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- PDB-6xc9: Immune receptor complex -

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基本情報

登録情報
データベース: PDB / ID: 6xc9
タイトルImmune receptor complex
要素
  • (T-CELL-RECEPTOR, A3.10- ...) x 2
  • Hybrid Insulin Peptide, MHC class II HLA-DQ-beta chain fusion
  • MHC class II HLA-DQ-alpha chain
キーワードIMMUNE SYSTEM / Immune Complex
機能・相同性
機能・相同性情報


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / membrane => GO:0016020 / endosome membrane / lysosomal membrane
類似検索 - 分子機能
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
MHC class II antigen / MHC class II HLA-DQ-alpha chain
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: 2.4 Å
データ登録者Tran, T.M. / Faridi, P. / Lim, J.J. / Ting, T.Y. / Onwukwe, G. / Bhattacharjee, P. / Tresoldi, M.C.E. / Cameron, J.F. / La-Gruta, L.N. / Purcell, W.A. ...Tran, T.M. / Faridi, P. / Lim, J.J. / Ting, T.Y. / Onwukwe, G. / Bhattacharjee, P. / Tresoldi, M.C.E. / Cameron, J.F. / La-Gruta, L.N. / Purcell, W.A. / Mannering, I.S. / Rossjohn, J. / Reid, H.H.
資金援助 オーストラリア, 1件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)APP1123586 オーストラリア
引用ジャーナル: Nat Commun / 年: 2021
タイトル: T cell receptor recognition of hybrid insulin peptides bound to HLA-DQ8.
著者: Tran, M.T. / Faridi, P. / Lim, J.J. / Ting, Y.T. / Onwukwe, G. / Bhattacharjee, P. / Jones, C.M. / Tresoldi, E. / Cameron, F.J. / La Gruta, N.L. / Purcell, A.W. / Mannering, S.I. / Rossjohn, J. / Reid, H.H.
履歴
登録2020年6月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年7月14日Provider: repository / タイプ: Initial release
改定 1.12022年1月26日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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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: MHC class II HLA-DQ-alpha chain
C: Hybrid Insulin Peptide, MHC class II HLA-DQ-beta chain fusion
D: T-CELL-RECEPTOR, A3.10-alpha chain
E: T-CELL-RECEPTOR, A3.10-beta chain
F: MHC class II HLA-DQ-alpha chain
H: Hybrid Insulin Peptide, MHC class II HLA-DQ-beta chain fusion
I: T-CELL-RECEPTOR, A3.10-alpha chain
J: T-CELL-RECEPTOR, A3.10-beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)200,50621
ポリマ－197,8198
非ポリマー2,68713
水7,044391
1
A: MHC class II HLA-DQ-alpha chain
C: Hybrid Insulin Peptide, MHC class II HLA-DQ-beta chain fusion
D: T-CELL-RECEPTOR, A3.10-alpha chain
E: T-CELL-RECEPTOR, A3.10-beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,1239
ポリマ－98,9104
非ポリマー1,2135
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14040 Å2
ΔGint-47 kcal/mol
Surface area37070 Å2
手法PISA
2
F: MHC class II HLA-DQ-alpha chain
H: Hybrid Insulin Peptide, MHC class II HLA-DQ-beta chain fusion
I: T-CELL-RECEPTOR, A3.10-alpha chain
J: T-CELL-RECEPTOR, A3.10-beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,38312
ポリマ－98,9104
非ポリマー1,4738
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15690 Å2
ΔGint-46 kcal/mol
Surface area36340 Å2
手法PISA
単位格子
Length a, b, c (Å)65.993, 114.790, 153.926
Angle α, β, γ (deg.)90.000, 90.066, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPPROPRO(chain 'A' and (resid 0 through 158 or (resid 159...AA0 - 1802 - 183
221ASPASPPROPRO(chain 'F' and (resid 0 through 1 or (resid 2...FE0 - 1802 - 183
132GLYGLYTHRTHR(chain 'C' and (resid 3 through 103 or resid 114 through 129 or resid 131 through 190))CB3 - 1036 - 119
142THRTHRLEULEU(chain 'C' and (resid 3 through 103 or resid 114 through 129 or resid 131 through 190))CB114 - 129130 - 145
152CYSCYSVALVAL(chain 'C' and (resid 3 through 103 or resid 114 through 129 or resid 131 through 190))CB131 - 189147 - 205
262GLYGLYTHRTHR(chain 'H' and ((resid 3 and (name N or name...HF3 - 1036 - 119
272THRTHRLEULEU(chain 'H' and ((resid 3 and (name N or name...HF114 - 129130 - 145
282CYSCYSVALVAL(chain 'H' and ((resid 3 and (name N or name...HF131 - 189147 - 205
193GLYGLYSERSERchain 'C'CB-2 - 141 - 17
2103GLYGLYSERSERchain 'H'HF-2 - 141 - 17
1114GLNGLNSERSER(chain 'D' and (resid 2 through 62 or (resid 63...DC2 - 302 - 30
1124ASNASNTYRTYR(chain 'D' and (resid 2 through 62 or (resid 63...DC36 - 5931 - 54
1134LYSLYSGLUGLU(chain 'D' and (resid 2 through 62 or (resid 63...DC62 - 6855 - 61
1144ASNASNGLNGLN(chain 'D' and (resid 2 through 62 or (resid 63...DC74 - 16262 - 150
1154SERSERPROPRO(chain 'D' and (resid 2 through 62 or (resid 63...DC166 - 217154 - 205
2164GLNGLNSERSER(chain 'I' and (resid 2 through 59 or (resid 62...IG2 - 302 - 30
2174ASNASNTYRTYR(chain 'I' and (resid 2 through 59 or (resid 62...IG36 - 5931 - 54
2184LYSLYSGLUGLU(chain 'I' and (resid 2 through 59 or (resid 62...IG62 - 6855 - 61
2194ASNASNGLNGLN(chain 'I' and (resid 2 through 59 or (resid 62...IG74 - 16262 - 150
2204SERSERPROPRO(chain 'I' and (resid 2 through 59 or (resid 62...IG166 - 217154 - 205
1215GLYGLYARGARG(chain 'E' and (resid 3 through 16 or resid 18...ED3 - 152 - 14
1225GLNGLNHISHIS(chain 'E' and (resid 3 through 16 or resid 18...ED18 - 2917 - 28
1235ARGARGSERSER(chain 'E' and (resid 3 through 16 or resid 18...ED37 - 5829 - 50
1245GLUGLUPROPRO(chain 'E' and (resid 3 through 16 or resid 18...ED63 - 7251 - 60
1255GLYGLYPHEPHE(chain 'E' and (resid 3 through 16 or resid 18...ED74 - 8161 - 68
1265SERSERALAALA(chain 'E' and (resid 3 through 16 or resid 18...ED83 - 25869 - 244
2275GLYGLYARGARG(chain 'J' and (resid 3 through 16 or resid 18...JH3 - 152 - 14
2285GLNGLNHISHIS(chain 'J' and (resid 3 through 16 or resid 18...JH18 - 2917 - 28
2295ARGARGSERSER(chain 'J' and (resid 3 through 16 or resid 18...JH37 - 5829 - 50
2305GLUGLUPROPRO(chain 'J' and (resid 3 through 16 or resid 18...JH63 - 7251 - 60
2315GLYGLYPHEPHE(chain 'J' and (resid 3 through 16 or resid 18...JH74 - 8161 - 68
2325SERSERALAALA(chain 'J' and (resid 3 through 16 or resid 18...JH83 - 25869 - 244

NCSアンサンブル:
ID
1
2
3
4
5

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要素

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タンパク質 , 2種, 4分子 AFCH

#1: タンパク質 MHC class II HLA-DQ-alpha chain


分子量: 21929.256 Da / 分子数: 2 / 変異: I72C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 組織: Skin, lymphoid, lungs, stomach and intestines / Cell: B Lymphocytes, dendritic cells, macrophages / 遺伝子: HLA-DQA1 / 器官: Parenchyma / プラスミド: pZip3 / 細胞株 (発現宿主): High Five (BTI-Tn-5B1-4) / 器官 (発現宿主): ovary / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 株 (発現宿主): DH10B / 参照: UniProt: Q30069
#2: タンパク質 Hybrid Insulin Peptide, MHC class II HLA-DQ-beta chain fusion


分子量: 26070.969 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 組織: Islets of Langerhans / Cell: Beta cells / 器官: Pancreas / プラスミド: pZip3 / 遺伝子: HLA-DQB / 細胞株 (発現宿主): High Five (BTI-Tn-5B1-4) / 器官 (発現宿主): ovary / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 株 (発現宿主): DH10B / 参照: UniProt: A0A6B9KAL0

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T-CELL-RECEPTOR, A3.10- ... , 2種, 4分子 DIEJ

#3: タンパク質 T-CELL-RECEPTOR, A3.10-alpha chain


分子量: 23482.980 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 組織: Islets of Langerhans / Cell: Beta cells / 遺伝子: TRAV38-1*03 / 器官: Pancreas / プラスミド: pPET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3)
#4: タンパク質 T-CELL-RECEPTOR, A3.10-beta chain


分子量: 27426.420 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 組織: Islets of Langerhans / Cell: Beta cells / 遺伝子: TRBV5-1*01 / 器官: Pancreas / プラスミド: pPET30 / 発現宿主: Escherichia coli BL21 (大腸菌) / 株 (発現宿主): BL21(DE3)

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糖 , 3種, 6分子

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


タイプ: oligosaccharide / 分子量: 586.542 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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}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 / 分子量: 570.542 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
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: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 4 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 2種, 398分子

#8: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C3H8O3
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 391 / 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: 2.94 Å3/Da / 溶媒含有率: 58.23 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 13% PEG 8000, 0.2 M Potassium dihydrogen phosphate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年2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: 0.9537 Å / 相対比: 1
反射解像度: 2.4→46.01 Å / Num. obs: 89707 / % possible obs: 99.94 % / 冗長度: 2 % / Biso Wilson estimate: 38.16 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.05908 / Rpim(I) all: 0.05908 / Net I/σ(I): 8.82
反射 シェル解像度: 2.4→2.486 Å / Rmerge(I) obs: 0.4443 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 8924 / CC1/2: 0.667 / CC star: 0.895 / Rpim(I) all: 0.4443 / Rrim(I) all: 0.6283 / % possible all: 99.98

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15_3459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: 4Z7U

4z7u


解像度: 2.4→46.01 Å / SU ML: 0.2505 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.1792
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2187 4465 4.98 %
Rwork0.1845 85214 -
obs0.1863 89679 99.96 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 50.36 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→46.01 Å
タンパク質核酸リガンド溶媒全体
原子数12951 0 175 391 13517
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003313474
X-RAY DIFFRACTIONf_angle_d0.621718345
X-RAY DIFFRACTIONf_chiral_restr0.04682037
X-RAY DIFFRACTIONf_plane_restr0.00422392
X-RAY DIFFRACTIONf_dihedral_angle_d15.7758011
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.32471480.27122845X-RAY DIFFRACTION99.97
2.43-2.460.29751440.24492833X-RAY DIFFRACTION100
2.46-2.490.27971340.24142818X-RAY DIFFRACTION99.97
2.49-2.520.30271270.23442853X-RAY DIFFRACTION100
2.52-2.550.29091460.23372844X-RAY DIFFRACTION100
2.55-2.590.30091540.22852782X-RAY DIFFRACTION99.93
2.59-2.620.26731340.22212872X-RAY DIFFRACTION99.97
2.62-2.660.26651520.21672847X-RAY DIFFRACTION99.93
2.66-2.70.2861440.21342842X-RAY DIFFRACTION99.97
2.7-2.750.26131330.20492862X-RAY DIFFRACTION100
2.75-2.790.22061410.19112774X-RAY DIFFRACTION99.97
2.79-2.850.21251680.18662827X-RAY DIFFRACTION99.97
2.85-2.90.23571320.18492848X-RAY DIFFRACTION100
2.9-2.960.24351450.17382833X-RAY DIFFRACTION99.93
2.96-3.020.20461410.17732885X-RAY DIFFRACTION100
3.02-3.090.22261490.18392821X-RAY DIFFRACTION100
3.09-3.170.20341470.18232823X-RAY DIFFRACTION99.97
3.17-3.260.22991380.17752817X-RAY DIFFRACTION100
3.26-3.350.17851620.16462843X-RAY DIFFRACTION100
3.35-3.460.20191400.1642853X-RAY DIFFRACTION100
3.46-3.580.21111500.16692845X-RAY DIFFRACTION99.97
3.58-3.730.22591570.17392819X-RAY DIFFRACTION99.93
3.73-3.90.23651420.17632885X-RAY DIFFRACTION99.93
3.9-4.10.19681420.17092822X-RAY DIFFRACTION100
4.1-4.360.2181540.16422840X-RAY DIFFRACTION100
4.36-4.70.17391640.15552840X-RAY DIFFRACTION100
4.7-5.170.18121410.16882864X-RAY DIFFRACTION100
5.17-5.920.20421550.19262859X-RAY DIFFRACTION100
5.92-7.450.22391900.21662845X-RAY DIFFRACTION100
7.45-46.010.20641910.18762873X-RAY DIFFRACTION99.35
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)
14.17770.8575-1.57940.7133-0.41152.36640.46120.42850.45580.0406-0.02780.2094-0.3548-0.0043-0.12370.26650.0085-0.00330.1974-0.01730.3339-18.96221.2552.367
20.3376-0.3069-0.46210.9178-0.3152.19280.28760.04370.0881-0.1955-0.09480.02470.10860.23410.00360.30750.0025-0.01040.228-0.02780.3394-16.67713.811-0.163
34.70481.0115-2.77913.2096-1.2994.8886-0.3480.0436-0.5946-0.26290.04040.1490.7756-0.31250.14160.4291-0.0423-0.03140.1918-0.01280.4177-18.2554.7571.755
42.538-0.9172-1.54952.5739-0.33694.43520.10090.3921-0.4108-0.6102-0.0985-0.05470.5310.26910.1770.46140.17230.00820.3189-0.05030.4753-7.3465.259-0.203
51.7816-1.5083-0.17362.52910.07461.428-0.094-0.23530.00770.1940.09920.2548-0.0437-0.3022-0.01980.2622-0.0009-0.0070.27720.00310.3747-25.27317.55814.545
60.16640.29560.29671.89832.1942.56140.33710.02210.1913-0.01060.46720.3647-0.9665-0.4015-0.26770.44440.18330.01760.4861-0.04430.5298-35.9927.6462.645
73.14280.9046-0.03770.5861-1.06023.3344-0.04710.3358-0.2108-0.22550.1919-0.28790.12090.1489-0.15090.3657-0.0185-0.05310.3585-0.0660.393-21.73113.622-24.55
80.91160.4695-0.60141.34720.76533.8238-0.10320.1620.1538-0.15710.2603-0.0182-0.05750.0908-0.04210.3041-0.0183-0.10180.2674-0.03030.3626-28.67914.917-12.935
95.76960.78614.8410.4608-0.10085.89990.392-0.1426-0.1057-0.2382-0.18130.35030.2246-0.2627-0.02530.3974-0.0015-0.10070.284-0.04090.4525-31.0934.327-16.919
100.65220.5485-0.18950.5725-0.14541.91810.1786-0.29110.0279-0.0059-0.14540.4506-0.2774-0.0666-0.07620.3505-0.0009-0.04960.22670.00340.3682-22.99521.796-3.794
111.25350.30280.18521.2866-0.0253.674-0.13190.492-0.0555-0.3186-0.11530.1945-0.2155-0.5043-0.02920.31520.0188-0.12740.3384-0.05360.3855-31.57413.187-19.961
122.81430.7209-1.49371.5328-0.04032.29140.06090.05640.0145-0.0695-0.03520.1869-0.1537-0.1918-0.04980.3037-0.0004-0.020.28350.00660.3559-23.94623.5264.45
131.005-0.2567-0.34331.26390.3462.31010.0835-0.15490.10440.06360.0338-0.0466-0.26990.0936-0.11990.3067-0.0139-0.03070.1843-0.02570.2794-16.47630.48511.863
141.452-0.8171-1.72491.80851.93735.5488-0.2804-0.477-0.15590.05630.21570.12240.05071.04460.00220.26860.0093-0.07190.36670.00010.34-4.73820.17110.422
151.1873-0.0949-0.1221.2154-0.77384.85470.02410.39470.2825-0.3787-0.13840.11340.02580.1590.07830.37190.0181-0.02280.48830.00480.3393-8.32116.998-23.189
160.82460.33150.36712.0643-0.60261.94370.18180.67080.3364-0.19450.062-0.3636-0.70540.63240.11260.4811-0.01040.03530.53120.12310.4739-5.20824.948-24.602
170.61850.1993-0.35960.0699-0.09520.2421-0.07750.31580.0707-0.196-0.0539-0.4525-0.07790.6474-0.09610.96530.02450.11610.79150.29490.8734-7.06732.161-34.633
181.28220.244-0.87260.8125-0.22262.4768-0.04640.71520.1113-0.4593-0.0763-0.0276-0.0572-0.1078-0.01740.5337-0.0165-0.05660.50790.08880.3554-13.23722.431-26.148
190.70190.3998-0.05421.26020.06994.6361-0.1730.73880.2311-0.6627-0.1504-0.5055-0.41610.40770.09660.56310.00090.09160.70840.05780.3795-1.44620.582-29.874
204.1018-2.1289-2.13275.40710.21984.2704-0.1480.10930.0436-0.29240.1468-0.6362-0.09020.60240.06970.3420.02270.02950.4986-0.07520.476-5.1269.8857.632
217.0382-5.3961-7.27094.17055.63087.58720.02570.1673-0.16040.1505-0.02210.21660.0166-0.1290.08080.2794-0.0599-0.04450.3185-0.04860.3502-16.01619.45613.558
223.279-1.1961-0.23462.29411.8873.0780.0995-0.45240.06060.58690.40780.8844-0.409-0.6118-0.06810.5110.04350.15690.58370.0280.5307-25.62323.43722.606
231.99986.94054.42477.9927.61128.13780.672-0.8746-0.1381-0.5512-0.50350.49660.9803-2.0689-0.26720.8746-0.0984-0.3741.23090.27820.9472-31.20617.90522.512
240.908-0.49910.43840.656-0.54213.12760.0531-0.0609-0.1294-0.0056-0.1016-0.10620.15470.540.14620.26010.0106-0.02520.44550.060.41021.2543.73232.115
252.15470.1973-0.79621.4855-0.16822.82730.2184-0.20140.0235-0.01420.04890.02550.06380.34160.22560.42390.08710.05110.68070.18380.66550.052-11.14860.605
262.86411.2881.72051.020.84271.30590.1995-0.0433-0.2538-0.11180.2948-0.02390.26540.41390.22130.64010.164-0.00070.75410.04680.733.407-20.55463.331
270.5427-0.4103-0.39680.6098-0.52032.07080.07720.0103-0.1835-0.1096-0.02710.20330.2533-0.19090.05830.2619-0.055-0.05390.28590.0480.3677-22.639-0.23731.806
281.36550.21270.66060.602-0.20131.6372-0.0766-0.2124-0.12960.01480.1424-0.0130.18970.16840.11060.29780.04660.01960.55180.18710.4706-9.5-6.60160.922
292.04461.29110.1872.24331.29762.5904-0.3447-0.55820.11670.0720.03360.52030.4754-0.2770.06320.2883-0.05960.06280.53090.25750.5641-25.104-9.47758.697
303.2448-0.67980.82260.5856-0.34732.24510.0673-0.24810.14320.1194-0.0110.03880.0431-0.0994-0.04450.2746-0.0034-0.05280.20150.02050.2884-51.854-9.559113.43
312.1841-0.44750.62423.1059-1.36394.2027-0.1124-0.18080.20110.38530.02970.081-0.3805-0.1667-0.02640.2973-0.0089-0.04270.2053-0.00570.3544-50.4331.817114.732
321.79770.0707-0.60311.6706-0.45772.0660.16060.1083-0.03450.0961-0.0578-0.0877-0.08780.05090.02750.24050.0173-0.04020.22430.02920.3234-52.052-3.63106.202
331.4438-0.5269-0.17830.74840.0982.2699-0.0086-0.26060.21390.2537-0.01250.16570.1366-0.3947-0.09640.2616-0.03750.00370.24150.02040.334-61.384-6.034128.458
346.8472-1.0345-5.78631.68120.22226.24070.4529-0.16480.27710.5268-0.52590.2858-0.323-0.2707-0.25470.5549-0.03270.04810.3927-0.07370.4732-64.4247.002131.567
351.52820.0487-0.38651.05710.12512.60290.0515-0.40940.2850.2369-0.03860.0997-0.1902-0.2311-0.10040.3075-0.0104-0.01890.3483-0.03510.3905-59.576-3.097129.483
362.02470.42090.08611.6157-0.05884.243-0.0141-0.5509-0.14870.3234-0.47970.00120.2745-0.2757-0.14930.3824-0.09680.05340.57960.03210.4612-68.852-6.882132.711
370.6315-0.42410.06151.5294-0.01132.2774-0.1091-0.08680.1483-0.01060.10540.09770.1938-0.3280.01580.2569-0.0305-0.04780.21290.0130.3059-55.781-13.677111.287
381.5760.7991-0.0651.38080.18552.4750.30730.10210.0109-0.047-0.138-0.07830.62750.13430.05290.27770.03870.00950.2163-0.01020.3409-44.079-17.954110.187
391.6067-0.1396-0.79790.9331-0.14091.5806-0.11360.2566-0.29170.0190.00310.15090.4146-0.22280.0750.3536-0.015-0.04290.2002-0.04440.3133-52.674-22.637102.149
402.56931.84240.70752.91331.87923.1056-0.42640.34330.3877-0.2941-0.03010.10370.01990.16960.09710.29670.0114-0.020.3853-0.06260.3531-41.265-14.698.11
411.4773-1.5910.13211.92211.03227.35610.13870.28610.2343-0.42170.0683-0.2701-0.52490.6110.00270.2514-0.04110.00420.37930.05470.4144-34.881-6.826112.434
420.48810.1062-0.49261.3683-0.79665.1984-0.1494-0.15070.22160.40390.00450.0697-0.28810.3353-0.03130.3782-0.0068-0.04950.2389-0.03460.3321-41.712-5.155138.956
430.92650.1946-0.1191.3438-0.2061.3828-0.0766-0.0936-0.19970.51950.057-0.2151-0.22340.16120.07330.4395-0.0245-0.090.33960.00020.3403-39.793-15.821145.883
440.8836-0.42710.95681.1884-0.53263.1480.111-0.2630.12420.33660.23590.3263-0.214-0.3249-0.08070.3547-0.0101-0.04240.2230.00260.3309-47.713-9.626137.862
451.0265-0.1370.64681.10670.14732.28060.1178-0.4601-0.06431.3296-0.3645-0.17450.27680.47460.14350.9857-0.1198-0.19360.37720.020.4299-39.019-11.709153.463
461.69590.0651-0.63071.745-0.18694.24570.0904-0.53160.210.6451-0.2907-0.1091-0.10170.9766-0.03580.5486-0.0745-0.11720.3439-0.04940.4215-34.599-6.561147.312
474.82492.9352.72886.29071.6876.2931-0.0052-0.2886-0.28170.5596-0.0883-0.4936-0.1870.62220.01260.3186-0.1177-0.00260.33080.10630.4835-38.496-0.369107.146
486.50866.14148.08985.88647.55752.0004-0.2345-0.01540.4315-0.07610.0763-0.2225-0.1329-0.21950.10.34080.12570.00860.4119-0.03750.3156-49.445-10.416102.087
493.10171.06020.36893.30251.01792.6104-0.43990.5746-0.0335-0.54710.18670.86960.3486-0.7521-0.03360.3733-0.0915-0.10480.48090.00690.581-59.397-14.97493.378
503.8586-6.2927-0.99961.99945.72716.2750.39210.67030.0974-0.3231-0.56820.0989-0.9017-1.2725-0.0110.1818-0.0521-0.25381.2312-0.1020.6593-64.296-9.20893.412
511.23630.3394-0.91370.6899-0.31673.03240.17420.01380.14610.0755-0.1317-0.1412-0.01790.57520.00960.23210.0204-0.01240.40410.1050.3712-32.9943.07884.729
520.31390.4711-0.47361.156-1.98364.21380.1421-0.1284-0.1312-0.09770.15960.07130.23010.2445-0.02430.3412-0.0428-0.04470.60830.12540.4418-24.75210.51563.187
534.7032-0.23631.12362.73-0.27443.98770.064-0.37820.05750.02890.1997-0.0834-0.2513-0.20570.00480.3510.02790.03560.40470.1020.3778-33.38320.36451.612
542.7695-0.9380.05363.4754-0.5463.87450.2831-0.51350.2605-0.2624-0.06110.4339-0.41380.2374-0.08690.416-0.12280.02140.48970.03360.5038-33.9516.1158.204
551.95311.3183-1.29311.8759-0.00153.30770.1927-0.01460.26480.1276-0.2282-0.0695-0.3805-0.1837-0.13960.4442-0.0275-0.02470.47890.03530.4613-28.94724.0352.595
560.82840.8294-0.42581.14-0.70451.8480.11220.15440.27120.0786-0.02870.1185-0.256-0.2953-0.13320.31570.0960.01770.41880.05120.4176-56.2546.30484.712
570.35260.04250.20340.2613-0.78392.59270.01580.14130.41590.22940.0833-0.1702-0.6947-0.3755-0.12220.39080.16060.01830.40910.15060.421-54.83615.53872.472
581.20970.0451-0.3760.8385-0.34861.4896-0.02350.0275-0.0501-0.03150.070.1472-0.2311-0.0813-0.12740.23120.01370.00790.35430.12740.3563-41.28814.31951.777
591.54080.42130.03171.96620.00963.0778-0.0547-0.15030.31990.17710.27260.1882-0.31750.1106-0.0870.25750.07150.00880.45520.09510.4378-44.18616.32660.753
601.3044-0.4734-0.58241.15240.6262.1244-0.0924-0.1012-0.13370.00730.16620.2722-0.2042-0.4184-0.09650.23210.0362-0.02950.52150.16890.4247-50.07512.97852.059
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 18 )A0 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 35 )A19 - 35
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 45 )A36 - 45
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 55 )A46 - 55
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 76 )A56 - 76
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 87 )A77 - 87
7X-RAY DIFFRACTION7chain 'A' and (resid 88 through 101 )A88 - 101
8X-RAY DIFFRACTION8chain 'A' and (resid 102 through 123 )A102 - 123
9X-RAY DIFFRACTION9chain 'A' and (resid 124 through 134 )A124 - 134
10X-RAY DIFFRACTION10chain 'A' and (resid 135 through 146 )A135 - 146
11X-RAY DIFFRACTION11chain 'A' and (resid 147 through 182 )A147 - 182
12X-RAY DIFFRACTION12chain 'C' and (resid 15 through 32 )C15 - 32
13X-RAY DIFFRACTION13chain 'C' and (resid 33 through 78 )C33 - 78
14X-RAY DIFFRACTION14chain 'C' and (resid 79 through 102)C79 - 102
15X-RAY DIFFRACTION15chain 'C' and (resid 103 through 136 )C103 - 136
16X-RAY DIFFRACTION16chain 'C' and (resid 137 through 147 )C137 - 147
17X-RAY DIFFRACTION17chain 'C' and (resid 148 through 158 )C148 - 158
18X-RAY DIFFRACTION18chain 'C' and (resid 159 through 183 )C159 - 183
19X-RAY DIFFRACTION19chain 'C' and (resid 184 through 204 )C184 - 204
20X-RAY DIFFRACTION20chain 'C' and (resid -2 through 2 )C-2 - 2
21X-RAY DIFFRACTION21chain 'C' and (resid 3 through 7 )C3 - 7
22X-RAY DIFFRACTION22chain 'C' and (resid 8 through 12 )C8 - 12
23X-RAY DIFFRACTION23chain 'C' and (resid 13 through 14 )C13 - 14
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 133 )D1 - 133
25X-RAY DIFFRACTION25chain 'D' and (resid 134 through 190 )D134 - 190
26X-RAY DIFFRACTION26chain 'D' and (resid 191 through 218 )D191 - 218
27X-RAY DIFFRACTION27chain 'E' and (resid 3 through 138 )E3 - 138
28X-RAY DIFFRACTION28chain 'E' and (resid 139 through 229 )E139 - 229
29X-RAY DIFFRACTION29chain 'E' and (resid 230 through 259 )E230 - 259
30X-RAY DIFFRACTION30chain 'F' and (resid 0 through 26 )F0 - 26
31X-RAY DIFFRACTION31chain 'F' and (resid 27 through 45 )F27 - 45
32X-RAY DIFFRACTION32chain 'F' and (resid 46 through 76 )F46 - 76
33X-RAY DIFFRACTION33chain 'F' and (resid 77 through 123 )F77 - 123
34X-RAY DIFFRACTION34chain 'F' and (resid 124 through 134 )F124 - 134
35X-RAY DIFFRACTION35chain 'F' and (resid 135 through 166 )F135 - 166
36X-RAY DIFFRACTION36chain 'F' and (resid 167 through 180 )F167 - 180
37X-RAY DIFFRACTION37chain 'H' and (resid 17 through 32 )H17 - 32
38X-RAY DIFFRACTION38chain 'H' and (resid 33 through 46 )H33 - 46
39X-RAY DIFFRACTION39chain 'H' and (resid 47 through 78 )H47 - 78
40X-RAY DIFFRACTION40chain 'H' and (resid 79 through 91 )H79 - 91
41X-RAY DIFFRACTION41chain 'H' and (resid 92 through 102 )H92 - 102
42X-RAY DIFFRACTION42chain 'H' and (resid 103 through 136 )H103 - 136
43X-RAY DIFFRACTION43chain 'H' and (resid 137 through 158 )H137 - 158
44X-RAY DIFFRACTION44chain 'H' and (resid 159 through 177 )H159 - 177
45X-RAY DIFFRACTION45chain 'H' and (resid 178 through 191 )H178 - 191
46X-RAY DIFFRACTION46chain 'H' and (resid 192 through 204 )H192 - 204
47X-RAY DIFFRACTION47chain 'H' and (resid -2 through 2 )H-2 - 2
48X-RAY DIFFRACTION48chain 'H' and (resid 3 through 7 )H3 - 7
49X-RAY DIFFRACTION49chain 'H' and (resid 8 through 12 )H8 - 12
50X-RAY DIFFRACTION50chain 'H' and (resid 13 through 14 )H13 - 14
51X-RAY DIFFRACTION51chain 'I' and (resid 2 through 119 )I2 - 119
52X-RAY DIFFRACTION52chain 'I' and (resid 120 through 133 )I120 - 133
53X-RAY DIFFRACTION53chain 'I' and (resid 134 through 162 )I134 - 162
54X-RAY DIFFRACTION54chain 'I' and (resid 163 through 182 )I163 - 182
55X-RAY DIFFRACTION55chain 'I' and (resid 183 through 217 )I183 - 217
56X-RAY DIFFRACTION56chain 'J' and (resid 3 through 117 )J3 - 117
57X-RAY DIFFRACTION57chain 'J' and (resid 118 through 138 )J118 - 138
58X-RAY DIFFRACTION58chain 'J' and (resid 139 through 176 )J139 - 176
59X-RAY DIFFRACTION59chain 'J' and (resid 177 through 202 )J177 - 202
60X-RAY DIFFRACTION60chain 'J' and (resid 203 through 259 )J203 - 259

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万見について

-
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://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