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- PDB-8as0: PD-1 extracellular domain in complex with Fab fragment from D12 a... -

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基本情報

登録情報
データベース: PDB / ID: 8as0
タイトルPD-1 extracellular domain in complex with Fab fragment from D12 antibody
要素
  • (D12 antibody ...) x 2
  • Programmed cell death protein 1PD-1
キーワードANTITUMOR PROTEIN / Monoclonal antibodies (モノクローナル抗体) / phage display technology / antibody library / human PD-1 (PD-1) / immunotherapy (免疫療法)
機能・相同性
機能・相同性情報


negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / 液性免疫 / PD-1 signaling / regulation of immune response / 獲得免疫系 ...negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / 液性免疫 / PD-1 signaling / regulation of immune response / 獲得免疫系 / Potential therapeutics for SARS / external side of plasma membrane / apoptotic process / 細胞膜
類似検索 - 分子機能
PD-1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / 抗体 / 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
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: 3.5 Å
データ登録者Ongaro, T. / Scietti, L. / Pluss, L. / Peissert, F. / Villa, A. / Puca, E. / De Luca, R. / Neri, D. / Forneris, F.
資金援助 イタリア, 米国, 3件
組織認可番号国
Italian Association for Cancer ResearchMFAG 20075 イタリア
The Giovanni Armenise-Harvard FoundationCDA 2013 米国
Ministero dell Universita e della RicercaDipartimenti di eccellenza 2018-2022 イタリア
引用ジャーナル: Protein Sci. / 年: 2022
タイトル: Selection of a PD-1 blocking antibody from a novel fully human phage display library.
著者: Peissert, F. / Pluss, L. / Giudice, A.M. / Ongaro, T. / Villa, A. / Elsayed, A. / Nadal, L. / Dakhel Plaza, S. / Scietti, L. / Puca, E. / De Luca, R. / Forneris, F. / Neri, D.
履歴
登録2022年8月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年11月23日Provider: repository / タイプ: Initial release
改定 1.12022年12月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22022年12月21日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.32024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
C: D12 antibody light chain, Fab fragment
B: D12 antibody heavy chain, Fab fragment
A: Programmed cell death protein 1
D: D12 antibody light chain, Fab fragment
E: D12 antibody heavy chain, Fab fragment
F: Programmed cell death protein 1
G: D12 antibody light chain, Fab fragment
H: D12 antibody heavy chain, Fab fragment
I: Programmed cell death protein 1
J: D12 antibody light chain, Fab fragment
K: D12 antibody heavy chain, Fab fragment
L: Programmed cell death protein 1
M: D12 antibody light chain, Fab fragment
N: D12 antibody heavy chain, Fab fragment
O: Programmed cell death protein 1
P: D12 antibody light chain, Fab fragment
Q: D12 antibody heavy chain, Fab fragment
R: Programmed cell death protein 1
V: D12 antibody light chain, Fab fragment
W: D12 antibody heavy chain, Fab fragment
X: Programmed cell death protein 1
S: D12 antibody light chain, Fab fragment
T: D12 antibody heavy chain, Fab fragment
Y: Programmed cell death protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)539,78745
ポリマ－529,67724
非ポリマー10,10921
水0
1
C: D12 antibody light chain, Fab fragment
B: D12 antibody heavy chain, Fab fragment
A: Programmed cell death protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,5135
ポリマ－66,2103
非ポリマー1,3032
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: D12 antibody light chain, Fab fragment
E: D12 antibody heavy chain, Fab fragment
F: Programmed cell death protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,5886
ポリマ－66,2103
非ポリマー1,3783
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: D12 antibody light chain, Fab fragment
H: D12 antibody heavy chain, Fab fragment
I: Programmed cell death protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,3696
ポリマ－66,2103
非ポリマー1,1593
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
J: D12 antibody light chain, Fab fragment
K: D12 antibody heavy chain, Fab fragment
L: Programmed cell death protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,7096
ポリマ－66,2103
非ポリマー1,4993
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
M: D12 antibody light chain, Fab fragment
N: D12 antibody heavy chain, Fab fragment
O: Programmed cell death protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,1645
ポリマ－66,2103
非ポリマー9542
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
P: D12 antibody light chain, Fab fragment
Q: D12 antibody heavy chain, Fab fragment
R: Programmed cell death protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,1645
ポリマ－66,2103
非ポリマー9542
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
V: D12 antibody light chain, Fab fragment
W: D12 antibody heavy chain, Fab fragment
X: Programmed cell death protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,8966
ポリマ－66,2103
非ポリマー1,6873
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
S: D12 antibody light chain, Fab fragment
T: D12 antibody heavy chain, Fab fragment
Y: Programmed cell death protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,3856
ポリマ－66,2103
非ポリマー1,1753
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)81.195, 187.092, 190.845
Angle α, β, γ (deg.)90.00, 90.24, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 1種, 8分子 AFILORXY

#3: タンパク質
Programmed cell death protein 1 / PD-1 / Protein PD-1 / hPD-1


分子量: 19073.203 Da / 分子数: 8 / 由来タイプ: 組換発現 / 詳細: expression tag at C-terminus: GLNDIFEAQKIEWHEHHHHHH / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PDCD1, PD1 / 細胞株 (発現宿主): CHO
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: Q15116

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抗体 , 2種, 16分子 CDGJMPVSBEHKNQWT

#1: 抗体
D12 antibody light chain, Fab fragment


分子量: 23343.863 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: AMG phage library / 細胞株 (発現宿主): CHO
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#2: 抗体
D12 antibody heavy chain, Fab fragment


分子量: 23792.594 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: AMG phage library / 細胞株 (発現宿主): CHO
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)

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糖 , 8種, 21分子

#4: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 748.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 多糖
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 732.682 Da / 分子数: 4 / 由来タイプ: 合成
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 570.542 Da / 分子数: 3 / 由来タイプ: 合成
記述子タイププログラム
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 424.401 Da / 分子数: 1 / 由来タイプ: 合成
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: 多糖 beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 732.682 Da / 分子数: 1 / 由来タイプ: 合成
記述子タイププログラム
DManpb1-3DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: 多糖 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 367.349 Da / 分子数: 2 / 由来タイプ: 合成
記述子タイププログラム
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#10: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 1056.964 Da / 分子数: 1 / 由来タイプ: 合成
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-3DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b3-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#11: 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 / N-アセチルグルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 8 / 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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詳細

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: 3.04 Å3/Da / 溶媒含有率: 59.55 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5 / 詳細: 22% PEG 3350, 250 mM sodium malonate, pH 4.5

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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: ESRF / ビームライン: MASSIF-1 / 波長: 0.965 Å
検出器タイプ: DECTRIS PILATUS3 2M / 検出器: PIXEL / 日付: 2021年7月1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: 0.965 Å / 相対比: 1
反射解像度: 3.5→190.84 Å / Num. obs: 68755 / % possible obs: 96.1 % / 冗長度: 1.7 % / CC1/2: 0.94 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.1 / Net I/σ(I): 3.9
反射 シェル解像度: 3.5→3.58 Å / 冗長度: 1.8 % / Rmerge(I) obs: 0.642 / Num. unique obs: 4708 / CC1/2: 0.431 / Rpim(I) all: 0.431 / % possible all: 97.6

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20_4459: ???)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: 5WT9, Alphafold2

5wt9


解像度: 3.5→95.42 Å / SU ML: 0.54 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 30.15 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2926 3524 5.13 %
Rwork0.2431 --
obs0.2456 68677 95.63 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.5→95.42 Å
タンパク質核酸リガンド溶媒全体
原子数33488 0 36 0 33524
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00434279
X-RAY DIFFRACTIONf_angle_d0.746582
X-RAY DIFFRACTIONf_dihedral_angle_d4.935015
X-RAY DIFFRACTIONf_chiral_restr0.0675363
X-RAY DIFFRACTIONf_plane_restr0.0075926
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.550.38061270.32912673X-RAY DIFFRACTION97
3.55-3.60.34681680.32192595X-RAY DIFFRACTION97
3.6-3.650.37061400.31932664X-RAY DIFFRACTION97
3.65-3.710.36161870.32562599X-RAY DIFFRACTION97
3.71-3.770.37161130.31472654X-RAY DIFFRACTION98
3.77-3.840.34491290.30192686X-RAY DIFFRACTION98
3.84-3.910.37881490.30922592X-RAY DIFFRACTION96
3.91-3.980.29251460.28282620X-RAY DIFFRACTION97
3.98-4.060.30221150.27482673X-RAY DIFFRACTION96
4.06-4.150.31591390.26482582X-RAY DIFFRACTION96
4.15-4.250.30171340.24522681X-RAY DIFFRACTION97
4.25-4.350.29041090.23422609X-RAY DIFFRACTION97
4.35-4.470.28881980.22562563X-RAY DIFFRACTION96
4.47-4.60.25871330.2162462X-RAY DIFFRACTION91
4.6-4.750.24131710.21022518X-RAY DIFFRACTION93
4.75-4.920.2791310.21252580X-RAY DIFFRACTION96
4.92-5.120.27161570.21222679X-RAY DIFFRACTION98
5.12-5.350.26381660.21432617X-RAY DIFFRACTION97
5.35-5.630.29151630.22132594X-RAY DIFFRACTION96
5.63-5.980.30861610.22662589X-RAY DIFFRACTION96
5.98-6.450.26411360.23322631X-RAY DIFFRACTION96
6.45-7.090.2904960.2522629X-RAY DIFFRACTION94
7.1-8.120.28391420.21882601X-RAY DIFFRACTION94
8.12-10.230.2345830.18532533X-RAY DIFFRACTION91
10.23-95.420.24951310.21972529X-RAY DIFFRACTION90
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)
11.45741.47470.54062.76680.55493.18540.2780.288-0.3248-0.4366-0.21520.56350.2962-1.18761.56240.7269-0.1012-0.10180.9663-0.73011.0787-1.237728.208222.7826
22.3555-0.4643-0.04642.24880.87921.7339-0.70250.02420.0721-0.0337-0.08090.5694-0.0806-0.4574-0.25620.4306-0.10420.27220.5626-0.24440.72247.805425.823625.7336
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1734.6491.3709-2.80972.3370.94443.36460.7051-1.34370.041-0.149-0.6498-1.2479-0.17861.02380.52251.2233-0.4450.17661.7767-0.17491.5174-15.8989129.129980.2272
1740.1872-0.11950.49080.0732-0.3211.3541-0.03530.17410.92470.6328-0.2479-1.6568-1.0116-0.3675-0.16361.5313-0.43260.09761.84220.03571.8233-14.2078139.082973.0787
1752.4986-2.96161.48216.2215-2.99951.9488-0.60480.23821.83510.6808-0.7174-0.1123-0.9147-0.98020.540.939-0.1621-0.06711.08070.10470.9497-18.7339128.077863.759
1760.0708-0.0655-0.02220.09310.0620.073-1.3370.71571.24021.3020.8054-1.37210.42631.76971.08711.4939-0.1818-0.12961.31140.21961.4039-2.4944124.712773.6379
1773.6989-1.844-0.41034.3924-0.93451.51410.2323-0.18940.180.3629-0.65820.7393-0.6197-0.2218-0.32261.36620.40930.02120.7585-0.30170.2224-20.8023125.042775.5574
178-0.00030.0043-0.00290.1429-0.15790.16990.99260.74510.2066-0.00590.35540.1477-1.3318-1.1855-0.54082.54280.5199-0.42691.4406-0.47331.8946-35.3686133.917578.4338
1790.4541-0.03690.78970.88060.34531.5702-0.39350.05170.808-0.2661-0.726-0.4466-1.35590.13150.25390.7372-0.2075-0.07010.6769-0.01170.8775-25.0793121.881677.3434
1802.8306-2.08561.65412.80050.09212.34420.0368-0.305-0.8352-0.8957-0.1414-1.55760.9165-0.1019-0.15891.0888-0.0170.04610.87710.20181.2662-5.1387116.30573.6634
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'C' and (resid 26 through 90 )
3X-RAY DIFFRACTION3chain 'C' and (resid 91 through 101 )
4X-RAY DIFFRACTION4chain 'C' and (resid 102 through 113 )
5X-RAY DIFFRACTION5chain 'C' and (resid 114 through 128 )
6X-RAY DIFFRACTION6chain 'C' and (resid 129 through 163 )
7X-RAY DIFFRACTION7chain 'C' and (resid 164 through 174 )
8X-RAY DIFFRACTION8chain 'C' and (resid 175 through 197 )
9X-RAY DIFFRACTION9chain 'C' and (resid 198 through 213 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 16 )
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 39 )
12X-RAY DIFFRACTION12chain 'B' and (resid 40 through 67 )
13X-RAY DIFFRACTION13chain 'B' and (resid 68 through 91 )
14X-RAY DIFFRACTION14chain 'B' and (resid 92 through 111 )
15X-RAY DIFFRACTION15chain 'B' and (resid 112 through 150 )
16X-RAY DIFFRACTION16chain 'B' and (resid 151 through 170 )
17X-RAY DIFFRACTION17chain 'B' and (resid 171 through 180 )
18X-RAY DIFFRACTION18chain 'B' and (resid 181 through 220 )
19X-RAY DIFFRACTION19chain 'A' and (resid 30 through 40 )
20X-RAY DIFFRACTION20chain 'A' and (resid 41 through 62 )
21X-RAY DIFFRACTION21chain 'A' and (resid 63 through 70 )
22X-RAY DIFFRACTION22chain 'A' and (resid 71 through 82 )
23X-RAY DIFFRACTION23chain 'A' and (resid 83 through 104 )
24X-RAY DIFFRACTION24chain 'A' and (resid 105 through 118 )
25X-RAY DIFFRACTION25chain 'A' and (resid 119 through 133 )
26X-RAY DIFFRACTION26chain 'A' and (resid 134 through 139 )
27X-RAY DIFFRACTION27chain 'A' and (resid 140 through 146 )
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 75 )
29X-RAY DIFFRACTION29chain 'D' and (resid 76 through 113 )
30X-RAY DIFFRACTION30chain 'D' and (resid 114 through 213 )
31X-RAY DIFFRACTION31chain 'E' and (resid 1 through 16 )
32X-RAY DIFFRACTION32chain 'E' and (resid 17 through 39 )
33X-RAY DIFFRACTION33chain 'E' and (resid 40 through 51 )
34X-RAY DIFFRACTION34chain 'E' and (resid 52 through 91 )
35X-RAY DIFFRACTION35chain 'E' and (resid 92 through 111 )
36X-RAY DIFFRACTION36chain 'E' and (resid 112 through 124 )
37X-RAY DIFFRACTION37chain 'E' and (resid 125 through 150 )
38X-RAY DIFFRACTION38chain 'E' and (resid 151 through 180 )
39X-RAY DIFFRACTION39chain 'E' and (resid 181 through 205 )
40X-RAY DIFFRACTION40chain 'E' and (resid 206 through 220 )
41X-RAY DIFFRACTION41chain 'F' and (resid 30 through 40 )
42X-RAY DIFFRACTION42chain 'F' and (resid 41 through 49 )
43X-RAY DIFFRACTION43chain 'F' and (resid 50 through 70 )
44X-RAY DIFFRACTION44chain 'F' and (resid 71 through 82 )
45X-RAY DIFFRACTION45chain 'F' and (resid 83 through 94 )
46X-RAY DIFFRACTION46chain 'F' and (resid 95 through 118 )
47X-RAY DIFFRACTION47chain 'F' and (resid 119 through 133 )
48X-RAY DIFFRACTION48chain 'F' and (resid 134 through 146 )
49X-RAY DIFFRACTION49chain 'G' and (resid 1 through 90 )
50X-RAY DIFFRACTION50chain 'G' and (resid 91 through 113 )
51X-RAY DIFFRACTION51chain 'G' and (resid 114 through 150 )
52X-RAY DIFFRACTION52chain 'G' and (resid 151 through 213 )
53X-RAY DIFFRACTION53chain 'H' and (resid 1 through 83 )
54X-RAY DIFFRACTION54chain 'H' and (resid 84 through 124 )
55X-RAY DIFFRACTION55chain 'H' and (resid 125 through 216 )
56X-RAY DIFFRACTION56chain 'I' and (resid 30 through 49 )
57X-RAY DIFFRACTION57chain 'I' and (resid 50 through 62 )
58X-RAY DIFFRACTION58chain 'I' and (resid 63 through 70 )
59X-RAY DIFFRACTION59chain 'I' and (resid 71 through 82 )
60X-RAY DIFFRACTION60chain 'I' and (resid 83 through 94 )
61X-RAY DIFFRACTION61chain 'I' and (resid 95 through 104 )
62X-RAY DIFFRACTION62chain 'I' and (resid 105 through 127 )
63X-RAY DIFFRACTION63chain 'I' and (resid 128 through 139 )
64X-RAY DIFFRACTION64chain 'I' and (resid 140 through 146 )
65X-RAY DIFFRACTION65chain 'J' and (resid 1 through 25 )
66X-RAY DIFFRACTION66chain 'J' and (resid 26 through 38 )
67X-RAY DIFFRACTION67chain 'J' and (resid 39 through 75 )
68X-RAY DIFFRACTION68chain 'J' and (resid 76 through 90 )
69X-RAY DIFFRACTION69chain 'J' and (resid 91 through 101 )
70X-RAY DIFFRACTION70chain 'J' and (resid 102 through 113 )
71X-RAY DIFFRACTION71chain 'J' and (resid 114 through 128 )
72X-RAY DIFFRACTION72chain 'J' and (resid 129 through 150 )
73X-RAY DIFFRACTION73chain 'J' and (resid 151 through 163 )
74X-RAY DIFFRACTION74chain 'J' and (resid 164 through 197 )
75X-RAY DIFFRACTION75chain 'J' and (resid 198 through 213 )
76X-RAY DIFFRACTION76chain 'K' and (resid 1 through 83 )
77X-RAY DIFFRACTION77chain 'K' and (resid 84 through 124 )
78X-RAY DIFFRACTION78chain 'K' and (resid 125 through 150 )
79X-RAY DIFFRACTION79chain 'K' and (resid 151 through 218 )
80X-RAY DIFFRACTION80chain 'L' and (resid 30 through 70 )
81X-RAY DIFFRACTION81chain 'L' and (resid 71 through 82 )
82X-RAY DIFFRACTION82chain 'L' and (resid 83 through 94 )
83X-RAY DIFFRACTION83chain 'L' and (resid 95 through 110 )
84X-RAY DIFFRACTION84chain 'L' and (resid 111 through 127 )
85X-RAY DIFFRACTION85chain 'L' and (resid 128 through 133 )
86X-RAY DIFFRACTION86chain 'L' and (resid 134 through 146 )
87X-RAY DIFFRACTION87chain 'M' and (resid 1 through 61 )
88X-RAY DIFFRACTION88chain 'M' and (resid 62 through 90 )
89X-RAY DIFFRACTION89chain 'M' and (resid 91 through 113 )
90X-RAY DIFFRACTION90chain 'M' and (resid 114 through 128 )
91X-RAY DIFFRACTION91chain 'M' and (resid 129 through 174 )
92X-RAY DIFFRACTION92chain 'M' and (resid 175 through 197 )
93X-RAY DIFFRACTION93chain 'M' and (resid 198 through 213 )
94X-RAY DIFFRACTION94chain 'N' and (resid 1 through 17 )
95X-RAY DIFFRACTION95chain 'N' and (resid 18 through 60 )
96X-RAY DIFFRACTION96chain 'N' and (resid 61 through 73 )
97X-RAY DIFFRACTION97chain 'N' and (resid 74 through 99 )
98X-RAY DIFFRACTION98chain 'N' and (resid 100 through 124 )
99X-RAY DIFFRACTION99chain 'N' and (resid 125 through 170 )
100X-RAY DIFFRACTION100chain 'N' and (resid 171 through 195 )
101X-RAY DIFFRACTION101chain 'N' and (resid 196 through 215 )
102X-RAY DIFFRACTION102chain 'O' and (resid 30 through 40 )
103X-RAY DIFFRACTION103chain 'O' and (resid 41 through 49 )
104X-RAY DIFFRACTION104chain 'O' and (resid 50 through 62 )
105X-RAY DIFFRACTION105chain 'O' and (resid 63 through 70 )
106X-RAY DIFFRACTION106chain 'O' and (resid 71 through 82 )
107X-RAY DIFFRACTION107chain 'O' and (resid 83 through 94 )
108X-RAY DIFFRACTION108chain 'O' and (resid 95 through 110 )
109X-RAY DIFFRACTION109chain 'O' and (resid 111 through 118 )
110X-RAY DIFFRACTION110chain 'O' and (resid 119 through 127 )
111X-RAY DIFFRACTION111chain 'O' and (resid 128 through 133 )
112X-RAY DIFFRACTION112chain 'O' and (resid 134 through 139 )
113X-RAY DIFFRACTION113chain 'O' and (resid 140 through 146 )
114X-RAY DIFFRACTION114chain 'P' and (resid 1 through 38 )
115X-RAY DIFFRACTION115chain 'P' and (resid 39 through 75 )
116X-RAY DIFFRACTION116chain 'P' and (resid 76 through 90 )
117X-RAY DIFFRACTION117chain 'P' and (resid 91 through 101 )
118X-RAY DIFFRACTION118chain 'P' and (resid 102 through 113 )
119X-RAY DIFFRACTION119chain 'P' and (resid 114 through 128 )
120X-RAY DIFFRACTION120chain 'P' and (resid 129 through 150 )
121X-RAY DIFFRACTION121chain 'P' and (resid 151 through 163 )
122X-RAY DIFFRACTION122chain 'P' and (resid 164 through 174 )
123X-RAY DIFFRACTION123chain 'P' and (resid 175 through 197 )
124X-RAY DIFFRACTION124chain 'P' and (resid 198 through 213 )
125X-RAY DIFFRACTION125chain 'Q' and (resid 1 through 16 )
126X-RAY DIFFRACTION126chain 'Q' and (resid 17 through 91 )
127X-RAY DIFFRACTION127chain 'Q' and (resid 92 through 111 )
128X-RAY DIFFRACTION128chain 'Q' and (resid 112 through 216 )
129X-RAY DIFFRACTION129chain 'R' and (resid 30 through 40 )
130X-RAY DIFFRACTION130chain 'R' and (resid 41 through 49 )
131X-RAY DIFFRACTION131chain 'R' and (resid 50 through 55 )
132X-RAY DIFFRACTION132chain 'R' and (resid 56 through 62 )
133X-RAY DIFFRACTION133chain 'R' and (resid 63 through 70 )
134X-RAY DIFFRACTION134chain 'R' and (resid 71 through 82 )
135X-RAY DIFFRACTION135chain 'R' and (resid 83 through 99 )
136X-RAY DIFFRACTION136chain 'R' and (resid 100 through 110 )
137X-RAY DIFFRACTION137chain 'R' and (resid 111 through 118 )
138X-RAY DIFFRACTION138chain 'R' and (resid 119 through 127 )
139X-RAY DIFFRACTION139chain 'R' and (resid 128 through 133 )
140X-RAY DIFFRACTION140chain 'R' and (resid 134 through 139 )
141X-RAY DIFFRACTION141chain 'R' and (resid 140 through 146 )
142X-RAY DIFFRACTION142chain 'V' and (resid 1 through 90 )
143X-RAY DIFFRACTION143chain 'V' and (resid 91 through 213 )
144X-RAY DIFFRACTION144chain 'W' and (resid 1 through 83 )
145X-RAY DIFFRACTION145chain 'W' and (resid 84 through 124 )
146X-RAY DIFFRACTION146chain 'W' and (resid 125 through 217 )
147X-RAY DIFFRACTION147chain 'X' and (resid 30 through 40 )
148X-RAY DIFFRACTION148chain 'X' and (resid 41 through 70 )
149X-RAY DIFFRACTION149chain 'X' and (resid 71 through 82 )
150X-RAY DIFFRACTION150chain 'X' and (resid 83 through 90 )
151X-RAY DIFFRACTION151chain 'X' and (resid 91 through 99 )
152X-RAY DIFFRACTION152chain 'X' and (resid 100 through 110 )
153X-RAY DIFFRACTION153chain 'X' and (resid 111 through 118 )
154X-RAY DIFFRACTION154chain 'X' and (resid 119 through 127 )
155X-RAY DIFFRACTION155chain 'X' and (resid 128 through 146 )
156X-RAY DIFFRACTION156chain 'S' and (resid 1 through 38 )
157X-RAY DIFFRACTION157chain 'S' and (resid 39 through 75 )
158X-RAY DIFFRACTION158chain 'S' and (resid 76 through 90 )
159X-RAY DIFFRACTION159chain 'S' and (resid 91 through 101 )
160X-RAY DIFFRACTION160chain 'S' and (resid 102 through 113 )
161X-RAY DIFFRACTION161chain 'S' and (resid 114 through 128 )
162X-RAY DIFFRACTION162chain 'S' and (resid 129 through 150 )
163X-RAY DIFFRACTION163chain 'S' and (resid 151 through 163 )
164X-RAY DIFFRACTION164chain 'S' and (resid 164 through 197 )
165X-RAY DIFFRACTION165chain 'S' and (resid 198 through 213 )
166X-RAY DIFFRACTION166chain 'T' and (resid 1 through 77 )
167X-RAY DIFFRACTION167chain 'T' and (resid 78 through 139 )
168X-RAY DIFFRACTION168chain 'T' and (resid 140 through 190 )
169X-RAY DIFFRACTION169chain 'T' and (resid 191 through 218 )
170X-RAY DIFFRACTION170chain 'Y' and (resid 30 through 40 )
171X-RAY DIFFRACTION171chain 'Y' and (resid 41 through 49 )
172X-RAY DIFFRACTION172chain 'Y' and (resid 50 through 70 )
173X-RAY DIFFRACTION173chain 'Y' and (resid 71 through 82 )
174X-RAY DIFFRACTION174chain 'Y' and (resid 83 through 94 )
175X-RAY DIFFRACTION175chain 'Y' and (resid 95 through 110 )
176X-RAY DIFFRACTION176chain 'Y' and (resid 111 through 118 )
177X-RAY DIFFRACTION177chain 'Y' and (resid 119 through 127 )
178X-RAY DIFFRACTION178chain 'Y' and (resid 128 through 133 )
179X-RAY DIFFRACTION179chain 'Y' and (resid 134 through 139 )
180X-RAY DIFFRACTION180chain 'Y' and (resid 140 through 146 )

+
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://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。

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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