978796-0.06007426574310.135863547092-0.2389108759170.769552225304-0.864335731325-0.3404251753010.379055042472-0.0103420188640.06434341920820.3830234898980.03039994232440.641737210961.4010690272-60.090729511680.3554461306
211.730861475330.583269610539-0.098004814791.86852381873-0.5057747770172.923007900850.015461593045-0.08180547245430.05042359434790.2983812198640.0238220367231-0.216380598412-0.2557111999010.445964970090.06226607506240.312764978538-0.0117126776051-0.05910063898860.284310777887-0.0227787914310.38792418255626.5612344873-25.405994642556.1482224862
221.359355448090.309602854105-0.0850776324272.033653567750.8646068087445.02356202130.1195918996750.08481576320460.4084389128170.171349581010.1006013849570.0896649968451-0.691870594286-0.0364998790978-0.02422048759650.301663957742-0.0130016036293-0.02090801149950.2454740899780.008868730466850.40240056821821.9185892106-21.146061001451.6287119007
231.01414897665-0.3828831885280.30905523012.75026525145-3.386057588173.13484241277-0.239762149932-0.4103451955580.01550351594170.8536841652440.02652458826320.422533226043-0.8742601106340.0310705612806-0.01582476409770.665632146116-0.0039125296006-0.04017035728680.367182264508-0.03753327681450.46233012224421.117979788-25.360016427374.8984306854
242.15842274458-0.465051508476-0.141680810482.37803345221-1.711290127083.4105446512-0.0104336453432-0.122101840475-0.07461703129750.0759395660815-0.0204764383519-0.0945147522885-0.08680701975360.05553283025320.006207170563040.2827693140610.0233540573862-0.005883806414990.314744146937-0.04475706728030.37058904186820.2767115684-49.923803249677.2899321802
252.517361762260.917207276892-0.2108388804673.54856928793-0.6106759075042.883311415560.14329717408-0.02104814018060.3954123966380.156620258102-0.0927395523150.502526122156-0.416517544962-0.143329903041-0.03332424587160.394900574939-0.0150047886090.01542324897830.3865379690650.07002941370460.4866063788617.4136088365-40.857836396973.5696021573
262.611274911210.3179564170890.1156648664322.849459530660.06914894375342.31918567649-0.0205259333088-0.139118258270.1107033437520.509308524321-0.0997535875953-0.0807960034485-0.3550508157090.384160878050.1201271895790.227153699455-0.0292608030425-0.03588859638280.309789690830.04694670153820.22964101219527.3289210652-44.209919933378.2773378033
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 144 )
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 18 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 51 )
7X-RAY DIFFRACTION7chain 'B' and (resid 52 through 63 )
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 89 )
9X-RAY DIFFRACTION9chain 'B' and (resid 90 through 133 )
10X-RAY DIFFRACTION10chain 'B' and (resid 134 through 149 )
11X-RAY DIFFRACTION11chain 'B' and (resid 150 through 188 )
12X-RAY DIFFRACTION12chain 'C' and (resid 69 through 81 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 30 )
14X-RAY DIFFRACTION14chain 'D' and (resid 31 through 56 )
15X-RAY DIFFRACTION15chain 'D' and (resid 57 through 88 )
16X-RAY DIFFRACTION16chain 'D' and (resid 89 through 125 )
17X-RAY DIFFRACTION17chain 'D' and (resid 126 through 154 )
18X-RAY DIFFRACTION18chain 'D' and (resid 155 through 192 )
19X-RAY DIFFRACTION19chain 'D' and (resid 193 through 206 )
20X-RAY DIFFRACTION20chain 'D' and (resid 207 through 217 )
21X-RAY DIFFRACTION21chain 'E' and (resid 3 through 44 )
22X-RAY DIFFRACTION22chain 'E' and (resid 45 through 120 )
23X-RAY DIFFRACTION23chain 'E' and (resid 121 through 135 )
24X-RAY DIFFRACTION24chain 'E' and (resid 136 through 173 )
25X-RAY DIFFRACTION25chain 'E' and (resid 174 through 199 )
26X-RAY DIFFRACTION26chain 'E' and (resid 200 through 256 )

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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