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- PDB-5ijc: The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex -

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基本情報

登録情報
データベース: PDB / ID: 5ijc
タイトルThe crystal structure of mouse TLR4/MD-2/neoseptin-3 complex
要素
  • Lymphocyte antigen 96
  • Toll-like receptor 4,Variable lymphocyte receptor B
キーワードIMMUNE SYSTEM / Immune response / protein complex / small molecule agonist
機能・相同性
機能・相同性情報


MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / Heme signaling / nitric oxide production involved in inflammatory response / Regulation of TLR by endogenous ligand / MHC class II biosynthetic process / TRIF-mediated programmed cell death / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex ...MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / Heme signaling / nitric oxide production involved in inflammatory response / Regulation of TLR by endogenous ligand / MHC class II biosynthetic process / TRIF-mediated programmed cell death / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of matrix metallopeptidase secretion / Toll-like receptor 4 binding / IKK complex recruitment mediated by RIP1 / mast cell activation / detection of lipopolysaccharide / positive regulation of lymphocyte proliferation / regulation of dendritic cell cytokine production / lipopolysaccharide receptor complex / negative regulation of interleukin-23 production / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / lymphocyte proliferation / B cell proliferation involved in immune response / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / activation of NF-kappaB-inducing kinase activity / positive regulation of stress-activated MAPK cascade / intestinal epithelial structure maintenance / positive regulation of interleukin-13 production / positive regulation of interleukin-1 production / macrophage activation / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / positive regulation of platelet activation / positive regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of interleukin-17 production / positive regulation of cytokine production involved in inflammatory response / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / positive regulation of macrophage cytokine production / positive regulation of smooth muscle cell migration / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of reactive oxygen species biosynthetic process / cellular response to lipoteichoic acid / negative regulation of type II interferon production / negative regulation of interleukin-6 production / B cell proliferation / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / phagocytosis / phagocytic cup / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / cellular response to platelet-derived growth factor stimulus / ruffle / positive regulation of B cell proliferation / ERK1 and ERK2 cascade / neurogenesis / nitric oxide biosynthetic process / positive regulation of interleukin-12 production / positive regulation of smooth muscle cell proliferation / activation of innate immune response / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / response to bacterium / lipopolysaccharide binding / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of type II interferon production / cellular response to amyloid-beta / positive regulation of inflammatory response / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cellular response to lipopolysaccharide / regulation of inflammatory response / response to lipopolysaccharide
類似検索 - 分子機能
Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / : / Leucine rich repeat N-terminal domain ...Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / TIR domain profile. / Alpha-Beta Horseshoe / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
neoseptin 3 / Variable lymphocyte receptor B / Lymphocyte antigen 96 / Toll-like receptor 4
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Eptatretus burgeri (ヌタウナギ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.57 Å
データ登録者Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. ...Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2016
タイトル: TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS.
著者: Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M.M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K.W. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B.
履歴
登録2016年3月1日登録サイト: RCSB / 処理サイト: RCSB
置き換え2016年4月27日ID: 5HG4
改定 1.02016年4月27日Provider: repository / タイプ: Initial release
改定 1.12016年5月4日Group: Database references
改定 2.02020年7月1日Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / citation / computing / database_PDB_caveat / diffrn / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / pdbx_version / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _cell.angle_beta / _cell.volume ..._cell.angle_beta / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity.src_method / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_low / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_netI_over_av_sigmaI / _reflns.pdbx_number_measured_all / _struct.pdbx_CASP_flag / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands / _symmetry.space_group_name_Hall
改定 3.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 3.12023年9月27日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 3.22024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Toll-like receptor 4,Variable lymphocyte receptor B
C: Lymphocyte antigen 96
B: Toll-like receptor 4,Variable lymphocyte receptor B
D: Lymphocyte antigen 96
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)193,27724
ポリマ－186,8234
非ポリマー6,45420
水3,837213
1
A: Toll-like receptor 4,Variable lymphocyte receptor B
D: Lymphocyte antigen 96
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,53712
ポリマ－93,4122
非ポリマー3,12510
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint20 kcal/mol
Surface area33330 Å2
手法PISA
2
C: Lymphocyte antigen 96
B: Toll-like receptor 4,Variable lymphocyte receptor B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,74012
ポリマ－93,4122
非ポリマー3,32810
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint19 kcal/mol
Surface area33790 Å2
手法PISA
単位格子
Length a, b, c (Å)70.752, 148.559, 131.720
Angle α, β, γ (deg.)90.000, 98.304, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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要素

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タンパク質 , 2種, 4分子 ABCD

#1: タンパク質 Toll-like receptor 4,Variable lymphocyte receptor B


分子量: 71649.758 Da / 分子数: 2
断片: TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)
由来タイプ: 組換発現
由来: (組換発現) Mus musculus (ハツカネズミ), (組換発現) Eptatretus burgeri (ヌタウナギ)
遺伝子: Tlr4, Lps, VLRB
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9QUK6, UniProt: Q4G1L2, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: タンパク質 Lymphocyte antigen 96 / Ly-96 / ESOP-1 / Protein MD-2


分子量: 21761.857 Da / 分子数: 2 / 断片: UNP residues 19-160 / 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: Ly96, Esop1, Md2
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9JHF9

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糖 , 2種, 16分子

#3: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 5 / 由来タイプ: 天然
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 11 / 由来タイプ: 天然 / 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 , 2種, 217分子

#5: 化合物
ChemComp-V2A / neoseptin 3 / tert-butyl (2S)-2-({4-amino-3-[2-(4-hydroxyphenyl)ethyl]benzene-1-carbonyl}amino)-4-phenylbutanoate


分子量: 474.591 Da / 分子数: 4 / 由来タイプ: 天然 / 式: C29H34N2O4 / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 213 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
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: 3.67 Å3/Da / 溶媒含有率: 66.45 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: 0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 12% PEG8000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.97918 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2015年6月17日
放射モノクロメーター: double crystal Si(111) / 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: 0.97918 Å / 相対比: 1
反射解像度: 2.55→50 Å / Num. obs: 84084 / % possible obs: 99.6 % / 冗長度: 3.8 % / Biso Wilson estimate: 37.67 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.063 / Rrim(I) all: 0.116 / Χ2: 0.88 / Net I/σ(I): 7.2 / Num. measured all: 315421
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.55-2.593.30.95940860.5580.6060.7197.5
2.59-2.643.40.85841600.7130.5340.73698.7
2.64-2.693.60.77541790.6650.4770.7899.50.914
2.69-2.753.70.62742000.7350.380.78499.90.736
2.75-2.813.80.56942170.8020.340.80599.90.665
2.81-2.873.80.46541710.850.2780.78999.90.544
2.87-2.943.90.38942020.8840.2320.83499.80.455
2.94-3.023.90.33142530.9140.1970.84699.90.386
3.02-3.113.80.25141840.9510.150.8711000.293
3.11-3.213.90.20541830.960.1220.95799.90.239
3.21-3.333.90.16742390.9730.0990.9899.90.194
3.33-3.463.90.13542150.9770.0811.06999.90.158
3.46-3.623.80.11342140.980.0681.10999.90.132
3.62-3.813.80.09441690.9850.0561.10599.90.11
3.81-4.053.80.08142450.9870.0491.04199.90.095
4.05-4.363.80.07442060.9890.0450.96799.80.087
4.36-4.83.80.06942330.9890.0420.90299.90.081
4.8-5.493.80.06742100.9880.0410.83499.80.079
5.49-6.923.70.06442630.9860.0390.73399.80.075
6.92-503.70.05642550.9910.0350.65898.60.066

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
PHENIX1.15.2_3472精密化
HKL-3000データ削減
HKL-3000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: PDB entry 5IJB

5ijb


解像度: 2.57→42.36 Å / SU ML: 0.2922 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 26.8528
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.234 2000 2.74 %RANDOM
Rwork0.1934 71117 --
obs0.1946 73117 85.33 %-
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
原子変位パラメータBiso mean: 44.48 Å2
精密化ステップサイクル: LAST / 解像度: 2.57→42.36 Å
タンパク質核酸リガンド溶媒全体
原子数11617 0 434 215 12266
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002512337
X-RAY DIFFRACTIONf_angle_d0.594616712
X-RAY DIFFRACTIONf_chiral_restr0.05561939
X-RAY DIFFRACTIONf_plane_restr0.00332102
X-RAY DIFFRACTIONf_dihedral_angle_d13.27737335
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.630.3616600.28762139X-RAY DIFFRACTION36.01
2.63-2.70.3327850.26733030X-RAY DIFFRACTION50.98
2.7-2.780.25811050.24123705X-RAY DIFFRACTION62.86
2.78-2.870.29951220.24084369X-RAY DIFFRACTION73.27
2.87-2.980.29021380.23874884X-RAY DIFFRACTION82.21
2.98-3.10.31791530.24655475X-RAY DIFFRACTION92.28
3.1-3.240.30791660.245893X-RAY DIFFRACTION99.04
3.24-3.410.24461670.2195907X-RAY DIFFRACTION99.82
3.41-3.620.26671660.18965922X-RAY DIFFRACTION99.89
3.62-3.90.19911680.17235961X-RAY DIFFRACTION99.82
3.9-4.290.17081670.15085927X-RAY DIFFRACTION99.82
4.29-4.910.19071670.13985954X-RAY DIFFRACTION99.8
4.91-6.190.2011680.17495980X-RAY DIFFRACTION99.77
6.19-42.360.22921680.20565971X-RAY DIFFRACTION98.49
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)
12.35903705888-0.392321694343-1.374317312260.977406751470.7087005238571.995574229720.0340596216012-0.416743486313-0.8186794380070.2667851000040.0285255938125-0.3134388054070.6163664851920.210645021733-0.01791515727681.322641444990.2319313428-0.3533111122010.6668168891920.0367987894420.71378471334731.399563852-29.4716139379.1784971339
21.08620471340.330340833958-0.1883566383991.02440113531-0.2386330112981.129377675810.216839412502-0.615743644885-0.04517464659150.460135863189-0.0980470717055-0.4622159878330.537617792910.416494198768-0.1683709928420.6668936840220.123476125803-0.3034692369480.762021472896-0.2800398991980.40631393579734.2029142492-7.1000383039882.7818198629
30.823103134185-0.00568046587377-0.2536883950630.7031424306490.4299362713330.8534846027180.0125502689584-0.1565139625560.1576466645140.05981753556010.04527108040590.0114897398478-0.07936785076710.09650986922360.162927256220.5113996249070.0123148078073-0.001918578811020.404425514689-0.3634411968830.41268862904427.349840278610.57827641272.0979418398
40.2557421485630.7111960507850.4287074428972.773562457990.5223094920381.292986517190.146948322599-0.197789587620.488534970159-0.1034048798720.05214100942810.17547065176-0.184096693364-0.006445131895260.04836736025750.3514448182420.0178785069695-0.02119861073770.346531573853-0.3264034401560.4830060238223.172585780212.673908074264.451234799
50.962517776767-0.0368948112577-0.23129446640.8695750624040.4388098942161.505984035550.0410128550556-0.0181562844660.480311169232-0.0802354801258-0.0205369024487-0.0730094673372-0.309872525263-0.1694423606720.009883073301550.158980996028-0.01817580286350.01095709539150.168197533239-0.01263744648430.28284771240324.74456206061.6608271406341.7575006187
60.9763962869660.2226299493810.5135743804122.30110712094-0.06124930996861.525757761670.1573960679350.19012409949-0.0325414654733-0.266483913683-0.085784530437-0.08322976888130.0607294410140.0606390365557-0.03760650666990.0835877758593-0.005174767090080.04738335662020.118095389948-0.004091798583430.13023260175831.6440387184-22.08615290529.0267103273
71.460582960780.761311888816-0.3191214117961.73539558783-0.1196146296441.19736996184-0.0929231314608-0.150998957722-0.5947617173620.03900739042260.17136373033-0.07806040975820.3143348601350.0577648313967-0.007437305835570.1931643486110.002417511936960.02478358863590.1653828613990.08954324520560.30013795254436.0894254942-42.113199180337.9913212003
87.21457402332-5.705046819434.569685374434.71310400406-3.512746271122.94490976807-0.0665841874123-0.1661878134280.08051777009140.3716297216910.1970574746180.05273453578640.0876463669047-0.153415617882-0.06843371359510.555028945407-0.162251849230.1928146729460.807992905483-0.1495033859380.45720785233-6.38172903131-15.978201090271.1581846648
92.14650856027-0.5001503704231.7661185290.716951862507-0.3322385752571.580797175210.2050799406140.0716866625369-0.210339259956-0.00770606212934-0.1282913927210.02481407361480.694452808314-0.0180637478736-0.05148156599620.817059000974-0.0632782736316-0.105412407480.5321135060610.02517450314810.1931721291554.48870231632-22.980015224871.2416466649
101.81033707374-2.37035861027-0.3596413968295.67495401377-0.8414468372254.33831886174-0.152620117428-0.5432717537810.2930464199280.3100646457060.1126433225410.141508727255-0.233798075396-0.716700356060.04746105022070.310907251959-0.05142597560150.05267695971470.5668078432-0.05737630827240.292931106412-4.1837412307-9.1972165251666.8389013887
116.60112979618-3.651865803620.8592621305712.65627302793-0.4757940659320.116480902367-0.143936359434-0.438396857270.1135449671290.5468842445570.2207252788490.106867593406-0.0715614306267-0.285631804538-0.08395315507150.3754396900110.04528446597130.0204144798230.410298089787-0.1186755708470.2448747768914.60936926838-7.8784943503970.4276428607
123.599959978991.607073253912.318099902391.246731233671.406466831041.822303918310.133201812186-0.142428572055-0.0693464222080.1771983689580.00354791452343-0.01222426283780.3157935963840.0448915946091-0.0483964533540.6331714896620.000975616923662-0.1266217513840.264486884881-0.07533441768390.17831701441413.9648489732-17.98008930963.5130230156
134.49212962664.122795929192.285362168993.783509501862.09706171321.162214677070.1691727626-0.295893913882-0.1792021487380.102673953069-0.203819462083-0.05318905883340.328186372881-0.2377564304240.005397890560960.481703321726-0.0427565800177-0.07413250348160.3004749420970.007870180211390.1791768731365.07928222786-22.346840525254.2046944061
143.29583766731-1.196930884150.004334599776063.405246503892.082844544753.904840897520.1850551107590.05075588481450.109542351114-0.1998564684520.219414089558-0.203990237882-0.1087062448730.095056604929-0.198661904980.478245458850.107552517919-0.1205616264850.357706955806-0.1572627914040.35564530520418.8683926135-5.770530328861.0689859959
153.31371983496-0.03289276271381.988328200271.164389475180.09027029386532.151273577750.0929144390149-0.289911316795-0.07317040356690.4551828148290.0162301016371-0.06213335038650.466655050601-0.0803106739043-0.1151408553360.4074031521290.00757569860013-0.01231453272920.235199922702-0.03948804333530.1474635378227.94008398902-13.40154478764.5134303298
160.296432720917-0.1672704356990.3837141972422.54074448033-0.3571479592222.952844473270.105650317061-0.480087682104-0.3251039146220.4946208640520.1563820228690.04818413962050.320123497597-0.169813199859-0.2355843166370.528947553315-0.0383526028038-0.01733231224980.298480653760.01191512894210.1597026570182.62310052879-20.79386260965.565469616
173.545370019521.07223634059-2.270986080351.81798398825-1.160583354842.22896946537-0.02175558470720.502188339171-0.536242035568-0.372585147626-0.1850333855940.146914358440.653432044027-0.165935732610.1461177232691.25553258014-0.0908178335888-0.2809379168520.520200841048-0.0009699035278230.580946611181-3.84585296194-20.0384502693-13.0970912858
180.947969580692-0.0266278420756-0.05873769118881.457831287390.342565360011.709167060460.1074311900030.3145698796370.15305679403-0.455195947225-0.04470957750590.5220803103610.0502341855247-0.438769740104-0.0892605201570.60668393106-0.0522174641354-0.2234990306230.4549674646080.2329117968190.472357054273-8.272960634965.21687459496-8.06016801047
191.76703759481-1.093344433410.02212836364363.3560690164-0.2121783202771.584017192770.1165380185980.08463318610280.657048215440.1367910315530.0779825661621-0.0149212319433-0.562923437165-0.0842445249667-0.1716724807250.5998640739550.0175883941874-0.04133808581120.2619536793420.1510468776450.506302683484-0.3835861665417.915220578412.1786322303
201.302642315440.0772388451721-0.2649731288691.3317559186-0.5499703620881.904327612120.0249544030005-0.06517202577330.3363589928620.117206926386-0.1261809133990.10538397859-0.386325231180.04766484948310.07094412115570.1694909238340.02021821707730.00470471941640.186056122411-0.01054037341060.24789350617-0.2861708666331.4105393310531.3074819889
210.1425193773630.2278178296680.309542679271.94092837667-0.08968591883761.274377048640.07196730761080.00383916398694-0.05563296767190.0601241103907-0.05071146549270.01998744372450.157796103150.0142075879571-0.03051135923560.06915155075450.01019697058340.01699329608220.159182131851-0.007161709020770.192593591462-3.63562022647-25.555172929937.2838440456
220.763704279189-0.640447821783-0.5782154887351.69972679380.1860450727750.947682988285-0.02185234210.315201849582-0.303185554915-0.2252177968040.0736772500698-0.1111636788470.4166435308510.0416549173444-0.04707247653670.3213492032740.0150713243877-0.008077729108060.258353797219-0.1391175785030.295094834385-5.47263750744-43.115085468923.023649558
231.738841359751.902298628792.262216602892.878949924413.051301256653.3591398099-0.04572153616180.223771732119-0.0286991058116-0.300522297724-0.143948716993-0.0803202475425-0.145854414032-0.1659853111980.07216777654030.544475665252-0.0372854209650.2321637285190.8666065078020.1073672181710.39691605979232.3628125696-3.90442435953-1.1808449753
241.623774983750.146194455941.466171078540.5741928220680.2795185344321.672650809830.3013749798020.0955562002992-0.19663094269-0.0926592856727-0.283216089651-0.09335085238310.671524451590.0784254396357-0.02575619537390.7400803416770.02803088395480.02058745701170.4548363628720.09944588210420.17083246312922.504719766-11.9650815111-3.18689376082
252.19275041831-0.4685641963761.857181284173.66329505554-0.7421725129386.3380532265-0.04704841441450.404006567330.415537973455-0.06174400271690.0278981571085-0.0784650080678-0.4070517184610.4071656261170.1424713775670.444049928401-0.0531776957293-0.001692355604450.4432871455010.1661492810420.39291486645229.43925759931.201387359864.78410973364
265.062353377692.828890659363.001702334022.132046171691.79961167181.83272166754-0.1253371069610.4419764961610.406453811375-0.4028380657590.10937747635-0.0153798571801-0.2418140541120.135705859650.01383566944330.477580515079-0.03344081721520.03292695323530.3250212505890.1619655818030.34139952166420.43723985392.273622017631.42131465621
271.86125102247-1.131606226761.190101863721.08303922547-0.7281333112820.8690678616770.03677127746730.09987143683330.0591376637768-0.1082581949150.005535401437830.03729451598850.225717254970.09302211906920.08884965675210.5770378468670.0130857458695-0.09356025920430.2165568063720.1185920491030.24329196262512.5715893063-10.46571097355.41342223231
283.08434493251-1.731496757961.447799429132.20362521183-1.002797888370.7429178346620.05630114425650.07201978799350.0973774310331-0.3584623395190.08038484729160.0613772151150.03656817285670.0910926218286-0.07752704382610.4573983259130.0218703164959-0.0355604140810.2951908665680.08872914289840.15526462092115.1121801257-8.7293522778312.3761790861
292.78461076875-0.3723887525831.775029550460.162401995396-0.248591496042.08880800279-0.1154447178560.1515292421690.181246627975-0.3008815746270.1030054858030.109301320955-0.1479587914940.09057945465190.09940680280780.5205907142380.015757439168-0.008032476932180.250177469920.1280818787120.27994638747417.8426942517-0.1615993506945.84084093738
305.642044040191.415960028271.036056658891.388276542380.3139109046150.193415859124-0.0019317873456-0.0352710079268-0.530686367559-0.3408252645090.007369649186090.1002209661640.3936983126380.216702077519-0.04247170085210.4808257763480.02291608926340.02476764488440.2928805479950.04037516174290.22805782757921.1034837393-12.32565807354.14916810399
311.323941874020.277214894528-0.9439022183410.1276192685-0.2443139524450.72835717379-0.282681803511-0.0983401309390.0955409446397-0.182308393777-0.0404695669031-0.02445269776910.3975869195230.0966140377090.3722098186770.325415588443-0.00817457003710.04734911221660.3665754632480.01558469519350.33557829903913.0639692901-10.374773930734.9879478284
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid 206 through 238 )
4X-RAY DIFFRACTION4chain 'A' and (resid 239 through 289 )
5X-RAY DIFFRACTION5chain 'A' and (resid 290 through 437 )
6X-RAY DIFFRACTION6chain 'A' and (resid 438 through 515 )
7X-RAY DIFFRACTION7chain 'A' and (resid 516 through 618 )
8X-RAY DIFFRACTION8chain 'C' and (resid 21 through 29 )
9X-RAY DIFFRACTION9chain 'C' and (resid 30 through 44 )
10X-RAY DIFFRACTION10chain 'C' and (resid 45 through 55 )
11X-RAY DIFFRACTION11chain 'C' and (resid 56 through 66 )
12X-RAY DIFFRACTION12chain 'C' and (resid 67 through 82 )
13X-RAY DIFFRACTION13chain 'C' and (resid 83 through 93 )
14X-RAY DIFFRACTION14chain 'C' and (resid 94 through 102 )
15X-RAY DIFFRACTION15chain 'C' and (resid 103 through 143 )
16X-RAY DIFFRACTION16chain 'C' and (resid 144 through 156 )
17X-RAY DIFFRACTION17chain 'B' and (resid 27 through 59 )
18X-RAY DIFFRACTION18chain 'B' and (resid 60 through 238 )
19X-RAY DIFFRACTION19chain 'B' and (resid 239 through 289 )
20X-RAY DIFFRACTION20chain 'B' and (resid 290 through 437 )
21X-RAY DIFFRACTION21chain 'B' and (resid 438 through 515 )
22X-RAY DIFFRACTION22chain 'B' and (resid 516 through 619 )
23X-RAY DIFFRACTION23chain 'D' and (resid 21 through 29 )
24X-RAY DIFFRACTION24chain 'D' and (resid 30 through 44 )
25X-RAY DIFFRACTION25chain 'D' and (resid 45 through 55 )
26X-RAY DIFFRACTION26chain 'D' and (resid 56 through 66 )
27X-RAY DIFFRACTION27chain 'D' and (resid 67 through 82 )
28X-RAY DIFFRACTION28chain 'D' and (resid 83 through 102 )
29X-RAY DIFFRACTION29chain 'D' and (resid 103 through 128 )
30X-RAY DIFFRACTION30chain 'D' and (resid 129 through 156 )
31X-RAY DIFFRACTION31chain 'A' and resid 709 or chain 'B' and (resid 701 through 702) or chain 'D' and resid 201

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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