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- PDB-7q5t: The tandem SH2 domains of SYK with a bound FCER1G diphospho-ITAM ... -

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基本情報

登録情報
データベース: PDB / ID: 7q5t
タイトルThe tandem SH2 domains of SYK with a bound FCER1G diphospho-ITAM peptide
要素
  • High affinity immunoglobulin epsilon receptor subunit gamma
  • Tyrosine-protein kinase SYK
キーワードTRANSFERASE / Signalling / kinase
機能・相同性
機能・相同性情報


IgE receptor activity / Fc-epsilon receptor I complex / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / Fc-gamma receptor III complex / interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / cellular response to lectin ...IgE receptor activity / Fc-epsilon receptor I complex / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / Fc-gamma receptor III complex / interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / cellular response to lectin / positive regulation of interleukin-3 production / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / serotonin secretion by platelet / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / neutrophil activation involved in immune response / positive regulation of mast cell cytokine production / positive regulation of mast cell degranulation / lymph vessel development / collagen-activated tyrosine kinase receptor signaling pathway / Fc-gamma receptor signaling pathway / regulation of platelet activation / cell activation / regulation of phagocytosis / Platelet Adhesion to exposed collagen / FLT3 signaling through SRC family kinases / IgE binding / cellular response to lipid / positive regulation of killing of cells of another organism / beta selection / macrophage activation involved in immune response / cellular response to molecule of fungal origin / early phagosome / leukotriene biosynthetic process / regulation of DNA-binding transcription factor activity / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of monocyte chemotactic protein-1 production / interleukin-3-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / positive regulation of granulocyte macrophage colony-stimulating factor production / Interleukin-2 signaling / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / Fc epsilon receptor (FCERI) signaling / IgG binding / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of B cell differentiation / T cell receptor complex / leukocyte cell-cell adhesion / mast cell degranulation / : / positive regulation of interleukin-4 production / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / positive regulation of receptor internalization / Fc-epsilon receptor signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I / phospholipase binding / positive regulation of type I interferon production / amyloid-beta clearance / tertiary granule membrane / positive regulation of interleukin-10 production / ficolin-1-rich granule membrane / FCGR activation / cellular response to low-density lipoprotein particle stimulus / positive regulation of bone resorption / phosphatase binding / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Signaling by CSF3 (G-CSF) / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of phagocytosis / GPVI-mediated activation cascade / positive regulation of interleukin-12 production / phosphotyrosine residue binding / neutrophil chemotaxis / positive regulation of TORC1 signaling / Integrin signaling / positive regulation of calcium-mediated signaling / regulation of ERK1 and ERK2 cascade / SH2 domain binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / B cell differentiation / positive regulation of superoxide anion generation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / integrin-mediated signaling pathway / positive regulation of interleukin-8 production / Regulation of signaling by CBL / animal organ morphogenesis / negative regulation of inflammatory response to antigenic stimulus / Cell surface interactions at the vascular wall / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation
類似検索 - 分子機能
High affinity immunoglobulin epsilon receptor subunit gamma / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain ...High affinity immunoglobulin epsilon receptor subunit gamma / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / High affinity immunoglobulin epsilon receptor subunit gamma / Tyrosine-protein kinase SYK
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å
データ登録者Bradshaw, W.J. / Katis, V.L. / Chen, Z. / Bountra, C. / von Delft, F. / Gileadi, O. / Brennan, P.E.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute on Aging (NIH/NIA)5U54AG065187-03 米国
引用ジャーナル: Structure / 年: 2024
タイトル: The mechanism of allosteric activation of SYK kinase derived from multiple phospho-ITAM-bound structures
著者: Bradshaw, W.J. / Harris, G. / Gileadi, O. / Katis, V.L.
履歴
登録2021年11月4日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年11月24日Provider: repository / タイプ: Initial release
改定 1.12024年1月31日Group: Data collection / Derived calculations / Refinement description
カテゴリ: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.22024年10月30日Group: Database references / Structure summary
カテゴリ: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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

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集合体

登録構造単位
AAA: Tyrosine-protein kinase SYK
BBB: Tyrosine-protein kinase SYK
CCC: Tyrosine-protein kinase SYK
DDD: Tyrosine-protein kinase SYK
EEE: Tyrosine-protein kinase SYK
FFF: Tyrosine-protein kinase SYK
GGG: High affinity immunoglobulin epsilon receptor subunit gamma
HHH: High affinity immunoglobulin epsilon receptor subunit gamma
III: High affinity immunoglobulin epsilon receptor subunit gamma
JJJ: High affinity immunoglobulin epsilon receptor subunit gamma
KKK: High affinity immunoglobulin epsilon receptor subunit gamma
LLL: High affinity immunoglobulin epsilon receptor subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)195,54826
ポリマ－194,29412
非ポリマー1,25314
水6,017334
1
AAA: Tyrosine-protein kinase SYK
JJJ: High affinity immunoglobulin epsilon receptor subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,6345
ポリマ－32,3822
非ポリマー2523
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-17 kcal/mol
Surface area14730 Å2
手法PISA
2
BBB: Tyrosine-protein kinase SYK
KKK: High affinity immunoglobulin epsilon receptor subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,6785
ポリマ－32,3822
非ポリマー2963
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-12 kcal/mol
Surface area14650 Å2
手法PISA
3
CCC: Tyrosine-protein kinase SYK
HHH: High affinity immunoglobulin epsilon receptor subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,6966
ポリマ－32,3822
非ポリマー3144
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-18 kcal/mol
Surface area14790 Å2
手法PISA
4
DDD: Tyrosine-protein kinase SYK
III: High affinity immunoglobulin epsilon receptor subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,6675
ポリマ－32,3822
非ポリマー2853
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-23 kcal/mol
Surface area14690 Å2
手法PISA
5
EEE: Tyrosine-protein kinase SYK
GGG: High affinity immunoglobulin epsilon receptor subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,4893
ポリマ－32,3822
非ポリマー1061
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-11 kcal/mol
Surface area14460 Å2
手法PISA
6
FFF: Tyrosine-protein kinase SYK
LLL: High affinity immunoglobulin epsilon receptor subunit gamma


分子量 (理論値)分子数
合計 (水以外)32,3822
ポリマ－32,3822
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-14 kcal/mol
Surface area14100 Å2
手法PISA
単位格子
Length a, b, c (Å)144.136, 88.035, 158.486
Angle α, β, γ (deg.)90.000, 113.575, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74AAA
84EEE
95AAA
105FFF
116BBB
126CCC
137BBB
147DDD
158BBB
168EEE
179BBB
189FFF
1910CCC
2010DDD
2111CCC
2211EEE
2312CCC
2412FFF
2513DDD
2613EEE
2714DDD
2814FFF
2915EEE
3015FFF
3116GGG
3216III
3317GGG
3417LLL
3518HHH
3618JJJ
3719HHH
3819KKK
3920III
4020LLL
4121JJJ
4221KKK

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPLYSLYSAAAA8 - 2614 - 257
221ASPASPLYSLYSBBBB8 - 2614 - 257
332SERSERLYSLYSAAAA9 - 2615 - 257
442SERSERLYSLYSCCCC9 - 2615 - 257
553ALAALAILEILEAAAA10 - 2626 - 258
663ALAALAILEILEDDDD10 - 2626 - 258
774SERSERLYSLYSAAAA9 - 2615 - 257
884SERSERLYSLYSEEEE9 - 2615 - 257
995SERSERILEILEAAAA9 - 2625 - 258
10105SERSERILEILEFFFF9 - 2625 - 258
11116SERSERGLYGLYBBBB9 - 2635 - 259
12126SERSERGLYGLYCCCC9 - 2635 - 259
13137ALAALAGLYGLYBBBB10 - 2636 - 259
14147ALAALAGLYGLYDDDD10 - 2636 - 259
15158SERSERLYSLYSBBBB9 - 2615 - 257
16168SERSERLYSLYSEEEE9 - 2615 - 257
17179SERSERILEILEBBBB9 - 2625 - 258
18189SERSERILEILEFFFF9 - 2625 - 258
191910ALAALAILEILECCCC10 - 2626 - 258
202010ALAALAILEILEDDDD10 - 2626 - 258
212111SERSERLYSLYSCCCC9 - 2615 - 257
222211SERSERLYSLYSEEEE9 - 2615 - 257
232312SERSERILEILECCCC9 - 2625 - 258
242412SERSERILEILEFFFF9 - 2625 - 258
252513ALAALAILEILEDDDD10 - 2626 - 258
262613ALAALAILEILEEEEE10 - 2626 - 258
272714ALAALAILEILEDDDD10 - 2626 - 258
282814ALAALAILEILEFFFF10 - 2626 - 258
292915SERSERILEILEEEEE9 - 2625 - 258
303015SERSERILEILEFFFF9 - 2625 - 258
313116GLYGLYLEULEUGGGG63 - 792 - 18
323216GLYGLYLEULEUIIII63 - 792 - 18
333317PTRPTRTHRTHRGGGG65 - 784 - 17
343417PTRPTRTHRTHRLLLL65 - 784 - 17
353518VALVALLEULEUHHHH64 - 793 - 18
363618VALVALLEULEUJJJJ64 - 793 - 18
373719GLYGLYLEULEUHHHH63 - 792 - 18
383819GLYGLYLEULEUKKKK63 - 792 - 18
393920PTRPTRTHRTHRIIII65 - 784 - 17
404020PTRPTRTHRTHRLLLL65 - 784 - 17
414121VALVALLEULEUJJJJ64 - 793 - 18
424221VALVALLEULEUKKKK64 - 793 - 18

NCSアンサンブル:
ID詳細
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42

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要素

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タンパク質 / タンパク質・ペプチド , 2種, 12分子 AAABBBCCCDDDEEEFFFGGGHHHIIIJJJKKKLLL

#1: タンパク質
Tyrosine-protein kinase SYK / Spleen tyrosine kinase / p72-Syk


分子量: 29906.971 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SYK / プラスミド: pNIC28-Bsa4 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P43405, non-specific protein-tyrosine kinase
#2: タンパク質・ペプチド
High affinity immunoglobulin epsilon receptor subunit gamma / Fc receptor gamma-chain / FcRgamma / Fc-epsilon RI-gamma / IgE Fc receptor subunit gamma / FceRI gamma


分子量: 2475.431 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P30273

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非ポリマー , 4種, 348分子

#3: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 9 / 由来タイプ: 合成 / 式: PO4
#4: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H10O3
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 334 / 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: 2.37 Å3/Da / 溶媒含有率: 48.14 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5
詳細: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME

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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: Diamond / ビームライン: I03 / 波長: 0.9762 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2021年1月20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: 0.9762 Å / 相対比: 1
反射解像度: 2.2→73.26 Å / Num. obs: 90843 / % possible obs: 98.3 % / 冗長度: 8.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.077 / Rrim(I) all: 0.164 / Χ2: 0.93 / Net I/σ(I): 7.5
反射 シェル解像度: 2.2→2.24 Å / 冗長度: 4.9 % / Rmerge(I) obs: 1.672 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3838 / CC1/2: 0.31 / Rpim(I) all: 1.1 / Rrim(I) all: 2.018 / Χ2: 0.97 / % possible all: 83.8

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0267精密化
DIALS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: 1A81

1a81


解像度: 2.2→73.26 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.783 / SU ML: 0.226 / 交差検証法: FREE R-VALUE / ESU R: 0.288 / ESU R Free: 0.222 / 詳細: Hydrogens have been added in their riding positions
Rfactor反射数%反射
Rfree0.255 1981 2.183 %
Rwork0.2075 88775 -
all0.209 --
obs-90756 98.264 %
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータBiso mean: 63.047 Å2
Baniso -1Baniso -2Baniso -3
1--1.865 Å20 Å21.846 Å2
2---2.006 Å20 Å2
3---1.636 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→73.26 Å
タンパク質核酸リガンド溶媒全体
原子数13083 0 71 334 13488
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01313448
X-RAY DIFFRACTIONr_bond_other_d0.0010.01512654
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.6518152
X-RAY DIFFRACTIONr_angle_other_deg1.2661.58429176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16451622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60622.378719
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.039152367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9561584
X-RAY DIFFRACTIONr_chiral_restr0.0690.21669
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215127
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023125
X-RAY DIFFRACTIONr_nbd_refined0.2110.22336
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.210817
X-RAY DIFFRACTIONr_nbtor_refined0.1630.26194
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.26386
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2364
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.252
X-RAY DIFFRACTIONr_nbd_other0.2180.2182
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3340.27
X-RAY DIFFRACTIONr_mcbond_it5.6816.3556512
X-RAY DIFFRACTIONr_mcbond_other5.6816.3546511
X-RAY DIFFRACTIONr_mcangle_it8.3689.5118117
X-RAY DIFFRACTIONr_mcangle_other8.3689.5128118
X-RAY DIFFRACTIONr_scbond_it6.1956.9426936
X-RAY DIFFRACTIONr_scbond_other6.1946.9426937
X-RAY DIFFRACTIONr_scangle_it9.32810.15210032
X-RAY DIFFRACTIONr_scangle_other9.32810.15210033
X-RAY DIFFRACTIONr_lrange_it12.52272.04514151
X-RAY DIFFRACTIONr_lrange_other12.52972.05614125
X-RAY DIFFRACTIONr_ncsr_local_group_10.1110.057753
X-RAY DIFFRACTIONr_ncsr_local_group_20.1060.057746
X-RAY DIFFRACTIONr_ncsr_local_group_30.1220.057464
X-RAY DIFFRACTIONr_ncsr_local_group_40.1230.057529
X-RAY DIFFRACTIONr_ncsr_local_group_50.1240.057331
X-RAY DIFFRACTIONr_ncsr_local_group_60.10.057859
X-RAY DIFFRACTIONr_ncsr_local_group_70.120.057511
X-RAY DIFFRACTIONr_ncsr_local_group_80.1190.057593
X-RAY DIFFRACTIONr_ncsr_local_group_90.110.057416
X-RAY DIFFRACTIONr_ncsr_local_group_100.1190.057524
X-RAY DIFFRACTIONr_ncsr_local_group_110.1220.057563
X-RAY DIFFRACTIONr_ncsr_local_group_120.1180.057380
X-RAY DIFFRACTIONr_ncsr_local_group_130.1250.057381
X-RAY DIFFRACTIONr_ncsr_local_group_140.1060.057309
X-RAY DIFFRACTIONr_ncsr_local_group_150.1110.057339
X-RAY DIFFRACTIONr_ncsr_local_group_160.2060.05335
X-RAY DIFFRACTIONr_ncsr_local_group_170.2360.05262
X-RAY DIFFRACTIONr_ncsr_local_group_180.1970.05331
X-RAY DIFFRACTIONr_ncsr_local_group_190.2250.05329
X-RAY DIFFRACTIONr_ncsr_local_group_200.2050.05272
X-RAY DIFFRACTIONr_ncsr_local_group_210.1970.05319
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.111350.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.111350.05008
23AAAX-RAY DIFFRACTIONLocal ncs0.106090.05008
24CCCX-RAY DIFFRACTIONLocal ncs0.106090.05008
35AAAX-RAY DIFFRACTIONLocal ncs0.122060.05008
36DDDX-RAY DIFFRACTIONLocal ncs0.122060.05008
47AAAX-RAY DIFFRACTIONLocal ncs0.123180.05007
48EEEX-RAY DIFFRACTIONLocal ncs0.123180.05007
59AAAX-RAY DIFFRACTIONLocal ncs0.124190.05008
510FFFX-RAY DIFFRACTIONLocal ncs0.124190.05008
611BBBX-RAY DIFFRACTIONLocal ncs0.100040.05008
612CCCX-RAY DIFFRACTIONLocal ncs0.100040.05008
713BBBX-RAY DIFFRACTIONLocal ncs0.119590.05008
714DDDX-RAY DIFFRACTIONLocal ncs0.119590.05008
815BBBX-RAY DIFFRACTIONLocal ncs0.119430.05008
816EEEX-RAY DIFFRACTIONLocal ncs0.119430.05008
917BBBX-RAY DIFFRACTIONLocal ncs0.110160.05008
918FFFX-RAY DIFFRACTIONLocal ncs0.110160.05008
1019CCCX-RAY DIFFRACTIONLocal ncs0.119190.05008
1020DDDX-RAY DIFFRACTIONLocal ncs0.119190.05008
1121CCCX-RAY DIFFRACTIONLocal ncs0.12180.05008
1122EEEX-RAY DIFFRACTIONLocal ncs0.12180.05008
1223CCCX-RAY DIFFRACTIONLocal ncs0.117740.05008
1224FFFX-RAY DIFFRACTIONLocal ncs0.117740.05008
1325DDDX-RAY DIFFRACTIONLocal ncs0.125010.05008
1326EEEX-RAY DIFFRACTIONLocal ncs0.125010.05008
1427DDDX-RAY DIFFRACTIONLocal ncs0.105960.05008
1428FFFX-RAY DIFFRACTIONLocal ncs0.105960.05008
1529EEEX-RAY DIFFRACTIONLocal ncs0.111390.05008
1530FFFX-RAY DIFFRACTIONLocal ncs0.111390.05008
1631GGGX-RAY DIFFRACTIONLocal ncs0.205560.05005
1632IIIX-RAY DIFFRACTIONLocal ncs0.205560.05005
1733GGGX-RAY DIFFRACTIONLocal ncs0.236370.05003
1734LLLX-RAY DIFFRACTIONLocal ncs0.236370.05003
1835HHHX-RAY DIFFRACTIONLocal ncs0.196810.05009
1836JJJX-RAY DIFFRACTIONLocal ncs0.196810.05009
1937HHHX-RAY DIFFRACTIONLocal ncs0.224810.05007
1938KKKX-RAY DIFFRACTIONLocal ncs0.224810.05007
2039IIIX-RAY DIFFRACTIONLocal ncs0.204950.05003
2040LLLX-RAY DIFFRACTIONLocal ncs0.204950.05003
2141JJJX-RAY DIFFRACTIONLocal ncs0.196730.05006
2142KKKX-RAY DIFFRACTIONLocal ncs0.196730.05006
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.3391190.3585684X-RAY DIFFRACTION85.1629
2.257-2.3190.3241350.3375997X-RAY DIFFRACTION92.6004
2.319-2.3860.3141330.3116212X-RAY DIFFRACTION98.7088
2.386-2.460.341320.2896111X-RAY DIFFRACTION99.984
2.46-2.540.3261050.2635982X-RAY DIFFRACTION99.9672
2.54-2.6290.2651500.2395741X-RAY DIFFRACTION99.9491
2.629-2.7290.3081360.2295529X-RAY DIFFRACTION99.9118
2.729-2.840.2721310.235320X-RAY DIFFRACTION99.9817
2.84-2.9660.3131260.2315079X-RAY DIFFRACTION99.9616
2.966-3.1110.29880.2264932X-RAY DIFFRACTION99.9801
3.111-3.2790.27980.2174679X-RAY DIFFRACTION100
3.279-3.4780.2621070.2124396X-RAY DIFFRACTION100
3.478-3.7180.2721070.2044143X-RAY DIFFRACTION100
3.718-4.0160.24680.1833927X-RAY DIFFRACTION100
4.016-4.3990.199820.1663541X-RAY DIFFRACTION100
4.399-4.9170.199760.1443232X-RAY DIFFRACTION100
4.917-5.6770.185670.1622866X-RAY DIFFRACTION100
5.677-6.950.267480.192439X-RAY DIFFRACTION100
6.95-9.8170.242520.1591885X-RAY DIFFRACTION100
9.817-73.260.214210.1941082X-RAY DIFFRACTION99.7288

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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