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- PDB-6gl1: HLA-E*01:03 in complex with the HIV epitope, RL9HIV -

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基本情報

登録情報
データベース: PDB / ID: 6gl1
タイトルHLA-E*01:03 in complex with the HIV epitope, RL9HIV
要素
  • ARG-MET-TYR-SER-PRO-THR-SER-ILE-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 lectin-like receptor binding / natural killer cell tolerance induction / 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 lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / integrase activity / negative regulation of natural killer cell mediated cytotoxicity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 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 / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / positive regulation of interleukin-4 production / Early Phase of HIV Life Cycle / beta-2-microglobulin binding / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of natural killer cell proliferation / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / 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 / Binding and entry of HIV virion / T cell receptor binding / negative regulation of T cell proliferation / viral life cycle / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / HIV-1 retropepsin / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / symbiont-mediated activation of host apoptosis / peptide antigen assembly with MHC class II protein complex / retroviral ribonuclease H / exoribonuclease H / cellular response to iron(III) ion / MHC class II protein complex / exoribonuclease H activity / 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 / Assembly Of The HIV Virion / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / Budding and maturation of HIV virion / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / host multivesicular body / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / protein processing / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / RNA-directed DNA polymerase activity / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / RNA-DNA hybrid ribonuclease activity / positive regulation of tumor necrosis factor production / 転移酵素; リンを含む基を移すもの; 核酸を移すもの / MHC class II protein complex binding / Interferon alpha/beta signaling
類似検索 - 分子機能
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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : ...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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / Reverse transcriptase thumb / Reverse transcriptase thumb domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / DNA/RNA polymerase superfamily / 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 / Gag-Pol polyprotein / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.623 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22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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry
改定 1.32024年10月16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
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-MET-TYR-SER-PRO-THR-SER-ILE-LEU
R: ARG-MET-TYR-SER-PRO-THR-SER-ILE-LEU
T: ARG-MET-TYR-SER-PRO-THR-SER-ILE-LEU
Q: ARG-MET-TYR-SER-PRO-THR-SER-ILE-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)178,82319
ポリマ－178,18112
非ポリマー6427
水5,513306
1
A: MHC class I antigen
B: Beta-2-microglobulin
P: ARG-MET-TYR-SER-PRO-THR-SER-ILE-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,7375
ポリマ－44,5453
非ポリマー1922
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-41 kcal/mol
Surface area19050 Å2
手法PISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
Q: ARG-MET-TYR-SER-PRO-THR-SER-ILE-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,6414
ポリマ－44,5453
非ポリマー961
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-33 kcal/mol
Surface area18790 Å2
手法PISA
3
E: MHC class I antigen
F: Beta-2-microglobulin
R: ARG-MET-TYR-SER-PRO-THR-SER-ILE-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,7375
ポリマ－44,5453
非ポリマー1922
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-42 kcal/mol
Surface area18940 Å2
手法PISA
4
G: MHC class I antigen
H: Beta-2-microglobulin
T: ARG-MET-TYR-SER-PRO-THR-SER-ILE-LEU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,7075
ポリマ－44,5453
非ポリマー1612
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-37 kcal/mol
Surface area18390 Å2
手法PISA
単位格子
Length a, b, c (Å)244.820, 48.220, 153.020
Angle α, β, γ (deg.)90.00, 117.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11G-301-

ZN

21H-201-

SO4

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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 PRTQ

#3: タンパク質・ペプチド
ARG-MET-TYR-SER-PRO-THR-SER-ILE-LEU


分子量: 1068.268 Da / 分子数: 4 / 由来タイプ: 合成
由来: (合成) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
参照: UniProt: P04585*PLUS

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非ポリマー , 3種, 313分子

#4: 化合物
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 6 / 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: 306 / 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: 2.25 Å3/Da / 溶媒含有率: 45.35 %
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, 0.05% dichloromethane

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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: 2.62→135.878 Å / Num. obs: 48641 / % possible obs: 100 % / 冗長度: 6.6 % / Net I/σ(I): 5.2
反射 シェル解像度: 2.62→2.66 Å / Rmerge(I) obs: 2.345 / Num. unique obs: 2439 / CC1/2: 0.447

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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
精密化構造決定の手法: 分子置換
開始モデル: 6GH1

6gh1


解像度: 2.623→135.878 Å / SU ML: 0.34 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 27.2
Rfactor反射数%反射
Rfree0.2728 2112 5.11 %
Rwork0.2234 --
obs0.2259 41354 85.34 %
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: 2.623→135.878 Å
タンパク質核酸リガンド溶媒全体
原子数12363 0 31 306 12700
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00312744
X-RAY DIFFRACTIONf_angle_d0.61617312
X-RAY DIFFRACTIONf_dihedral_angle_d13.4187532
X-RAY DIFFRACTIONf_chiral_restr0.0431773
X-RAY DIFFRACTIONf_plane_restr0.0042263
LS精密化 シェル解像度: 2.623→2.717 Å /
Rfactor反射数
Rfree0.3156 -
Rwork0.303 -
obs-587
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)
13.1249-1.1159-1.0781.30860.86153.06810.02570.63860.0373-0.2524-0.12330.0374-0.1427-0.35570.07110.15910.0139-0.04330.2926-0.030.210419.64980.448746.6877
22.60571.469-1.30861.3725-1.81223.7517-0.1929-0.2293-0.39570.02520.0814-0.32210.31940.04730.06410.14710.028-0.02860.2454-0.03140.222619.2615-1.440562.7456
33.6516-1.6512-0.56450.8586-0.11841.4949-0.05640.2291-0.3295-0.0744-0.04660.06160.241-0.12620.0860.26590.0211-0.00010.1052-0.02620.285328.5672-8.715655.4093
44.42150.91331.08363.75690.67044.04060.3177-0.1486-0.01570.1078-0.0109-0.51490.22760.191-0.29590.1530.0522-0.02350.20080.01710.213854.3746-5.519959.2191
53.7632-0.9576-1.84864.77891.69886.1799-0.29390.47130.3335-0.4055-0.30690.0254-0.46490.4250.44550.3547-0.0981-0.19870.28360.06940.308244.16696.938850.1834
62.10091.6862-1.14482.2665-0.55752.9973-0.00611.3740.9028-0.5609-0.3154-0.2121-0.7078-0.01720.07690.43550.01220.00170.59850.32090.450339.850912.049344.9147
72.50980.3875-0.99171.9262-0.24743.8078-0.34350.3423-0.1085-0.6908-0.2613-0.11780.05011.22690.46310.41770.0907-0.18210.350.43110.199539.84456.741147.4143
82.5484-0.3496-1.38840.3075-0.0441.59630.16340.03421.0625-0.08750.2132-0.1828-0.33830.9487-0.0980.2843-0.2751-0.0253-0.00350.36291.081945.374615.14151.2463
93.4375-1.14170.0053.5097-1.6172.99540.1362-1.0858-0.05920.8297-0.0137-0.4314-0.3293-0.2378-0.07180.21280.0343-0.05210.6305-0.05320.277862.7647-20.263522.3324
103.61180.2811-1.23662.0211-1.08453.42290.028-0.5004-0.1353-0.0906-0.1031-0.13610.19990.26620.04720.1350.0425-0.06320.2745-0.01770.289370.6512-22.186310.2672
114.54190.1877-0.35732.3427-0.31622.69740.01680.2664-0.1441-0.29090.17110.60830.0843-0.0548-0.15840.2485-0.0471-0.06650.1314-0.0520.339432.6847-24.36110.3438
121.7720.0377-3.33935.6708-2.27627.6164-0.0322-0.17660.0193-0.455-0.3481-0.6874-0.56550.26770.16830.20250.033-0.08810.1847-0.08730.504348.9668-8.139211.2634
132.3771-1.158-0.67150.47530.29450.7508-0.1138-1.30090.84230.49420.0724-0.17880.04320.4312-0.05140.22960.11440.15660.3669-0.27810.543743.6887-10.686322.3935
142.6774-3.0305-0.49183.85530.90210.51250.3969-0.23080.17390.73760.0662-0.3702-0.99040.9187-0.44260.68330.1867-0.01020.8857-0.3740.465245.5862-4.375229.7204
154.6667-0.0652-0.32590.6495-0.5351.17220.329-1.8418-0.0068-0.27430.53060.2847-0.2155-0.8638-0.1480.2399-0.3271-0.1632-0.0194-0.43390.136547.0481-12.143720.5514
161.52690.7151-1.6490.5854-0.68011.48510.2178-0.48640.4390.70950.04550.4026-0.6559-0.1255-0.07260.3818-0.3402-0.0696-0.9407-0.57411.108446.9120.031716.4627
171.2409-0.4364-0.53161.6744-0.57071.68630.27150.14630.1284-0.24640.46240.08410.0867-0.4743-0.21380.1790.19620.06050.462-0.25570.698635.0269-7.462218.0625
183.8421-0.2302-0.29981.80530.21844.06280.0001-0.02180.0029-0.0952-0.04740.1583-0.3875-0.29210.04340.1325-0.0456-0.09750.19640.01970.2197-27.089510.140611.0751
192.7697-0.1203-1.40622.94162.30366.6919-0.16-0.8371-0.7112-0.0354-0.15010.26150.26980.01330.24810.3358-0.0202-0.10610.51210.15820.326-26.07150.728320.2602
203.0805-0.3098-1.53111.69560.65435.2052-0.1931-0.4016-0.89470.21170.00340.24870.8978-0.28260.15170.3182-0.0194-0.04220.36930.11750.3876-30.3994-5.130117.3981
215.2091.21152.4561.6948-0.40311.5820.05040.4075-0.69240.03490.2449-0.42490.26051.0032-0.2650.29410.16890.02240.8059-0.05350.33787.68792.255417.636
226.29464.843-3.60445.7047-4.10115.91950.4004-0.497-0.64780.5394-0.7531-0.4304-0.3164-0.2270.20110.28590.007-0.08720.4028-0.02310.1929-10.345413.280426.6867
231.69610.2991-1.58334.5376-0.85885.2356-0.40170.55610.8197-0.6464-0.1277-1.0522-0.22181.38680.33860.557-0.11070.03161.09150.30160.48186.375519.41118.6422
243.2264-0.0111-0.39323.4112-0.59534.7019-0.27220.17020.5329-0.6974-0.0896-0.2001-0.41380.20540.24170.3875-0.0539-0.10260.38410.12750.2594-5.796316.848316.8656
256.35021.1829-3.88582.9219-1.33494.65250.3039-0.60681.3540.2382-0.21220.1532-1.3931-0.0689-0.0060.42590.0067-0.23760.4981-0.15960.3214-12.769722.175322.8844
267.04375.89850.70247.5156-0.95234.9235-0.32690.36071.2009-0.02430.57811.171-1.0173-0.0889-0.30510.63420.0555-0.06360.30730.10980.5198-7.545528.823315.5303
276.32121.5952-0.52451.85370.30772.5594-0.3518-0.13530.294-0.4038-0.1855-0.25320.05740.33430.46510.23140.1157-0.0660.25170.06710.1913-12.648113.478817.3084
284.9913-0.6292-0.13763.1837-0.94584.89470.1813-0.19281.6629-0.16150.0701-0.7873-0.84371.7024-0.20240.5845-0.2032-0.04570.7468-0.0430.6928.270129.442216.3983
297.83950.636-4.99741.8369-2.39026.9248-0.1161-0.24340.7545-0.14390.47510.0198-0.55820.2775-0.21920.4321-0.0118-0.06970.3672-0.08760.3801-7.280323.846824.39
301.3222-0.3513-2.3142.8794-0.71985.1921-0.8997-0.93881.21760.2396-0.18-1.0722-0.40060.56040.37430.3699-0.054-0.25540.6356-0.2150.0952-2.099620.612226.4467
312.8214-1.64740.31161.5417-0.68023.9937-0.09070.46590.47550.3744-0.03210.62-0.22980.20990.03090.18140.0404-0.03630.20940.0230.2698-12.5195.401855.9259
324.79572.2972-1.06613.9278-1.15633.7771-0.0053-1.01620.12890.8001-0.19040.6453-0.47720.73350.29890.50330.06440.09240.08130.14270.1949-12.52056.953267.5874
332.8658-0.4461-0.90061.1015-0.27672.1714-0.17750.5551-0.6277-0.01030.0626-0.0440.41520.09830.17780.2350.0057-0.02020.345-0.0880.2614-5.6921-3.255150.9213
344.5546-0.4391-0.67563.073-0.4062.4976-0.64540.986-0.52420.44120.09680.26780.8088-0.78410.3962-0.1284-0.37250.30710.6592-0.15330.4413-40.5359-0.83357.591
352.06060.14250.88051.1568-0.06511.5366-0.47171.0808-1.1481-0.74370.09390.18840.8939-0.87620.24860.4403-0.38660.1440.8447-0.37360.5203-39.4066-2.313752.2381
364.1191-1.171-1.69222.65980.56095.240.25670.794-0.1796-0.1184-0.5521-0.3133-0.1480.00780.15090.16860.0264-0.06620.49570.03110.2506-25.699211.244343.9817
371.28761.1490.97962.3825-0.46792.28320.13110.57180.23610.2529-0.10520.5908-0.1772-0.94330.06990.0572-0.0604-0.00850.30040.0040.1776-35.539713.115457.8417
383.761-2.1662-2.34415.5243-0.15764.57520.67510.17820.84171.0580.3897-0.4301-1.78040.6985-0.50240.4461-0.0776-0.02710.330.06170.1456-25.717321.774153.5665
393.1988-1.749-1.96863.52191.6926.9235-0.02140.5873-0.91170.19010.32620.08580.3398-0.0074-0.1680.1937-0.0853-0.15410.2069-0.12850.1581-17.96344.366949.1602
404.38240.4667-4.481.67851.61996.90480.57260.54770.8283-0.1281-0.10720.063-1.3354-0.462-0.3810.28130.021-0.01680.22170.01640.2947-32.902118.776554.9146
411.012-0.9669-0.23431.36531.25192.4742-0.27090.75840.5232-0.8189-0.2910.3245-0.1144-1.40910.2030.43130.1265-0.04940.75540.20630.1808-32.979418.229945.2916
428.0135-5.3094-5.92873.47124.20547.8534-0.8780.9629-1.33880.32780.14731.467-0.32490.30070.69120.28940.06340.01310.43150.09760.469911.3576-3.757553.5872
433.64510.0535-3.12141.2517-1.57494.5474-0.04710.4098-0.47790.42950.11770.03540.0377-0.7765-0.15280.48630.002-0.15580.3416-0.00480.4838-34.59691.717613.2779
449.92941.2952-5.90224.5742-0.64358.02570.3249-0.58270.0104-0.150.1547-1.2032-0.07391.4137-0.27310.24190.01750.08030.3928-0.0370.3875-1.1369-2.374855.028
450.0202-0.0819-0.13870.24840.32160.41730.2637-1.1299-1.2053-0.0918-0.2575-1.2215-0.14170.68880.16440.068-0.0301-0.09690.69530.30340.660275.0625-23.263614.4837
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 274 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 78 )
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 100 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 56 )
10X-RAY DIFFRACTION10chain 'C' and (resid 57 through 174 )
11X-RAY DIFFRACTION11chain 'C' and (resid 175 through 274 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 12 )
13X-RAY DIFFRACTION13chain 'D' and (resid 13 through 42 )
14X-RAY DIFFRACTION14chain 'D' and (resid 43 through 52 )
15X-RAY DIFFRACTION15chain 'D' and (resid 53 through 78 )
16X-RAY DIFFRACTION16chain 'D' and (resid 79 through 91 )
17X-RAY DIFFRACTION17chain 'D' and (resid 92 through 100 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 84 )
19X-RAY DIFFRACTION19chain 'E' and (resid 85 through 118 )
20X-RAY DIFFRACTION20chain 'E' and (resid 119 through 174 )
21X-RAY DIFFRACTION21chain 'E' and (resid 175 through 274 )
22X-RAY DIFFRACTION22chain 'F' and (resid 1 through 12 )
23X-RAY DIFFRACTION23chain 'F' and (resid 13 through 20 )
24X-RAY DIFFRACTION24chain 'F' and (resid 21 through 31 )
25X-RAY DIFFRACTION25chain 'F' and (resid 32 through 42 )
26X-RAY DIFFRACTION26chain 'F' and (resid 43 through 52 )
27X-RAY DIFFRACTION27chain 'F' and (resid 53 through 72 )
28X-RAY DIFFRACTION28chain 'F' and (resid 73 through 78 )
29X-RAY DIFFRACTION29chain 'F' and (resid 79 through 85 )
30X-RAY DIFFRACTION30chain 'F' and (resid 86 through 100 )
31X-RAY DIFFRACTION31chain 'G' and (resid 1 through 37 )
32X-RAY DIFFRACTION32chain 'G' and (resid 38 through 56 )
33X-RAY DIFFRACTION33chain 'G' and (resid 57 through 174 )
34X-RAY DIFFRACTION34chain 'G' and (resid 175 through 201 )
35X-RAY DIFFRACTION35chain 'G' and (resid 202 through 274 )
36X-RAY DIFFRACTION36chain 'H' and (resid 1 through 12 )
37X-RAY DIFFRACTION37chain 'H' and (resid 13 through 31 )
38X-RAY DIFFRACTION38chain 'H' and (resid 32 through 52 )
39X-RAY DIFFRACTION39chain 'H' and (resid 53 through 62 )
40X-RAY DIFFRACTION40chain 'H' and (resid 63 through 84 )
41X-RAY DIFFRACTION41chain 'H' and (resid 85 through 100 )
42X-RAY DIFFRACTION42chain 'P' and (resid 1 through 9 )
43X-RAY DIFFRACTION43chain 'R' and (resid 1 through 9 )
44X-RAY DIFFRACTION44chain 'T' and (resid 1 through 9 )
45X-RAY DIFFRACTION45chain 'Q' and (resid 1 through 9 )

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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://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