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- PDB-5kd7: Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Be... -

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基本情報

登録情報
データベース: PDB / ID: 5kd7
タイトルCrystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PV9) of HIV gp120 MN Isolate (IGPGRAFYV)
要素
  • Beta-2-microglobulinΒ2-ミクログロブリン
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
キーワードIMMUNE SYSTEM (免疫系) / MAJOR HISTOMPATIBILITY COMPLEX CLASS I / MHC-I (MHCクラスI分子) / H2-Dd / H-2Dd / HIV peptide / PVI10 / PV9 / GLYCOPROTEIN (糖タンパク質) / IMMUNE RESPONSE (免疫応答)
機能・相同性
機能・相同性情報


TAP1 binding / TAP2 binding / 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 ...TAP1 binding / TAP2 binding / 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 / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / Dectin-2 family / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / detection of bacterium / Neutrophil degranulation / T cell receptor binding / host cell endosome membrane / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane
類似検索 - 分子機能
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Gp120 (HIV) / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Gp120 (HIV) / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / Β2-ミクログロブリン / 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 / 抗体 / Immunoglobulin-like fold / Immunoglobulin-like / サンドイッチ / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Β2-ミクログロブリン / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Human immunodeficiency virus type 1 group M subtype B (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: 2.35 Å
データ登録者Jiang, J. / Natarajan, K. / Margulies, D.
引用ジャーナル: J. Immunol. / 年: 2018
タイトル: Effects of Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T Cell Immunity.
著者: Frey, B.F. / Jiang, J. / Sui, Y. / Boyd, L.F. / Yu, B. / Tatsuno, G. / Billeskov, R. / Solaymani-Mohammadi, S. / Berman, P.W. / Margulies, D.H. / Berzofsky, J.A.
履歴
登録2016年6月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年10月11日Provider: repository / タイプ: Initial release
改定 1.12018年2月7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_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22018年2月28日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32020年2月19日Group: Derived calculations / Source and taxonomy
カテゴリ: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
改定 1.42023年9月27日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
P: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
C: H-2 class I histocompatibility antigen, D-D alpha chain
D: Beta-2-microglobulin
E: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
F: H-2 class I histocompatibility antigen, D-D alpha chain
G: Beta-2-microglobulin
H: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
I: H-2 class I histocompatibility antigen, D-D alpha chain
J: Beta-2-microglobulin
K: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)179,72821
ポリマ－179,10912
非ポリマー6199
水3,963220
1
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
P: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,9636
ポリマ－44,7773
非ポリマー1863
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-15 kcal/mol
Surface area19180 Å2
手法PISA
2
C: H-2 class I histocompatibility antigen, D-D alpha chain
D: Beta-2-microglobulin
E: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,8394
ポリマ－44,7773
非ポリマー621
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-23 kcal/mol
Surface area19230 Å2
手法PISA
3
F: H-2 class I histocompatibility antigen, D-D alpha chain
G: Beta-2-microglobulin
H: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,0867
ポリマ－44,7773
非ポリマー3084
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-26 kcal/mol
Surface area19380 Å2
手法PISA
4
I: H-2 class I histocompatibility antigen, D-D alpha chain
J: Beta-2-microglobulin
K: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,8394
ポリマ－44,7773
非ポリマー621
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-22 kcal/mol
Surface area18940 Å2
手法PISA
単位格子
Length a, b, c (Å)51.420, 75.360, 120.030
Angle α, β, γ (deg.)93.52, 87.14, 96.50
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 ACFIBDGJ

#1: タンパク質
H-2 class I histocompatibility antigen, D-D alpha chain / H-2D(D)


分子量: 32005.594 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: H2-D1 / プラスミド: PET21-B / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P01900
#2: タンパク質
Beta-2-microglobulin / Β2-ミクログロブリン


分子量: 11791.545 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: B2m / プラスミド: PET3A / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P01887

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タンパク質・ペプチド , 1種, 4分子 PEHK

#3: タンパク質・ペプチド
Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)


分子量: 980.141 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus type 1 group M subtype B (isolate MN) (ヒト免疫不全ウイルス)
発現宿主: synthetic construct (人工物) / 参照: UniProt: P05877*PLUS

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非ポリマー , 3種, 229分子

#4: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル / エチレングリコール


分子量: 62.068 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル / グリセリン


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#6: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 220 / 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: 2.57 Å3/Da / 溶媒含有率: 52.09 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: 12% PEG 20000, 0.1M MES buffer

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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: APS / ビームライン: 22-ID / 波長: 1.0333 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2015年6月25日
放射モノクロメーター: SI 100 / 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: 1.0333 Å / 相対比: 1
反射解像度: 2.35→74.8 Å / Num. obs: 72767 / % possible obs: 97.9 % / 冗長度: 3.9 % / Biso Wilson estimate: 31.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.7
反射 シェル解像度: 2.35→2.43 Å / 冗長度: 4 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 1.8 / % possible all: 96.5

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155: ???)精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3ECB

3ecb


解像度: 2.35→42.719 Å / SU ML: 0.32 / 交差検証法: THROUGHOUT / σ(F): 2 / 位相誤差: 29.39 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2488 2011 2.77 %
Rwork0.1977 --
obs0.1992 72716 97.81 %
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: 2.35→42.719 Å
タンパク質核酸リガンド溶媒全体
原子数12377 0 40 220 12637
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00512810
X-RAY DIFFRACTIONf_angle_d0.77717388
X-RAY DIFFRACTIONf_dihedral_angle_d14.727589
X-RAY DIFFRACTIONf_chiral_restr0.0451764
X-RAY DIFFRACTIONf_plane_restr0.0052267
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3499-2.40870.32471440.2914932X-RAY DIFFRACTION96
2.4087-2.47380.33041310.2764999X-RAY DIFFRACTION97
2.4738-2.54660.33631360.25724998X-RAY DIFFRACTION97
2.5466-2.62880.34961560.25424960X-RAY DIFFRACTION97
2.6288-2.72270.32791420.24495051X-RAY DIFFRACTION97
2.7227-2.83170.30841440.23725033X-RAY DIFFRACTION97
2.8317-2.96060.29191470.24145043X-RAY DIFFRACTION98
2.9606-3.11660.31151380.24465060X-RAY DIFFRACTION98
3.1166-3.31180.25251460.21775084X-RAY DIFFRACTION98
3.3118-3.56740.27451540.20665095X-RAY DIFFRACTION99
3.5674-3.92620.22811350.18155124X-RAY DIFFRACTION99
3.9262-4.49380.18141460.14975073X-RAY DIFFRACTION99
4.4938-5.65960.16831420.14065164X-RAY DIFFRACTION99
5.6596-42.72640.20311500.15885089X-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)
12.83841.83080.12318.6234-0.74882.4521-0.1054-0.0591-0.13610.3769-0.1852-0.68060.2070.4090.26550.41960.1601-0.06970.37870.03880.2292-21.135751.77491.1833
22.1061-0.02140.32723.1158-0.53282.7611-0.1039-0.03030.06770.2730.0166-0.0244-0.0913-0.28710.08650.33590.1551-0.03950.3660.00520.1584-31.573959.8191-3.0158
34.16680.41261.6477.4601-1.3864.24220.12690.28910.28810.07030.09710.7111-0.0177-0.913-0.11960.31030.17160.00050.55960.03450.2783-39.745662.0837-9.9292
41.20040.2323-0.38691.6967-0.46562.6780.014-0.26660.0199-0.3109-0.34130.24470.7763-0.95830.2990.2215-0.05040.00210.3839-0.03080.2681-30.930440.458520.7882
50.39070.4987-0.80580.8006-0.52134.03560.1337-0.37970.07090.1091-0.29460.44180.7587-1.44410.07220.3184-0.24350.02930.8026-0.04530.3257-34.769140.810131.7793
62.38691.5726-0.90931.53710.32512.0481-0.0578-0.018-0.01020.07590.01350.1161-0.2864-0.23630.03320.26720.0157-0.03350.1293-0.01180.1128-21.181550.524325.2497
71.7521-1.85052.42872.9272-2.66383.8393-0.0490.23140.1273-0.3838-0.2472-0.1677-0.63130.56490.28340.33150.00780.03730.23070.05080.2507-15.357555.923720.4376
88.8246-5.21016.91985.8497-4.09146.88640.49860.2077-0.2782-1.04-0.27570.0060.3111-0.1139-0.16240.28050.01690.05490.15470.02720.2709-19.363952.334119.1814
92.0285-1.38741.26975.4898-3.07073.652-0.0927-0.15850.27830.1688-0.2592-0.2253-0.8848-0.10320.33580.4529-0.0385-0.03310.16790.00330.2526-18.322359.238727.9204
102.20852.41450.05013.9994-2.14263.56560.04670.14780.16320.0228-0.13660.1431-0.2075-0.10570.08350.22250.1102-0.02590.3228-0.03860.2657-30.270659.4644-9.6049
111.7684-0.8089-0.44236.0273-0.46941.3574-0.04910.20780.1482-0.4223-0.1207-0.1748-0.56230.3710.10910.5002-0.1112-0.11360.18170.01350.3245-2.599690.222941.9664
122.3310.3493-0.91093.37650.14862.8842-0.0242-0.02090.0836-0.1618-0.15210.3402-0.2718-0.31240.16260.2257-0.0371-0.11680.1942-0.0090.2307-13.979381.221749.1688
132.1863-0.2265-0.31731.8102-1.06995.34520.02040.4237-0.1360.0566-0.0666-0.0477-0.0844-0.09760.02730.27080.0369-0.0270.1527-0.06860.2852-14.144499.824923.1664
141.9796-2.50271.15493.9357-2.39743.07390.30480.4776-0.5841-0.705-0.02140.81720.3715-0.8361-0.20760.4228-0.0364-0.14430.6596-0.15550.5241-18.14293.473615.7225
151.7657-0.3878-1.04722.3061.39293.23560.43171.3247-0.3019-0.7425-0.46790.3927-0.3339-0.96590.03360.5480.1972-0.06270.7117-0.06580.3109-19.555100.488810.4243
166.31475.8633-5.81065.444-5.39545.3464-0.1492-0.0535-0.6965-0.0195-0.2114-0.29431.2617-0.00770.34050.9573-0.0779-0.04550.336-0.18830.4367-10.422672.552828.1125
174.40765.54-4.5116.9245-5.6474.59460.33130.44380.5580.02880.30640.8842-0.3194-0.0499-0.67440.437-0.0469-0.00590.31070.02870.4037-1.114895.437216.0995
183.17723.3724-3.55016.6137-6.56257.64320.1224-0.0567-0.0369-0.02670.0414-0.01710.29790.2872-0.18330.44190.0222-0.08460.1608-0.04630.2556-2.949184.721525.514
197.89244.273-7.23742.6396-3.48097.2866-0.3669-0.171-0.6278-0.0349-0.359-0.48820.53740.43560.67540.56880.3643-0.07770.5407-0.02880.49176.274882.829120.4169
204.4395-0.1543-4.43133.920.48764.45080.5431-0.59820.19450.30280.0475-0.97320.01460.8706-0.56820.5450.1995-0.03630.842-0.12190.60479.477986.846222.0098
213.02742.13522.41226.21230.18152.4153-0.10891.0311.1097-0.39520.52410.5876-1.2093-0.0506-0.3750.5076-0.0532-0.10740.27560.06510.3083-11.0183.68734.9442
225.59842.8068-5.00084.5541-2.91257.91890.26530.3902-0.1082-0.1773-0.1714-0.5067-0.16410.1913-0.14720.25250.0747-0.04370.364-0.09420.29883.394891.226318.8787
233.75874.7724-3.6046.9475-4.1114.51820.1648-0.0723-0.5799-0.2103-0.1221-0.89450.47010.38160.13530.65560.34680.05350.3058-0.00590.46463.256581.628818.1567
243.3124-1.2606-1.86542.4470.79351.47380.06510.3616-0.199-0.7283-0.29350.13080.0377-0.08980.1831.11010.28250.0380.323-0.07220.6689-3.111471.691621.8692
258.31824.4282-3.90982.7007-3.35566.58860.28790.5106-0.1548-1.07730.01080.04360.36730.1554-0.29950.51510.1505-0.06350.3294-0.12530.3003-1.801887.705411.288
260.2054-0.19240.10420.5144-0.76061.3532-0.13270.00240.3990.3176-0.15970.0199-0.31250.17340.26380.3052-0.0527-0.11880.1889-0.03610.375-10.524982.583953.8081
271.6498-0.0342-0.22433.028-0.62543.1829-0.11020.0769-0.1065-0.2141-0.0988-0.40110.61720.40690.1570.33460.18070.09930.45030.0270.229-17.071953.060491.6796
281.9208-0.1841-0.07781.62930.0343.0513-0.0604-0.41160.11030.27120.135-0.28690.0361.01110.00930.14960.0408-0.02820.4691-0.05350.2908-1.3149.296957.787
295.3455-5.8024-5.29946.21575.73565.2397-0.2232-0.46290.1590.42510.45030.0244-0.31380.1605-0.20010.4462-0.00160.00710.3656-0.01310.3655-22.49754.835868.0182
305.15773.77624.60373.18214.1298.74270.45360.655-0.6591-0.31860.2515-0.6380.75420.4339-0.64070.59540.22380.03070.29130.02990.3156-11.864935.613556.0209
314.8919-4.3098-3.98455.31946.29818.3096-0.34010.039-0.0053-0.04950.2444-0.16360.54020.13640.06540.3434-0.00590.08820.33350.04650.1533-18.906145.798866.2713
320.872-1.1857-0.90439.46496.97415.1207-0.0237-0.053-0.05010.1261-0.17040.41710.3804-0.57750.19330.5019-0.22270.11480.57460.05720.2272-29.054847.857869.0799
335.19851.98193.00372.10431.01287.39170.2443-0.5723-0.60250.3591-0.14450.00120.7148-0.553-0.09070.6065-0.40030.12320.64360.01010.3739-28.357737.76964.0255
346.9238-6.4025-1.10767.0953.59235.80550.0219-0.40090.05030.1023-0.0361-0.20850.92630.15130.05760.30150.05380.01360.397-0.01010.1629-19.123653.341479.5171
351.7995-0.11780.52134.45872.64515.22630.0158-0.0204-0.0959-0.0521-0.26650.28060.6643-0.62640.22620.2859-0.12070.10180.40590.04230.2264-25.077545.201862.6529
363.0946-1.7171-3.52053.78491.00096.90040.03370.0850.4332-0.3941-0.173-0.30330.16860.35340.08980.2433-0.0545-0.02650.4120.11630.2201-20.057747.656954.9619
372.25160.51-1.94281.19451.62125.6298-0.3907-0.062-0.0241-0.01810.17770.15650.0740.14810.23220.25790.15510.00930.53050.11650.2792-19.478355.346198.5191
380.32910.0166-0.09060.87020.36320.97110.0936-0.22590.2114-0.01470.2027-0.2116-0.89240.7247-0.05541.2802-0.5785-0.20110.5441-0.49170.0078-4.010988.111377.1688
393.00651.70370.65163.13740.90361.3281-0.18030.04960.4839-0.16980.1595-0.2312-0.55520.41570.00221.8061-0.82980.00690.639-0.19640.5559-1.185299.653174.2108
403.04510.7860.1661.92060.07350.7232-0.1622-0.16860.1116-0.20670.2414-0.1598-1.09720.8753-0.05620.6707-0.3345-0.00560.6282-0.10970.233-5.525481.785671.1945
414.40650.0139-0.44163.63721.59835.6909-0.21510.2702-0.2647-0.26280.4307-0.32040.35651.7019-0.13980.3434-0.0293-0.02350.5858-0.0680.2786-0.897970.228668.0736
420.4574-0.33380.5980.48990.78876.716-0.58170.80280.143-0.25560.7837-0.428-0.27990.4786-0.11910.7793-0.5034-0.15151.3992-0.24571.047213.165391.552685.9048
433.7379-1.15670.43011.62621.16363.5628-0.79330.02790.03790.15140.2541-0.32460.52870.18490.48450.58230.2137-0.20540.9199-0.4931.360913.042685.2033101.9139
443.9868-0.40652.40880.1298-0.61963.2182-0.27580.2776-0.2279-0.0720.18280.25580.5186-0.31680.05830.7788-0.2695-0.01070.9431-0.2330.81539.665982.804100.577
451.94720.1444-0.19341.1949-0.30974.9580.0398-0.352-0.43720.3250.0313-0.48420.30660.5258-0.17430.6532-0.087-0.25451.1816-0.43590.99679.745282.8878107.8655
463.10181.227-2.62291.9285-0.25132.6575-0.0859-0.20330.13410.1982-0.2503-0.43910.52340.8270.31850.76330.2333-0.16851.0539-0.15491.13719.498584.1923107.4869
473.5157-1.3091-3.24722.31970.32253.4296-0.17890.4436-0.687-0.03820.3989-0.02150.5135-0.1327-0.19770.390.0125-0.05510.3629-0.00520.3132-11.141374.853790.158
487.43622.07997.57563.62742.04267.72130.1654-0.07750.03150.4950.5443-1.5913-0.15151.3474-0.67080.5424-0.1838-0.04270.9776-0.17220.4813-2.048987.8793100.8439
491.04210.44031.56570.69951.40473.37230.2646-0.70920.59651.03080.0876-0.6638-0.64360.4429-0.14291.0733-0.3687-0.14531.1034-0.55060.7316-0.740895.1755101.5028
501.62961.92811.31652.62392.24162.4716-0.0337-0.44340.70640.2091-0.36480.5074-0.7569-0.63760.50210.73510.0663-0.15820.6319-0.23020.3472-13.55788.498994.5376
511.8623-1.0028-2.09661.43510.90512.41290.0186-0.20010.7585-0.08030.14190.2314-1.0044-0.3189-0.19811.10650.0014-0.14120.7811-0.36510.7937-13.328998.810199.6737
523.6995.06911.5297.85094.94599.60760.4075-0.27690.56190.34910.1278-0.8675-0.63930.7803-0.49520.4133-0.24640.0940.5572-0.11680.4253-3.279683.389784.1302
531.01012.55652.00238.21156.2354.7382-0.2355-0.37650.7803-0.5777-0.0081-0.1756-1.33630.0020.25051.181-0.222-0.07970.7107-0.26510.5282-5.123494.439595.259
542.87734.33442.5446.55493.87262.3113-0.1368-0.26350.3560.2528-0.07240.1175-0.41490.19330.15661.14470.1015-0.08431.2235-0.59510.8456-6.48299.306113.9113
555.49773.56773.14042.0057.03114.85210.2182-0.77330.51210.899-0.60570.3403-0.0501-0.50650.34540.6573-0.0532-0.04090.7967-0.17820.4053-14.668784.647399.5355
562.342-1.3692-0.53252.084-1.17571.84450.2921-0.4001-0.02980.2860.1156-0.7303-0.09190.4409-0.34130.7605-0.022-0.02171.0332-0.28260.4504-4.935588.5359107.842
571.753-0.8830.52080.49310.04372.07420.0308-0.37080.03090.5018-0.2949-0.1569-0.70380.41270.19970.557-0.347-0.01610.63160.06730.2506-4.452780.3965.1374
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 219 )
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 274 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 19 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 77 )
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 99 )
10X-RAY DIFFRACTION10chain 'P' and (resid 1 through 9 )
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 56 )
12X-RAY DIFFRACTION12chain 'C' and (resid 57 through 162 )
13X-RAY DIFFRACTION13chain 'C' and (resid 163 through 219 )
14X-RAY DIFFRACTION14chain 'C' and (resid 220 through 240 )
15X-RAY DIFFRACTION15chain 'C' and (resid 241 through 274 )
16X-RAY DIFFRACTION16chain 'D' and (resid 0 through 5 )
17X-RAY DIFFRACTION17chain 'D' and (resid 6 through 19 )
18X-RAY DIFFRACTION18chain 'D' and (resid 20 through 35 )
19X-RAY DIFFRACTION19chain 'D' and (resid 36 through 41 )
20X-RAY DIFFRACTION20chain 'D' and (resid 42 through 52 )
21X-RAY DIFFRACTION21chain 'D' and (resid 53 through 61 )
22X-RAY DIFFRACTION22chain 'D' and (resid 62 through 77 )
23X-RAY DIFFRACTION23chain 'D' and (resid 78 through 83 )
24X-RAY DIFFRACTION24chain 'D' and (resid 84 through 90 )
25X-RAY DIFFRACTION25chain 'D' and (resid 91 through 99 )
26X-RAY DIFFRACTION26chain 'E' and (resid 1 through 9 )
27X-RAY DIFFRACTION27chain 'F' and (resid 2 through 174 )
28X-RAY DIFFRACTION28chain 'F' and (resid 175 through 276 )
29X-RAY DIFFRACTION29chain 'G' and (resid 0 through 11 )
30X-RAY DIFFRACTION30chain 'G' and (resid 12 through 19 )
31X-RAY DIFFRACTION31chain 'G' and (resid 20 through 30 )
32X-RAY DIFFRACTION32chain 'G' and (resid 31 through 41 )
33X-RAY DIFFRACTION33chain 'G' and (resid 42 through 51 )
34X-RAY DIFFRACTION34chain 'G' and (resid 52 through 61 )
35X-RAY DIFFRACTION35chain 'G' and (resid 62 through 90 )
36X-RAY DIFFRACTION36chain 'G' and (resid 91 through 99 )
37X-RAY DIFFRACTION37chain 'H' and (resid 1 through 9 )
38X-RAY DIFFRACTION38chain 'I' and (resid 2 through 37 )
39X-RAY DIFFRACTION39chain 'I' and (resid 38 through 56 )
40X-RAY DIFFRACTION40chain 'I' and (resid 57 through 118 )
41X-RAY DIFFRACTION41chain 'I' and (resid 119 through 162 )
42X-RAY DIFFRACTION42chain 'I' and (resid 163 through 198 )
43X-RAY DIFFRACTION43chain 'I' and (resid 199 through 219 )
44X-RAY DIFFRACTION44chain 'I' and (resid 220 through 240 )
45X-RAY DIFFRACTION45chain 'I' and (resid 241 through 252 )
46X-RAY DIFFRACTION46chain 'I' and (resid 253 through 275 )
47X-RAY DIFFRACTION47chain 'J' and (resid 0 through 5 )
48X-RAY DIFFRACTION48chain 'J' and (resid 6 through 11 )
49X-RAY DIFFRACTION49chain 'J' and (resid 12 through 30 )
50X-RAY DIFFRACTION50chain 'J' and (resid 31 through 41 )
51X-RAY DIFFRACTION51chain 'J' and (resid 42 through 51 )
52X-RAY DIFFRACTION52chain 'J' and (resid 52 through 61 )
53X-RAY DIFFRACTION53chain 'J' and (resid 62 through 71 )
54X-RAY DIFFRACTION54chain 'J' and (resid 72 through 77 )
55X-RAY DIFFRACTION55chain 'J' and (resid 78 through 90 )
56X-RAY DIFFRACTION56chain 'J' and (resid 91 through 99 )
57X-RAY DIFFRACTION57chain 'K' 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