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- PDB-6veq: Con-Ins G1 in complex with the human insulin microreceptor in tur... -

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基本情報

登録情報
データベース: PDB / ID: 6veq
タイトルCon-Ins G1 in complex with the human insulin microreceptor in turn in complex with Fv 83-7
要素
  • Con-Ins G1 B chain
  • Con-Ins G1a A chain
  • Fv 83-7 heavy chain
  • Fv 83-7 light chain
  • Insulin receptor
  • Insulin receptor subunit alpha
キーワードTOXIN
機能・相同性
機能・相同性情報


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 / positive regulation of protein-containing complex disassembly / insulin receptor activity / exocrine pancreas development ...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 / positive regulation of protein-containing complex disassembly / insulin receptor activity / exocrine pancreas development / dendritic spine maintenance / cargo receptor activity / insulin binding / adrenal gland development / neuronal cell body membrane / PTB domain binding / Signaling by Insulin receptor / IRS activation / positive regulation of respiratory burst / amyloid-beta clearance / positive regulation of receptor internalization / regulation of embryonic development / insulin receptor substrate binding / protein kinase activator activity / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / heart morphogenesis / transport across blood-brain barrier / phosphatidylinositol 3-kinase binding / Insulin receptor recycling / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / positive regulation of glycolytic process / positive regulation of D-glucose import / learning / receptor protein-tyrosine kinase / hormone activity / caveola / cellular response to growth factor stimulus / receptor internalization / memory / male gonad development / cellular response to insulin stimulus / glucose metabolic process / positive regulation of nitric oxide biosynthetic process / insulin receptor signaling pathway / late endosome / glucose homeostasis / amyloid-beta binding / protein autophosphorylation / toxin activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / endosome membrane / 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 / positive regulation of cell migration / G protein-coupled receptor signaling pathway / axon / protein domain specific binding / external side of plasma membrane / positive regulation of cell population proliferation / symbiont entry into host cell / regulation of DNA-templated transcription / GTP binding / positive regulation of DNA-templated transcription / protein-containing complex binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / plasma 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 / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / 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 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Con-Ins G1b / Con-Ins G1a / Insulin receptor
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Mus musculus (ハツカネズミ)
Conus geographus (アンボイナ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.25 Å
データ登録者Menting, J.G. / Chou, D.H.-C. / Lawrence, M.C. / Xiong, X.
資金援助 オーストラリア, 米国, 2件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)APP1143546 オーストラリア
Other private5-CDA-2018-572-A-N 米国
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2020
タイトル: A structurally minimized yet fully active insulin based on cone-snail venom insulin principles.
著者: Xiong, X. / Menting, J.G. / Disotuar, M.M. / Smith, N.A. / Delaine, C.A. / Ghabash, G. / Agrawal, R. / Wang, X. / He, X. / Fisher, S.J. / MacRaild, C.A. / Norton, R.S. / Gajewiak, J. / ...著者: Xiong, X. / Menting, J.G. / Disotuar, M.M. / Smith, N.A. / Delaine, C.A. / Ghabash, G. / Agrawal, R. / Wang, X. / He, X. / Fisher, S.J. / MacRaild, C.A. / Norton, R.S. / Gajewiak, J. / Forbes, B.E. / Smith, B.J. / Safavi-Hemami, H. / Olivera, B. / Lawrence, M.C. / Chou, D.H.
履歴
登録2020年1月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年6月3日Provider: repository / タイプ: Initial release
改定 1.12020年6月17日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22020年7月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / chem_comp ...atom_site / 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 / _chem_comp.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 2.12023年10月11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 2.22023年11月15日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: Con-Ins G1a A chain
B: Con-Ins G1 B chain
E: Insulin receptor subunit alpha
F: Insulin receptor
C: Fv 83-7 heavy chain
D: Fv 83-7 light chain
K: Insulin receptor subunit alpha
L: Insulin receptor
I: Fv 83-7 heavy chain
J: Fv 83-7 light chain
H: Con-Ins G1 B chain
G: Con-Ins G1a A chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)148,15726
ポリマ－143,48312
非ポリマー4,67414
水00
1
A: Con-Ins G1a A chain
B: Con-Ins G1 B chain
E: Insulin receptor subunit alpha
F: Insulin receptor
C: Fv 83-7 heavy chain
D: Fv 83-7 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)74,17514
ポリマ－71,7416
非ポリマー2,4338
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
K: Insulin receptor subunit alpha
L: Insulin receptor
I: Fv 83-7 heavy chain
J: Fv 83-7 light chain
H: Con-Ins G1 B chain
G: Con-Ins G1a A chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)73,98212
ポリマ－71,7416
非ポリマー2,2416
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)106.160, 227.120, 228.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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要素

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タンパク質・ペプチド , 3種, 6分子 AGBHFL

#1: タンパク質・ペプチド Con-Ins G1a A chain


分子量: 2358.720 Da / 分子数: 2 / 断片: residues 95-114 / 由来タイプ: 合成 / 由来: (合成) Conus geographus (アンボイナ) / 参照: UniProt: A0A0B5AC95
#2: タンパク質・ペプチド Con-Ins G1 B chain


分子量: 2802.083 Da / 分子数: 2 / 断片: residues 30-52 / 由来タイプ: 合成 / 由来: (合成) Conus geographus (アンボイナ) / 参照: UniProt: A0A0B5A8Q2
#4: タンパク質・ペプチド Insulin receptor / IR


分子量: 1922.143 Da / 分子数: 2 / 断片: residues 731-746 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P06213, receptor protein-tyrosine kinase

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抗体 , 2種, 4分子 CIDJ

#5: 抗体 Fv 83-7 heavy chain


分子量: 15058.748 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Brevibacillus brevis (バクテリア)
#6: 抗体 Fv 83-7 light chain


分子量: 13367.913 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Brevibacillus brevis (バクテリア)

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タンパク質 / 非ポリマー , 2種, 6分子 EK

#10: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 4 / 由来タイプ: 組換発現 / 式: SO4
#3: タンパク質 Insulin receptor subunit alpha / IR


分子量: 36231.762 Da / 分子数: 2 / 断片: residues 28-337 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: INSR / プラスミド: pEE14 / 器官 (発現宿主): ovary
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
Variant (発現宿主): LEC 8 MUTANT / 参照: UniProt: P06213, receptor protein-tyrosine kinase

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糖 , 3種, 10分子

#7: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 748.682 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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 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
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: 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: 6 / 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

研究の焦点であるリガンドがあるかN

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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: 4.81 Å3/Da / 溶媒含有率: 74.45 %
結晶化温度: 300 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 1.7 M ammonium sulphate 50 mM MOPS-NaOH (pH 7.0)

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.953646 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2017年3月22日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.953646 Å / 相対比: 1
反射解像度: 3.25→50 Å / Num. obs: 43876 / % possible obs: 99.8 % / 冗長度: 5.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.259 / Net I/σ(I): 6.44
反射 シェル解像度: 3.25→3.35 Å / 冗長度: 6 % / Rmerge(I) obs: 2.748 / Mean I/σ(I) obs: 0.59 / Num. unique obs: 3751 / CC1/2: 0.163 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.13-2998_1692)精密化
XDSデータ削減
XSCALE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: 4OGA

4oga


解像度: 3.25→48.146 Å / SU ML: 0.53 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 29.98
Rfactor反射数%反射
Rfree0.277 1743 3.98 %
Rwork0.2279 --
obs0.2299 43845 99.82 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 3.25→48.146 Å
タンパク質核酸リガンド溶媒全体
原子数8965 0 302 0 9267
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0029531
X-RAY DIFFRACTIONf_angle_d0.50412971
X-RAY DIFFRACTIONf_dihedral_angle_d8.9825732
X-RAY DIFFRACTIONf_chiral_restr0.0421462
X-RAY DIFFRACTIONf_plane_restr0.0031624
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.34560.39371450.37413447X-RAY DIFFRACTION99
3.3456-3.45360.39471430.35893473X-RAY DIFFRACTION100
3.4536-3.5770.35181430.33423465X-RAY DIFFRACTION100
3.577-3.72010.35831440.28833466X-RAY DIFFRACTION100
3.7201-3.88940.2841430.25893481X-RAY DIFFRACTION100
3.8894-4.09430.27841450.24033500X-RAY DIFFRACTION100
4.0943-4.35070.27851450.20733493X-RAY DIFFRACTION100
4.3507-4.68640.20181440.16963476X-RAY DIFFRACTION100
4.6864-5.15750.20381430.17173523X-RAY DIFFRACTION100
5.1575-5.90260.23161480.18943530X-RAY DIFFRACTION100
5.9026-7.43230.26051430.2393570X-RAY DIFFRACTION100
7.4323-48.1460.31081570.21943678X-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)
16.9944-1.05794.79462.7322-2.70646.3605-1.8601-2.9062-0.4058-1.41490.88941.79080.9621-1.36881.04381.08160.101-0.35251.0590.36392.3648-46.0967-87.5529-51.8778
25.8474.6476-2.79414.7895-3.54433.54970.7043-1.4983-0.3147-0.784-1.211.7135-0.42292.08160.06572.1639-0.0267-0.85321.889-0.12162.5919-46.8459-88.0102-57.5356
34.90182.4696-1.77257.34961.9795.2747-0.0829-0.17170.50862.0208-2.3640.14980.86441.32791.73422.3104-0.24530.12380.93670.50991.7559-38.826-80.8555-55.0073
44.97951.8543-4.05332.45411.19788.43052.57571.3466-0.5537-2.4091-1.04331.1198-1.28280.6635-0.65481.9311-0.3635-0.25231.27950.36511.6353-41.2372-91.4228-59.8543
59.09442.96841.46792.1024-0.95066.7794-0.3334-0.06561.6298-1.6693-0.07761.51152.12831.07430.34361.7767-0.2288-0.09511.17040.1571.381-32.8891-89.2858-55.858
60.99570.6438-0.77644.4824-2.26663.5988-0.07890.4171.0865-0.2170.0082-0.1202-0.58710.23410.04931.0723-0.17660.14771.01380.06311.1169-25.1565-92.8937-36.328
74.0351-2.21480.44384.7232-1.76613.44-0.31870.5396-0.4019-0.5316-0.00480.19680.3859-0.12730.32451.0787-0.09030.18361.0315-0.07340.8954-29.3738-109.1532-36.0391
80.0413-2.2543-1.95170.42641.99714.0142-0.29080.1170.26550.23310.2439-0.37340.5370.19450.08420.9114-0.0604-0.01050.9348-0.02691.0152-27.5463-101.6927-16.9394
93.8374-1.2529-1.72972.88260.73781.98390.06230.0521-0.6332-0.7566-0.0914-0.2350.5887-0.0024-0.05141.3214-0.0024-0.1691.0492-0.03971.4957-46.7608-76.544-16.9613
106.79770.327-1.05274.55191.2868.8645-2.10310.68350.1908-1.94520.33481.9548-1.0742-2.19551.65941.6435-0.00290.02551.2886-0.08141.0793-40.6514-93.6115-45.236
111.98350.32277.8671.31151.95838.2312-0.9733-0.57672.4452-0.73830.3922-0.0642-2.2233-1.0988-0.49492.6633-0.18880.47441.06720.34761.5861-36.7004-81.9756-42.6997
123.7810.0454-1.96624.77781.06535.3116-0.241-0.07130.43670.80360.3025-0.97210.95210.6801-0.01970.9074-0.1031-0.20851.1087-0.11131.1872-19.1422-85.932111.1857
133.15351.7979-1.65294.7621-0.95362.19530.0571-0.04850.69080.0012-0.0683-0.5432-0.67720.3752-0.07640.9527-0.1124-0.05280.9235-0.22281.1372-28.19-81.55049.2777
141.68361.65153.36482.14820.46365.26910.3321-0.17480.01240.52960.0541-0.72730.33720.2402-0.42020.8497-0.0297-0.14220.9908-0.15121.1141-25.6801-85.601714.1428
153.2964-1.72262.79642.8999-3.2964.54050.1974-2.013-1.58850.19322.26790.33050.72740.58463.35280.96820.2326-0.61691.0353-0.3111-1.1849-45.6149-87.226813.1571
165.2259-3.79522.48094.414-4.70016.2103-0.7472-0.8364-1.4138-1.14081.3762.35150.3378-1.6394-0.4470.9911-0.16030.05460.97030.15091.05-45.6678-106.21423.7152
174.23936.08230.01212.0144-2.83955.2687-0.5960.001-0.33861.7431.4175-0.7589-1.5106-3.6609-0.7080.90850.2083-0.07721.14650.05980.5706-48.0397-96.930914.5615
185.25680.4886-1.00650.845-2.63778.43110.5609-0.14440.7659-0.6880.52610.47321.1490.1978-0.96761.0785-0.0889-0.25251.014-0.11261.0438-45.9991-90.8287-1.6503
195.93182.7549-0.88046.89992.90092.273-0.919-1.2788-0.69910.03970.5692-1.49460.1022-1.0231-0.01561.0529-0.0977-0.25220.91160.08740.3089-36.6253-98.155813.1367
205.02190.61483.30844.33740.18526.0754-0.2941-0.2444-0.789-0.46691.1721-0.3681-0.30831.0712-0.36230.8407-0.0843-0.0280.7685-0.01620.8543-31.4817-100.171314.3085
216.2784-2.40351.71298.1026-6.21045.01580.59130.04780.1524-1.2679-0.55631.07312.51240.6233-0.06351.0020.0431-0.12670.8563-0.29821.2893-37.9098-104.78215.0553
226.2839-2.85870.66346.0854-0.5695.0323-0.08941.66130.50871.9097-1.16170.904-0.50170.31340.94471.0333-0.0574-0.26251.0155-0.08790.833-47.2618-100.39439.375
231.72651.365-0.17482.4267-2.73467.5483-0.1669-1.334-2.76320.80520.4249-2.140.37622.0979-0.12330.81220.2827-0.17631.1744-0.061.394-38.1571-110.40319.655
246.5137-0.1262-0.62677.4612-1.39151.7914-0.5015-1.3180.18040.19240.29230.2684-1.1501-1.92760.77960.73950.0102-0.26120.8926-0.24060.7188-38.7343-95.001414.5807
257.691-2.11170.15194.5743.40264.84810.48530.1257-0.3679-1.1795-0.27640.3874-2.67330.8878-0.33941.1568-0.0944-0.01540.8936-0.20910.9862-38.9751-86.7657.2038
261.58992.0696-4.10815.309-4.9662.00140.7320.7962-0.4627-1.3553-0.3714-0.7305-1.8157-0.3939-1.18241.0128-0.11520.03880.9992-0.19460.7778-40.7015-105.2427.5555
272.9568-2.5527-1.13434.35450.52692.29930.5129-0.8363-1.3455-0.5801-0.31280.67840.241-0.03610.04010.9581-0.3601-0.17051.31520.03761.4352-80.8946-96.3215-64.0976
283.0281-1.8555-0.32581.17950.93760.42120.1330.54990.1111-0.19740.28090.10340.9906-0.3713-0.45161.5561-0.2692-0.12251.26020.27331.123-75.8215-95.9125-71.6287
290.86811.1075-1.25237.2928-2.14066.1224-0.0227-0.1755-1.0403-0.5006-0.42460.04370.7939-0.03560.36140.97430.00810.02671.1940.08041.4679-65.3376-89.6078-66.0402
302.6921-0.66150.96282.092-0.76242.21930.0514-0.5092-0.7296-0.7910.0692-0.56050.86920.2174-0.07311.1736-0.00190.33421.29320.3531.5895-57.6043-81.4731-73.7454
312.8357-1.4924-0.95675.59213.10171.88550.23920.14820.3201-1.03390.16480.1825-0.9678-0.1202-0.44311.1351-0.0391-0.15421.22510.38971.6709-76.9182-69.8319-61.7909
321.5183-0.07640.3450.11150.52032.84050.0404-0.01030.43440.09380.052-0.24220.3365-0.1948-0.07430.9845-0.1052-0.2931.11670.3451.1068-85.9364-84.2786-45.0019
332.61920.02973.54112.4217-2.10526.9214-0.1676-0.5622-0.192-0.02911.46751.04050.1046-2.2918-1.2611.0815-0.095-0.22781.22750.37781.52-84.1502-91.3853-30.3433
341.7768-0.87441.55542.3342.37718.56981.3356-1.18270.52550.0663-0.8824-1.42641.1813-1.1927-0.43592.02050.08030.2211.43740.2981.1915-64.0148-104.6586-56.4014
352.05250.2322-1.6177.5955-0.73172.34160.59552.21711.09820.7230.69320.50320.5075-0.9934-1.03141.32380.2062-0.1761.31260.2280.9981-96.1184-55.0257-58.2542
362.3278-1.1332-2.13319.07652.00622.0438-1.8143-0.191-0.2752-1.15210.85522.3555-1.42354.61410.96850.7526-0.00930.07142.09170.79591.5732-115.7347-52.2938-45.7769
376.2042-3.22412.13431.83620.14655.232-0.06570.07530.6327-0.2113-0.1361-0.2851-1.40340.80360.48420.7846-0.0857-0.20270.72460.35391.2155-98.7305-59.0776-48.1271
382.5163.10630.65813.4481.89454.31780.35760.67660.21330.16680.68430.3807-0.4933-0.597-0.94311.11390.0187-0.12821.26180.28841.2215-102.8913-67.5355-44.452
396.7797-1.6206-1.84773.45261.36792.632-0.1704-0.04621.09370.067-0.1020.4662-0.1536-0.65690.21851.1250.1054-0.26621.26240.26861.3197-104.7117-58.0316-47.7347
401.37351.02340.7767.3336-0.56710.7675-0.48181.22160.8826-0.12230.0211-3.5585-1.6081-0.12350.47321.14810.0191-0.1251.05530.36341.1846-89.7552-59.4046-50.1868
415.8749-0.98074.26431.8045-0.93853.569-0.53461.361-0.38781.83540.6879-1.57160.4152.27180.33191.05580.152-0.17041.4552-0.03711.7543-109.8213-48.2272-44.7602
428.43026.4210.95452.00811.6876.90161.4963-0.80961.75630.3734-2.1279-2.5091-1.93051.25060.61481.28560.2161-0.17110.75590.04211.2106-89.3958-56.5759-29.9454
434.4279-3.18231.05113.6131.27253.35020.614-0.56711.46021.2159-0.6201-2.3179-0.74120.39750.08121.3981-0.3008-0.39061.16180.15221.841-79.5925-45.4556-32.4566
446.96329.1102-1.80921.9729-2.622.04520.4436-0.9005-2.9321-0.9702-0.3262-2.80990.35080.4561-0.31531.14360.0325-0.87161.45250.26221.1064-80.9182-69.7277-36.5838
451.1692-1.1475-0.92022.65630.23692.2624-0.1206-0.07230.05691.2332-0.1594-0.6958-0.2426-0.44340.42980.7861-0.0597-0.2690.9530.4381.4171-85.8956-51.5497-44.264
465.9083-3.6629-6.47119.30822.47737.64360.92610.26911.5311-0.81380.6985-1.21870.0638-0.0388-1.09331.1247-0.12-0.531.58680.48321.6282-76.1573-55.0022-45.9156
472.307-4.75290.89332.0368-0.18575.7743-0.6965-0.77652.14191.30821.94290.68820.6499-0.6327-1.10111.1645-0.1197-0.89421.30640.13852.4199-77.2316-55.6709-34.7549
483.20025.12811.04878.73232.53483.71790.54870.74142.84460.6743-1.65480.2997-1.1361-0.4629-1.18861.06330.2204-0.40490.84390.82422.0477-82.8648-46.8567-40.3284
493.1871-1.494-0.70834.9938-0.5732.88390.1570.0891-1.39561.51810.3433-1.00490.56890.7016-0.55261.0193-0.189-0.33810.87460.22751.6961-91.0662-63.3499-38.081
503.19193.1201-1.05335.89643.55527.7233-0.56051.7713-1.82132.5574-2.3051-2.52231.1105-1.91331.8631.24170.0739-0.2421.24010.2391.7929-85.4859-40.6826-35.3172
511.4219-2.1677-1.69823.50023.33464.3715-0.59890.12630.43950.93632.24893.07630.9467-1.2306-1.4961.09550.1544-0.27821.321-0.15113.0789-56.5488-116.2927-60.5281
522.5312-0.9856-5.09680.42772.04992.0221-2.02080.0798-0.3735-0.5751-0.1188-4.55233.2968-1.1620.41772.1710.33740.65180.70340.30792.2303-63.8401-113.7094-65.9898
531.98072.2783-6.17921.8028-3.0865.87420.65690.2617-4.53560.54520.0777-2.73010.3988-1.1643-1.34071.7358-0.1432-0.45821.09670.87112.7103-60.8709-113.3754-52.7111
542.01171.9444-3.15386.13162.53236.4796-4.0663-1.8476-0.730.8411.79864.19561.5549-0.47092.14571.54280.08660.18791.14290.44182.8043-64.5377-118.7465-56.6301
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:6 )A1 - 6
2X-RAY DIFFRACTION2( CHAIN A AND RESID 7:12 )A7 - 12
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 13:19 OR RESID 20:20 ) )A13 - 19
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 13:19 OR RESID 20:20 ) )A20
5X-RAY DIFFRACTION4( CHAIN B AND RESID 4:8 )B4 - 8
6X-RAY DIFFRACTION5( CHAIN B AND RESID 9:19 )B9 - 19
7X-RAY DIFFRACTION6( CHAIN E AND RESID 5:106 )E5 - 106
8X-RAY DIFFRACTION7( CHAIN E AND RESID 107:170 )E107 - 170
9X-RAY DIFFRACTION8( CHAIN E AND RESID 171:255 )E171 - 255
10X-RAY DIFFRACTION9( CHAIN E AND RESID 256:309 )E256 - 309
11X-RAY DIFFRACTION10( CHAIN F AND RESID 705:713 )F705 - 713
12X-RAY DIFFRACTION11( CHAIN F AND RESID 714:719 )F714 - 719
13X-RAY DIFFRACTION12( CHAIN C AND RESID 1:32 )C1 - 32
14X-RAY DIFFRACTION13( CHAIN C AND RESID 33:76 )C33 - 76
15X-RAY DIFFRACTION14( CHAIN C AND RESID 77:118 )C77 - 118
16X-RAY DIFFRACTION15( CHAIN D AND RESID 1:7 )D1 - 7
17X-RAY DIFFRACTION16( CHAIN D AND RESID 8:18 )D8 - 18
18X-RAY DIFFRACTION17( CHAIN D AND RESID 19:25 )D19 - 25
19X-RAY DIFFRACTION18( CHAIN D AND RESID 26:38 )D26 - 38
20X-RAY DIFFRACTION19( CHAIN D AND RESID 39:45 )D39 - 45
21X-RAY DIFFRACTION20( CHAIN D AND RESID 46:54 )D46 - 54
22X-RAY DIFFRACTION21( CHAIN D AND RESID 55:67 )D55 - 67
23X-RAY DIFFRACTION22( CHAIN D AND RESID 68:81 )D68 - 81
24X-RAY DIFFRACTION23( CHAIN D AND RESID 82:89 )D82 - 89
25X-RAY DIFFRACTION24( CHAIN D AND RESID 90:96 )D90 - 96
26X-RAY DIFFRACTION25( CHAIN D AND RESID 97:106 )D97 - 106
27X-RAY DIFFRACTION26( CHAIN D AND RESID 107:114 )D107 - 114
28X-RAY DIFFRACTION27( CHAIN K AND RESID 5:36 )K5 - 36
29X-RAY DIFFRACTION28( CHAIN K AND RESID 37:60 )K37 - 60
30X-RAY DIFFRACTION29( CHAIN K AND RESID 61:143 )K61 - 143
31X-RAY DIFFRACTION30( CHAIN K AND RESID 144:193 )K144 - 193
32X-RAY DIFFRACTION31( CHAIN K AND RESID 194:233 )K194 - 233
33X-RAY DIFFRACTION32( CHAIN K AND RESID 234:291 )K234 - 291
34X-RAY DIFFRACTION33( CHAIN K AND RESID 292:309 )K292 - 309
35X-RAY DIFFRACTION34( CHAIN L AND RESID 705:715 )L705 - 715
36X-RAY DIFFRACTION35( CHAIN I AND RESID 1:7 )I1 - 7
37X-RAY DIFFRACTION36( CHAIN I AND RESID 8:17 )I8 - 17
38X-RAY DIFFRACTION37( CHAIN I AND RESID 18:51 )I18 - 51
39X-RAY DIFFRACTION38( CHAIN I AND RESID 52:72 )I52 - 72
40X-RAY DIFFRACTION39( CHAIN I AND RESID 73:98 )I73 - 98
41X-RAY DIFFRACTION40( CHAIN I AND RESID 99:111 )I99 - 111
42X-RAY DIFFRACTION41( CHAIN I AND RESID 112:117 )I112 - 117
43X-RAY DIFFRACTION42( CHAIN J AND RESID 1:9 )J1 - 9
44X-RAY DIFFRACTION43( CHAIN J AND RESID 10:25 )J10 - 25
45X-RAY DIFFRACTION44( CHAIN J AND RESID 26:38 )J26 - 38
46X-RAY DIFFRACTION45( CHAIN J AND RESID 39:55 )J39 - 55
47X-RAY DIFFRACTION46( CHAIN J AND RESID 56:67 )J56 - 67
48X-RAY DIFFRACTION47( CHAIN J AND RESID 68:81 )J68 - 81
49X-RAY DIFFRACTION48( CHAIN J AND RESID 82:96 )J82 - 96
50X-RAY DIFFRACTION49( CHAIN J AND RESID 97:106 )J97 - 106
51X-RAY DIFFRACTION50( CHAIN J AND RESID 107:111 )J107 - 111
52X-RAY DIFFRACTION51( CHAIN H AND RESID 4:8 )H4 - 8
53X-RAY DIFFRACTION52( CHAIN H AND RESID 9:19 )H9 - 19
54X-RAY DIFFRACTION53( CHAIN G AND RESID 1:7 )G1 - 7
55X-RAY DIFFRACTION54( CHAIN G AND ( RESID 8:19 OR RESID 20:20 ) )G8 - 19
56X-RAY DIFFRACTION54( CHAIN G AND ( RESID 8:19 OR RESID 20:20 ) )G20

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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

-
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