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- PDB-8vd0: Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2 -

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基本情報

登録情報
データベース: PDB / ID: 8vd0
タイトルHuman TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2
要素
  • (T-CELL-RECEPTOR, TCR ET650-4 ...) x 2
  • Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera
  • MHC class II HLA-DQ-alpha chain
キーワードIMMUNE SYSTEM / Immune T cell receptor-pMHC II 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 / 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 ...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
PHOSPHATE ION / MHC class II HLA-DQ-beta-1 / 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. / Lim, J.J. / Loh, T.Y. / Mannering, I.S. / Rossjohn, J. / Reid, H.H.
資金援助 オーストラリア, 2件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)2008981 オーストラリア
National Health and Medical Research Council (NHMRC, Australia)APP1123586 オーストラリア
引用ジャーナル: J.Biol.Chem. / 年: 2024
タイトル: A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8.
著者: Tran, M.T. / Lim, J.J. / Loh, T.J. / Mannering, S.I. / Rossjohn, J. / Reid, H.H.
履歴
登録2023年12月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年8月7日Provider: repository / タイプ: Initial release
改定 1.12024年8月14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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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 (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera
F: MHC class II HLA-DQ-alpha chain
H: Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera
D: T-CELL-RECEPTOR, TCR ET650-4 alpha
E: T-CELL-RECEPTOR, TCR ET650-4 beta
I: T-CELL-RECEPTOR, TCR ET650-4 alpha
J: T-CELL-RECEPTOR, TCR ET650-4 beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)194,13231
ポリマ－191,3518
非ポリマー2,78123
水6,738374
1
A: MHC class II HLA-DQ-alpha chain
C: Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera
D: T-CELL-RECEPTOR, TCR ET650-4 alpha
E: T-CELL-RECEPTOR, TCR ET650-4 beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,86614
ポリマ－95,6764
非ポリマー1,19110
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
F: MHC class II HLA-DQ-alpha chain
H: Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera
I: T-CELL-RECEPTOR, TCR ET650-4 alpha
J: T-CELL-RECEPTOR, TCR ET650-4 beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,26617
ポリマ－95,6764
非ポリマー1,59013
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)72.193, 139.303, 120.495
Angle α, β, γ (deg.)90.000, 93.698, 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詳細
d_1ens_1(chain "A" and (resid 1 through 96 or (resid 97...
d_2ens_1(chain "F" and (resid 1 through 179 or resid 202 or resid 204 through 205))
d_1ens_2(chain "B" and (resid 3 through 103 or (resid 113...
d_2ens_2(chain "G" and (resid 3 through 21 or (resid 22...
d_1ens_3chain "C"
d_2ens_3(chain "H" and resid -2 through 13)
d_1ens_4(chain "D" and (resid 2 through 146 or (resid 147...
d_2ens_4(chain "I" and (resid 2 through 144 or (resid 145...
d_1ens_5(chain "E" and (resid 3 through 215 or (resid 216...
d_2ens_5(chain "J" and (resid 3 through 185 or (resid 186...

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
d_11ens_1ILEILEGLUGLUAA1 - 1793 - 182
d_12ens_1NAGNAGNAGNAGAI201
d_13ens_1GOLGOLGOLGOLAK203
d_14ens_1GOLGOLGOLGOLAL204
d_21ens_1ILEILEGLUGLUFC1 - 1793 - 182
d_22ens_1NAGNAGNAGNAGFP202
d_23ens_1GOLGOLGOLGOLFR204
d_24ens_1GOLGOLGOLGOLFS205
d_11ens_2SERSERARGARGCB21 - 20724 - 210
d_21ens_2SERSERARGARGHD21 - 20724 - 210
d_11ens_3GLYGLYGLYGLYCB-2 - 131 - 16
d_21ens_3GLYGLYGLYGLYHD-2 - 131 - 16
d_11ens_4METMETLYSLYSDE2 - 1971 - 180
d_12ens_4ASPASPSERSERDE199 - 219182 - 202
d_13ens_4GOLGOLGOLGOLDV301
d_21ens_4METMETSERSERIG2 - 2191 - 202
d_22ens_4GOLGOLGOLGOLIZ301
d_11ens_5GLYGLYASPASPEF3 - 2661 - 240
d_12ens_5GOLGOLGOLGOLEX301
d_21ens_5GLYGLYASPASPJH3 - 2661 - 240
d_22ens_5GOLGOLGOLGOLJCA301

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixベクター
1given(0.892212938115, -0.151955489872, 0.425282967162), (-0.169206364361, -0.985576575871, 0.00283184654439), (0.418718615923, -0.0744871948237, -0.905056008481)-21.345634003, 28.1064348397, 22.2294407684
2given(0.888739508085, -0.163668411854, 0.42819941351), (-0.183203583472, -0.983064731258, 0.00449234463936), (0.420212486454, -0.0824401911606, -0.903673105226)-21.2268351023, 28.2437611467, 22.0744421191
3given(0.888442774975, -0.164085284623, 0.428655403518), (-0.191790989578, -0.981190965154, 0.0219204520259), (0.416995985487, -0.101687311255, -0.903202102974)-21.2849393811, 28.7113609605, 22.20735766
4given(0.894102186793, -0.176117267313, 0.411781480552), (-0.211466127799, -0.976503437898, 0.0415103910705), (0.394795334782, -0.124192366622, -0.910336695793)-21.3551802869, 29.4425733139, 22.5280538531
5given(0.893616920645, -0.151418230331, 0.422517832359), (-0.188283814698, -0.981006000033, 0.0466522563504), (0.407428526567, -0.121242514915, -0.905153162905)-21.399437662, 29.154069438, 22.3484027263

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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 / DQA1*03:01 (DQ8-alpha chain


分子量: 21150.596 Da / 分子数: 2 / 変異: I75C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DQA1 / プラスミド: pZip3 / 細胞株 (発現宿主): High Five (BTI-Tn-5B1-4) / 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 (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera


分子量: 24450.369 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pZip3 / 遺伝子: HLA-DQB1 / 細胞株 (発現宿主): High Five (BTI-Tn-5B1-4) / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 株 (発現宿主): DH10B / 参照: UniProt: O19707

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T-CELL-RECEPTOR, TCR ET650-4 ... , 2種, 4分子 DIEJ

#3: タンパク質 T-CELL-RECEPTOR, TCR ET650-4 alpha


分子量: 22921.559 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: Human CD4+ T cell clone isolated from PBMC of recent onset T1D patient
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRAV26-1*01 / プラスミド: pET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): Escherichia coli (E.coli)
#4: タンパク質 T-CELL-RECEPTOR, TCR ET650-4 beta


分子量: 27153.135 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: Human CD4+ T cell clone isolated from PBMC of recent onset T1D patient
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRBV5-1*01 / プラスミド: pET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): Escherichia coli (E.coli)

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糖 , 1種, 5分子

#5: 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: 5 / 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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非ポリマー , 3種, 392分子

#6: 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: 12 / 由来タイプ: 合成 / 式: C3H8O3
#7: 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
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 374 / 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: 3.16 Å3/Da / 溶媒含有率: 61.11 %
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 / pH: 8
詳細: 0.2 M K Na tartrate, 15% w/v PEG 20,000 with seeding and additive C8 silver bullet

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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: 0.95372 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年8月6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: 0.95372 Å / 相対比: 1
反射解像度: 2.4→46.98 Å / Num. obs: 91516 / % possible obs: 98.7 % / 冗長度: 5 % / Biso Wilson estimate: 43.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.047 / Rrim(I) all: 0.078 / Net I/σ(I): 13.3
反射 シェル解像度: 2.4→2.44 Å / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4473 / CC1/2: 0.865 / Rpim(I) all: 0.258 / Rrim(I) all: 0.584

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
autoXDSデータ削減
Coot0.9.8.92モデル構築
XDSccp4-8.0データスケーリング
PHASERccp4-8.0位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.4→45.51 Å / SU ML: 0.2715 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 24.0085
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.22 4596 5.03 %
Rwork0.1883 86860 -
obs0.1899 91456 98.6 %
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: 52.96 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→45.51 Å
タンパク質核酸リガンド溶媒全体
原子数12736 0 172 374 13282
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002113216
X-RAY DIFFRACTIONf_angle_d0.517518006
X-RAY DIFFRACTIONf_chiral_restr0.04551995
X-RAY DIFFRACTIONf_plane_restr0.00422329
X-RAY DIFFRACTIONf_dihedral_angle_d12.09774663
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS3.89707972665
ens_2d_2BCX-RAY DIFFRACTIONTorsion NCS0.53277651086
ens_3d_2CFX-RAY DIFFRACTIONTorsion NCS0.328478891329
ens_4d_2GIX-RAY DIFFRACTIONTorsion NCS2.98226043605
ens_5d_2HJX-RAY DIFFRACTIONTorsion NCS1.51042414024
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.30211430.24432843X-RAY DIFFRACTION98.13
2.43-2.460.27681570.25472886X-RAY DIFFRACTION98.19
2.46-2.490.31421480.2342894X-RAY DIFFRACTION97.44
2.49-2.520.27251550.23492804X-RAY DIFFRACTION98.4
2.52-2.550.27811590.22432868X-RAY DIFFRACTION98.18
2.55-2.590.29511430.21912883X-RAY DIFFRACTION97.49
2.59-2.620.26551600.24112899X-RAY DIFFRACTION98.74
2.62-2.660.27671320.25182852X-RAY DIFFRACTION97.9
2.66-2.70.29151880.25992836X-RAY DIFFRACTION98.15
2.7-2.750.35811580.25752922X-RAY DIFFRACTION98.56
2.75-2.790.30081400.24372870X-RAY DIFFRACTION98.01
2.79-2.850.27931730.22942858X-RAY DIFFRACTION98.79
2.85-2.90.27851480.22492904X-RAY DIFFRACTION97.82
2.9-2.960.25341540.20832874X-RAY DIFFRACTION98.86
2.96-3.020.24621290.20692916X-RAY DIFFRACTION98.29
3.02-3.090.23251580.21392896X-RAY DIFFRACTION98.9
3.09-3.170.23321590.21442879X-RAY DIFFRACTION98.54
3.17-3.260.28891580.21722887X-RAY DIFFRACTION98.74
3.26-3.350.23571490.21592905X-RAY DIFFRACTION98.9
3.35-3.460.25141380.19852914X-RAY DIFFRACTION98.67
3.46-3.580.23331470.18442907X-RAY DIFFRACTION98.83
3.58-3.730.20531480.18252902X-RAY DIFFRACTION99.15
3.73-3.90.20771440.17272924X-RAY DIFFRACTION99.03
3.9-4.10.17811820.16972883X-RAY DIFFRACTION99.09
4.1-4.360.1751400.14492934X-RAY DIFFRACTION99.1
4.36-4.70.15741750.13662886X-RAY DIFFRACTION99.16
4.7-5.170.17531470.142960X-RAY DIFFRACTION99.11
5.17-5.910.19711360.16722957X-RAY DIFFRACTION99.49
5.92-7.440.20411670.1882935X-RAY DIFFRACTION99.33
7.45-45.510.17141610.17142982X-RAY DIFFRACTION99.15
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)
17.18879574634-0.3016735252932.143787617841.31359223721-0.01726438706613.352565999960.00182067457815-0.329958111204-0.206933213290.238286261420.0914530847973-0.009654034282220.2683892675040.140228213575-0.09150116476140.3652899294950.0242956687066-0.09526354754260.4067436830720.01548175691560.24989419233117.268-5.592-1.869
21.32838648930.235568449179-0.009347065748971.98577887680.5897606801232.285559104830.0595757578514-0.4454785697840.2016002538640.12680789572-0.0381752841597-0.0280452654164-0.360232253064-0.0318559366546-0.0573126696880.359232411368-0.0172940368204-0.06228526628070.294699523688-0.0001570933531550.2775973457069.2180.995-0.733
34.036541797821.306911085231.485312144733.21322980560.6159484159377.04450422265-0.0610097098899-0.5749219415880.8951590258530.136438356651-0.2172490557130.277505284924-0.961797079253-0.1332315277990.2247520264450.46498023719-0.01356393492840.005845233433310.362801783167-0.1026653916950.40725103385712.62911.6250.961
41.22572566880.504552070872-0.2080525486781.700813894120.9307214358022.31523929384-0.06971523371420.304647379355-0.209226653688-0.1440040301740.0617754021820.1187504651460.479428165536-0.164085001490.03600023171130.36830925549-0.0199349290138-0.07197822501680.313662650921-0.03351021677370.3510595407154.08-7.401-12.044
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552.153881740671.21033537698-0.7910599884272.77931172572-0.9626571577212.895649641060.01446382828130.37619117419-0.0631880395185-0.1708986978550.1295069475740.1330257813960.0313374943417-0.43859226853-0.1433896166060.2517984641110.0334819487643-0.01322825335940.381044717701-0.00690682156790.249035489573-29.7079.84550.327
563.09584209210.2087212780280.4375172443791.87073106481-0.6807119498224.549630051080.0291990458014-0.224965333299-0.5095125312850.206951497020.05587697302940.1117547290740.51421712694-0.302351065866-0.08615384414020.395216276056-0.06740811744370.02096074743660.3469858488880.07613270932580.50041866379-33.623-6.22276.809
573.49692026516-0.6812468649110.4841856329652.16246612956-0.4982961304323.078525134990.03232763284420.118972167835-0.24545334433-0.207275413975-0.0386562707909-0.07243743974740.3292966907470.1401919403330.02350046568390.278262497959-0.0173915308642-0.03392316094720.3522758231040.04309830401040.388108639495-31.016-3.52575.386
583.736314577520.07222770537890.6233747049592.478492611880.1130663866953.97684635802-0.133684846427-0.637943409588-0.1517721182610.1608276465420.08048120480710.1300814321420.0136897485267-0.5871569479580.04617418560850.252897980776-0.02720034954240.001796174949740.4819906547180.04469074292530.378818400121-37.629-0.45180.439
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:14 )A0 - 14
2X-RAY DIFFRACTION2( CHAIN A AND RESID 15:35 )A15 - 35
3X-RAY DIFFRACTION3( CHAIN A AND RESID 36:55 )A36 - 55
4X-RAY DIFFRACTION4( CHAIN A AND RESID 56:87 )A56 - 87
5X-RAY DIFFRACTION5( CHAIN A AND RESID 88:160 )A88 - 160
6X-RAY DIFFRACTION6( CHAIN A AND RESID 161:181 )A161 - 181
7X-RAY DIFFRACTION7( CHAIN C AND RESID 21:36 )C21 - 36
8X-RAY DIFFRACTION8( CHAIN C AND RESID 37:72 )C37 - 72
9X-RAY DIFFRACTION9( CHAIN C AND RESID 73:82 )C73 - 82
10X-RAY DIFFRACTION10( CHAIN C AND RESID 83:95 )C83 - 95
11X-RAY DIFFRACTION11( CHAIN C AND RESID 96:106 )C96 - 106
12X-RAY DIFFRACTION12( CHAIN C AND RESID 107:115 )C107 - 115
13X-RAY DIFFRACTION13( CHAIN C AND RESID 116:151 )C116 - 151
14X-RAY DIFFRACTION14( CHAIN C AND RESID 152:162 )C152 - 162
15X-RAY DIFFRACTION15( CHAIN C AND RESID 163:195 )C163 - 195
16X-RAY DIFFRACTION16( CHAIN C AND RESID 196:207 )C196 - 207
17X-RAY DIFFRACTION17( CHAIN C AND RESID -2:2 )C-2 - 2
18X-RAY DIFFRACTION18( CHAIN C AND RESID 3:7 )C3 - 7
19X-RAY DIFFRACTION19( CHAIN C AND RESID 8:13 )C8 - 13
20X-RAY DIFFRACTION20( CHAIN F AND RESID 1:26 )F1 - 26
21X-RAY DIFFRACTION21( CHAIN F AND RESID 27:55 )F27 - 55
22X-RAY DIFFRACTION22( CHAIN F AND RESID 56:76 )F56 - 76
23X-RAY DIFFRACTION23( CHAIN F AND RESID 77:87 )F77 - 87
24X-RAY DIFFRACTION24( CHAIN F AND RESID 88:101 )F88 - 101
25X-RAY DIFFRACTION25( CHAIN F AND RESID 102:123 )F102 - 123
26X-RAY DIFFRACTION26( CHAIN F AND RESID 124:134 )F124 - 134
27X-RAY DIFFRACTION27( CHAIN F AND RESID 135:179 )F135 - 179
28X-RAY DIFFRACTION28( CHAIN H AND RESID 21:36 )H21 - 36
29X-RAY DIFFRACTION29( CHAIN H AND RESID 37:50 )H37 - 50
30X-RAY DIFFRACTION30( CHAIN H AND RESID 51:72 )H51 - 72
31X-RAY DIFFRACTION31( CHAIN H AND RESID 73:82 )H73 - 82
32X-RAY DIFFRACTION32( CHAIN H AND RESID 83:106 )H83 - 106
33X-RAY DIFFRACTION33( CHAIN H AND RESID 107:121 )H107 - 121
34X-RAY DIFFRACTION34( CHAIN H AND RESID 131:151 )H131 - 151
35X-RAY DIFFRACTION35( CHAIN H AND RESID 152:162 )H152 - 162
36X-RAY DIFFRACTION36( CHAIN H AND RESID 163:181 )H163 - 181
37X-RAY DIFFRACTION37( CHAIN H AND RESID 182:195 )H182 - 195
38X-RAY DIFFRACTION38( CHAIN H AND RESID 196:207 )H196 - 207
39X-RAY DIFFRACTION39( CHAIN H AND RESID -2:7 )H-2 - 7
40X-RAY DIFFRACTION40( CHAIN H AND RESID 8:12 )H8 - 12
41X-RAY DIFFRACTION41( CHAIN H AND RESID 13:14 )H13 - 14
42X-RAY DIFFRACTION42( CHAIN D AND RESID 2:37 )D2 - 37
43X-RAY DIFFRACTION43( CHAIN D AND RESID 38:122 )D38 - 122
44X-RAY DIFFRACTION44( CHAIN D AND RESID 123:170 )D123 - 170
45X-RAY DIFFRACTION45( CHAIN D AND RESID 171:219 )D171 - 219
46X-RAY DIFFRACTION46( CHAIN E AND RESID 3:24 )E3 - 24
47X-RAY DIFFRACTION47( CHAIN E AND RESID 25:119 )E25 - 119
48X-RAY DIFFRACTION48( CHAIN E AND RESID 120:134 )E120 - 134
49X-RAY DIFFRACTION49( CHAIN E AND RESID 135:213 )E135 - 213
50X-RAY DIFFRACTION50( CHAIN E AND RESID 214:266 )E214 - 266
51X-RAY DIFFRACTION51( CHAIN I AND RESID 2:37 )I2 - 37
52X-RAY DIFFRACTION52( CHAIN I AND RESID 38:91 )I38 - 91
53X-RAY DIFFRACTION53( CHAIN I AND RESID 92:155 )I92 - 155
54X-RAY DIFFRACTION54( CHAIN I AND RESID 156:219 )I156 - 219
55X-RAY DIFFRACTION55( CHAIN J AND RESID 3:119 )J3 - 119
56X-RAY DIFFRACTION56( CHAIN J AND RESID 120:150 )J120 - 150
57X-RAY DIFFRACTION57( CHAIN J AND RESID 151:198 )J151 - 198
58X-RAY DIFFRACTION58( CHAIN J AND RESID 199:266 )J199 - 266

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://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