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- PDB-4zxb: Structure of the human insulin receptor ectodomain, IRDeltabeta c... -

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基本情報

登録情報
データベース: PDB / ID: 4zxb
タイトルStructure of the human insulin receptor ectodomain, IRDeltabeta construct, in complex with four Fab molecules
要素
  • Fab 83-14 heavy chain
  • Fab 83-14 light chain
  • Fab 83-7 heavy chain
  • Fab 83-7 light chain
  • Insulin receptor
キーワードHORMONE RECEPTOR/IMMUNE SYSTEM / receptor tyrosine kinase extracellular domain antibody fragments / HORMONE RECEPTOR-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


positive regulation of B cell activation / regulation of female gonad development / positive regulation of meiotic cell cycle / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / insulin-like growth factor II binding / positive regulation of developmental growth / early endosome to late endosome transport / male sex determination / positive regulation of type IIa hypersensitivity ...positive regulation of B cell activation / regulation of female gonad development / positive regulation of meiotic cell cycle / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / insulin-like growth factor II binding / positive regulation of developmental growth / early endosome to late endosome transport / male sex determination / positive regulation of type IIa hypersensitivity / insulin receptor complex / insulin-like growth factor I binding / exocrine pancreas development / positive regulation of type I hypersensitivity / positive regulation of protein-containing complex disassembly / antibody-dependent cellular cytotoxicity / dendritic spine maintenance / cargo receptor activity / insulin binding / immunoglobulin complex, circulating / neuronal cell body membrane / adrenal gland development / PTB domain binding / phagocytosis, engulfment / Signaling by Insulin receptor / endosome to lysosome transport / IRS activation / antigen processing and presentation / positive regulation of endocytosis / positive regulation of respiratory burst / amyloid-beta clearance / regulation of embryonic development / immunoglobulin mediated immune response / positive regulation of receptor internalization / regulation of proteolysis / protein kinase activator activity / insulin receptor substrate binding / epidermis development / complement activation, classical pathway / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / transport across blood-brain barrier / heart morphogenesis / antigen binding / activation of protein kinase B activity / positive regulation of phagocytosis / Insulin receptor recycling / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / multivesicular body / positive regulation of MAP kinase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / B cell differentiation / positive regulation of glycolytic process / learning / positive regulation of D-glucose import / response to bacterium / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / caveola / positive regulation of immune response / receptor internalization / memory / cellular response to insulin stimulus / male gonad development / positive regulation of nitric oxide biosynthetic process / late endosome / insulin receptor signaling pathway / glucose homeostasis / amyloid-beta binding / positive regulation of protein phosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein autophosphorylation / protein tyrosine kinase activity / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / endosome membrane
類似検索 - 分子機能
Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / 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. / Alpha-Beta Horseshoe ...Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / 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. / Alpha-Beta Horseshoe / : / 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 / : / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / : / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Kappa light chain / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 2A / Insulin receptor / Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 解像度: 3.3 Å
データ登録者Croll, T. / Smith, B.J. / Margetts, M.B. / Whittaker, J. / Weiss, M.A. / Ward, C.W. / Lawrence, M.C.
資金援助 オーストラリア, 5件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)1005896 オーストラリア
National Health and Medical Research Council (NHMRC, Australia)1058233 オーストラリア
Hazel and Pip Appel Fund オーストラリア
National Health and Medical Research Council (NHMRC, Australia)361646 オーストラリア
Victorian State Government Operational Infrastructure Support Grant オーストラリア
引用ジャーナル: Structure / 年: 2016
タイトル: Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain.
著者: Croll, T.I. / Smith, B.J. / Margetts, M.B. / Whittaker, J. / Weiss, M.A. / Ward, C.W. / Lawrence, M.C.
履歴
登録2015年5月20日登録サイト: RCSB / 処理サイト: RCSB
置き換え2016年2月24日ID: 2DTG, 3LOH
改定 1.02016年2月24日Provider: repository / タイプ: Initial release
改定 1.12016年3月9日Group: Database references
改定 1.22017年9月6日Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
カテゴリ: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.32020年1月8日Group: Author supporting evidence / Data collection / カテゴリ: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
改定 2.02020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.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 / _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20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: Fab 83-7 heavy chain
B: Fab 83-7 light chain
C: Fab 83-14 heavy chain
D: Fab 83-14 light chain
E: Insulin receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)202,01115
ポリマ－197,2175
非ポリマー4,79510
水00
1
A: Fab 83-7 heavy chain
B: Fab 83-7 light chain
C: Fab 83-14 heavy chain
D: Fab 83-14 light chain
E: Insulin receptor
ヘテロ分子

A: Fab 83-7 heavy chain
B: Fab 83-7 light chain
C: Fab 83-14 heavy chain
D: Fab 83-14 light chain
E: Insulin receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)404,02330
ポリマ－394,43410
非ポリマー9,58920
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
単位格子
Length a, b, c (Å)121.870, 321.250, 199.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
対称性点対称性: (シェーンフリース記号: C2 (2回回転対称))

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要素

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タンパク質 , 1種, 1分子 E

#5: タンパク質 Insulin receptor


分子量: 102279.945 Da / 分子数: 1
Mutation: Y144H, V731A, T732G, V733N, A734N, residues 735-753 deleted
由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pEE14 / 細胞株 (発現宿主): Lec8
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: P06213

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抗体 , 4種, 4分子 ABCD

#1: 抗体 Fab 83-7 heavy chain


分子量: 23414.266 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: Original Mab obtained from a mouse hybridoma cell line
由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Mus musculus (ハツカネズミ) / 参照: UniProt: U5LP42
#2: 抗体 Fab 83-7 light chain


分子量: 24385.072 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: The original Mab was obtained from a mouse hybridoma
由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Mus musculus (ハツカネズミ) / 参照: UniProt: P01837
#3: 抗体 Fab 83-14 heavy chain


分子量: 23622.672 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: The original mAb was obtained from a mouse hybridoma
由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Igh-1a / 発現宿主: Mus musculus (ハツカネズミ) / 参照: UniProt: P01865
#4: 抗体 Fab 83-14 light chain


分子量: 23514.807 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: The original mAb was obtained form a mouse hybridoma
由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Igkc, Igk-C / 発現宿主: Mus musculus (ハツカネズミ) / 参照: UniProt: A2P1G9

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糖 , 5種, 10分子

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


タイプ: oligosaccharide / 分子量: 570.542 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1098.016 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
DGlcpNAcb1-2DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-4/a4-b1_a6-f1_b4-c1_c6-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: 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: 2 / 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
#10: 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: 3 / 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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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: 4.95 Å3/Da / 溶媒含有率: 75.15 %
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: 6.5
詳細: Crystals were produced by vapour diffusion using 1 microlitre of the complex (2.6 mg/ml) in 10 mM HEPES (pH 7.5), 0.02% sodium azide and 10% D-trehalose solution and 1 microlitres of well ...詳細: Crystals were produced by vapour diffusion using 1 microlitre of the complex (2.6 mg/ml) in 10 mM HEPES (pH 7.5), 0.02% sodium azide and 10% D-trehalose solution and 1 microlitres of well solution containing 10% PEG 8000, 0.1 M MES (pH 6.5) and 0.1 M MgAc2.

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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: Photon Factory / ビームライン: BL-5A / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2006年6月22日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.3→35 Å / Num. obs: 57953 / % possible obs: 97.9 % / 冗長度: 7 % / Biso Wilson estimate: 90.48 Å2 / Net I/σ(I): 11.39
反射 シェル解像度: 3.3→3.4 Å / 冗長度: 3.6 % / Mean I/σ(I) obs: 0.78 / % possible all: 86.6

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解析

ソフトウェア
名称バージョン分類
BUSTER2.10.2精密化
XDSデータ削減
XSCALEデータスケーリング
BUSTER位相決定
精密化解像度: 3.3→34.46 Å / Cor.coef. Fo:Fc: 0.9258 / Cor.coef. Fo:Fc free: 0.9127 / SU R Cruickshank DPI: 0.978 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.854 / SU Rfree Blow DPI: 0.359 / SU Rfree Cruickshank DPI: 0.37
Rfactor反射数%反射Selection details
Rfree0.2368 2911 5.03 %RANDOM
Rwork0.2054 ---
obs0.207 57926 98.01 %-
原子変位パラメータBiso mean: 134.12 Å2
Baniso -1Baniso -2Baniso -3
1--13.5969 Å20 Å20 Å2
2--16.8154 Å20 Å2
3----3.2185 Å2
Refine analyzeLuzzati coordinate error obs: 0.912 Å
精密化ステップサイクル: LAST / 解像度: 3.3→34.46 Å
タンパク質核酸リガンド溶媒全体
原子数12601 0 317 0 12918
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113273HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3318079HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4561SINUSOIDAL20
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes296HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1888HARMONIC5
X-RAY DIFFRACTIONt_it13273HARMONIC5
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion10.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1804SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14752SEMIHARMONIC4
LS精密化 シェル解像度: 3.3→3.39 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.2253 187 5.08 %
Rwork0.2317 3492 -
all0.2314 3679 -
obs--98.01 %
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)
12.3673-0.36530.28082.51280.92644.4298-0.0918-0.2473-0.17980.30170.2361-0.126-0.86170.0831-0.14430.5568-0.2862-0.1189-0.01430.0293-0.435839.0482120.17438.395
22.57262.2125-0.09755.3161-1.03194.2521-0.1527-0.3018-0.13090.65630.21630.0679-0.3692-0.1664-0.06350.4308-0.3040.05960.06940.0531-0.341531.7307110.87615.1132
35.81860.50610.29644.94120.60058.2918-0.38090.7786-0.1162-0.0643-0.0723-0.4277-0.6040.89280.4532-0.3092-0.10840.11710.25540.0186-0.15589.740775.488434.4809
44.6001-1.94010.88852.3341-0.18046.50670.3116-0.4383-0.4478-0.1637-0.1606-0.552-0.1129-0.2055-0.1511-0.34510.1209-0.0444-0.1231-0.0645-0.0409-22.336473.634442.0641
50.1532-1.86620.39098.22550.29012.62910.28740.40110.1506-0.9266-0.3907-0.6432-0.17740.03240.10330.45430.29110.0039-0.2286-0.0276-0.3066-38.2847122.63234.6693
65.1623-4.2455-3.543401.37011.00480.00440.2138-0.09580.109-0.1712-0.2463-0.12020.13640.16680.23080.26490.18880.231-0.1165-0.3447-24.383109.83952.9279
75.0274-0.8554-0.23357.43230.76991.99060.20030.1802-0.3207-0.6632-0.3563-0.05480.26290.37610.15610.58270.265-0.2514-0.25260.0218-0.4138-49.3398159.98836.749
81.71410.5916-1.58933.6610.12155.21150.3917-0.2938-0.23230.3628-0.3645-0.5726-0.15630.1441-0.0272-0.0282-0.22650.0297-0.03420.0214-0.079243.0115116.431-9.7451
91.9931-1.80930.16476.9263-1.89995.43080.46930.08090.39320.5535-0.13990.2656-0.7851-0.8693-0.3294-0.0306-0.13190.2392-0.0017-0.0363-0.166224.4946126.699-6.9001
103.43641.6755-0.96945.1925-1.3142.72760.1946-0.24540.12210.0467-0.08050.4966-0.68010.3843-0.11410.323-0.11380.304-0.09080.0089-0.272649.5995139.179-29.0461
116.1173-0.636-4.61021.4727-0.38215.11050.35510.57240.1421-0.24460.080.5383-0.1018-0.571-0.43510.37770.04710.2276-0.2810.0887-0.100437.8926143.646-39.5123
123.04770.6931-0.79384.46430.98261.6356-0.0375-0.82440.24390.2951-0.53291.0615-0.6162-0.89640.5704-0.41660.3040.14170.5208-0.2674-0.0826-49.727777.080339.3958
1310.35483.56612.1120.76345.11213.7571-0.0750.2787-0.27510.27180.06840.15070.063-0.35620.0066-0.6080.28440.04950.608-0.24170.5805-74.685859.738224.9776
145.00961.39362.54136.02514.17386.76640.01670.4848-0.1526-0.5792-0.14570.3425-0.5303-0.55310.129-0.31060.18580.13430.236-0.0694-0.1355-38.163666.173724.0044
1511.70.22082.91070.9430.16149.4792-0.11560.7288-0.0349-0.662-0.09440.4477-0.0845-0.63170.21-0.6080.304-0.17410.608-0.27220.0653-67.090258.88839.9081
160.0105-0.1581-0.108800.40450.2055-0.0008-0.00150.01150.0028-0.01010.00340.0050.0130.0109-0.0872-0.1831-0.03150.1682-0.21020.049748.840798.316345.4003
170-0.46050.43530.1488-0.02380.45570.0069-0.0438-0.00810.0028-0.0507-0.0120.01350.01040.04380.1675-0.05790.0750.1433-0.0445-0.138156.1411104.11124.7759
1802.20280.27240.0683-2.21970.1148-0.0050.0279-0.05890.0456-0.01450.0071-0.1061-0.02890.01950.3317-0.09710.0875-0.06580.1656-0.165425.1793124.52222.7587
190.0331-0.19610.1330.07050.214100.0049-0.0213-0.00730.0116-0.039-0.01540.0420.02110.03410.1061-0.1002-0.0484-0.0594-0.13070.011947.2529128.54324.9909
200.176-0.2187-0.23130.1712-0.53570.1776-0.0030.014-0.0177-0.05580.0324-0.01970.04740.0515-0.02940.0977-0.20030.05480.00390.19170.023543.7815103.73310.161
210.1375-0.1776-0.71990.0595-1.113200.0082-0.0008-0.00830.07290.0075-0.02360.07550.0454-0.0157-0.33140.04140.30290.1715-0.07470.187727.195656.421832.2473
220.1007-0.19180.10570.1958-0.05220.39350.0031-0.0019-0.01040.0097-0.01160.01410.022-0.02140.00850.0339-0.186-0.0730.07340.09480.03367.887470.944516.8348
230.1669-0.2181-0.40850-0.04320.07230.00530.0046-0.01960.0198-0.0018-0.0073-0.0024-0.0215-0.0035-0.06410.18220.17450.21790.00030.0315-10.361990.875628.3903
2400.0573-1.34910-0.31130.34470.00980.0009-0.02650.0161-0.0114-0.0005-0.03860.03930.00160.1794-0.01170.2707-0.04390.21430.0562-28.5665126.56921.2713
250.08250.03590.550200.60850.40810.0016-0.01560.0063-0.0342-0.0266-0.0118-0.0215-0.02190.02490.03660.1072-0.0047-0.05370.11280.1979-44.408173.28226.2346
260.69571.8179-1.60831.73381.07981.3618-0.0029-0.0135-0.00070.03070.05810.05690.0237-0.0622-0.0552-0.1928-0.07030.13720.1561-0.20750.182730.682757.288329.1719
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ E|1 - E|162 E|168 - E|172 E|177 - E|191 }
2X-RAY DIFFRACTION2{ E|192 - E|267 E|274 - E|311 }
3X-RAY DIFFRACTION3{ E|312 - E|464 }
4X-RAY DIFFRACTION4{ E|465 - E|515 E|531 - E|594 }
5X-RAY DIFFRACTION5{ E|595 - E|656 E|754 - E|817 }
6X-RAY DIFFRACTION6{ E|694 - E|710 }
7X-RAY DIFFRACTION7{ E|818 - E|910 }
8X-RAY DIFFRACTION8{ A|1 - A|112 }
9X-RAY DIFFRACTION9{ B|1 - B|109 }
10X-RAY DIFFRACTION10{ A|113 - A|133 A|139 - A|219 }
11X-RAY DIFFRACTION11{ B|110 - B|218 }
12X-RAY DIFFRACTION12{ C|1 - C|84 C|89 - C|109 }
13X-RAY DIFFRACTION13{ C|110 - C|126 C|135 - C|183 C|194 - C|209 }
14X-RAY DIFFRACTION14{ D|1 - D|106 }
15X-RAY DIFFRACTION15{ D|107 - D|147 D|159 - D|179 D|196 - D|209 }
16X-RAY DIFFRACTION16{ E|1001 }
17X-RAY DIFFRACTION17{ E|1002 - E|1003 E|1004 }
18X-RAY DIFFRACTION18{ E|1005 - E|1007 }
19X-RAY DIFFRACTION19{ E|1008 }
20X-RAY DIFFRACTION20{ E|1009 - E|1010 E|1011 }
21X-RAY DIFFRACTION21{ E|1012 - E|1014 }
22X-RAY DIFFRACTION22{ E|1018 E|1019 }
23X-RAY DIFFRACTION23{ E|1020 }
24X-RAY DIFFRACTION24{ E|1021 - E|1022 E|1023 }
25X-RAY DIFFRACTION25{ E|1024 E|1025 }
26X-RAY DIFFRACTION26{ E|1015 - E|1016 E|1017 }

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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