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- PDB-6gh4: HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln. -

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基本情報

登録情報
データベース: PDB / ID: 6gh4
タイトルHLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln.
要素
  • ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
  • Beta-2-microglobulin
  • MHC class I antigen
キーワードIMMUNE SYSTEM / Complex / Histocompatibility antigen
機能・相同性
機能・相同性情報


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / trans-2-enoyl-CoA reductase (NADH) activity / positive regulation of natural killer cell mediated cytotoxicity / mycolic acid biosynthetic process / positive regulation of interleukin-13 production / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / positive regulation of natural killer cell proliferation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / NAD+ binding / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / peptidoglycan-based cell wall / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / fatty acid binding / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium
類似検索 - 分子機能
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / NAD(P)-binding domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
HLA class I histocompatibility antigen, alpha chain E / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin / Enoyl-[acyl-carrier-protein] reductase [NADH]
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Mycobacteriaceae (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.16 Å
データ登録者Walters, L.C. / Gillespie, G.M. / McMichael, A.J. / Rozbesky, D. / Jones, E.Y. / Harlos, K.
資金援助 米国, 1件
組織認可番号国
Bill & Melinda Gates FoundationOPP1133649 米国
引用ジャーナル: Nat Commun / 年: 2018
タイトル: Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding.
著者: Walters, L.C. / Harlos, K. / Brackenridge, S. / Rozbesky, D. / Barrett, J.R. / Jain, V. / Walter, T.S. / O'Callaghan, C.A. / Borrow, P. / Toebes, M. / Hansen, S.G. / Sacha, J. / Abdulhaqq, S. ...著者: Walters, L.C. / Harlos, K. / Brackenridge, S. / Rozbesky, D. / Barrett, J.R. / Jain, V. / Walter, T.S. / O'Callaghan, C.A. / Borrow, P. / Toebes, M. / Hansen, S.G. / Sacha, J. / Abdulhaqq, S. / Greene, J.M. / Fruh, K. / Marshall, E. / Picker, L.J. / Jones, E.Y. / McMichael, A.J. / Gillespie, G.M.
履歴
登録2018年5月4日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年8月8日Provider: repository / タイプ: Initial release
改定 1.12018年8月22日Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.22024年1月17日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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 I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
E: MHC class I antigen
F: Beta-2-microglobulin
G: MHC class I antigen
H: Beta-2-microglobulin
P: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
Q: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
R: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
Y: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)178,62720
ポリマ－177,88912
非ポリマー7388
水18,3031016
1
A: MHC class I antigen
B: Beta-2-microglobulin
P: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,6645
ポリマ－44,4723
非ポリマー1922
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: MHC class I antigen
D: Beta-2-microglobulin
Q: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,8267
ポリマ－44,4723
非ポリマー3544
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: MHC class I antigen
F: Beta-2-microglobulin
R: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,5684
ポリマ－44,4723
非ポリマー961
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: MHC class I antigen
H: Beta-2-microglobulin
Y: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,5684
ポリマ－44,4723
非ポリマー961
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)48.317, 76.412, 111.309
Angle α, β, γ (deg.)99.39, 99.83, 93.50
Int Tables number1
Space group name H-MP1

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要素

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タンパク質 , 2種, 8分子 ACEGBDFH

#1: タンパク質
MHC class I antigen


分子量: 31597.713 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-E / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): plysS / 参照: UniProt: E2G051, UniProt: P13747*PLUS
#2: タンパク質
Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): plysS / 参照: UniProt: P61769

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タンパク質・ペプチド , 1種, 4分子 PQRY

#3: タンパク質・ペプチド
ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU


分子量: 995.218 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Mycobacteriaceae (バクテリア) / 参照: UniProt: P9WGR1*PLUS

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非ポリマー , 3種, 1024分子

#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 7 / 由来タイプ: 合成 / 式: SO4
#5: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Zn
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1016 / 由来タイプ: 天然 / 式: H2O

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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: 2.24 Å3/Da / 溶媒含有率: 45 %
結晶化温度: 293.5 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: 2.4 M Ammonium Sulphate, 0.1 M HEPES, pH 7

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I24 / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年4月22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: 0.9795 Å / 相対比: 1
反射解像度: 2.16→67.47 Å / Num. obs: 81277 / % possible obs: 98 % / 冗長度: 3.3 % / CC1/2: 0.976 / Rmerge(I) obs: 0.177 / Net I/σ(I): 4.3
反射 シェル解像度: 2.16→2.2 Å / 冗長度: 2.6 % / Num. unique obs: 3904 / CC1/2: 0.504 / % possible all: 92.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
xia2データ削減
xia2データスケーリング
MOLREP位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 6GH1

6gh1


解像度: 2.16→67.467 Å / SU ML: 0.29 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 27.67
Rfactor反射数%反射
Rfree0.2416 3945 4.88 %
Rwork0.2021 --
obs0.2041 80857 97.48 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.16→67.467 Å
タンパク質核酸リガンド溶媒全体
原子数12544 0 36 1022 13602
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00312943
X-RAY DIFFRACTIONf_angle_d0.58817592
X-RAY DIFFRACTIONf_dihedral_angle_d13.8747654
X-RAY DIFFRACTIONf_chiral_restr0.0431795
X-RAY DIFFRACTIONf_plane_restr0.0042309
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.158-2.18430.39831390.31232618X-RAY DIFFRACTION89
2.1843-2.21190.37871120.30632654X-RAY DIFFRACTION95
2.2119-2.24110.32551180.2932673X-RAY DIFFRACTION96
2.2411-2.27180.3151270.28642709X-RAY DIFFRACTION96
2.2718-2.30420.33891340.27792774X-RAY DIFFRACTION96
2.3042-2.33860.36621310.27482679X-RAY DIFFRACTION97
2.3386-2.37520.2961380.25372739X-RAY DIFFRACTION97
2.3752-2.41410.33871360.24912750X-RAY DIFFRACTION97
2.4141-2.45570.33611480.23252724X-RAY DIFFRACTION97
2.4557-2.50040.2471130.2322753X-RAY DIFFRACTION97
2.5004-2.54850.2761580.23772763X-RAY DIFFRACTION97
2.5485-2.60050.28961410.23122703X-RAY DIFFRACTION97
2.6005-2.6570.27921530.23162781X-RAY DIFFRACTION98
2.657-2.71890.27551560.22312735X-RAY DIFFRACTION98
2.7189-2.78680.27161600.21952692X-RAY DIFFRACTION98
2.7868-2.86220.24711390.20552806X-RAY DIFFRACTION98
2.8622-2.94640.24651390.20622748X-RAY DIFFRACTION98
2.9464-3.04150.23921290.20072789X-RAY DIFFRACTION99
3.0415-3.15020.23951350.19192767X-RAY DIFFRACTION99
3.1502-3.27640.20851400.17992793X-RAY DIFFRACTION99
3.2764-3.42550.22281400.17312776X-RAY DIFFRACTION99
3.4255-3.6060.18511520.16992767X-RAY DIFFRACTION99
3.606-3.8320.18991530.162797X-RAY DIFFRACTION99
3.832-4.12780.18251230.15542791X-RAY DIFFRACTION99
4.1278-4.54310.18781570.14712768X-RAY DIFFRACTION99
4.5431-5.20030.1971610.15182799X-RAY DIFFRACTION99
5.2003-6.5510.20611550.20112776X-RAY DIFFRACTION99
6.551-67.49970.23971580.20362788X-RAY DIFFRACTION99
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)
16.98252.21821.33982.78340.87223.8618-0.1212-0.39350.2722-0.22450.04280.2354-0.0782-0.40180.0620.1290.02290.02410.14160.03110.0864-2.2487-3.2095-11.2271
23.7810.32222.66911.42370.2343.7926-0.07110.05190.1935-0.07110.1296-0.1345-0.40960.0656-0.02070.1666-0.03870.02630.1498-0.00950.14594.02896.2599-13.7915
31.32262.43510.70816.1155-0.05191.8574-0.19680.22170.0127-0.4960.18410.12450.032-0.1808-0.01820.11040.01960.00970.19720.01010.1032-1.7731-6.095-21.0508
45.88012.3221-1.33063.62810.02611.6887-0.1227-0.58060.0662-0.2669-0.02510.28490.0793-0.14960.10770.14430.0071-0.00540.16490.04690.0895-5.8028-12.4104-10.7459
52.38030.674-0.04591.95550.0750.67230.0773-0.2622-0.19550.2659-0.0309-0.2362-0.07230.2103-0.04580.16280.0107-0.02590.20280.0320.13336.2629-16.9432-7.2698
62.2081.88290.15483.78990.65431.2864-0.13850.3472-0.2187-0.31560.2981-0.47720.03020.324-0.11310.1149-0.02150.04840.3369-0.00560.139610.2249-13.0964-15.2647
72.41590.0392-2.64911.39161.62947.71320.0799-0.12360.23450.0591-0.00910.0533-0.22160.0502-0.04750.10370.0151-0.01760.1733-0.00140.16415.94757.772616.9637
82.0896-0.98861.51653.7124-4.09198.8-0.105-0.2187-0.22150.08490.24320.10860.2248-0.5201-0.05030.2377-0.0133-0.0010.1146-0.04120.21492.2011.485717.6657
92.91940.6303-1.86711.77360.26983.89880.0577-0.56460.03660.142-0.049-0.17290.15440.3482-0.10.10060.0268-0.01820.25590.01920.17823.88125.220425.5507
105.6473-2.6534-1.82193.13572.08232.9743-0.2812-0.86150.4690.09660.5204-0.44840.27510.9852-0.41290.1843-0.0728-0.03290.3792-0.06380.282314.15787.306619.9077
113.63351.5596-0.03896.87370.97982.2435-0.342-0.0007-0.28590.05170.1660.098-0.0542-0.09270.16690.03610.0650.00980.2244-0.0120.2001-9.8818-1.81375.3589
126.3038-5.1375-1.38134.23181.15240.6592-0.1536-0.51810.8866-0.38910.0902-0.6429-0.61870.1203-0.03260.4941-0.0155-0.05970.2745-0.1070.4101-1.689121.524310.8066
130.88480.118-0.25252.62113.04363.6538-0.02350.09220.2932-0.4176-0.05510.2356-0.4322-0.28530.06070.14730.0375-0.01720.22910.00590.1777-10.53686.77071.9608
143.349-0.2758-1.89893.47781.6073.24550.05760.05040.5682-0.1799-0.1705-0.2258-0.5604-0.0925-0.01040.14380.0594-0.04020.2685-0.02850.0958-8.90935.6467-1.8946
153.79771.07330.19982.48191.10176.12050.18670.1120.2769-0.0093-0.4884-0.0732-0.9585-0.11030.14560.18220.0419-0.0160.2426-0.00080.0938-6.657610.41870.7989
160.6951.52450.18427.13132.61912.6476-0.08840.05350.4480.4108-0.09740.6682-0.1092-0.50790.18570.19490.0852-0.01860.376-0.05690.3701-17.09499.50197.8933
173.01531.3529-0.74721.8937-0.32632.2522-0.1663-0.62250.20560.4981-0.01320.4361-0.07190.1351-0.00490.1950.12460.0350.4515-0.09330.3014-11.225711.089514.1069
181.0222-0.0196-0.12312.84580.61242.585-0.04110.0270.03-0.11550.00810.18450.0964-0.12950.03690.1325-0.00530.02560.21310.02120.104219.4173-10.502234.7063
191.38510.922-0.18024.51080.48431.6241-0.03130.0135-0.2010.07110.1279-0.52270.34740.3131-0.10090.27870.054-0.01320.2767-0.00420.142832.2499-18.110836.9006
201.63430.3483-1.05561.7396-1.39566.8020.082-0.231-0.06310.376-0.021-0.1008-0.11850.3048-0.03890.20360.0249-0.00460.1446-0.01610.192727.5462-0.266768.759
212.5376-2.6355-0.53829.78233.71643.0893-0.0134-0.0727-0.0007-0.0011-0.1265-0.07530.5778-0.06850.17980.32140.00860.03820.24560.06010.138416.0566-16.257956.8557
227.0058-0.7688-6.02712.1494-0.34965.68790.5508-0.14621.80750.41080.44930.2143-0.6755-0.2952-1.06280.36530.00720.05680.24980.01760.501210.59667.496763.4491
232.2795-2.6246-1.11165.34831.10192.5656-0.00020.19830.2182-0.31650.0130.05410.0595-0.627-0.01610.1355-0.02220.01520.28820.07660.22129.9521-9.617654.629
247.1564-1.2402-1.75741.87351.49663.11570.241.11620.3937-0.2907-0.09640.7361-0.517-1.3371-0.30190.25120.0794-0.04790.54680.05140.43730.7344-4.52753.8343
256.4732-3.4315-3.87784.33362.23433.22350.04930.36990.4859-0.0279-0.0789-0.2083-0.041-0.06110.07990.1732-0.063-0.00180.23870.03740.116416.0309-9.085950.3703
260.06330.56640.26095.03392.31781.06840.544-0.54090.64310.574-0.09240.4138-0.1596-0.0552-0.22680.49130.17820.29980.8621-0.00080.47340.64611.470968.9593
272.7524-2.969-1.77184.48733.222.4922-0.39330.0027-0.14070.40120.14750.37580.4801-0.53860.05580.2956-0.15740.09730.45020.11190.24556.1525-17.194958.2956
283.52232.48310.79057.34981.55014.28040.2107-0.6272-0.05990.7247-0.16450.1932-0.2189-0.29830.00680.29060.07420.08970.42090.08310.22629.5662-6.289767.1611
290.3979-0.36560.24094.5027-0.10182.3239-0.01180.0703-0.1114-0.2038-0.00710.1483-0.20550.00990.00330.14-0.03010.02060.1930.01730.100719.179933.054568.321
303.6253-1.1975-2.15144.82732.2157.5462-0.05820.0524-0.38760.29420.08070.40680.61890.04670.04030.1385-0.07260.01510.18930.00710.236318.105322.842774.1529
310.5648-0.8274-0.09647.7802-0.3971.8004-0.1236-0.1023-0.00350.18770.2079-0.0391-0.1265-0.0841-0.11360.11-0.03820.01710.22480.00560.115819.81938.096278.4875
323.5389-1.52290.09654.04-0.41091.36250.05450.14820.1648-0.2789-0.0363-0.429-0.14540.22170.00740.2624-0.07530.05860.2592-0.00960.13928.718943.54466.5284
330.9546-0.11090.12711.89410.7811.3878-0.03080.09320.0078-0.02660.1804-0.1671-0.11670.1814-0.14410.0939-0.05560.08690.23630.03020.130529.888630.77862.1225
343.7029-1.17860.24441.3942-0.45183.2233-0.02080.75390.4895-0.80380.1362-0.3607-0.40070.40550.00630.5317-0.15960.15050.36540.0040.268424.269125.992740.0166
352.7377-0.08780.72262.0096-0.6943.72910.07140.69820.007-0.54780.0181-0.1185-0.39360.7086-0.06260.4368-0.08480.07540.3899-0.01770.209326.638722.30334.6601
365.48120.1961-1.8698.69521.98541.65240.3513-0.26960.53940.39590.49750.2485-0.47220.1521-0.57120.4271-0.05170.02030.13870.00960.18613.557446.145255.0671
375.8317-3.0661-0.44375.2995-1.09936.11120.1715-0.12060.0559-0.28370.03270.0234-0.5850.2551-0.18630.26520.0012-0.00710.2018-0.05710.138312.032728.664747.7258
385.91525.28143.32014.90562.57722.9726-0.39450.409-1.1504-0.32780.3057-0.41920.6689-0.28720.15240.3153-0.0351-0.02010.2477-0.06440.44969.908213.067945.9583
392.6723-0.0590.30121.4793-0.75652.3202-0.17210.2715-0.3741-0.33720.40950.02660.1257-0.0688-0.1650.1421-0.0057-0.05540.2583-0.00610.182311.025226.230352.5118
406.52665.86017.27277.62276.02758.46040.0046-0.76030.38110.1834-0.36180.7717-0.2613-0.97660.36420.16840.02810.05660.25980.00990.23694.836234.010256.4513
415.51740.23324.89296.22931.27135.5425-0.2367-0.9628-1.13190.61170.57790.5152-0.5744-1.0602-0.12860.26480.08510.04260.34430.04440.34-0.460523.845656.3144
420.7040.50091.32316.05370.07272.6114-0.21980.2328-0.1960.08020.252-0.4977-0.1390.21710.07750.1471-0.01170.05840.26250.03950.15120.062136.620460.3778
435.70992.14241.85174.46211.82071.41260.2528-0.2432-0.66150.3241-0.040.08190.08410.291-0.16930.1613-0.0375-0.00980.30820.04930.12789.656725.052855.9497
445.71241.1385-2.11653.52284.52548.8159-0.00750.4189-0.4419-1.11570.14110.5336-0.1265-0.72510.07590.31950.0414-0.11240.479-0.21330.6739-1.416517.41841.9342
452.69012.85352.40344.07513.85983.7644-0.0586-0.14930.1943-0.3437-0.28980.6818-0.2916-0.08980.30760.19030.0669-0.0170.3579-0.02130.40752.787937.111951.1439
463.6536-3.5105-3.33955.61490.65816.23820.22240.77740.2649-0.5854-0.1301-0.14960.3644-0.4287-0.25310.2742-0.0694-0.0920.3080.00680.26746.559826.559642.1926
474.7621-1.7274-0.63433.20230.78723.1638-0.099-0.1085-0.40220.3991-0.03630.38050.4786-0.14820.0840.234-0.06750.04570.17510.00110.151420.974240.800211.1686
481.445-0.4141-0.39152.76450.63341.00920.0817-0.21680.12760.2917-0.14480.0260.02530.05220.02640.1952-0.0510.02960.2495-0.01410.091123.27854.917612.6804
491.5090.36520.54291.45330.46595.5876-0.03080.3213-0.0968-0.15670.15220.02280.09910.0464-0.11680.1416-0.04180.03470.17130.00470.160926.48336.2868-21.1476
501.64590.40180.925.7525-0.3621.1969-0.3479-0.20450.08260.0870.4819-0.2067-0.00890.0842-0.1150.0367-0.0043-0.01630.2016-0.0060.147813.092535.631-8.9537
510.76640.13580.54544.79372.5441.86960.0497-0.177-0.13880.3301-0.10510.23370.2545-0.24920.03910.1462-0.03450.01440.24320.03520.150210.245636.3574-1.5049
521.0068-1.1611-0.23374.69192.33412.73470.03840.0409-0.29760.0222-0.08930.43890.1779-0.16860.0220.1254-0.05680.04250.21050.02970.21659.038829.5913-6.894
531.9308-2.404-0.45436.44593.92974.35740.12080.5026-0.1479-0.3622-0.35280.3058-0.1737-0.48930.13260.1853-0.029-0.01220.30860.03180.16315.068136.9768-11.6538
547.33656.59852.96588.43531.41273.8073-0.38790.5266-0.0619-1.2050.3255-0.0142-0.29560.15270.00590.1863-0.02410.07650.1993-0.00930.24734.2267-10.2348-19.3506
550.2569-0.69930.35928.5018-1.9541.00950.25940.0659-0.0115-1.4367-0.4027-0.20280.40210.35310.13310.20930.07350.05640.2539-0.01530.276327.4646-15.85729.5058
562.15210.0381-0.03961.89470.93192.3446-0.1542-0.01350.051.34360.01520.27480.27510.40470.16040.32760.0170.04120.2326-0.0080.113526.888438.612477.426
579.2867-5.946-2.91024.81832.93684.057-0.6047-0.59180.2921.06970.3806-0.2240.62630.17050.08540.2772-0.00540.00890.14370.00550.187323.864452.575618.2487
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 219 )
8X-RAY DIFFRACTION8chain 'A' and (resid 220 through 240 )
9X-RAY DIFFRACTION9chain 'A' and (resid 241 through 262 )
10X-RAY DIFFRACTION10chain 'A' and (resid 263 through 274 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 12 )
12X-RAY DIFFRACTION12chain 'B' and (resid 13 through 20 )
13X-RAY DIFFRACTION13chain 'B' and (resid 21 through 42 )
14X-RAY DIFFRACTION14chain 'B' and (resid 43 through 62 )
15X-RAY DIFFRACTION15chain 'B' and (resid 63 through 72 )
16X-RAY DIFFRACTION16chain 'B' and (resid 73 through 91 )
17X-RAY DIFFRACTION17chain 'B' and (resid 92 through 100 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 84 )
19X-RAY DIFFRACTION19chain 'C' and (resid 85 through 174 )
20X-RAY DIFFRACTION20chain 'C' and (resid 175 through 274 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 12 )
22X-RAY DIFFRACTION22chain 'D' and (resid 13 through 20 )
23X-RAY DIFFRACTION23chain 'D' and (resid 21 through 42 )
24X-RAY DIFFRACTION24chain 'D' and (resid 43 through 52 )
25X-RAY DIFFRACTION25chain 'D' and (resid 53 through 72 )
26X-RAY DIFFRACTION26chain 'D' and (resid 73 through 78 )
27X-RAY DIFFRACTION27chain 'D' and (resid 79 through 91 )
28X-RAY DIFFRACTION28chain 'D' and (resid 92 through 100 )
29X-RAY DIFFRACTION29chain 'E' and (resid 1 through 37 )
30X-RAY DIFFRACTION30chain 'E' and (resid 38 through 56 )
31X-RAY DIFFRACTION31chain 'E' and (resid 57 through 84 )
32X-RAY DIFFRACTION32chain 'E' and (resid 85 through 137 )
33X-RAY DIFFRACTION33chain 'E' and (resid 138 through 197 )
34X-RAY DIFFRACTION34chain 'E' and (resid 198 through 240 )
35X-RAY DIFFRACTION35chain 'E' and (resid 241 through 274 )
36X-RAY DIFFRACTION36chain 'F' and (resid 1 through 6 )
37X-RAY DIFFRACTION37chain 'F' and (resid 7 through 12 )
38X-RAY DIFFRACTION38chain 'F' and (resid 13 through 20 )
39X-RAY DIFFRACTION39chain 'F' and (resid 21 through 31 )
40X-RAY DIFFRACTION40chain 'F' and (resid 32 through 42 )
41X-RAY DIFFRACTION41chain 'F' and (resid 43 through 52 )
42X-RAY DIFFRACTION42chain 'F' and (resid 53 through 62 )
43X-RAY DIFFRACTION43chain 'F' and (resid 63 through 72 )
44X-RAY DIFFRACTION44chain 'F' and (resid 73 through 78 )
45X-RAY DIFFRACTION45chain 'F' and (resid 79 through 91 )
46X-RAY DIFFRACTION46chain 'F' and (resid 92 through 100 )
47X-RAY DIFFRACTION47chain 'G' and (resid 1 through 56 )
48X-RAY DIFFRACTION48chain 'G' and (resid 57 through 174 )
49X-RAY DIFFRACTION49chain 'G' and (resid 175 through 274 )
50X-RAY DIFFRACTION50chain 'H' and (resid 1 through 20 )
51X-RAY DIFFRACTION51chain 'H' and (resid 21 through 62 )
52X-RAY DIFFRACTION52chain 'H' and (resid 63 through 84 )
53X-RAY DIFFRACTION53chain 'H' and (resid 85 through 100 )
54X-RAY DIFFRACTION54chain 'P' and (resid 1 through 9 )
55X-RAY DIFFRACTION55chain 'Q' and (resid 1 through 9 )
56X-RAY DIFFRACTION56chain 'R' and (resid 1 through 9 )
57X-RAY DIFFRACTION57chain 'Y' and (resid 1 through 9 )

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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