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- PDB-7ox5: hIL-9:hIL-9Ra complex -

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基本情報

登録情報
データベース: PDB / ID: 7ox5
タイトルhIL-9:hIL-9Ra complex
要素
  • Interleukin-9
  • Interleukin-9 receptor
キーワードCYTOKINE / IL-9 / complex
機能・相同性
機能・相同性情報


interleukin-9 receptor activity / interleukin-9 binding / interleukin-9 receptor binding / Interleukin-9 signaling / interleukin-9-mediated signaling pathway / positive regulation of interleukin-5 production / cytokine receptor activity / regulation of receptor signaling pathway via JAK-STAT / B cell proliferation / immunoglobulin mediated immune response ...interleukin-9 receptor activity / interleukin-9 binding / interleukin-9 receptor binding / Interleukin-9 signaling / interleukin-9-mediated signaling pathway / positive regulation of interleukin-5 production / cytokine receptor activity / regulation of receptor signaling pathway via JAK-STAT / B cell proliferation / immunoglobulin mediated immune response / regulation of peptidyl-tyrosine phosphorylation / B cell differentiation / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / regulation of cell population proliferation / positive regulation of cell growth / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular region / plasma membrane
類似検索 - 分子機能
Interleukin-9 / Interleukin-7/Interleukin-9, conserved site / Interleukin-7 and -9 signature. / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
Interleukin-9 / Interleukin-9 receptor
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: 3.09 Å
データ登録者De Vos, T. / Savvides, S.N.
資金援助 ベルギー, 1件
組織認可番号国
Research Foundation - Flanders (FWO)1S56318N ベルギー
引用ジャーナル: Biorxiv / 年: 2022
タイトル: Structural basis for the mechanism and antagonism of receptor signaling mediated by Interleukin-9 (IL-9)
著者: De Vos, T. / Godar, M. / Bick, F. / Papageorgiou, A.C. / Evangelidis, T. / Markovic, I. / Mortier, E. / Dumoutier, L. / Tripsianes, K. / Blanchetot, C. / Savvides, S.N.
履歴
登録2021年6月22日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年12月28日Provider: repository / タイプ: Initial release
改定 1.12023年1月11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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Interleukin-9 receptor
B: Interleukin-9
C: Interleukin-9 receptor
D: Interleukin-9
E: Interleukin-9 receptor
F: Interleukin-9
G: Interleukin-9 receptor
H: Interleukin-9
I: Interleukin-9 receptor
J: Interleukin-9
K: Interleukin-9 receptor
L: Interleukin-9
M: Interleukin-9 receptor
N: Interleukin-9
O: Interleukin-9 receptor
P: Interleukin-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)320,81326
ポリマ－319,85316
非ポリマー96110
水1086
1
A: Interleukin-9 receptor
B: Interleukin-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,1744
ポリマ－39,9822
非ポリマー1922
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-23 kcal/mol
Surface area17450 Å2
手法PISA
2
C: Interleukin-9 receptor
D: Interleukin-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,0783
ポリマ－39,9822
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-38 kcal/mol
Surface area17020 Å2
手法PISA
3
E: Interleukin-9 receptor
F: Interleukin-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,0783
ポリマ－39,9822
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-21 kcal/mol
Surface area16280 Å2
手法PISA
4
G: Interleukin-9 receptor
H: Interleukin-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,1744
ポリマ－39,9822
非ポリマー1922
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-34 kcal/mol
Surface area16710 Å2
手法PISA
5
I: Interleukin-9 receptor
J: Interleukin-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,1744
ポリマ－39,9822
非ポリマー1922
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-36 kcal/mol
Surface area16690 Å2
手法PISA
6
K: Interleukin-9 receptor
L: Interleukin-9


分子量 (理論値)分子数
合計 (水以外)39,9822
ポリマ－39,9822
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-10 kcal/mol
Surface area16330 Å2
手法PISA
7
M: Interleukin-9 receptor
N: Interleukin-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,0783
ポリマ－39,9822
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-27 kcal/mol
Surface area16500 Å2
手法PISA
8
O: Interleukin-9 receptor
P: Interleukin-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,0783
ポリマ－39,9822
非ポリマー961
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-22 kcal/mol
Surface area16590 Å2
手法PISA
単位格子
Length a, b, c (Å)85.450, 107.810, 159.550
Angle α, β, γ (deg.)90.000, 90.770, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 53 through 69 or resid 78...
21(chain C and (resid 53 through 69 or resid 78...
31(chain G and (resid 53 through 69 or resid 78...
41(chain I and (resid 53 through 125 or resid 133...
51(chain K and (resid 53 through 69 or resid 78...
61(chain M and (resid 53 through 69 or resid 78...
71(chain O and (resid 53 through 69 or resid 78...
12(chain B and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))
22(chain D and (resid 20 through 113 or resid 116 through 138))
32(chain F and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))
42(chain H and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))
52(chain J and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))
62(chain L and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))
72(chain N and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))
82(chain P and (resid 20 through 60 or resid 67 through 138))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 53 through 69 or resid 78...A53 - 69
121(chain A and (resid 53 through 69 or resid 78...A78 - 90
131(chain A and (resid 53 through 69 or resid 78...A92 - 98
141(chain A and (resid 53 through 69 or resid 78...A47 - 256
151(chain A and (resid 53 through 69 or resid 78...A218 - 229
161(chain A and (resid 53 through 69 or resid 78...A47 - 256
171(chain A and (resid 53 through 69 or resid 78...A218 - 229
181(chain A and (resid 53 through 69 or resid 78...A241 - 256
211(chain C and (resid 53 through 69 or resid 78...C53 - 69
221(chain C and (resid 53 through 69 or resid 78...C78 - 90
231(chain C and (resid 53 through 69 or resid 78...C92 - 98
241(chain C and (resid 53 through 69 or resid 78...C102 - 125
251(chain C and (resid 53 through 69 or resid 78...C52 - 257
261(chain C and (resid 53 through 69 or resid 78...C52 - 257
271(chain C and (resid 53 through 69 or resid 78...C218 - 229
281(chain C and (resid 53 through 69 or resid 78...C241 - 256
311(chain G and (resid 53 through 69 or resid 78...G53 - 69
321(chain G and (resid 53 through 69 or resid 78...G78 - 90
331(chain G and (resid 53 through 69 or resid 78...G92 - 98
341(chain G and (resid 53 through 69 or resid 78...G102 - 125
351(chain G and (resid 53 through 69 or resid 78...G52 - 256
361(chain G and (resid 53 through 69 or resid 78...G52 - 256
371(chain G and (resid 53 through 69 or resid 78...G2 - 8
381(chain G and (resid 53 through 69 or resid 78...G241 - 256
411(chain I and (resid 53 through 125 or resid 133...I53 - 125
421(chain I and (resid 53 through 125 or resid 133...I133 - 210
431(chain I and (resid 53 through 125 or resid 133...I218 - 229
441(chain I and (resid 53 through 125 or resid 133...I241 - 256
511(chain K and (resid 53 through 69 or resid 78...K53 - 69
521(chain K and (resid 53 through 69 or resid 78...K78 - 90
531(chain K and (resid 53 through 69 or resid 78...K92 - 98
541(chain K and (resid 53 through 69 or resid 78...K102 - 125
551(chain K and (resid 53 through 69 or resid 78...K133 - 210
561(chain K and (resid 53 through 69 or resid 78...K218 - 256
611(chain M and (resid 53 through 69 or resid 78...M53 - 69
621(chain M and (resid 53 through 69 or resid 78...M78 - 90
631(chain M and (resid 53 through 69 or resid 78...M92 - 98
641(chain M and (resid 53 through 69 or resid 78...M102 - 125
651(chain M and (resid 53 through 69 or resid 78...M51 - 257
661(chain M and (resid 53 through 69 or resid 78...M51 - 257
671(chain M and (resid 53 through 69 or resid 78...M218 - 229
681(chain M and (resid 53 through 69 or resid 78...M241 - 256
711(chain O and (resid 53 through 69 or resid 78...O53 - 69
721(chain O and (resid 53 through 69 or resid 78...O78 - 90
731(chain O and (resid 53 through 69 or resid 78...O92 - 98
741(chain O and (resid 53 through 69 or resid 78...O102 - 210
751(chain O and (resid 53 through 69 or resid 78...O218 - 229
761(chain O and (resid 53 through 69 or resid 78...O241 - 256
112(chain B and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))B20 - 60
122(chain B and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))B67 - 113
132(chain B and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))B116 - 138
212(chain D and (resid 20 through 113 or resid 116 through 138))D20 - 113
222(chain D and (resid 20 through 113 or resid 116 through 138))D116 - 138
312(chain F and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))F20 - 60
322(chain F and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))F67 - 113
332(chain F and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))F116 - 138
412(chain H and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))H20 - 60
422(chain H and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))H67 - 113
432(chain H and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))H116 - 138
512(chain J and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))J20 - 60
522(chain J and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))J67 - 113
532(chain J and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))J116 - 138
612(chain L and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))L20 - 60
622(chain L and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))L67 - 113
632(chain L and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))L116 - 138
712(chain N and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))N20 - 60
722(chain N and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))N67 - 113
732(chain N and (resid 20 through 60 or resid 67 through 113 or resid 116 through 138))N116 - 138
812(chain P and (resid 20 through 60 or resid 67 through 138))P20 - 60
822(chain P and (resid 20 through 60 or resid 67 through 138))P67 - 138

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Interleukin-9 receptor / IL-9 receptor / IL-9R


分子量: 25430.586 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL9R / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q01113
#2: タンパク質
Interleukin-9 / IL-9 / Cytokine P40 / T-cell growth factor P40


分子量: 14551.010 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL9 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P15248
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 10 / 由来タイプ: 合成 / 式: SO4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 6 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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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: 2.3 Å3/Da / 溶媒含有率: 46.46 %
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: 5.6
詳細: 0.1 M ammonium sulfate, 0.1 M TRIS, pH 5.6, 18% PEG 1500

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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: SOLEIL / ビームライン: PROXIMA 2 / 波長: 0.98 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2016年11月19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: 0.98 Å / 相対比: 1
反射解像度: 3.09→47.69 Å / Num. obs: 52814 / % possible obs: 98.9 % / 冗長度: 3.5 % / Biso Wilson estimate: 100.794 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.39
反射 シェル解像度: 3.09→3.27 Å / Num. unique obs: 8141 / CC1/2: 0.281

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHASER位相決定
PHENIX1.19.1精密化
PDB_EXTRACT3.27データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 2B5I

2b5i


解像度: 3.09→47.69 Å / SU ML: 0.56 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 30.81 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2796 2640 5.01 %
Rwork0.2198 50102 -
obs0.2228 52742 98.82 %
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 max: 300.87 Å2 / Biso mean: 135.4342 Å2 / Biso min: 49.22 Å2
精密化ステップサイクル: final / 解像度: 3.09→47.69 Å
タンパク質核酸リガンド溶媒全体
原子数19758 0 50 6 19814
Biso mean--141.07 100.24 -
残基数----2494
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3406X-RAY DIFFRACTION8.377TORSIONAL
12C3406X-RAY DIFFRACTION8.377TORSIONAL
13G3406X-RAY DIFFRACTION8.377TORSIONAL
14I3406X-RAY DIFFRACTION8.377TORSIONAL
15K3406X-RAY DIFFRACTION8.377TORSIONAL
16M3406X-RAY DIFFRACTION8.377TORSIONAL
17O3406X-RAY DIFFRACTION8.377TORSIONAL
21B2624X-RAY DIFFRACTION8.377TORSIONAL
22D2624X-RAY DIFFRACTION8.377TORSIONAL
23F2624X-RAY DIFFRACTION8.377TORSIONAL
24H2624X-RAY DIFFRACTION8.377TORSIONAL
25J2624X-RAY DIFFRACTION8.377TORSIONAL
26L2624X-RAY DIFFRACTION8.377TORSIONAL
27N2624X-RAY DIFFRACTION8.377TORSIONAL
28P2624X-RAY DIFFRACTION8.377TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.09-3.140.36391170.33792169228682
3.14-3.20.38611400.335826582798100
3.2-3.270.35371420.328926932835100
3.27-3.340.43211360.362825852721100
3.34-3.420.40561410.347426912832100
3.42-3.50.39591390.311726212760100
3.5-3.60.33471390.287426522791100
3.6-3.710.31331410.263826842825100
3.71-3.820.3111390.253926412780100
3.82-3.960.30581400.246526462786100
3.96-4.120.30631400.244426702810100
4.12-4.310.30091410.216726682809100
4.31-4.530.26481390.198726522791100
4.53-4.820.22511400.181426522792100
4.82-5.190.23691400.190126582798100
5.19-5.710.29241410.18782688282999
5.71-6.540.26021410.212926682809100
6.54-8.230.24711400.204626752815100
8.23-47.690.23711440.17432731287599
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)
12.10460.84581.87781.62730.1761.98020.1134-0.0425-0.09210.1752-0.22460.09990.058-0.4826-0.00010.71910.04630.0450.9464-0.03080.8273-21.9739-19.4689-1.3551
21.88380.46921.77470.11670.52872.0633-0.01530.39910.0336-0.61670.197-0.1129-0.8306-0.68260.00010.81880.1382-0.04951.0395-0.01660.8551-21.9235-11.2442-5.154
33.12033.34632.39247.25052.37681.32581.0519-0.77130.01460.5473-1.36720.99340.67-0.4684-0.23030.69190.2487-0.28550.81650.01430.4499-28.8173-18.3698-4.5806
40.5828-0.68440.2531.9207-1.40450.96490.85070.4528-0.3258-0.0259-0.6292-0.78330.6540.5601-0.00120.51060.03930.00160.69440.03460.8829-0.9653-6.031516.4683
50.1302-0.04930.50671.04510.34270.58270.21060.02420.3189-0.2091-1.0704-0.20721.2409-0.7291-0.03250.6647-0.02820.00730.7574-0.03840.8422-7.6339-3.892116.3242
63.14691.5155-2.13220.9981-0.33133.19760.3982-0.9903-0.69860.2092-0.06821.09840.1844-0.66250.00011.1959-0.1795-0.01020.92690.09650.9039-2.653-8.654527.9861
72.0227-2.4045.37463.5765-2.42837.13012.0016-2.9614-1.51561.7164-0.581-0.61430.1481-0.53282.54150.9509-0.2737-0.171.00370.19651.03-5.2257-11.0320.8417
80.09320.79380.12759.08743.34032.01340.62340.01270.024-0.2964-2.26331.889-2.226-2.7799-0.70041.58350.27360.39241.13120.10551.1647-24.83144.582211.8646
90.84430.2492-0.29130.3762-0.22742.5213-0.45080.90841.43040.397-0.7285-1.19520.0362-0.068-0.02780.8928-0.1766-0.06221.0022-0.13730.9852-7.9696-10.394317.1987
100.22770.0615-0.60010.86170.3082.0945-0.0995-0.9413-0.0798-0.11990.25950.1947-0.54460.2507-0.00011.018-0.04560.24950.84-0.04581.0549-10.445810.38882.4425
112.88373.3499-0.18294.11010.04870.9745-0.48980.02230.54020.30310.2844-0.6093-0.6750.5383-01.0220.14030.19950.988-0.05470.912-5.605115.6597-10.0635
120.27560.0483-0.60340.5354-0.32021.17890.62151.23570.3055-0.053-0.31620.68650.7306-0.88050.0020.61240.1340.23220.82370.15260.864-15.82834.5302-6.3977
130.53720.39110.74860.16280.18031.035-0.1816-1.7159-1.1416-0.0795-0.5443-1.0372-0.38280.50710.00041.09850.14780.00711.60210.23831.1109-23.449517.0609-12.5878
140.64240.00120.48210.13930.05822.23320.4013-0.12871.57890.4101-0.40291.2043-1.60720.3754-0.26940.75550.3570.28910.7639-0.05351.28-14.490118.1154-3.0567
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 105 )A47 - 105
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 125 )A106 - 125
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 143 )A126 - 143
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 169 )A144 - 169
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 187 )A170 - 187
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 218 )A188 - 218
7X-RAY DIFFRACTION7chain 'A' and (resid 219 through 228 )A219 - 228
8X-RAY DIFFRACTION8chain 'A' and (resid 229 through 239 )A229 - 239
9X-RAY DIFFRACTION9chain 'A' and (resid 240 through 256 )A240 - 256
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 39 )B20 - 39
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 85 )B40 - 85
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 101 )B86 - 101
13X-RAY DIFFRACTION13chain 'B' and (resid 102 through 115 )B102 - 115
14X-RAY DIFFRACTION14chain 'B' and (resid 116 through 138 )B116 - 138
15X-RAY DIFFRACTION15chain 'C' and (resid 52 through 68 )C52 - 68
16X-RAY DIFFRACTION16chain 'C' and (resid 69 through 96 )C69 - 96
17X-RAY DIFFRACTION17chain 'C' and (resid 97 through 117 )C97 - 117
18X-RAY DIFFRACTION18chain 'C' and (resid 118 through 143 )C118 - 143
19X-RAY DIFFRACTION19chain 'C' and (resid 144 through 169 )C144 - 169
20X-RAY DIFFRACTION20chain 'C' and (resid 170 through 187 )C170 - 187
21X-RAY DIFFRACTION21chain 'C' and (resid 188 through 209 )C188 - 209
22X-RAY DIFFRACTION22chain 'C' and (resid 210 through 228 )C210 - 228
23X-RAY DIFFRACTION23chain 'C' and (resid 229 through 238 )C229 - 238
24X-RAY DIFFRACTION24chain 'C' and (resid 239 through 257 )C239 - 257
25X-RAY DIFFRACTION25chain 'D' and (resid 20 through 75 )D20 - 75
26X-RAY DIFFRACTION26chain 'D' and (resid 76 through 85 )D76 - 85
27X-RAY DIFFRACTION27chain 'D' and (resid 86 through 107 )D86 - 107
28X-RAY DIFFRACTION28chain 'D' and (resid 108 through 120 )D108 - 120
29X-RAY DIFFRACTION29chain 'D' and (resid 121 through 141 )D121 - 141
30X-RAY DIFFRACTION30chain 'E' and (resid 52 through 136 )E52 - 136
31X-RAY DIFFRACTION31chain 'E' and (resid 137 through 256 )E137 - 256
32X-RAY DIFFRACTION32chain 'F' and (resid 20 through 39 )F20 - 39
33X-RAY DIFFRACTION33chain 'F' and (resid 40 through 75 )F40 - 75
34X-RAY DIFFRACTION34chain 'F' and (resid 76 through 85 )F76 - 85
35X-RAY DIFFRACTION35chain 'F' and (resid 86 through 115 )F86 - 115
36X-RAY DIFFRACTION36chain 'F' and (resid 116 through 138 )F116 - 138
37X-RAY DIFFRACTION37chain 'G' and (resid 52 through 105 )G52 - 105
38X-RAY DIFFRACTION38chain 'G' and (resid 106 through 127 )G106 - 127
39X-RAY DIFFRACTION39chain 'G' and (resid 128 through 158 )G128 - 158
40X-RAY DIFFRACTION40chain 'G' and (resid 159 through 198 )G159 - 198
41X-RAY DIFFRACTION41chain 'G' and (resid 199 through 219 )G199 - 219
42X-RAY DIFFRACTION42chain 'G' and (resid 220 through 239 )G220 - 239
43X-RAY DIFFRACTION43chain 'G' and (resid 240 through 256 )G240 - 256
44X-RAY DIFFRACTION44chain 'H' and (resid 20 through 85 )H20 - 85
45X-RAY DIFFRACTION45chain 'H' and (resid 86 through 101 )H86 - 101
46X-RAY DIFFRACTION46chain 'H' and (resid 102 through 115 )H102 - 115
47X-RAY DIFFRACTION47chain 'H' and (resid 116 through 138 )H116 - 138
48X-RAY DIFFRACTION48chain 'I' and (resid 53 through 143 )I53 - 143
49X-RAY DIFFRACTION49chain 'I' and (resid 144 through 158 )I144 - 158
50X-RAY DIFFRACTION50chain 'I' and (resid 159 through 169 )I159 - 169
51X-RAY DIFFRACTION51chain 'I' and (resid 170 through 187 )I170 - 187
52X-RAY DIFFRACTION52chain 'I' and (resid 188 through 198 )I188 - 198
53X-RAY DIFFRACTION53chain 'I' and (resid 199 through 228 )I199 - 228
54X-RAY DIFFRACTION54chain 'I' and (resid 229 through 239 )I229 - 239
55X-RAY DIFFRACTION55chain 'I' and (resid 240 through 256 )I240 - 256
56X-RAY DIFFRACTION56chain 'J' and (resid 20 through 39 )J20 - 39
57X-RAY DIFFRACTION57chain 'J' and (resid 40 through 56 )J40 - 56
58X-RAY DIFFRACTION58chain 'J' and (resid 57 through 75 )J57 - 75
59X-RAY DIFFRACTION59chain 'J' and (resid 76 through 85 )J76 - 85
60X-RAY DIFFRACTION60chain 'J' and (resid 86 through 101 )J86 - 101
61X-RAY DIFFRACTION61chain 'J' and (resid 102 through 120 )J102 - 120
62X-RAY DIFFRACTION62chain 'J' and (resid 121 through 138 )J121 - 138
63X-RAY DIFFRACTION63chain 'K' and (resid 53 through 124 )K53 - 124
64X-RAY DIFFRACTION64chain 'K' and (resid 125 through 158 )K125 - 158
65X-RAY DIFFRACTION65chain 'K' and (resid 159 through 218 )K159 - 218
66X-RAY DIFFRACTION66chain 'K' and (resid 219 through 257 )K219 - 257
67X-RAY DIFFRACTION67chain 'L' and (resid 20 through 39 )L20 - 39
68X-RAY DIFFRACTION68chain 'L' and (resid 40 through 75 )L40 - 75
69X-RAY DIFFRACTION69chain 'L' and (resid 76 through 101 )L76 - 101
70X-RAY DIFFRACTION70chain 'L' and (resid 102 through 120 )L102 - 120
71X-RAY DIFFRACTION71chain 'L' and (resid 121 through 140 )L121 - 140
72X-RAY DIFFRACTION72chain 'M' and (resid 51 through 105 )M51 - 105
73X-RAY DIFFRACTION73chain 'M' and (resid 106 through 117 )M106 - 117
74X-RAY DIFFRACTION74chain 'M' and (resid 118 through 136 )M118 - 136
75X-RAY DIFFRACTION75chain 'M' and (resid 137 through 158 )M137 - 158
76X-RAY DIFFRACTION76chain 'M' and (resid 159 through 169 )M159 - 169
77X-RAY DIFFRACTION77chain 'M' and (resid 170 through 198 )M170 - 198
78X-RAY DIFFRACTION78chain 'M' and (resid 199 through 209 )M199 - 209
79X-RAY DIFFRACTION79chain 'M' and (resid 210 through 228 )M210 - 228
80X-RAY DIFFRACTION80chain 'M' and (resid 229 through 257 )M229 - 257
81X-RAY DIFFRACTION81chain 'N' and (resid 20 through 56 )N20 - 56
82X-RAY DIFFRACTION82chain 'N' and (resid 57 through 85 )N57 - 85
83X-RAY DIFFRACTION83chain 'N' and (resid 86 through 120 )N86 - 120
84X-RAY DIFFRACTION84chain 'N' and (resid 121 through 138 )N121 - 138
85X-RAY DIFFRACTION85chain 'O' and (resid 49 through 62 )O49 - 62
86X-RAY DIFFRACTION86chain 'O' and (resid 63 through 79 )O63 - 79
87X-RAY DIFFRACTION87chain 'O' and (resid 80 through 96 )O80 - 96
88X-RAY DIFFRACTION88chain 'O' and (resid 97 through 105 )O97 - 105
89X-RAY DIFFRACTION89chain 'O' and (resid 106 through 158 )O106 - 158
90X-RAY DIFFRACTION90chain 'O' and (resid 159 through 169 )O159 - 169
91X-RAY DIFFRACTION91chain 'O' and (resid 170 through 186 )O170 - 186
92X-RAY DIFFRACTION92chain 'O' and (resid 187 through 198 )O187 - 198
93X-RAY DIFFRACTION93chain 'O' and (resid 199 through 218 )O199 - 218
94X-RAY DIFFRACTION94chain 'O' and (resid 219 through 239 )O219 - 239
95X-RAY DIFFRACTION95chain 'O' and (resid 240 through 256 )O240 - 256
96X-RAY DIFFRACTION96chain 'P' and (resid 20 through 39 )P20 - 39
97X-RAY DIFFRACTION97chain 'P' and (resid 40 through 68 )P40 - 68
98X-RAY DIFFRACTION98chain 'P' and (resid 69 through 85 )P69 - 85
99X-RAY DIFFRACTION99chain 'P' and (resid 86 through 107 )P86 - 107
100X-RAY DIFFRACTION100chain 'P' and (resid 108 through 120 )P108 - 120
101X-RAY DIFFRACTION101chain 'P' and (resid 121 through 138 )P121 - 138

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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

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る