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- PDB-7nx3: Crystal structure of ALK in complex with Fab324 -

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基本情報

登録情報
データベース: PDB / ID: 7nx3
タイトルCrystal structure of ALK in complex with Fab324
要素
  • ALK tyrosine kinase receptor
  • Fab324 HeavyChain
  • Fab324 Light Chain
キーワードPROTEIN BINDING / Cell Surface Receptor Cytokine binding
機能・相同性
機能・相同性情報


ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway ...ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway / response to environmental enrichment / ALK mutants bind TKIs / swimming behavior / regulation of neuron differentiation / positive regulation of dendrite development / Signaling by ALK / phosphorylation / response to stress / adult behavior / neuron development / negative regulation of lipid catabolic process / peptidyl-tyrosine autophosphorylation / energy homeostasis / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / hippocampus development / 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 / positive regulation of NF-kappaB transcription factor activity / Signaling by ALK fusions and activated point mutants / heparin binding / regulation of cell population proliferation / protein autophosphorylation / protein tyrosine kinase activity / regulation of apoptotic process / receptor complex / signal transduction / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / plasma membrane
類似検索 - 分子機能
: / ALK/LTK, Glycine-rich domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily ...: / ALK/LTK, Glycine-rich domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Concanavalin A-like lectin/glucanase domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
ALK tyrosine kinase receptor
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: 2.81 Å
データ登録者De Munck, S. / Savvides, S.N.
資金援助 ベルギー, 1件
組織認可番号国
Research Foundation - Flanders (FWO) ベルギー
引用ジャーナル: Nature / 年: 2021
タイトル: Structural basis of cytokine-mediated activation of ALK family receptors.
著者: De Munck, S. / Provost, M. / Kurikawa, M. / Omori, I. / Mukohyama, J. / Felix, J. / Bloch, Y. / Abdel-Wahab, O. / Bazan, J.F. / Yoshimi, A. / Savvides, S.N.
履歴
登録2021年3月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年10月27日Provider: repository / タイプ: Initial release
改定 1.12021年11月3日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
改定 1.22021年12月15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_author.identifier_ORCID
改定 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.42024年10月9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: ALK tyrosine kinase receptor
B: Fab324 HeavyChain
C: Fab324 Light Chain
D: Fab324 Light Chain
E: Fab324 HeavyChain
F: ALK tyrosine kinase receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)179,63814
ポリマ－177,8696
非ポリマー1,7708
水00
1
A: ALK tyrosine kinase receptor
D: Fab324 Light Chain
E: Fab324 HeavyChain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)89,8197
ポリマ－88,9343
非ポリマー8854
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Fab324 HeavyChain
C: Fab324 Light Chain
F: ALK tyrosine kinase receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)89,8197
ポリマ－88,9343
非ポリマー8854
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)109.700, 137.470, 144.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROILEILE(chain 'A' and (resid 679 through 795 or (resid 796...AA679 - 79532 - 148
121TRPTRPASNASN(chain 'A' and (resid 679 through 795 or (resid 796...AA814 - 986167 - 339
231PROPROILEILE(chain 'F' and (resid 679 through 796 or resid 814 through 986))FF679 - 79532 - 148
241TRPTRPASNASN(chain 'F' and (resid 679 through 796 or resid 814 through 986))FF814 - 986167 - 339
152VALVALPROPRO(chain 'B' and (resid 2 through 130 or (resid 131...BB2 - 1312 - 131
162SERSERPROPRO(chain 'B' and (resid 2 through 130 or (resid 131...BB142 - 220142 - 220
272VALVALPROPRO(chain 'E' and (resid 2 through 131 or resid 142 through 220))EE2 - 1312 - 131
282SERSERPROPRO(chain 'E' and (resid 2 through 131 or resid 142 through 220))EE142 - 220142 - 220
193ASPASPARGARG(chain 'C' and (resid 1 through 159 or resid 161 through 191 or resid 193 through 215))CC1 - 1591 - 159
1103ASNASNGLUGLU(chain 'C' and (resid 1 through 159 or resid 161 through 191 or resid 193 through 215))CC161 - 191161 - 191
1113HISHISARGARG(chain 'C' and (resid 1 through 159 or resid 161 through 191 or resid 193 through 215))CC193 - 215193 - 215
2123ASPASPARGARG(chain 'D' and (resid 1 through 159 or resid 161 through 191 or resid 193 through 215))DD1 - 1591 - 159
2133ASNASNGLUGLU(chain 'D' and (resid 1 through 159 or resid 161 through 191 or resid 193 through 215))DD161 - 191161 - 191
2143HISHISARGARG(chain 'D' and (resid 1 through 159 or resid 161 through 191 or resid 193 through 215))DD193 - 215193 - 215

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質 ALK tyrosine kinase receptor / Anaplastic lymphoma kinase


分子量: 40499.660 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ALK / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9UM73, receptor protein-tyrosine kinase
#2: 抗体 Fab324 HeavyChain


分子量: 24516.209 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: Homo sapiens (ヒト)
#3: 抗体 Fab324 Light Chain


分子量: 23918.410 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: Homo sapiens (ヒト)
#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 / 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: 8 / 由来タイプ: 合成 / 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
研究の焦点であるリガンドがあるかN
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: 3.59 Å3/Da / 溶媒含有率: 65.72 %
結晶化温度: 287 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 40mMPolyamines, 0.1M Gly-Gly/AMPD pH8.5 12.5% w/v PEG4000 20% w/v 1,2,6-Hexanetriol

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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: ESRF / ビームライン: ID23-2 / 波長: 0.8731 Å
検出器タイプ: DECTRIS PILATUS3 2M / 検出器: PIXEL / 日付: 2018年3月1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: 0.8731 Å / 相対比: 1
反射解像度: 2.8→48.04 Å / Num. obs: 55385 / % possible obs: 99 % / 冗長度: 5.8 % / Biso Wilson estimate: 39.47 Å2 / Rrim(I) all: 0.25 / Net I/σ(I): 7.7
反射 シェル解像度: 2.81→2.96 Å / Num. unique obs: 6835 / Rrim(I) all: 1.2

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
PHENIX1.17.1_3660精密化
XDSデータ削減
XDS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: 5NUZ

5nuz


解像度: 2.81→48.04 Å / SU ML: 0.3401 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 29.1544
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2664 2009 3.76 %
Rwork0.2276 51376 -
obs0.2291 53385 99.03 %
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: 49.13 Å2
精密化ステップサイクル: LAST / 解像度: 2.81→48.04 Å
タンパク質核酸リガンド溶媒全体
原子数10652 0 112 0 10764
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004811023
X-RAY DIFFRACTIONf_angle_d0.866814965
X-RAY DIFFRACTIONf_chiral_restr0.07191620
X-RAY DIFFRACTIONf_plane_restr0.00651946
X-RAY DIFFRACTIONf_dihedral_angle_d14.38083892
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.880.34971220.30983222X-RAY DIFFRACTION87.68
2.88-2.960.30411480.2913613X-RAY DIFFRACTION100
2.96-3.040.29871470.27913657X-RAY DIFFRACTION99.97
3.04-3.140.29311350.26783668X-RAY DIFFRACTION99.74
3.14-3.250.30671510.25883647X-RAY DIFFRACTION99.82
3.25-3.380.30321440.25543661X-RAY DIFFRACTION99.92
3.38-3.540.26811410.24693681X-RAY DIFFRACTION99.92
3.54-3.720.24591330.23153686X-RAY DIFFRACTION99.87
3.72-3.960.27611460.21853685X-RAY DIFFRACTION99.97
3.96-4.260.24581440.20263704X-RAY DIFFRACTION99.95
4.26-4.690.20091480.16543718X-RAY DIFFRACTION100
4.69-5.370.23921460.18223745X-RAY DIFFRACTION99.97
5.37-6.760.25151500.22223773X-RAY DIFFRACTION99.95
6.76-48.040.29251540.23843916X-RAY DIFFRACTION99.56
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)
12.10325414996-0.4791794428390.2985084685232.78043086792-0.1906893403112.71049507808-0.1860322127-0.3818031602320.01514202134690.399317975459-0.0184334680731-0.03549414465690.0318270721325-0.0564138605970.1199523245170.1924092169540.0231108463452-0.03858189148740.2496092937360.007367066268340.159277892165-4.8173240944-20.2181220959-21.2662007807
24.88818021348-1.993926882942.319588243642.93716062648-2.123386650673.757614341770.176510470281-0.05056973468280.281192242224-0.2171824143980.132039615398-0.005511048304010.08493404326310.0153780411248-0.1603291528490.193838889224-0.015248907160.02651714533850.124086923606-0.09551534645010.294593281851-8.6890362935-9.47787539994-31.8865702707
37.071019995091.09689358159-1.780672827678.326272502390.4794537196755.219929302460.104987507341-0.6951119486060.02892910142650.3150586084080.41792023082-0.8660604466020.126688538390.760427756532-0.4375368048120.3113099246060.134989595278-0.001651469406570.278941192696-0.06732908204160.3424902367188.80306972851-22.5299735487-23.6105966968
43.20105733687-3.844596943723.002625385164.62509705575-3.616369231112.822734408860.2390409130960.0206358026679-0.326592979443-1.105402144090.001911331066430.2272942980510.5596129520350.0811706223657-0.3243469466250.527042608594-0.0385656008450.01132655995540.246657412481-0.002464269601560.275529344226-6.44448449199-16.4634732656-44.9350596087
51.05493321584-0.9938799979760.7339753164323.35453685458-0.3695315582220.9073650601280.04399754928060.1117958436980.33041270854-0.147767136938-0.201876931826-0.5022705922290.01962343876090.2144321512090.1227218732070.22117185753-0.01562191186640.06927105144560.2386725276550.05361550804960.3647645981952.87093884694-10.2049334389-37.0858991997
62.867973093430.620485654816-0.8930155356221.605508825731.923653935263.32651258554-0.165844375612-0.0307960794274-0.246859050570.000467893092673-0.2065712573980.4447254656650.3590788221920.175872563070.2413457632040.1870148711380.04552413918270.003638309970670.2442395541480.03473216730050.200279403234-6.18512183458-29.3819666018-27.7676727768
71.455530223321.125622137230.3695045279593.69006455091-1.87400045161.7495970899-0.0887080212388-0.345152005228-0.1177393450310.663259898247-0.232043647070.212019198125-0.00848052833166-0.4470229911670.1691762699290.3745976679980.03862469612960.2335739680260.4686893897950.06336133728860.300268608956-54.2416705195-12.3228067807-16.475616813
81.72364705632-0.404240724710.4433901511182.33592206098-0.7447238294322.56089304135-0.0359463220244-0.22858595953-0.1316285185820.130759260979-0.01758789156160.3284891903070.0175080668237-0.02961086594620.01270837271640.173567003511-0.004534313483810.06384028339450.184248763132-0.04024179571260.297573100283-50.8482174097-11.9859243529-27.000162763
92.14272805889-0.5973231312140.266421764410.999617797611-0.3489222924482.25006006807-0.440652383995-1.07078761432-0.4039526823520.220546707780.4377359896620.1128168327250.564664498320.4382806177250.08248155086340.6783042464910.3269296302390.2721472645961.149163081250.4340587885770.416188977867-36.694745185-29.45748700540.700016851592
104.50748840451-0.557010022604-0.3775224045161.64111628014-1.025058473075.92716142175-0.410081772517-0.715259945261-0.9205919062230.1915487687780.0153937714-0.205346597920.5413311874180.7646157559420.2775914054490.6366282555610.210683376890.3663388233430.8993628933990.3952758140150.589209725317-37.1208965637-32.8884241248-3.63762727305
110.903463047057-0.6147159794930.7024566420442.50415252777-0.5558533847820.541967551721-0.323006193487-1.39496507522-0.1536761319091.188428710410.0222079457623-0.3029728054970.5424495161620.6944629163240.1557558676691.056669566780.3531091487990.0812326103851.833371574090.1764523379740.496903150679-30.9218247101-29.17636890089.50240765872
120.4176836925630.03959980199290.04465195962731.44096600985-1.053990942961.12147461002-0.024083894079-0.128241766325-0.0941746157337-0.000147756527423-0.270992116889-0.3500228804150.5326201638870.8859371226410.2830523987670.995616090960.2646328308430.3876147238481.525232951510.4632707548950.685181733551-36.6490586593-30.991580265510.8605594891
134.043301135270.2375123453372.581818902280.6734897852460.4581204059181.83402850696-0.1013916734980.060744170295-0.614413579080.1353860036520.339631476166-0.09168378499230.06659938142820.0287720822538-0.2517247998040.209595036407-0.02281308958610.04195467641510.1645481672430.003215464534970.338011948578-26.5625998614-20.3872159529-30.5285092773
144.99253772958-0.04777310332583.264125977911.384108091830.5731698755044.165983773330.208899063590.527170989395-0.531736700854-0.234899495726-0.2413406493380.16210977592-0.0154359909068-0.0678189857563-0.07119257924640.2214727034220.03810759286440.0931506750010.324235442548-0.04026596206810.130342912677-34.2055085309-13.7895824619-42.2324807257
153.427004870950.5852060184720.6449848993612.47205592761-0.5784440110341.21207561043-0.118092134392-0.2228041782660.21521447231-0.02799049715710.327657834799-0.117709478603-0.07177009244760.115661021387-0.06008421359940.235473164682-0.0009853453500170.06755383869720.17304034837-0.02702746383240.212666525695-30.5269216326-9.64570599118-30.5556432673
163.48061015737-0.9410414586730.5200475545292.14242652938-0.769708635260.893901660272-0.318976114942-0.47132940135-0.3435730979770.2359558312170.3368368744960.214734001933-0.02644905728-0.169316231174-0.04202183216990.3143760805780.01837415586420.08463229015980.1747521573110.01507368685040.231729081121-29.2859355388-17.9931174978-26.1520788617
170.210859545424-0.0143765565242-0.03689006234210.3434238252310.3644205424970.56245151318-0.178621030563-0.369809351711-0.5656507381820.2520153828620.04143443471990.2382817536760.2766158327-0.126362965760.5350834921460.7404727265270.2553252709860.5478807701641.114131844860.7150166102341.44255397519-32.1170539724-42.53793833252.95959529015
180.310244763430.3991458417860.2702294379930.916281735830.3165793650410.24123761866-0.480756355323-0.255735870671-1.035620311250.1409330592680.03397640064830.1750422655620.502053527888-0.391199474674-0.07973603809140.7444249862410.1513714663030.6408229029270.7032749900550.3752380348411.15775986533-27.7861456641-39.7522185031-9.52019075674
190.109239945961-0.3214564457890.1900025205031.39845667778-0.4412321291250.338456995664-0.443418246759-0.125166994557-1.28722500358-0.2734948396280.2573628946930.1251610146120.743740963963-0.322380798764-0.06356328637030.900834226752-0.06093458721410.4818319872570.6557944224890.3759613615651.39836597267-33.9587311372-45.7087542334-12.2569046381
205.03633190982-1.05918381018-3.418717986317.33305253445-0.7644921990093.48422420559-0.418039514675-0.9206214234850.06055404010021.04532157447-0.336723704843-0.0427414715283-0.01182656716490.3766314620760.6921750472760.4614798777040.2070852990780.0270087611560.805978377266-0.05109328882070.380106957042-23.5280897734-24.5690444747-11.1603656771
210.9117303133160.03497973730941.445589314955.53966969004-1.332175039212.623877451410.0988643759483-0.00943124762298-0.7654424202130.2506322221820.1077780746250.3138175576710.152011452221-0.457049807425-0.1319089382970.807475417310.2556414445290.4550810343960.9534893935090.6719066153661.74209604834-33.5320640063-49.208773239-4.04365549991
220.6158095779491.38975311847-0.4013563077465.59372824535-3.314677695722.62121815164-0.0974052221098-0.63200122285-0.570896154743-0.02965001445930.2260747630810.4948463923170.241971578401-0.187104774786-0.1380959139160.9407412247860.387349969640.4094337078510.8300651181240.6354885753871.31617993814-20.9560252829-46.0726861088-7.37307643873
232.8595096801-0.582339022495-0.9817564279080.7971499248570.07949143558410.8219800926-0.149865367240.3399009485230.448364126130.01165328879020.1145366694960.01297891275870.0863889483113-0.154728318753-0.05528947422940.30547488506-0.0699255665651-0.03731775600750.1537878219370.02673840696840.289625344721-24.232717917525.5692225696-37.1303110888
242.72780321594-0.850300008049-0.3811516347681.194216854420.4433951173850.832456852389-0.109408733149-0.1617726341610.226593071991-0.02751287175240.151302168859-0.0416750991572-0.09487683984550.000138420281129-0.04152942348070.176063261157-0.00642283436393-0.05262158568310.121513927144-0.009002783337270.262163212017-24.786647214122.4824760862-29.0179319828
251.977638099391.452261641461.502119994941.770282539670.8999267423191.57382635269-0.569029141622-0.5488479394251.023933075680.4453620045210.47976752122-0.579757963352-0.5059649596550.3829593591540.3683374508640.6261020679510.222169048899-0.6639555138380.744941037849-0.6237479656620.918697381043-24.556859228448.8844074255-5.82507417456
260.445025369933-0.694481061156-0.4439255932881.085440429020.6936803487950.4427373108530.1537285794160.01339614053151.15157485602-0.692332646523-0.26899645726-1.3180094391-0.6797415343280.02950293381860.1688448353181.335846939920.305584343729-0.6869907323560.627943777793-0.1593419901471.75877668728-24.652704512459.5826341841-13.4357827473
273.945471196165.77947732131.267677781848.949623862933.231568767354.66738286186-0.613961730826-0.1451048041090.8503169870640.1136852816050.748590797441-0.0528671675846-0.6528912372120.0303073003118-0.3246797782380.402665795490.0759915039847-0.2251974936760.375651265498-0.05997923866720.637199562878-26.142185952740.5647152225-13.2934407873
280.1364930275250.2534120229180.005157389712120.6192372311780.1826915513270.192245813519-0.218263225817-0.4067030858650.8585181151260.01090004975320.0563527430606-0.127464543931-0.3597724574270.001733780225720.1242965563381.179306927090.188407384936-0.7047126306150.500358120978-0.5459836601281.60467234253-25.417334116957.4567507923-7.41960495675
291.52952004156-0.1185421992150.3158652906861.05687697070.8109841559612.20026271723-0.0829637167224-0.379361431442-0.00454304066310.0377153496080.14968515863-0.101307116858-0.14209622349-0.0769179431333-0.08520302514450.19417494010.0030772770163-0.05574420437560.2610675389050.009028283314870.288281259764-6.1758770248925.7173326792-19.5474481524
303.38312957896-0.0879745594323-1.538843175892.427843336240.4991476273081.4493010326-0.160218943354-1.35362703424-0.05258644024920.48808274115-0.01800498588290.0635354262106-0.732473701874-1.0332052126-0.07530077432580.481077200780.27268046965-0.07492101126071.28108655502-0.1616036379690.375262125555-20.656156786240.0415643622.2743191839
312.70533072294-0.794551298423-0.7627494234262.772122182811.197426752682.37735429391-0.0887377863596-0.1166323714440.09113687884280.105861345250.1138922219940.0115225012474-0.118975578741-0.260594115489-0.02070758990920.1533296074360.00597741876839-0.03857479891830.1579522904550.05349141358170.217263639669-50.651459231826.1145744027-25.164808237
323.92251582881-5.72049324356-3.139318030588.537738284034.721067838732.606474134510.5461950029340.4331812165140.231340243688-1.47897536592-0.313261532816-0.479076027322-0.8693816436720.0024104403871-0.2834100635450.533671132232-0.02151515424510.02748483576570.304435371187-0.03084023783370.260194963209-48.46564207524.5971418047-45.4287399145
331.57110642116-0.937718266622-0.4681248361153.07648496398-0.02461283408130.673653667698-0.06211631803150.242296426239-0.182814557114-0.2522955012050.006064383754130.3375545540820.0335561810226-0.1590305923330.0246144603620.230536420221-0.00453323744481-0.08361650333710.253355391472-0.008723462726470.291490944195-57.701037769418.5766856094-37.4151151734
342.33119080648-0.519869087152-0.03809555026042.21518132819-0.9847817050211.55889214393-0.0372620126621-0.3041401741650.5569352460030.09323111339980.0594029348003-0.41696564448-0.1523214339170.12495810955-0.1761060426720.156976431104-0.0161120354615-0.006877469842150.29133588129-0.06100057308280.281245570549-48.741829598738.0559768927-28.4282740271
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 678 through 765 )
2X-RAY DIFFRACTION2chain 'A' and (resid 766 through 824 )
3X-RAY DIFFRACTION3chain 'A' and (resid 825 through 841 )
4X-RAY DIFFRACTION4chain 'A' and (resid 842 through 861 )
5X-RAY DIFFRACTION5chain 'A' and (resid 862 through 965 )
6X-RAY DIFFRACTION6chain 'A' and (resid 966 through 986 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 25 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 176 )
10X-RAY DIFFRACTION10chain 'B' and (resid 177 through 192 )
11X-RAY DIFFRACTION11chain 'B' and (resid 193 through 210 )
12X-RAY DIFFRACTION12chain 'B' and (resid 211 through 220 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 18 )
14X-RAY DIFFRACTION14chain 'C' and (resid 19 through 36 )
15X-RAY DIFFRACTION15chain 'C' and (resid 37 through 79 )
16X-RAY DIFFRACTION16chain 'C' and (resid 80 through 117 )
17X-RAY DIFFRACTION17chain 'C' and (resid 118 through 130 )
18X-RAY DIFFRACTION18chain 'C' and (resid 131 through 154 )
19X-RAY DIFFRACTION19chain 'C' and (resid 155 through 167 )
20X-RAY DIFFRACTION20chain 'C' and (resid 168 through 178 )
21X-RAY DIFFRACTION21chain 'C' and (resid 179 through 201 )
22X-RAY DIFFRACTION22chain 'C' and (resid 202 through 216 )
23X-RAY DIFFRACTION23chain 'D' and (resid 1 through 36 )
24X-RAY DIFFRACTION24chain 'D' and (resid 37 through 117 )
25X-RAY DIFFRACTION25chain 'D' and (resid 118 through 148 )
26X-RAY DIFFRACTION26chain 'D' and (resid 149 through 159 )
27X-RAY DIFFRACTION27chain 'D' and (resid 160 through 178 )
28X-RAY DIFFRACTION28chain 'D' and (resid 179 through 216 )
29X-RAY DIFFRACTION29chain 'E' and (resid 2 through 165 )
30X-RAY DIFFRACTION30chain 'E' and (resid 166 through 220 )
31X-RAY DIFFRACTION31chain 'F' and (resid 678 through 841 )
32X-RAY DIFFRACTION32chain 'F' and (resid 842 through 861 )
33X-RAY DIFFRACTION33chain 'F' and (resid 862 through 965 )
34X-RAY DIFFRACTION34chain 'F' and (resid 966 through 986 )

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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