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- PDB-6gh1: HLA-E*01:03 in complex with Mtb44 -

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基本情報

登録情報
データベース: PDB / ID: 6gh1
タイトルHLA-E*01:03 in complex with Mtb44
要素
  • Beta-2-microglobulin
  • Enoyl-[acyl-carrier-protein] reductase [NADH]
  • 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 / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / trans-2-enoyl-CoA reductase (NADH) activity ...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 / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / trans-2-enoyl-CoA reductase (NADH) activity / MHC class Ib protein complex / mycolic acid biosynthetic process / natural killer cell lectin-like receptor binding / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / enoyl-[acyl-carrier-protein] reductase (NADH) / negative regulation of natural killer cell mediated cytotoxicity / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 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 immunoglobulin production / positive regulation of interleukin-4 production / protection from natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / beta-2-microglobulin binding / NAD+ binding / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / negative regulation of T cell proliferation / T cell receptor binding / peptidoglycan-based cell wall / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / fatty acid binding / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / positive regulation of cellular senescence / sensory perception of smell / tertiary granule lumen / MHC class II protein complex binding / DAP12 signaling / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / protein refolding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation
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 / Short-chain dehydrogenase/reductase SDR / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...: / 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 / Short-chain dehydrogenase/reductase SDR / 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 / Immunoglobulin-like fold / Immunoglobulins / 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)
Mycobacterium tuberculosis (結核菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.1 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_symmetry
改定 1.32024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
P: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: MHC class I antigen
D: Beta-2-microglobulin
Q: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: MHC class I antigen
F: Beta-2-microglobulin
R: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: MHC class I antigen
H: Beta-2-microglobulin
Z: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)179,04725
ポリマ－177,82912
非ポリマー1,21813
水14,016778
1
C: MHC class I antigen
D: Beta-2-microglobulin
Q: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,8427
ポリマ－44,4573
非ポリマー3844
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
G: MHC class I antigen
H: Beta-2-microglobulin
Z: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,7156
ポリマ－44,4573
非ポリマー2583
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
3
A: MHC class I antigen
B: Beta-2-microglobulin
P: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,7466
ポリマ－44,4573
非ポリマー2883
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-45 kcal/mol
Surface area19150 Å2
手法PISA
4
E: MHC class I antigen
F: Beta-2-microglobulin
R: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,7466
ポリマ－44,4573
非ポリマー2883
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-55 kcal/mol
Surface area19030 Å2
手法PISA
単位格子
Length a, b, c (Å)48.380, 76.600, 111.150
Angle α, β, γ (deg.)99.33, 99.56, 93.66
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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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 PQRZ

#3: タンパク質・ペプチド
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


分子量: 980.247 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Mycobacterium tuberculosis (結核菌)
参照: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)

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非ポリマー , 3種, 791分子

#4: 化合物
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 12 / 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: 778 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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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: 45.19 %
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: 6 / 詳細: 2.4 M Ammonium Sulphate, 0.1 M MES, pH 6

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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: I04 / 波長: 0.9686 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年7月15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: 0.9686 Å / 相対比: 1
反射解像度: 2.09→53.91 Å / Num. obs: 81176 / % possible obs: 89.1 % / 冗長度: 1.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.085 / Net I/σ(I): 2.8
反射 シェル解像度: 2.09→2.13 Å / 冗長度: 1.5 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.668 / % possible all: 47

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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
MOLREP位相決定
Cootモデル構築
xia2データ削減
xia2データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 1MHE

1mhe


解像度: 2.1→48.021 Å / SU ML: 0.27 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 25.57 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2288 4090 5.05 %
Rwork0.191 --
obs0.1929 80979 89.76 %
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
精密化ステップサイクル: LAST / 解像度: 2.1→48.021 Å
タンパク質核酸リガンド溶媒全体
原子数12548 0 61 779 13388
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00212967
X-RAY DIFFRACTIONf_angle_d0.54117630
X-RAY DIFFRACTIONf_dihedral_angle_d14.8357653
X-RAY DIFFRACTIONf_chiral_restr0.0411800
X-RAY DIFFRACTIONf_plane_restr0.0032308
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12470.3865640.29631433X-RAY DIFFRACTION48
2.1247-2.15060.3364920.27031557X-RAY DIFFRACTION53
2.1506-2.17790.2893920.26661713X-RAY DIFFRACTION58
2.1779-2.20650.2548920.27481860X-RAY DIFFRACTION63
2.2065-2.23670.30931250.26822053X-RAY DIFFRACTION70
2.2367-2.26870.32321320.27072386X-RAY DIFFRACTION81
2.2687-2.30260.32031430.25822781X-RAY DIFFRACTION93
2.3026-2.33850.31411470.24522742X-RAY DIFFRACTION94
2.3385-2.37690.31131380.22992838X-RAY DIFFRACTION95
2.3769-2.41790.3141480.23672852X-RAY DIFFRACTION96
2.4179-2.46180.25841440.21882820X-RAY DIFFRACTION96
2.4618-2.50920.27681500.22852855X-RAY DIFFRACTION97
2.5092-2.56040.27781490.22142897X-RAY DIFFRACTION97
2.5604-2.6160.25571720.22942802X-RAY DIFFRACTION97
2.616-2.67690.30111590.22452940X-RAY DIFFRACTION98
2.6769-2.74380.27461750.21792843X-RAY DIFFRACTION97
2.7438-2.8180.25591660.21192851X-RAY DIFFRACTION97
2.818-2.90090.27371570.2012899X-RAY DIFFRACTION98
2.9009-2.99450.2631460.19982903X-RAY DIFFRACTION98
2.9945-3.10160.23721410.18912870X-RAY DIFFRACTION98
3.1016-3.22570.25391520.18382963X-RAY DIFFRACTION98
3.2257-3.37250.21581490.16912858X-RAY DIFFRACTION98
3.3725-3.55020.18461620.17042884X-RAY DIFFRACTION98
3.5502-3.77260.21671430.15472887X-RAY DIFFRACTION97
3.7726-4.06370.17491550.14742893X-RAY DIFFRACTION98
4.0637-4.47240.1661700.14652852X-RAY DIFFRACTION98
4.4724-5.11890.17041470.14772891X-RAY DIFFRACTION98
5.1189-6.44690.20331520.19522887X-RAY DIFFRACTION98
6.4469-48.03330.2021280.19922879X-RAY DIFFRACTION96
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)
13.61020.88150.66063.7933-0.25692.63020.0161-0.01660.199-0.18350.05840.0475-0.2788-0.0638-0.05830.2484-0.02020.06810.1858-0.03620.13920.74571.7157-12.5332
21.44310.436-0.19813.3765-0.24851.5776-0.0314-0.0017-0.0632-0.17060.060.01560.06280.0293-0.02450.25130.00060.03530.2405-0.05950.18930.4694-11.987-13.04
34.07513.64971.50337.68533.81342.0094-0.34450.4096-0.372-0.67920.6019-0.8694-0.19830.338-0.25860.1907-0.01440.00680.33110.02250.199110.0256-13.0826-15.1249
43.09390.25-2.21531.42420.227.5432-0.0196-0.45830.00820.0982-0.00080.04120.14010.22340.01750.2034-0.02460.00210.2231-0.04460.25875.66966.006519.4117
57.0519-2.7519-4.962.86942.86696.1354-0.55610.8135-0.8494-0.6146-0.00450.96651.0965-1.0030.61210.3803-0.06950.04620.2428-0.02450.2703-13.0882-9.80581.6661
66.88275.34784.27824.4054.29836.6091-0.3165-0.05080.14380.00660.46550.5153-0.2957-0.2634-0.15790.17720.0603-0.02440.28430.00260.225-7.06626.44459.0374
76.8772-6.6617-1.97929.19682.4270.66520.0783-0.63711.2907-0.68940.5843-1.7851-1.45310.9981-0.65690.5179-0.10230.01030.3358-0.03230.4794-1.863121.48510.6596
82.5709-0.4394-1.30085.63181.89953.6903-0.10510.1380.2267-0.2871-0.01840.26-0.3178-0.32480.17830.18660.0084-0.02660.1968-0.01790.1749-10.79336.82151.9876
92.7135-0.6952-0.97183.62741.19933.390.18511.07181.1057-0.4569-0.47570.2353-0.9079-1.103-0.01370.46250.1524-0.11650.39290.03440.4528-15.38115.8334-0.9123
101.4037-0.937-0.29573.33424.33566.32090.04170.20440.253-0.3208-0.074-0.3755-0.404-0.1182-0.02540.14940.01910.03490.20690.01510.2342-4.90023.3339-0.9629
112.5597-2.7675-2.38748.56185.4056.5816-0.247-0.34340.31060.5131-0.14830.9002-0.8655-1.31970.57530.60550.1817-0.01870.547-0.12810.5988-13.965322.891414.2358
120.28191.05061.05086.31184.21135.1783-0.1572-0.22970.31770.2885-0.02680.44190.2094-0.64520.13160.19090.03870.00690.4689-0.07840.4063-18.86113.20014.8237
137.20520.2497-2.33285.0157-2.06722.8315-0.2804-0.94590.0530.94440.18430.1759-0.35980.0830.09390.37330.18390.04190.5545-0.10540.3251-11.244411.015414.0581
145.55254.6331-2.33345.1905-1.48096.1188-1.44981.0433-0.4626-1.85481.2062-0.11120.5009-0.09180.17660.45340.00050.06820.3232-0.02830.30744.2468-10.4357-19.4075
151.73230.9209-0.23385.5522-0.49082.624-0.05750.12090.05240.02330.11410.3080.1618-0.23-0.03860.18820.00620.0430.2389-0.02030.1831-29.0057-10.504834.6782
161.57170.727-0.51885.76140.37762.2341-0.04360.0666-0.23810.17840.0934-0.58550.46920.254-0.05250.33010.068-0.00580.3482-0.05780.2303-16.2056-18.176936.9574
171.90410.5697-0.36552.7945-2.40188.38420.1955-0.2975-0.02640.5947-0.2239-0.068-0.05230.39440.00610.34-0.01730.00820.1857-0.0490.2731-20.7136-0.181468.7086
185.485-4.7773-3.33048.63966.39416.3952-0.2007-0.0792-0.14680.17950.04690.11460.9799-0.33230.17130.47170.04950.0520.19610.06040.3071-32.339-16.24456.8711
199.0092-5.5207-7.20067.01376.01096.47920.0556-0.64662.19020.30310.06480.22960.4454-0.6420.04890.4906-0.04140.04030.4525-0.1420.6425-37.81467.667163.3286
204.5905-3.9139-1.25384.45850.73386.1112-0.4102-0.13690.72570.36660.5985-0.54320.1925-0.0919-0.17050.203-0.00870.03640.1750.02040.3253-35.5811-5.310956.3027
216.199-7.1563-6.0729.6168.07447.89520.16520.3291-0.2152-0.482-0.48780.83830.3853-1.00820.23770.3965-0.10660.09640.39680.05730.2831-41.209-13.869352.9897
227.6126-0.7069-5.17264.56750.65893.6737-0.03721.50980.8911-0.43540.34530.71720.4116-1.3909-0.19460.3613-0.0321-0.0830.6120.02160.4156-47.5846-4.542553.6881
238.0221-6.5157-5.65437.87215.0635.76940.1640.28790.60660.1354-0.0585-0.11620.0343-0.1195-0.14330.2065-0.09180.0240.21330.01830.2657-32.3149-9.09250.4072
247.3983-3.4194-7.50742.13783.5917.63660.59470.02420.7120.62910.7360.8197-0.7055-0.7489-1.21450.51940.16560.17780.7999-0.02130.7216-47.83361.783968.7177
255.3311-6.0662-6.98526.89667.95459.17350.08770.19260.4528-0.70210.11380.0126-0.2854-0.0588-0.3280.3976-0.03610.0040.33460.04090.3927-43.8669-10.943359.5473
267.5145-0.0205-0.29373.1902-1.110.40050.4835-1.1945-0.33310.6081-0.51510.6895-0.4823-0.0743-0.27440.8502-0.54410.30570.4909-0.01310.4679-40.5717-22.948957.4823
279.74995.80173.08623.68123.10167.96990.4594-1.07390.05870.6261-0.80850.2747-0.0906-0.73840.40580.396-0.0310.18450.5136-0.04610.4539-38.7257-6.091867.1593
282.29780.12591.67355.401-1.33861.59990.16830.3107-0.0749-1.9472-0.1115-0.35080.08310.5058-0.04950.3541-0.07340.0860.36660.0020.2938-20.8267-15.919929.4452
293.2698-2.05270.16283.46780.61411.9865-0.0072-0.4815-0.30140.44020.01430.35760.2048-0.1153-0.01620.2679-0.08060.04950.2487-0.01470.2409-23.7968-32.80114.2707
301.8564-0.71750.2182.80510.6021.32160.0269-0.15430.13530.0989-0.0883-0.0901-0.06840.07230.06240.1932-0.0520.0430.2259-0.00560.1835-18.9533-19.15110.2448
311.46260.24570.59691.91590.13538.4854-0.08380.3251-0.1316-0.25750.2119-0.002-0.07170.0159-0.10260.1923-0.0470.06520.2118-0.02890.2508-17.4019-40.0661-21.0351
322.60290.03371.08675.79570.15882.658-0.2081-0.15180.04220.10020.3089-0.0628-0.0394-0.1832-0.19270.1219-0.01350.01290.16460.01920.1141-30.8336-40.6121-8.8775
330.868-0.51530.59754.55112.64723.1890.1097-0.2011-0.17080.1508-0.20810.35680.2184-0.35460.09320.1667-0.02810.03880.2754-0.01990.2095-33.6686-39.8759-1.4783
341.7546-1.3081-0.5663.66762.32184.31130.09080.3586-0.1961-0.1731-0.22070.30180.1707-0.32890.16030.1596-0.08950.02090.29910.01320.2892-36.5182-43.657-8.7446
356.1071-5.3461-3.75454.70713.53796.9226-1.1047-0.8640.41351.51240.8367-0.6191-0.07380.25940.24260.3692-0.0239-0.04450.3650.00050.2874-19.9345-23.495718.3825
360.9556-0.9920.06195.96910.24032.4397-0.05390.0056-0.12480.04520.08020.2135-0.109-0.0681-0.02380.1819-0.06230.04450.2255-0.01730.2015-24.2183-43.646373.2602
370.6857-0.42420.09443.5802-0.07340.99820.0562-0.08420.183-0.36830.0417-0.5058-0.27950.2919-0.09980.3941-0.07840.1020.3631-0.06460.3081-12.5768-34.900469.5072
383.5783-0.17540.90192.1209-0.04475.66040.06120.6220.3036-0.48890.0096-0.14-0.39730.4124-0.03090.4152-0.04580.07970.2878-0.01940.2917-18.613-53.397438.7548
398.18582.63993.37064.12545.48917.2769-0.29470.10810.8257-0.92430.72120.0672-0.77830.1836-0.28870.46050.07070.05370.2490.02540.3357-30.0873-30.155455.0903
408.9352-5.44-2.42344.0266-0.40195.57030.61380.43760.3031-0.7359-0.91890.7328-0.60990.13720.30960.30020.0236-0.01090.2093-0.02210.2625-31.5218-47.845747.7987
417.83146.15184.91694.86833.7253.4944-0.12510.2813-1.873-0.2433-0.4979-0.62241.1202-0.6510.150.4035-0.08510.04370.379-0.16530.7035-33.6516-63.370346.0704
424.21435.30754.64356.73775.40087.40520.2071-0.1509-0.1873-0.4129-0.3710.22930.02280.1350.17920.31290.02720.01710.2482-0.07470.252-32.4873-50.180752.5703
437.92298.238.36529.28999.19469.17190.0356-0.93050.24650.274-0.74390.8918-0.2777-1.23170.60250.32160.02610.0850.30980.01440.3543-38.6953-42.342356.4428
448.9115-3.15116.50067.71520.92587.793-0.3122-1.3622-0.71340.80790.28990.7272-0.5954-1.3850.11860.46810.03940.09920.5104-0.07460.348-43.9735-52.559156.3741
451.9374-1.57611.87535.60061.42863.8421-0.04020.6503-0.0023-0.31910.1922-0.5153-0.0110.1569-0.07680.2663-0.05360.07610.3448-0.01370.2083-23.4943-39.719160.2906
466.93087.16294.97298.2515.38856.03010.1894-0.0974-0.84330.23610.02160.07420.31310.3204-0.26030.1629-0.00090.05450.1843-0.01740.3793-33.8683-51.412555.9628
475.41385.30764.79345.20334.6864.8919-0.10941.4832-0.4124-1.76950.56540.39420.2218-0.1220.02820.6487-0.0844-0.04470.746-0.19780.5888-44.641-59.042141.8179
485.61714.16264.02793.31043.32663.4142-0.1565-0.67070.19420.1826-0.35221.4128-0.2687-0.50070.30580.31160.10130.01760.3874-0.12590.5223-40.7957-39.393751.152
493.8468-3.7207-1.70449.83194.33184.75070.59931.5688-0.3859-1.787-0.51630.1537-0.3316-0.1129-0.13260.4495-0.0297-0.00870.5728-0.07180.3102-37.0445-49.936142.2156
506.5682-3.7207-0.31593.2478-2.04574.7233-1.08310.08670.12140.84680.8254-1.0072-0.45130.60620.24550.3526-0.0915-0.05340.2976-0.03050.2363-16.3426-37.242777.543
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 174 )
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 274 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 6 )
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 12 )
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 20 )
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 72 )
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 78 )
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 91 )
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 100 )
14X-RAY DIFFRACTION14chain 'P' and (resid 1 through 9 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 84 )
16X-RAY DIFFRACTION16chain 'C' and (resid 85 through 174 )
17X-RAY DIFFRACTION17chain 'C' and (resid 175 through 274 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 12 )
19X-RAY DIFFRACTION19chain 'D' and (resid 13 through 20 )
20X-RAY DIFFRACTION20chain 'D' and (resid 21 through 31 )
21X-RAY DIFFRACTION21chain 'D' and (resid 32 through 42 )
22X-RAY DIFFRACTION22chain 'D' and (resid 43 through 52 )
23X-RAY DIFFRACTION23chain 'D' and (resid 53 through 72 )
24X-RAY DIFFRACTION24chain 'D' and (resid 73 through 78 )
25X-RAY DIFFRACTION25chain 'D' and (resid 79 through 84 )
26X-RAY DIFFRACTION26chain 'D' and (resid 85 through 91 )
27X-RAY DIFFRACTION27chain 'D' and (resid 92 through 100 )
28X-RAY DIFFRACTION28chain 'Q' and (resid 1 through 9 )
29X-RAY DIFFRACTION29chain 'E' and (resid 1 through 84 )
30X-RAY DIFFRACTION30chain 'E' and (resid 85 through 174 )
31X-RAY DIFFRACTION31chain 'E' and (resid 175 through 274 )
32X-RAY DIFFRACTION32chain 'F' and (resid 1 through 20 )
33X-RAY DIFFRACTION33chain 'F' and (resid 21 through 62 )
34X-RAY DIFFRACTION34chain 'F' and (resid 63 through 100 )
35X-RAY DIFFRACTION35chain 'R' and (resid 1 through 9 )
36X-RAY DIFFRACTION36chain 'G' and (resid 1 through 84 )
37X-RAY DIFFRACTION37chain 'G' and (resid 85 through 174 )
38X-RAY DIFFRACTION38chain 'G' and (resid 175 through 274 )
39X-RAY DIFFRACTION39chain 'H' and (resid 1 through 6 )
40X-RAY DIFFRACTION40chain 'H' and (resid 7 through 12 )
41X-RAY DIFFRACTION41chain 'H' and (resid 13 through 20 )
42X-RAY DIFFRACTION42chain 'H' and (resid 21 through 31 )
43X-RAY DIFFRACTION43chain 'H' and (resid 32 through 42 )
44X-RAY DIFFRACTION44chain 'H' and (resid 43 through 52 )
45X-RAY DIFFRACTION45chain 'H' and (resid 53 through 62 )
46X-RAY DIFFRACTION46chain 'H' and (resid 63 through 72 )
47X-RAY DIFFRACTION47chain 'H' and (resid 73 through 78 )
48X-RAY DIFFRACTION48chain 'H' and (resid 79 through 91 )
49X-RAY DIFFRACTION49chain 'H' and (resid 92 through 100 )
50X-RAY DIFFRACTION50chain 'Z' 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://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