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- PDB-1lk2: 1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide -

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基本情報

登録情報
データベース: PDB / ID: 1lk2
タイトル1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide
要素
  • Beta-2-microglobulin
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
  • INSULIN RECEPTOR, BETA-SUBUNIT
キーワードIMMUNE SYSTEM / Class I MHC-peptide complex / high resolution / anisotropic and TLS refinement
機能・相同性
機能・相同性情報


Signaling by Insulin receptor / IRS activation / Insulin receptor signalling cascade / Signal attenuation / Insulin receptor recycling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth ...Signaling by Insulin receptor / IRS activation / Insulin receptor signalling cascade / Signal attenuation / Insulin receptor recycling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / exocrine pancreas development / nuclear lumen / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / insulin binding / adrenal gland development / PTB domain binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / positive regulation of respiratory burst / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / regulation of embryonic development / positive regulation of receptor internalization / insulin receptor substrate binding / protein kinase activator activity / epidermis development / positive regulation of glycogen biosynthetic process / cellular defense response / heart morphogenesis / phosphatidylinositol 3-kinase binding / insulin-like growth factor receptor binding / Neutrophil degranulation / positive regulation of mitotic nuclear division / positive regulation of glycolytic process / animal organ morphogenesis / lumenal side of endoplasmic reticulum membrane / positive regulation of D-glucose import / 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 / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / 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 / receptor protein-tyrosine kinase / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / caveola / peptide antigen binding / cellular response to growth factor stimulus / receptor internalization / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / male gonad development / phagocytic vesicle membrane / recycling endosome membrane / negative regulation of epithelial cell proliferation / positive regulation of nitric oxide biosynthetic process / sensory perception of smell / positive regulation of cellular senescence / late endosome / nuclear envelope / insulin receptor signaling pathway / glucose homeostasis / T cell differentiation in thymus / negative regulation of neuron projection development / amyloid-beta binding / protein autophosphorylation / protein refolding / protein tyrosine kinase activity / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / lysosome / receptor complex / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / defense response to bacterium / positive regulation of cell migration / G protein-coupled receptor signaling pathway / external side of plasma membrane / positive regulation of cell population proliferation
類似検索 - 分子機能
Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / 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 / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / : / Fibronectin type 3 domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Fibronectin type-III domain profile. / Beta-2-Microglobulin / Fibronectin type III / Fibronectin type III superfamily / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Tyrosine-protein kinase, active site / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
PHOSPHATE ION / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Insulin receptor
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.35 Å
データ登録者Luz, J.G. / Rudolph, M.G. / Wilson, I.A. / Eisen, H.
引用ジャーナル: J.Immunol. / 年: 2004
タイトル: A peptide that antagonizes TCR-mediated reactions with both syngeneic and allogeneic agonists: functional and structural aspects.
著者: Rudolph, M.G. / Shen, L.Q. / Lamontagne, S.A. / Luz, J.G. / Delaney, J.R. / Ge, Q. / Cho, B.K. / Palliser, D. / McKinley, C.A. / Chen, J. / Wilson, I.A. / Eisen, H.N.
履歴
登録2002年4月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02003年11月11日Provider: repository / タイプ: Initial release
改定 1.12008年4月28日Group: Version format compliance
改定 1.22011年7月13日Group: Non-polymer description / Version format compliance
改定 1.32019年7月24日Group: Data collection / Derived calculations / Refinement description
カテゴリ: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年11月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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, K-B ALPHA CHAIN
B: Beta-2-microglobulin
P: INSULIN RECEPTOR, BETA-SUBUNIT
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,3259
ポリマ－44,2873
非ポリマー1,0386
水6,972387
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-36 kcal/mol
Surface area19090 Å2
手法PISA
単位格子
Length a, b, c (Å)135.549, 87.650, 45.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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要素

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タンパク質 , 2種, 2分子 AB

#1: タンパク質 H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN / MHC CLASS I H-2KB HEAVY CHAIN


分子量: 31648.322 Da / 分子数: 1
断片: EXTRACELLULAR DOMAIN, SEQUENCE DATABASE RESIDUES 22-295, NUMBERED 1-274
由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: pET22b(+) / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P01901
#2: タンパク質 Beta-2-microglobulin


分子量: 11704.359 Da / 分子数: 1 / 断片: SEQUENCE DATABASE RESIDUES 21-119, NUMBERED 1-99 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: pET22b(+) / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (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, 1分子 P

#3: タンパク質・ペプチド INSULIN RECEPTOR, BETA-SUBUNIT / GNYSFYAL peptide


分子量: 934.005 Da / 分子数: 1 / 断片: sequence database residues 423-430, numbered 1-8 / 由来タイプ: 合成
詳細: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS FOUND NATURALLY IN MUS MUSCULUS.
参照: UniProt: P15208

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糖 , 2種, 2分子

#4: 多糖 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 367.349 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 1 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 4種, 391分子

#6: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 1 / 由来タイプ: 合成 / 式: PO4
#7: 化合物 ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#8: 化合物 ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / (4R)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 387 / 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: 3.02 Å3/Da / 溶媒含有率: 59.33 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: K/Na-Phosphate, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
結晶化
*PLUS
詳細: Stura, E.A., (1992) J. Mol. Biol., 228, 975.

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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: SSRL / ビームライン: BL9-1 / 波長: 0.97 Å
検出器タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2000年2月13日 / 詳細: Flat mirror (vertical focusing)
放射モノクロメーター: single crystal Si(311) bent monochromator (horizontal focusing)
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: 0.97 Å / 相対比: 1
反射解像度: 1.35→30 Å / Num. obs: 117515 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.4 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.053 / Net I/σ(I): 23.95
反射 シェル解像度: 1.35→1.37 Å / 冗長度: 2.5 % / Mean I/σ(I) obs: 1.13 / Num. unique all: 5606 / Rsym value: 0.813 / % possible all: 95.3
反射
*PLUS
Rmerge(I) obs: 0.053
反射 シェル
*PLUS
% possible obs: 95.3 % / Num. unique obs: 5606 / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.1

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解析

ソフトウェア
名称バージョン分類
REFMAC5精密化
SCALEPACKデータスケーリング
CNS精密化
DENZOデータ削減
CNS位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.35→18.35 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.001 / SU ML: 0.041 / Isotropic thermal model: anisotropic / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.047 / ESU R Free: 0.043 / 立体化学のターゲット値: Engh & Huber / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.1639 5552 5 %RANDOM
Rwork0.14949 ---
obs0.15023 104434 93.64 %-
all-109986 --
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 9.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.18 Å2
精密化ステップサイクル: LAST / 解像度: 1.35→18.35 Å
タンパク質核酸リガンド溶媒全体
原子数3119 0 67 387 3573
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213342
X-RAY DIFFRACTIONr_bond_other_d0.0010.022916
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9594548
X-RAY DIFFRACTIONr_angle_other_deg1.1936797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6383378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.93415606
X-RAY DIFFRACTIONr_chiral_restr0.1660.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023618
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02692
X-RAY DIFFRACTIONr_nbd_refined0.2180.3582
X-RAY DIFFRACTIONr_nbd_other0.2010.32755
X-RAY DIFFRACTIONr_nbtor_other0.5660.54
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.5370
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.352
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.522
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1280.51
X-RAY DIFFRACTIONr_mcbond_it1.1241.51916
X-RAY DIFFRACTIONr_mcangle_it1.69123118
X-RAY DIFFRACTIONr_scbond_it2.75531426
X-RAY DIFFRACTIONr_scangle_it4.0434.51430
X-RAY DIFFRACTIONr_rigid_bond_restr1.16323342
X-RAY DIFFRACTIONr_sphericity_free20.989387
X-RAY DIFFRACTIONr_sphericity_bonded3.5873249
LS精密化 シェル解像度: 1.35→1.385 Å / Total num. of bins used: 20 /
Rfactor反射数
Rfree0.282 357
Rwork0.261 6364
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)
111.35920.96833.56831.29990.38972.0030.02670.191-0.3310.00110.0149-0.08010.07770.0987-0.04150.06550.0070.0110.04290.00780.015748.367147.6778-0.57
215.2112.32483.12923.65281.35492.79380.1625-0.2456-0.14020.2304-0.07180.5526-0.0233-0.3899-0.09070.0958-0.00860.01210.14050.00380.147725.609446.8227-3.3321
313.1154-3.9882.89421.5264-1.39831.6037-0.0185-0.1284-0.10690.04120.00070.066-0.0083-0.08290.01790.063-0.00280.01170.0314-0.01070.010942.95548.06032.7054
412.137-2.3825-5.8672.7053-0.89696.8109-0.238-0.1885-0.38-0.00760.0235-0.19330.32410.14140.21450.0756-0.00620.0030.0304-0.00330.02849.728946.14437.3466
519.45941.11316.53332.99153.03337.7910.1616-0.4183-0.590.34460.04730.20170.3621-0.3102-0.20890.08040.00420.00890.07820.00550.030837.316449.11536.6088
68.4306-0.48165.34462.0936-0.4067.10990.0094-0.62650.04180.13230.03320.30890.0692-0.816-0.04260.1088-0.0040.02940.13540.00180.065537.788450.625411.2805
72.5238-0.29982.01415.4545-0.50425.8905-0.0118-0.07560.11780.09520.0683-0.1948-0.2410.2202-0.05650.0828-0.00250.00160.0797-0.00980.048849.80553.915815.5799
82.34580.46133.68920.75071.754610.0158-0.1-0.09460.08-0.0316-0.03840.1133-0.226-0.32240.13840.08880.00820.00610.04180.00990.064535.899556.7535-2.7568
95.3931-0.09053.31284.1721-5.232616.65530.07820.1817-0.1463-0.27660.33040.7136-0.0095-1.2758-0.40860.12270.0031-0.05280.1891-0.00990.178126.765545.7639-15.134
1017.6744.40586.36961.88781.52162.594-0.05430.01570.2513-0.0268-0.0748-0.0289-0.07780.0510.12910.0699-0.00470.01240.06470.01370.012248.113849.3361-5.2211
1114.68130.499711.69732.90261.247323.15970.19020.6297-0.2621-0.16660.0394-0.4774-0.02390.4316-0.22970.07260.00060.02180.11280.02090.115663.666252.9449-2.347
1215.94858.10434.87044.34472.83153.42850.00960.0393-0.3056-0.12780.0043-0.1337-0.01820.181-0.01390.08620.00170.00370.06020.01940.006445.644549.1877-10.7195
135.89142.1962-2.65732.6364-2.64974.7154-0.00050.1639-0.329-0.2783-0.03450.00160.2708-0.0570.03490.09920.0036-0.01060.0806-0.01080.013641.220546.2189-15.7451
1424.763214.79635.584314.552512.909913.01210.0888-0.7249-0.2348-0.24580.0856-0.3725-0.3021-0.0536-0.17440.08470.00430.00420.11580.02380.012250.57452.8323-13.8448
1513.69353.448412.369910.63774.240121.0918-0.29050.03020.2273-0.42740.1842-0.382-0.41580.84780.10630.1096-0.03250.0290.1723-0.00380.061954.596255.851-15.6014
162.94663.85053.94928.592.0695.33410.01010.23-0.3828-0.02270.0711-0.01660.1490.1606-0.08120.1230.00990.01350.0721-0.00990.018245.266548.8651-21.2958
174.33451.88491.01069.30373.47576.2402-0.08410.14560.1697-0.30870.03320.0224-0.22410.07680.05090.08750.02210.00580.06420.01290.026442.243557.7668-20.906
187.0821-1.30391.37065.5865-3.556510.60770.00730.50090.0482-0.2504-0.2608-0.3111-0.01410.50470.25350.08570.00230.00790.09530.01860.070651.841161.0634-8.4763
194.3789-0.10780.29492.4681-2.92978.5-0.0234-0.03120.29340.0955-0.045-0.0048-0.29190.15630.06840.0548-0.0088-0.00760.0385-0.00860.071456.272156.54766.8126
205.9426-0.06031.326817.79155.227319.2064-0.1145-0.1265-0.17990.2764-0.02740.22290.166-0.17190.14190.06490.01120.00270.0775-0.0010.102757.665446.873113.9445
21-0.1701-4.02771.694934.08614.9199-0.167-0.0883-0.1293-0.03780.26850.0979-0.57460.01950.0233-0.00950.0941-0.0060.01930.1241-0.01130.146360.749136.281413.2303
2216.624122.11129.509337.016316.19126.60740.1386-0.1947-0.34190.4508-0.2748-0.21210.2916-0.19920.13620.1562-0.00040.01980.08980.04350.173855.182114.3188.3217
2361.2126-2.0544-10.921217.7263.1588.7901-0.09462.7663-1.9406-1.967-0.0145-0.41450.0212-0.94510.10920.4498-0.06470.09380.2913-0.09960.266551.56974.6139-2.5922
242.03241.7504-0.33518.62228.56734.7897-0.07480.0694-0.28760.17350.0363-0.17440.2417-0.00090.03850.09730.01230.00950.06720.02520.133854.915317.73995.8145
255.377-0.6584-2.40835.86853.66464.64180.23470.16120.2611-0.33430.0982-0.2597-0.3840.1076-0.33290.0674-0.00440.03790.06520.00670.123758.728633.96046.286
266.67872.93430.200617.47150.42271.3965-0.16960.1668-0.2586-0.79770.1625-0.77810.00630.29950.00710.1633-0.00780.06820.134-0.03260.200863.391418.8837-0.3456
274.45480.94690.58215.01551.31944.56650.08140.6448-0.5518-0.56720.1508-0.64480.34930.475-0.23220.16860.0530.04880.1744-0.05050.208356.08325.26640.3784
281.6443-0.4014-0.348611.40743.49392.1052-0.07020.1867-0.3557-0.378-0.0001-0.28610.1437-0.01820.07030.13380.01420.04780.0745-0.01290.154955.505417.93950.9912
2919.105111.83084.057938.43272.59838.0519-0.10470.0443-2.09010.44810.0179-1.04630.81110.19450.08680.27910.05780.08620.1205-0.00810.591660.72384.22191.8697
3024.7543-4.4749-7.93646.2389-35.946253.544-0.1929-0.2593-1.8828-1.0329-0.5464-1.92622.40621.29370.73930.28780.12430.02310.1457-0.04670.667267.10157.37082.7442
312.88685.0264-0.099722.17763.1182-0.5214-0.15840.028-0.6766-0.4410.0789-0.56280.070.19940.07950.11130.01730.04770.1071-0.01040.260465.155420.46412.9404
3213.7686-3.87351.502-0.2065-0.30884.4745-0.0129-0.4591-0.03810.20940.1809-0.2337-0.05720.2649-0.1680.0859-0.02330.02730.1488-0.03570.159267.620630.22298.8118
3365.126162.03919.622681.1282-0.45859.05871.0435-0.7136-2.52230.879-0.5073-2.24680.8089-0.5429-0.53620.2108-0.001-0.0410.19320.06490.34564.214.81728.1216
3421.5112-9.377119.992916.4632-11.310353.48790.22271.44140.5015-0.7348-0.7269-0.1437-0.59540.62090.50420.24890.0008-0.02720.1404-0.00120.128437.467730.9399-8.3001
355.09070.61634.57632.67460.78457.55470.06640.0208-0.2117-0.16050.05230.10740.12370.0367-0.11870.07410.0090.00470.03090.00680.070942.767225.9586.5452
364.21973.072-3.96185.5257-4.82715.07730.2514-0.7805-0.53830.5487-0.465-0.58050.04250.56070.21360.1642-0.0443-0.04340.20350.07220.132648.421724.442920.5049
372.5916-0.14963.11681.8127-3.525512.91210.079-0.0632-0.003-0.0302-0.02890.09450.2396-0.0325-0.05020.06350.00170.0070.0183-0.00390.062942.43230.30248.1633
384.55471.261-2.02744.7467-1.37718.62430.18980.20670.0578-0.12730.10460.4477-0.128-0.3463-0.29440.1184-0.0167-0.02510.04630.01580.098334.600735.3915-3.424
392.04042.9818-2.484514.828-16.670519.3622-0.0407-0.12260.1521-0.20750.16530.3460.0901-0.2776-0.12460.09560.00360.01720.0598-0.01210.113532.969928.183811.3986
409.459913.2048-6.135626.828-10.36474.32090.9392-0.43041.23411.554-0.40181.6965-0.62640.0039-0.53740.1874-0.02730.10340.1179-0.03920.200931.984730.89116.3435
4110.18124.4925-8.85822.4137-2.944712.16790.05710.11680.34810.10360.0620.777-0.3401-0.2762-0.11910.08910.00550.00130.0333-0.0060.090238.898538.46378.6205
421.29490.67921.1772.2939-2.022420.3214-0.05740.07310.017-0.1272-0.0847-0.0993-0.16360.60630.1420.0865-0.0098-0.00090.06030.00680.089544.072639.7013-4.9392
431.72130.38470.63524.1949-4.21839.74270.016-0.2333-0.01270.2605-0.06550.0688-0.32620.05160.04940.0461-0.00460.01390.0465-0.0020.081741.352933.150510.3892
447.56342.36785.62254.225-1.89638.76110.4184-0.5-0.53060.31-0.2419-0.29420.27920.0271-0.17650.1222-0.0299-0.00590.1350.03320.126338.799919.312719.8477
455.1884-6.95019.7716.4301-15.786823.93890.0047-0.4313-0.2101-0.36390.62080.86980.3089-1.1781-0.62540.0902-0.0198-0.00570.08980.02020.13331.015227.074.9477
46-0.19413.817-4.574418.3077-18.429425.0732-0.30360.2973-0.1314-1.02620.55540.54551.0661-0.4376-0.25180.2184-0.0718-0.07090.120.00730.17729.471726.7561-3.2265
477.4040.37.54482.1293-3.105513.95290.0943-0.0112-0.1413-0.5649-0.01720.13890.0530.007-0.07710.1525-0.006-0.00670.0314-0.01060.102935.121620.7356.3751
4815.4866-8.5976-5.97288.50056.0199-0.097-0.0878-0.2854-0.59110.0839-0.03690.08180.32570.4820.12470.1584-0.00210.01060.09050.03160.208444.610718.047211.8423
494.2572-0.44485.07730.3663-0.43288.04180.0499-0.00050.0216-0.0822-0.04120.0302-0.0026-0.1933-0.00870.08850.01260.0020.0691-0.00350.074941.870358.0917-6.9533
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 121 - 12
2X-RAY DIFFRACTION2AA13 - 2113 - 21
3X-RAY DIFFRACTION3AA22 - 2822 - 28
4X-RAY DIFFRACTION4AA28 - 3428 - 34
5X-RAY DIFFRACTION5AA34 - 3734 - 37
6X-RAY DIFFRACTION6AA37 - 5037 - 50
7X-RAY DIFFRACTION7AA50 - 5650 - 56
8X-RAY DIFFRACTION8AA57 - 8557 - 85
9X-RAY DIFFRACTION9AA85 - 9485 - 94
10X-RAY DIFFRACTION10AA94 - 10394 - 103
11X-RAY DIFFRACTION11AA103 - 111103 - 111
12X-RAY DIFFRACTION12AA111 - 118111 - 118
13X-RAY DIFFRACTION13AA118 - 124118 - 124
14X-RAY DIFFRACTION14AA124 - 126124 - 126
15X-RAY DIFFRACTION15AA126 - 133126 - 133
16X-RAY DIFFRACTION16AA133 - 137133 - 137
17X-RAY DIFFRACTION17AA138 - 151138 - 151
18X-RAY DIFFRACTION18AA152 - 162152 - 162
19X-RAY DIFFRACTION19AA163 - 175163 - 175
20X-RAY DIFFRACTION20AA176 - 179176 - 179
21X-RAY DIFFRACTION21AA179 - 186179 - 186
22X-RAY DIFFRACTION22AA186 - 193186 - 193
23X-RAY DIFFRACTION23AA193 - 198193 - 198
24X-RAY DIFFRACTION24AA198 - 206198 - 206
25X-RAY DIFFRACTION25AA206 - 214206 - 214
26X-RAY DIFFRACTION26AA214 - 219214 - 219
27X-RAY DIFFRACTION27AA219 - 241219 - 241
28X-RAY DIFFRACTION28AA241 - 250241 - 250
29X-RAY DIFFRACTION29AA250 - 254250 - 254
30X-RAY DIFFRACTION30AA254 - 256254 - 256
31X-RAY DIFFRACTION31AA257 - 262257 - 262
32X-RAY DIFFRACTION32AA262 - 270262 - 270
33X-RAY DIFFRACTION33AA270 - 274270 - 274
34X-RAY DIFFRACTION34BB1 - 61 - 6
35X-RAY DIFFRACTION35BB6 - 116 - 11
36X-RAY DIFFRACTION36BB11 - 2111 - 21
37X-RAY DIFFRACTION37BB21 - 2821 - 28
38X-RAY DIFFRACTION38BB28 - 3628 - 36
39X-RAY DIFFRACTION39BB36 - 4136 - 41
40X-RAY DIFFRACTION40BB41 - 5041 - 50
41X-RAY DIFFRACTION41BB50 - 5250 - 52
42X-RAY DIFFRACTION42BB52 - 6252 - 62
43X-RAY DIFFRACTION43BB62 - 7062 - 70
44X-RAY DIFFRACTION44BB70 - 7870 - 78
45X-RAY DIFFRACTION45BB78 - 8378 - 83
46X-RAY DIFFRACTION46BB83 - 9183 - 91
47X-RAY DIFFRACTION47BB91 - 9491 - 94
48X-RAY DIFFRACTION48BB94 - 9994 - 99
49X-RAY DIFFRACTION49PC1 - 81 - 8
ソフトウェア
*PLUS
バージョン: 5 / 分類: refinement
精密化
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.164 / Rfactor Rwork: 0.149
溶媒の処理
*PLUS
原子変位パラメータ
*PLUS
拘束条件
*PLUS
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.19
LS精密化 シェル
*PLUS
最低解像度: 1.39 Å

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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