[日本語] English
万見
- PDB-7q5w: The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM ... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7q5w
タイトルThe tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide
要素
  • TYRO protein tyrosine kinase-binding protein
  • Tyrosine-protein kinase SYK
キーワードTRANSFERASE / Signalling / kinase
機能・相同性
機能・相同性情報


myeloid leukocyte activation / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of receptor localization to synapse / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / positive regulation of natural killer cell activation / negative regulation of transforming growth factor beta1 production / positive regulation of microglial cell mediated cytotoxicity / Other semaphorin interactions ...myeloid leukocyte activation / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of receptor localization to synapse / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / positive regulation of natural killer cell activation / negative regulation of transforming growth factor beta1 production / positive regulation of microglial cell mediated cytotoxicity / Other semaphorin interactions / interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / cellular response to lectin / gamma-delta T cell differentiation / serotonin secretion by platelet / positive regulation of interleukin-3 production / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / 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 / regulation of platelet activation / collagen-activated tyrosine kinase receptor signaling pathway / cell activation / positive regulation of killing of cells of another organism / regulation of phagocytosis / beta selection / macrophage activation involved in immune response / positive regulation of protein localization to cell surface / cellular response to molecule of fungal origin / early phagosome / FLT3 signaling through SRC family kinases / leukotriene biosynthetic process / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of monocyte chemotactic protein-1 production / interleukin-3-mediated signaling pathway / cellular response to lipid / regulation of DNA-binding transcription factor activity / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / Signal regulatory protein family interactions / negative regulation of type I interferon production / T cell receptor complex / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / mast cell degranulation / negative regulation of interleukin-10 production / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of interleukin-4 production / Dectin-2 family / negative regulation of B cell proliferation / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / phospholipase binding / positive regulation of receptor internalization / positive regulation of interleukin-10 production / cellular response to low-density lipoprotein particle stimulus / negative regulation of long-term synaptic potentiation / FCGR activation / response to axon injury / positive regulation of type I interferon production / positive regulation of bone resorption / phosphatase binding / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / cellular defense response / Signaling by CSF3 (G-CSF) / forebrain development / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / positive regulation of TORC1 signaling / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of interleukin-12 production / neutrophil chemotaxis / phosphotyrosine residue binding / Integrin signaling / FCERI mediated Ca+2 mobilization / SH2 domain binding / B cell differentiation / FCGR3A-mediated IL10 synthesis / regulation of ERK1 and ERK2 cascade / osteoclast differentiation / secretory granule membrane / positive regulation of superoxide anion generation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of interleukin-1 beta production
類似検索 - 分子機能
TYRO protein tyrosine kinase-binding protein / 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 ...TYRO protein tyrosine kinase-binding protein / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / TYRO protein tyrosine kinase-binding protein / 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: To Be Published
タイトル: The tandem SH2 domains of SYK
著者: Bradshaw, W.J. / Katis, V.L. / Chen, Z. / Bountra, C. / von Delft, F. / Gileadi, O. / Brennan, P.E.
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

-
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

-
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: TYRO protein tyrosine kinase-binding protein
HHH: TYRO protein tyrosine kinase-binding protein
III: TYRO protein tyrosine kinase-binding protein
JJJ: TYRO protein tyrosine kinase-binding protein
KKK: TYRO protein tyrosine kinase-binding protein
LLL: TYRO protein tyrosine kinase-binding protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)195,40823
ポリマ－194,38412
非ポリマー1,02411
水5,459303
1
AAA: Tyrosine-protein kinase SYK
JJJ: TYRO protein tyrosine kinase-binding protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,5544
ポリマ－32,3972
非ポリマー1572
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-13 kcal/mol
Surface area14620 Å2
手法PISA
2
BBB: Tyrosine-protein kinase SYK
LLL: TYRO protein tyrosine kinase-binding protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,5544
ポリマ－32,3972
非ポリマー1572
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-9 kcal/mol
Surface area14950 Å2
手法PISA
3
CCC: Tyrosine-protein kinase SYK
KKK: TYRO protein tyrosine kinase-binding protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,5984
ポリマ－32,3972
非ポリマー2012
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-12 kcal/mol
Surface area14580 Å2
手法PISA
4
DDD: Tyrosine-protein kinase SYK
GGG: TYRO protein tyrosine kinase-binding protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,5544
ポリマ－32,3972
非ポリマー1572
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-12 kcal/mol
Surface area14610 Å2
手法PISA
5
EEE: Tyrosine-protein kinase SYK
III: TYRO protein tyrosine kinase-binding protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,6554
ポリマ－32,3972
非ポリマー2572
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-14 kcal/mol
Surface area14360 Å2
手法PISA
6
FFF: Tyrosine-protein kinase SYK
HHH: TYRO protein tyrosine kinase-binding protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,4923
ポリマ－32,3972
非ポリマー951
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-14 kcal/mol
Surface area14710 Å2
手法PISA
単位格子
Length a, b, c (Å)117.949, 131.928, 141.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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
3216HHH
3317GGG
3417III
3518GGG
3618JJJ
3719GGG
3819KKK
3920GGG
4020LLL
4121HHH
4221III
4322HHH
4422JJJ
4523HHH
4623KKK
4724HHH
4824LLL
4925III
5025JJJ
5126III
5226KKK
5327III
5427LLL
5528JJJ
5628KKK
5729JJJ
5829LLL
5930KKK
6030LLL

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
111SERSERILEILEAAAA9 - 2625 - 258
221SERSERILEILEBBBB9 - 2625 - 258
332SERSERGLNGLNAAAA9 - 2605 - 256
442SERSERGLNGLNCCCC9 - 2605 - 256
553SERSERLYSLYSAAAA9 - 2615 - 257
663SERSERLYSLYSDDDD9 - 2615 - 257
774SERSERILEILEAAAA9 - 2625 - 258
884SERSERILEILEEEEE9 - 2625 - 258
995SERSERLYSLYSAAAA9 - 2615 - 257
10105SERSERLYSLYSFFFF9 - 2615 - 257
11116SERSERGLNGLNBBBB9 - 2605 - 256
12126SERSERGLNGLNCCCC9 - 2605 - 256
13137SERSERLYSLYSBBBB9 - 2615 - 257
14147SERSERLYSLYSDDDD9 - 2615 - 257
15158SERSERILEILEBBBB9 - 2625 - 258
16168SERSERILEILEEEEE9 - 2625 - 258
17179SERSERLYSLYSBBBB9 - 2615 - 257
18189SERSERLYSLYSFFFF9 - 2615 - 257
191910ASPASPGLNGLNCCCC8 - 2604 - 256
202010ASPASPGLNGLNDDDD8 - 2604 - 256
212111SERSERGLNGLNCCCC9 - 2605 - 256
222211SERSERGLNGLNEEEE9 - 2605 - 256
232312ASPASPGLNGLNCCCC8 - 2604 - 256
242412ASPASPGLNGLNFFFF8 - 2604 - 256
252513SERSERLYSLYSDDDD9 - 2615 - 257
262613SERSERLYSLYSEEEE9 - 2615 - 257
272714ASPASPLYSLYSDDDD8 - 2614 - 257
282814ASPASPLYSLYSFFFF8 - 2614 - 257
292915SERSERLYSLYSEEEE9 - 2615 - 257
303015SERSERLYSLYSFFFF9 - 2615 - 257
313116PROPROLEULEUGGGG90 - 1053 - 18
323216PROPROLEULEUHHHH90 - 1053 - 18
333317PROPROLEULEUGGGG90 - 1053 - 18
343417PROPROLEULEUIIII90 - 1053 - 18
353518PROPROLEULEUGGGG90 - 1053 - 18
363618PROPROLEULEUJJJJ90 - 1053 - 18
373719PROPROLEULEUGGGG90 - 1053 - 18
383819PROPROLEULEUKKKK90 - 1053 - 18
393920PROPROASNASNGGGG90 - 1063 - 19
404020PROPROASNASNLLLL90 - 1063 - 19
414121PROPROASNASNHHHH90 - 1063 - 19
424221PROPROASNASNIIII90 - 1063 - 19
434322PROPROLEULEUHHHH90 - 1053 - 18
444422PROPROLEULEUJJJJ90 - 1053 - 18
454523PROPROASNASNHHHH90 - 1063 - 19
464623PROPROASNASNKKKK90 - 1063 - 19
474724PROPROLEULEUHHHH90 - 1053 - 18
484824PROPROLEULEULLLL90 - 1053 - 18
494925PROPROLEULEUIIII90 - 1053 - 18
505025PROPROLEULEUJJJJ90 - 1053 - 18
515126PROPROASNASNIIII90 - 1063 - 19
525226PROPROASNASNKKKK90 - 1063 - 19
535327PROPROLEULEUIIII90 - 1053 - 18
545427PROPROLEULEULLLL90 - 1053 - 18
555528PROPROLEULEUJJJJ90 - 1053 - 18
565628PROPROLEULEUKKKK90 - 1053 - 18
575729SERSERLEULEUJJJJ89 - 1052 - 18
585829SERSERLEULEULLLL89 - 1052 - 18
595930PROPROLEULEUKKKK90 - 1053 - 18
606030PROPROLEULEULLLL90 - 1053 - 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
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60

-
要素

-
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-Bsa7 / 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
TYRO protein tyrosine kinase-binding protein / DNAX-activation protein 12 / Killer-activating receptor-associated protein / KAR-associated protein


分子量: 2490.357 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: O43914

-
非ポリマー , 5種, 314分子

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


分子量: 94.971 Da / 分子数: 6 / 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: 天然 / 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: 1 / 由来タイプ: 合成 / 式: C4H10O3
#6: 化合物 ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / ジエチレングリコ-ルジエチルエ-テル


分子量: 162.227 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H18O3
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 303 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.93 Å3/Da / 溶媒含有率: 58.01 %
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

-
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: 0.9763 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2021年6月27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: 0.9763 Å / 相対比: 1
反射解像度: 2.2→65.96 Å / Num. obs: 112454 / % possible obs: 100 % / 冗長度: 24.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.039 / Rrim(I) all: 0.137 / Χ2: 0.69 / Net I/σ(I): 14
反射 シェル解像度: 2.2→2.24 Å / 冗長度: 25.8 % / Rmerge(I) obs: 4.191 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5513 / CC1/2: 0.571 / Rpim(I) all: 1.195 / Rrim(I) all: 4.259 / Χ2: 0.51 / % possible all: 100

-
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→65.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.193 / SU ML: 0.214 / 交差検証法: FREE R-VALUE / ESU R: 0.253 / ESU R Free: 0.206 / 詳細: Hydrogens have been added in their riding positions
Rfactor反射数%反射
Rfree0.2663 2018 1.796 %
Rwork0.2336 110340 -
all0.234 --
obs-112358 99.986 %
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: 61.064 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å2-0 Å2-0 Å2
2---3.288 Å20 Å2
3---2.138 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→65.96 Å
タンパク質核酸リガンド溶媒全体
原子数13148 0 60 303 13511
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01313498
X-RAY DIFFRACTIONr_bond_other_d0.0010.01512666
X-RAY DIFFRACTIONr_angle_refined_deg1.421.64818215
X-RAY DIFFRACTIONr_angle_other_deg1.2071.58429210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0951625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02722.592737
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.967152367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8331584
X-RAY DIFFRACTIONr_chiral_restr0.0610.21654
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023152
X-RAY DIFFRACTIONr_nbd_refined0.2030.22258
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.211077
X-RAY DIFFRACTIONr_nbtor_refined0.1610.26217
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.26778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2363
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.233
X-RAY DIFFRACTIONr_nbd_other0.2130.2156
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.27
X-RAY DIFFRACTIONr_mcbond_it5.0766.226530
X-RAY DIFFRACTIONr_mcbond_other5.0746.2196529
X-RAY DIFFRACTIONr_mcangle_it7.5779.3168142
X-RAY DIFFRACTIONr_mcangle_other7.5779.3178143
X-RAY DIFFRACTIONr_scbond_it5.1546.6846968
X-RAY DIFFRACTIONr_scbond_other5.1546.6856969
X-RAY DIFFRACTIONr_scangle_it7.9339.80810072
X-RAY DIFFRACTIONr_scangle_other7.9339.80910073
X-RAY DIFFRACTIONr_lrange_it10.65569.87514099
X-RAY DIFFRACTIONr_lrange_other10.66169.87514070
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.057873
X-RAY DIFFRACTIONr_ncsr_local_group_20.090.057708
X-RAY DIFFRACTIONr_ncsr_local_group_30.0850.057807
X-RAY DIFFRACTIONr_ncsr_local_group_40.0980.057717
X-RAY DIFFRACTIONr_ncsr_local_group_50.090.057737
X-RAY DIFFRACTIONr_ncsr_local_group_60.0880.057697
X-RAY DIFFRACTIONr_ncsr_local_group_70.0940.057789
X-RAY DIFFRACTIONr_ncsr_local_group_80.0940.057763
X-RAY DIFFRACTIONr_ncsr_local_group_90.0910.057770
X-RAY DIFFRACTIONr_ncsr_local_group_100.0710.057918
X-RAY DIFFRACTIONr_ncsr_local_group_110.0940.057695
X-RAY DIFFRACTIONr_ncsr_local_group_120.0980.057732
X-RAY DIFFRACTIONr_ncsr_local_group_130.0950.057753
X-RAY DIFFRACTIONr_ncsr_local_group_140.0970.057759
X-RAY DIFFRACTIONr_ncsr_local_group_150.0910.057820
X-RAY DIFFRACTIONr_ncsr_local_group_160.1360.05343
X-RAY DIFFRACTIONr_ncsr_local_group_170.1060.05353
X-RAY DIFFRACTIONr_ncsr_local_group_180.140.05345
X-RAY DIFFRACTIONr_ncsr_local_group_190.1170.05335
X-RAY DIFFRACTIONr_ncsr_local_group_200.1470.05361
X-RAY DIFFRACTIONr_ncsr_local_group_210.1610.05367
X-RAY DIFFRACTIONr_ncsr_local_group_220.1360.05345
X-RAY DIFFRACTIONr_ncsr_local_group_230.1920.05340
X-RAY DIFFRACTIONr_ncsr_local_group_240.1640.05335
X-RAY DIFFRACTIONr_ncsr_local_group_250.130.05345
X-RAY DIFFRACTIONr_ncsr_local_group_260.1590.05350
X-RAY DIFFRACTIONr_ncsr_local_group_270.1290.05343
X-RAY DIFFRACTIONr_ncsr_local_group_280.1590.05328
X-RAY DIFFRACTIONr_ncsr_local_group_290.1970.05354
X-RAY DIFFRACTIONr_ncsr_local_group_300.1230.05334
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.084110.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.084110.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.089510.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.089510.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.08470.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.08470.05009
47AAAX-RAY DIFFRACTIONLocal ncs0.09820.05009
48EEEX-RAY DIFFRACTIONLocal ncs0.09820.05009
59AAAX-RAY DIFFRACTIONLocal ncs0.089940.05009
510FFFX-RAY DIFFRACTIONLocal ncs0.089940.05009
611BBBX-RAY DIFFRACTIONLocal ncs0.087640.05009
612CCCX-RAY DIFFRACTIONLocal ncs0.087640.05009
713BBBX-RAY DIFFRACTIONLocal ncs0.094030.05009
714DDDX-RAY DIFFRACTIONLocal ncs0.094030.05009
815BBBX-RAY DIFFRACTIONLocal ncs0.093660.05009
816EEEX-RAY DIFFRACTIONLocal ncs0.093660.05009
917BBBX-RAY DIFFRACTIONLocal ncs0.091020.05009
918FFFX-RAY DIFFRACTIONLocal ncs0.091020.05009
1019CCCX-RAY DIFFRACTIONLocal ncs0.070570.05009
1020DDDX-RAY DIFFRACTIONLocal ncs0.070570.05009
1121CCCX-RAY DIFFRACTIONLocal ncs0.093710.05009
1122EEEX-RAY DIFFRACTIONLocal ncs0.093710.05009
1223CCCX-RAY DIFFRACTIONLocal ncs0.097960.05009
1224FFFX-RAY DIFFRACTIONLocal ncs0.097960.05009
1325DDDX-RAY DIFFRACTIONLocal ncs0.094970.05009
1326EEEX-RAY DIFFRACTIONLocal ncs0.094970.05009
1427DDDX-RAY DIFFRACTIONLocal ncs0.097190.05009
1428FFFX-RAY DIFFRACTIONLocal ncs0.097190.05009
1529EEEX-RAY DIFFRACTIONLocal ncs0.091130.05009
1530FFFX-RAY DIFFRACTIONLocal ncs0.091130.05009
1631GGGX-RAY DIFFRACTIONLocal ncs0.135670.05008
1632HHHX-RAY DIFFRACTIONLocal ncs0.135670.05008
1733GGGX-RAY DIFFRACTIONLocal ncs0.105890.05008
1734IIIX-RAY DIFFRACTIONLocal ncs0.105890.05008
1835GGGX-RAY DIFFRACTIONLocal ncs0.140040.05007
1836JJJX-RAY DIFFRACTIONLocal ncs0.140040.05007
1937GGGX-RAY DIFFRACTIONLocal ncs0.117270.05006
1938KKKX-RAY DIFFRACTIONLocal ncs0.117270.05006
2039GGGX-RAY DIFFRACTIONLocal ncs0.146760.05007
2040LLLX-RAY DIFFRACTIONLocal ncs0.146760.05007
2141HHHX-RAY DIFFRACTIONLocal ncs0.161230.05008
2142IIIX-RAY DIFFRACTIONLocal ncs0.161230.05008
2243HHHX-RAY DIFFRACTIONLocal ncs0.136360.05008
2244JJJX-RAY DIFFRACTIONLocal ncs0.136360.05008
2345HHHX-RAY DIFFRACTIONLocal ncs0.1920.05007
2346KKKX-RAY DIFFRACTIONLocal ncs0.1920.05007
2447HHHX-RAY DIFFRACTIONLocal ncs0.164370.05008
2448LLLX-RAY DIFFRACTIONLocal ncs0.164370.05008
2549IIIX-RAY DIFFRACTIONLocal ncs0.130330.05008
2550JJJX-RAY DIFFRACTIONLocal ncs0.130330.05008
2651IIIX-RAY DIFFRACTIONLocal ncs0.159490.05006
2652KKKX-RAY DIFFRACTIONLocal ncs0.159490.05006
2753IIIX-RAY DIFFRACTIONLocal ncs0.128660.05007
2754LLLX-RAY DIFFRACTIONLocal ncs0.128660.05007
2855JJJX-RAY DIFFRACTIONLocal ncs0.159330.05006
2856KKKX-RAY DIFFRACTIONLocal ncs0.159330.05006
2957JJJX-RAY DIFFRACTIONLocal ncs0.196590.05007
2958LLLX-RAY DIFFRACTIONLocal ncs0.196590.05007
3059KKKX-RAY DIFFRACTIONLocal ncs0.122790.05006
3060LLLX-RAY DIFFRACTIONLocal ncs0.122790.05006
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.3961180.3858066X-RAY DIFFRACTION99.9756
2.257-2.3190.381550.3627879X-RAY DIFFRACTION99.9751
2.319-2.3860.3561390.3297680X-RAY DIFFRACTION99.9872
2.386-2.460.3781350.3027449X-RAY DIFFRACTION99.9736
2.46-2.540.3231030.2917213X-RAY DIFFRACTION99.9727
2.54-2.6290.2951230.2927014X-RAY DIFFRACTION100
2.629-2.7280.321270.2636749X-RAY DIFFRACTION100
2.728-2.840.2851170.2476482X-RAY DIFFRACTION99.9848
2.84-2.9660.3431040.2696255X-RAY DIFFRACTION100
2.966-3.110.319930.296007X-RAY DIFFRACTION100
3.11-3.2790.317840.2685734X-RAY DIFFRACTION100
3.279-3.4770.3211130.2615386X-RAY DIFFRACTION100
3.477-3.7170.2981160.255046X-RAY DIFFRACTION100
3.717-4.0140.291100.2234730X-RAY DIFFRACTION100
4.014-4.3970.184920.1834378X-RAY DIFFRACTION100
4.397-4.9140.184880.173969X-RAY DIFFRACTION100
4.914-5.6720.247720.193520X-RAY DIFFRACTION100
5.672-6.9410.226580.1933019X-RAY DIFFRACTION100
6.941-9.790.174470.1512373X-RAY DIFFRACTION100
9.79-65.960.196240.1961391X-RAY DIFFRACTION99.5778

+
万見について

-
お知らせ

-
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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlc1.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

+
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

+
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

+
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。

-
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