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- PDB-5u8q: Structure of the ectodomain of the human Type 1 insulin-like grow... -

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基本情報

登録情報
データベース: PDB / ID: 5u8q
タイトルStructure of the ectodomain of the human Type 1 insulin-like growth factor receptor in complex with IGF-I
要素
  • (Insulin-like growth factor ...インスリン様成長因子) x 2
  • Fv 24-60 heavy chain
  • Fv 24-60 light chain
キーワードTRANSFERASE (転移酵素) / Receptor tyrosine kinase (受容体型チロシンキナーゼ) / Type 1 insulin-like growth factor receptor / insulin-like growth-factor I
機能・相同性
機能・相同性情報


glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / cardiac atrium development / proteoglycan biosynthetic process / negative regulation of cholangiocyte apoptotic process / positive regulation of glycoprotein biosynthetic process ...glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / cardiac atrium development / proteoglycan biosynthetic process / negative regulation of cholangiocyte apoptotic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / insulin-like growth factor receptor activity / negative regulation of neuroinflammatory response / positive regulation of steroid hormone biosynthetic process / protein kinase complex / positive regulation of cell growth involved in cardiac muscle cell development / negative regulation of vascular associated smooth muscle cell apoptotic process / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / bone mineralization involved in bone maturation / IRS-related events triggered by IGF1R / insulin-like growth factor binding / exocytic vesicle / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to zinc ion starvation / cellular response to aldosterone / cell activation / positive regulation of calcineurin-NFAT signaling cascade / insulin receptor complex / negative regulation of hepatocyte apoptotic process / cellular response to testosterone stimulus / insulin-like growth factor I binding / positive regulation of transcription regulatory region DNA binding / insulin receptor activity / transcytosis / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / positive regulation of Ras protein signal transduction / positive regulation of protein-containing complex disassembly / cellular response to angiotensin / myoblast differentiation / myoblast proliferation / positive regulation of insulin-like growth factor receptor signaling pathway / muscle organ development / cellular response to insulin-like growth factor stimulus / response to L-glutamate / negative regulation of interleukin-1 beta production / dendritic spine maintenance / insulin binding / establishment of cell polarity / negative regulation of amyloid-beta formation / negative regulation of MAPK cascade / positive regulation of activated T cell proliferation / positive regulation of axon regeneration / positive regulation of cardiac muscle hypertrophy / positive regulation of smooth muscle cell migration / amyloid-beta clearance / negative regulation of release of cytochrome c from mitochondria / positive regulation of cytokinesis / positive regulation of osteoblast proliferation / negative regulation of smooth muscle cell apoptotic process / regulation of JNK cascade / estrous cycle / negative regulation of tumor necrosis factor production / insulin receptor substrate binding / G-protein alpha-subunit binding / 上皮間葉転換 / Synthesis, secretion, and deacylation of Ghrelin / response to vitamin E / positive regulation of glycogen biosynthetic process / positive regulation of DNA binding / positive regulation of osteoblast differentiation / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / 横行小管 / insulin-like growth factor receptor binding / activation of protein kinase B activity / cerebellum development / positive regulation of glycolytic process / cellular response to dexamethasone stimulus / 軸索誘導 / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / response to nicotine / phosphatidylinositol 3-kinase/protein kinase B signal transduction / skeletal system development / cellular response to estradiol stimulus / positive regulation of epithelial cell proliferation / カベオラ / positive regulation of protein secretion / hippocampus development / cellular response to glucose stimulus
類似検索 - 分子機能
インスリン様成長因子1 / Insulin-like, subunit E / Insulin-like / インスリン様成長因子 / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site ...インスリン様成長因子1 / Insulin-like, subunit E / Insulin-like / インスリン様成長因子 / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / 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 / フィブロネクチンIII型ドメイン / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 抗体 / 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 / Immunoglobulin-like / サンドイッチ / Orthogonal Bundle / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
D-MALATE / インスリン様成長因子1 / インスリン様成長因子1受容体
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 3.27104018461 Å
データ登録者Lawrence, M. / Xu, Y.
引用ジャーナル: Nat Commun / 年: 2018
タイトル: How ligand binds to the type 1 insulin-like growth factor receptor.
著者: Xu, Y. / Kong, G.K. / Menting, J.G. / Margetts, M.B. / Delaine, C.A. / Jenkin, L.M. / Kiselyov, V.V. / De Meyts, P. / Forbes, B.E. / Lawrence, M.C.
履歴
登録2016年12月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年2月28日Provider: repository / タイプ: Initial release
改定 1.12018年3月14日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

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集合体

登録構造単位
A: Insulin-like growth factor 1 receptor
B: Insulin-like growth factor I
H: Fv 24-60 heavy chain
L: Fv 24-60 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)137,01913
ポリマ－134,4324
非ポリマー2,5879
水0
1
A: Insulin-like growth factor 1 receptor
B: Insulin-like growth factor I
H: Fv 24-60 heavy chain
L: Fv 24-60 light chain
ヘテロ分子

A: Insulin-like growth factor 1 receptor
B: Insulin-like growth factor I
H: Fv 24-60 heavy chain
L: Fv 24-60 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)274,03826
ポリマ－268,8638
非ポリマー5,17518
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area21280 Å2
ΔGint-34 kcal/mol
Surface area107620 Å2
手法PISA
単位格子
Length a, b, c (Å)88.690, 197.660, 117.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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要素

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Insulin-like growth factor ... , 2種, 2分子 AB

#1: タンパク質 Insulin-like growth factor 1 receptor / インスリン様成長因子1受容体 / Insulin-like growth factor I receptor / IGF-I receptor


分子量: 101085.461 Da / 分子数: 1
変異: residues 718-741 are replaced with the sequence AGNN
由来タイプ: 組換発現
詳細: A17delta-beta construct, see Whitten et al., J. Mol. Biol., v394, pp878-92 (2009).
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IGF1R / プラスミド: FIII-IGFR.ECD
詳細 (発現宿主): see Whitten et al., J. Mol. Biol., v394, pp878-92 (2009).
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: P08069, 受容体型チロシンキナーゼ
#2: タンパク質 Insulin-like growth factor I / インスリン様成長因子1 / IGF-I / Mechano growth factor / MGF / Somatomedin-C


分子量: 7663.752 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Mature IGF-1 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IGF1, IBP1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P05019

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抗体 , 2種, 2分子 HL

#3: 抗体 Fv 24-60 heavy chain


分子量: 13948.477 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: hybridoma / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: pgpHFT-SUMO-scFV
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
#4: 抗体 Fv 24-60 light chain


分子量: 11733.944 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: hybridoma / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: pgpHFT-SUMO-scFV
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)

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糖 , 3種, 6分子

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


タイプ: oligosaccharideオリゴ糖 / 分子量: 424.401 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
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
#6: 多糖 alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 748.682 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
DManpa1-4DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(4+1)][a-D-Manp]{}}}}}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 / N-アセチルグルコサミン


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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非ポリマー , 2種, 3分子

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


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO4
#8: 化合物 ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / D-りんご酸 / リンゴ酸


分子量: 134.087 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H6O5

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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: 3.84 Å3/Da / 溶媒含有率: 67.94 %
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: 7
詳細: 1.2 M ammonium sulfate, 0.1 M imidazole-malate pH 7.0. IGF-1 was included by soaking directly into the mother crystal. For full details see the primary citation.

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年8月20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: 0.9537 Å / 相対比: 1
反射解像度: 3.27→50 Å / Num. obs: 32228 / % possible obs: 98.6 % / 冗長度: 7.2 % / Biso Wilson estimate: 110.958573147 Å2 / CC1/2: 0.775 / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.1
反射 シェル解像度: 3.27→3.46 Å / 冗長度: 6.7 % / Rmerge(I) obs: 2.07 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4896 / CC1/2: 0.775 / % possible all: 92.5

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解析

ソフトウェア
名称バージョン分類
phenix.refine1.11.1-2575_1692精密化
PHENIX1.11.1-2575_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: 5U8R

5u8r


解像度: 3.27104018461→22.1725 Å / SU ML: 0.543083052018 / 交差検証法: FREE R-VALUE / σ(F): 1.32594454353 / 位相誤差: 38.9050389519
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.303184371053 1524 4.7461849891 %
Rwork0.259826709676 30586 -
obs0.261887829198 32110 98.5725249424 %
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: 177.857907853 Å2
精密化ステップサイクル: LAST / 解像度: 3.27104018461→22.1725 Å
タンパク質核酸リガンド溶媒全体
原子数8537 0 167 0 8704
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001888328003078934
X-RAY DIFFRACTIONf_angle_d0.51966972220212148
X-RAY DIFFRACTIONf_chiral_restr0.04419986906341337
X-RAY DIFFRACTIONf_plane_restr0.003002686560651549
X-RAY DIFFRACTIONf_dihedral_angle_d11.59457349395364
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.271-3.37630.4306593320951310.4146208473552493X-RAY DIFFRACTION89.8322492297
3.3763-3.49650.4153946439581260.354111906282736X-RAY DIFFRACTION98.9968868903
3.4965-3.63590.395193229591490.3347725295162731X-RAY DIFFRACTION99.0712074303
3.6359-3.80060.3342212373461180.3273953984832799X-RAY DIFFRACTION98.9484396201
3.8006-3.99990.340131322961370.2993325354792751X-RAY DIFFRACTION99.1077556623
3.9999-4.24880.3141207008621410.252682472972785X-RAY DIFFRACTION99.3885869565
4.2488-4.57420.2589289923141460.2223510546842786X-RAY DIFFRACTION99.6262317363
4.5742-5.02970.2357703822271550.2023083509792804X-RAY DIFFRACTION99.8313090418
5.0297-5.74640.2546930106031410.2156402634972827X-RAY DIFFRACTION99.7647058824
5.7464-7.19850.3350429455031360.2706702584562879X-RAY DIFFRACTION99.8675057966
7.1985-22.1730.2993476661281440.2518898262882995X-RAY DIFFRACTION99.6824388695
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)
17.260622382791.211649196490.5625063734531.127751345210.9176177161541.821907716020.04448273048522.78641590942-0.759989793321-0.409759345860.453253084058-0.3602628309490.3377980949150.646343069291-0.4663037076342.52285965106-0.03276974008570.207416733571.9333040848-0.3993916783551.2098348284526.242238147429.7959641751-49.9070965647
22.416224651011.28209347549-1.347760854983.05903772868-1.411746698262.99092303732-0.176918781321-0.382894877979-0.1549643930460.151093803521-0.011778922466-0.971817122121-0.2033484332260.116126425640.1401772907062.51834573730.0858730134607-0.05289049700330.850977729714-0.1358974879981.2505908347718.46897190913.2341461151.40061954234
38.34063969760.142141880748-1.233307291153.66353553053-1.072506174356.00277170237-0.0787508962612-0.3619554559091.02607186779-0.03003012453710.3659480826730.524849611954-0.863254506437-0.15465632657-0.2346440078833.15629989950.310328531202-0.02725318819170.8962340990760.09353215244030.6326946884019.53755747653-17.81746557716.43606342494
40.226106473073-0.363161573844-0.003147495487220.6511517018663.020781096912.260370509250.317221175448-0.0310575761470.147466672174-0.337862762643-0.0372439529166-0.02406905964840.05537508574110.289045329251-0.2994846285852.853773710310.08928394821720.09418889818741.5663410456-0.04498574138790.86865663179618.1668807835-23.3123327905-57.9279677721
55.530678545080.618537635538-1.084543918323.63681088215-1.61641643059.79140260422-0.1542449275492.422595742750.1152578714040.3532672851951.24020793598-0.595791678382-0.0652181824344-0.330228469346-0.7493048850612.37047385071-0.0539696845963-0.0696304941051.98659514759-0.204065290520.599162315325-2.1148671219624.6525890177-44.9978350675
68.063337220670.5279949846291.388026113924.60264369988-2.685668368272.795399024780.7178938814940.914804109386-1.179096971-1.47405852601-0.4348383902710.8086222467050.935952402686-0.437846436207-0.1594980430532.275184474310.4934743201730.2641543026661.28603664427-0.1151304008330.9263982041562.8837980373819.9558071461-35.6240861936
72.551026221350.6720856178621.388754060573.259214939854.01784462395.81783230787-0.203679629262-0.981448391784-0.8863960917741.26934451967-0.1187872303070.2376192552890.22744068290.990424026266-0.07069503524852.997962333230.52098051626-0.2308170585421.56819165015-0.171231027755-0.064749205703-3.7378014011427.0094624701-35.3262356704
83.67168017575-4.13357417997-0.8464567200224.908775934471.555644425063.716303928531.50323103572-0.8673656512390.697497802504-0.926392035296-0.3049894477920.372355091422-0.219723764017-0.325655367218-1.039267340311.91349119899-0.0780923608268-0.1595859038670.8563040424050.126214490960.7914233366414.252382156856.2685786603-17.5537103355
94.307254601373.604442184430.1548576521687.56650754083-1.182100347314.36856479844-1.30664301651-0.18019488615-0.441858395439-2.06114056158-0.6577234962920.3799887326431.07315338931-1.025903125031.622803432932.06498387545-0.1597490401310.03190997738490.96785069744-0.1846205871930.75735392765117.362358204452.8656903792-22.8101957998
104.69937147001-1.443364058271.848600283247.67418529505-2.434233727641.161208061410.814680662679-0.0277196663562-0.363877443601-1.52006676255-0.459219952145-0.917096694655-1.625961574571.29516316409-0.4422902030391.62937998998-0.4680518961930.08217803248050.864735046547-0.01975077838950.51607937947823.12332617746.7007145403-15.2554935925
112.192250874193.265513734521.064612901965.165765174452.743930963524.64326698576-0.2780408606860.115652108633-0.84752992448-0.213627044648-0.5280417150050.3948179759140.321601664124-0.2767782511430.1539512825011.79495825978-0.185406707480.465632249562-0.394382100688-0.5481297247591.2725931375422.861776010837.7849803173-27.5043551741
125.71893682585-5.05446378077-5.416542382864.479336206114.801430804055.156935550491.40689822514-1.18264107943-0.4935559385412.47724063974-1.170542680311.545242862241.06747366778-0.560075645948-0.2916029083131.96640095339-0.3543171549240.2642953980441.07132357043-0.06027117051861.0724662653116.125136164337.6774790677-12.2211524149
134.80133757993-6.49889877904-2.634394776999.535036707593.999855031051.72704771249-2.640832504670.237608061072-0.7783942137040.00330656411352-0.9191909279031.549889790810.189622067411-1.334943808923.445248455661.81354999234-0.5169116349570.02280233188041.07374130566-0.2302920702080.95845954547813.223816295742.6397193958-19.8966732133
147.33550462351-5.7067020739-4.613423350226.363852746874.886161005513.76647324662-0.9919080768542.50266386346-1.39020561064-1.61928083729-0.842407241643-0.4850914105011.76311442882-4.700674790861.567094033782.740765415960.116518508086-0.2438818228961.59014566634-0.2290806402360.77661907863116.133448835448.2377371474-25.2920410027
156.1189364877-4.221312124372.933442368741.994157285652.304558036493.938767657480.809227518464-2.26250773089-0.5481979347981.076375249851.032765057950.550004800814-1.22188533732-0.877695833141-0.978900382372.37325523461-0.1226958046120.3951940793761.638432405130.07890536751860.7499941230576.3357119191348.3619268252-8.02776403046
169.20683424338-0.265239992033-1.154451946598.853407360824.795503464012.713141225510.299237224499-1.590508326211.87082101210.896106881324-0.4202471832110.884596791876-0.958819581468-1.069166224530.351855012972.573428594820.202759152561-0.4087433949940.940768871535-0.06556469521050.61818625464419.382978685152.142970797-12.5903479309
172.75587784231.57617321588-2.018979853681.688956490320.8110054369968.92951369237-0.8787396799331.61523946004-0.211401271475-1.363922618680.735281662162-0.4736664258940.5307127416430.2340571234860.1440329401392.11752749853-0.4747615690140.1116851022620.997996966263-0.1120761687541.0332722732723.548349324950.1993779758-14.6840117964
183.59994447722-0.9141866628080.5218043870454.802107467833.680239955897.375768800420.788984510034-0.8626539691541.535159437742.632130582370.1581913846140.982993866745-0.958734934139-0.245782533787-0.9089669861872.49847772403-0.06916494564840.2332065794781.052526686480.2399555804141.0995352359329.92891545546.84620680964.49885506836
195.07763616335-3.44132087933-1.317027030653.60829938531-1.790063363417.346047505970.0577276711624-0.290543960421-0.5144649378131.949351297-0.6686138840680.3983238460861.452965088160.8662743664320.5489321091162.00178211268-0.115604891062-0.01968509823620.984672154820.1341594632520.88821316791835.774565826245.9405861506-0.66789993115
202.483045341990.2902958351940.5649683370372.508798843453.331169471435.02290042790.332051147674-0.283175567428-0.1620020816360.358700027014-0.210518161678-0.114468224809-2.611269488940.994238287873-0.2537199921721.9144494469-0.365398443984-0.1030209081371.372275547480.09813329518550.93321975142538.071976488351.0897134424-8.26682678688
216.395760072226.61803039594-5.713501005176.99756498005-5.966772510795.1645384316-1.1999303146-1.59640038616-1.632067478743.4884488385-1.08167549756-3.03618227932-0.0217548466642-0.7378341658662.104973457121.889379103060.2571068059160.2551183480550.9210115232070.09919996262731.7115673548639.164298537243.5312595221.33550982575
225.30018125456-2.179627410511.767188827279.346191214654.213395430373.9407802318-0.232049136997-0.318554189094-0.499240559316-0.1759442468990.158077871347-1.12480609285-0.1750068912171.202171176140.1645776516332.13153889605-0.1852501539090.01351501404440.9163627551210.02682944768260.77324609243735.842219986655.0995567319-2.07820363312
236.050841302113.53445886385-1.339716898828.581607026520.2655784771321.53681679791-0.0502098808607-1.01031479967-0.4333253441730.5478987017590.213122363980.387182298980.108074866614-0.0887561672515-0.5123310644462.3581989691-0.475074475022-0.02916983909270.9882567037060.4203554240820.72061915717828.834378198746.7010730024-2.1176483633
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 266 )
2X-RAY DIFFRACTION2chain 'A' and (resid 267 through 456 )
3X-RAY DIFFRACTION3chain 'A' and (resid 457 through 575 )
4X-RAY DIFFRACTION4chain 'A' and (resid 576 through 900 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 21 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 53 )
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 63 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 17 )
9X-RAY DIFFRACTION9chain 'H' and (resid 18 through 25 )
10X-RAY DIFFRACTION10chain 'H' and (resid 26 through 51 )
11X-RAY DIFFRACTION11chain 'H' and (resid 52 through 57 )
12X-RAY DIFFRACTION12chain 'H' and (resid 58 through 64 )
13X-RAY DIFFRACTION13chain 'H' and (resid 65 through 73 )
14X-RAY DIFFRACTION14chain 'H' and (resid 74 through 83 )
15X-RAY DIFFRACTION15chain 'H' and (resid 84 through 91 )
16X-RAY DIFFRACTION16chain 'H' and (resid 92 through 97 )
17X-RAY DIFFRACTION17chain 'H' and (resid 98 through 118 )
18X-RAY DIFFRACTION18chain 'L' and (resid 1 through 13 )
19X-RAY DIFFRACTION19chain 'L' and (resid 14 through 38 )
20X-RAY DIFFRACTION20chain 'L' and (resid 39 through 67 )
21X-RAY DIFFRACTION21chain 'L' and (resid 68 through 75 )
22X-RAY DIFFRACTION22chain 'L' and (resid 76 through 90 )
23X-RAY DIFFRACTION23chain 'L' and (resid 91 through 107 )

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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