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- PDB-6tyh: Four-Disulfide Insulin Analog A22/B22 -

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基本情報

登録情報
データベース: PDB / ID: 6tyh
タイトルFour-Disulfide Insulin Analog A22/B22
要素
  • Insulin A chain
  • Insulin B chain
キーワードHORMONE / Signalling / metabolism
機能・相同性
機能・相同性情報


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / Insulin receptor recycling / transport vesicle / insulin-like growth factor receptor binding / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / Regulation of insulin secretion / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / cell-cell signaling / insulin receptor signaling pathway / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding
類似検索 - 分子機能
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
類似検索 - ドメイン・相同性
ACETONE / PHENOL / Insulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 1.60001899481 Å
データ登録者Blakely, A.D. / Xiong, X.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK120430 米国
引用ジャーナル: Chem Sci / 年: 2020
タイトル: Novel four-disulfide insulin analog with high aggregation stability and potency.
著者: Xiong, X. / Blakely, A. / Karra, P. / VandenBerg, M.A. / Ghabash, G. / Whitby, F. / Zhang, Y.W. / Webber, M.J. / Holland, W.L. / Hill, C.P. / Chou, D.H.
履歴
登録2019年8月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年11月13日Provider: repository / タイプ: Initial release
改定 1.12019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22020年3月11日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.32024年10月30日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
I: Insulin A chain
J: Insulin B chain
K: Insulin A chain
L: Insulin B chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,36127
ポリマ－35,20012
非ポリマー1,16115
水4,161231
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area20020 Å2
ΔGint-263 kcal/mol
Surface area14080 Å2
手法PISA
単位格子
Length a, b, c (Å)47.231, 61.821, 60.468
Angle α, β, γ (deg.)90.000, 112.814, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

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タンパク質・ペプチド , 2種, 12分子 ACEGIKBDFHJL

#1: タンパク質・ペプチド
Insulin A chain


分子量: 2486.841 Da / 分子数: 6 / 断片: ADD ENGINEERED MUTATION INSTEAD OF EXPRESSION TAG / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308
#2: タンパク質・ペプチド
Insulin B chain


分子量: 3379.902 Da / 分子数: 6 / Mutation: R22C / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308

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非ポリマー , 6種, 246分子

#3: 化合物
ChemComp-IPH / PHENOL / フェノ-ル


分子量: 94.111 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C6H6O
#4: 化合物 ChemComp-ACN / ACETONE / アセトン


分子量: 58.079 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H6O
#5: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#6: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#7: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 231 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるか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: 2.35 Å3/Da / 溶媒含有率: 47.71 % / 解説: Thick plate crystals
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: Sodium Citrate, Phenol, Acetone, Zinc acetate

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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: SSRL / ビームライン: BL9-2 / 波長: 0.97946 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2019年5月12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: 0.97946 Å / 相対比: 1
反射解像度: 1.6→35.6 Å / Num. obs: 81415 / % possible obs: 98.5 % / 冗長度: 13.2 % / Biso Wilson estimate: 21.35 Å2 / CC1/2: 1 / Net I/σ(I): 20.8
反射 シェル解像度: 1.6→1.65 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4121 / CC1/2: 0.87 / Rpim(I) all: 0.263 / % possible all: 97.01

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解析

ソフトウェア
名称バージョン分類
PHENIX1.12_2829精密化
Cootモデル構築
XDSデータ削減
XDSデータスケーリング
AutoSol位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 1.60001899481→35.5952808097 Å / SU ML: 0.164928287021 / 交差検証法: FREE R-VALUE / σ(F): 1.3364811245 / 位相誤差: 20.7705324969
Rfactor反射数%反射
Rfree0.195794509938 8100 9.9 %
Rwork0.162466996866 --
obs0.165802433142 81415 98.5 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 35.0875371384 Å2
精密化ステップサイクル: LAST / 解像度: 1.60001899481→35.5952808097 Å
タンパク質核酸リガンド溶媒全体
原子数2379 0 73 231 2683
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006491379359252711
X-RAY DIFFRACTIONf_angle_d0.8325739040193695
X-RAY DIFFRACTIONf_chiral_restr0.0493526148438401
X-RAY DIFFRACTIONf_plane_restr0.00416334529703472
X-RAY DIFFRACTIONf_dihedral_angle_d13.79279071021591
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.60001899481-1.61820.3060158082852160.2805544621011930X-RAY DIFFRACTION76.0453579022
1.6182-1.63720.2894865591492780.2483358583672530X-RAY DIFFRACTION99.433427762
1.6372-1.65720.2422191314742640.2340277194732387X-RAY DIFFRACTION98.6602158541
1.6572-1.67820.2178993690772800.225962025862523X-RAY DIFFRACTION98.6971830986
1.6782-1.70030.2434241456842710.206786919692454X-RAY DIFFRACTION98.8393180994
1.7003-1.72360.2570202638532740.2064263351762435X-RAY DIFFRACTION98.8686131387
1.7236-1.74820.2457262156732610.222184987862443X-RAY DIFFRACTION98.5422740525
1.7482-1.77430.2606372808822720.2219942303642477X-RAY DIFFRACTION98.1785714286
1.7743-1.8020.2611226162432660.2168053074382448X-RAY DIFFRACTION97.5557153127
1.802-1.83150.2364419662172630.2077002963752427X-RAY DIFFRACTION97.0418470418
1.8315-1.86310.2376206939682760.1992630156332435X-RAY DIFFRACTION99.1224862888
1.8631-1.8970.2163834180832760.1848726090352508X-RAY DIFFRACTION99.1452991453
1.897-1.93350.2387574345772730.1893026756542440X-RAY DIFFRACTION98.225923244
1.9335-1.97290.2152413956372730.1775927250162465X-RAY DIFFRACTION98.951933502
1.9729-2.01580.2006852264592740.1824949829152489X-RAY DIFFRACTION98.8197424893
2.0158-2.06270.2142820475442730.1804841958092487X-RAY DIFFRACTION98.0810234542
2.0627-2.11430.2362070285392860.175443095722390X-RAY DIFFRACTION97.5574188844
2.1143-2.17150.2161064010372710.1683632754222407X-RAY DIFFRACTION97.0993473532
2.1715-2.23530.2061437030972700.1688356343162456X-RAY DIFFRACTION97.7411258516
2.2353-2.30750.2027815682192650.1649196314412442X-RAY DIFFRACTION99.0849194729
2.3075-2.38990.1891984988032710.1541832893672473X-RAY DIFFRACTION99.2405063291
2.3899-2.48560.1996435300692830.1573448558942531X-RAY DIFFRACTION99.0496304118
2.4856-2.59870.2078508468962590.1633153701582467X-RAY DIFFRACTION98.8397389413
2.5987-2.73570.2066282720182790.163745906932440X-RAY DIFFRACTION98.052650559
2.7357-2.9070.1955875913482530.1611011733682449X-RAY DIFFRACTION98.0406386067
2.907-3.13130.2055589333982680.1605620166972502X-RAY DIFFRACTION99.4256999282
3.1313-3.44620.1823944251452930.1503643004372476X-RAY DIFFRACTION99.5685005394
3.4462-3.94430.165128026012640.1307499409162464X-RAY DIFFRACTION98.7690079652
3.9443-4.96730.1563833787212660.1234677340562468X-RAY DIFFRACTION99.1298042059
4.9673-35.5952080.1623464619322780.155644034842476X-RAY DIFFRACTION98.9224137931
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)
13.145792524350.625076903916-4.695197196026.61896717649-1.227244544817.02955341359-0.1833010156231.746492214261.39184298894-0.8081416750960.2294745499030.691405958059-0.248580778523-0.332623719911-0.1651756075750.381846884251-0.0648762869876-0.1025226678250.6140212696730.2439518699850.50125906245810.89680569551.56650087876-2.76047598658
22.48827242775-2.52961269639-3.675748259354.822407266112.593593225756.04579665935-0.2001130925231.82839689642-0.128868586148-0.8651208942610.2184295712391.571393224540.395011638627-0.548621660063-0.1380132848330.401348061922-0.0320374979796-0.1334413744210.9261645084010.0361604522920.4348931586743.02571199035-7.39438191937-2.18387041587
33.526224800752.62155603415-2.53925521965.50517550201-2.480505562794.26049287613-0.04683606315630.380239036734-0.211023276296-0.06574594599260.005341632628240.1430308753040.0290050592923-0.3542054842650.03119307706410.190430653485-0.004740010252590.009593791128440.131803898387-0.01366646611560.15563670353213.3405717097-6.309320882293.64975106045
45.026864125525.17040048713-3.976740584465.49772306189-4.273131510993.33065250242-0.356352852421.250437479490.903771713271-0.8297311039960.1816773911990.9042800739720.00877481341086-0.09029329079250.255833279250.568303137241-0.0495475233043-0.04860442846210.4817636763120.0273178878810.36322813983712.5773330813-11.3119423055-2.93567316032
54.362062752624.25988438218-4.755200023514.31169556179-4.846730944935.451842157080.22098939584-1.07041174192-0.4207120804440.639982837336-0.636068355918-0.500492134305-0.05300621334770.7657499201840.3814415219110.358507040557-0.0207898170825-0.04603074640920.3523651435930.06639044642670.35785363101324.8259186448-14.610912272530.2635808808
66.622980298173.58566124461-4.795089240436.47977289962-0.8632542067446.866275583650.77397328094-0.8430690266570.1083144177541.21244221866-0.345956375377-0.274996213105-0.2299281457540.602249240497-0.3142750301760.392158797775-0.0300411113788-0.08196980040680.3164797891490.004259037730950.29835593107724.9941585422-6.4723732523130.5659655015
73.442729480661.013434417790.508263513867.077745548933.249768104174.29943001-0.0290313777234-0.109045393789-0.192540840108-0.00443714783240.0259971390799-0.549147732444-0.06164839121660.1128877930510.04330944105310.145531901220.01171243008110.03031611933280.145868984910.02800599434070.15763776120323.5618863263-8.1817281738521.1609741582
84.54425540866-4.17864455396-0.9650071051295.57499077994-1.14706924666.352243325980.100397731198-0.870586438668-0.5383125948810.2788003506430.203221226617-0.7702875761310.9320671519190.143975943004-0.3186244859390.317148320859-0.0363280623056-0.0559297645910.2928299473180.08020737778280.37657532748632.5780899194-11.270285846122.2596345358
99.056174370347.904911827843.553634166938.735197191090.1073911481746.51468871796-0.3681566604180.1037516903920.934564139943-0.9879391554110.2850079844070.202287359152-0.912127246221-0.1353124934370.1460451047930.5834920444180.0670102877660.06505456736720.336625944591-0.05378987346470.3632754364116.761874431112.736499516316.6093100983
106.811439615550.819669390518-2.156403409854.307180279971.086379848435.8567085382-0.344536915748-0.406042104463-0.1175394331930.07813305782290.2063940433540.06759873014890.3155577462240.1903998765570.1620551129040.3036679079870.03210324846660.03048891804170.192904944985-0.03840718885190.24514632510413.54658827239.1148320302427.6724817956
115.38028781479-0.121925831543-1.18888339116.42695908605-0.8227577173036.21223083253-0.02052876646930.2589920829170.143502768359-0.1983208429660.06646140170030.206527568434-0.2391184585830.16416809885-0.09305529876280.206115295910.004856675558880.0157503675970.079069832242-0.006377132313610.18990395392313.5426983662.7910164870317.3040863257
126.29247296205-1.090176007740.2264766776233.897534216321.526170942560.66618822941-0.04232564507550.6065509927150.444350327992-0.151548474388-0.2813626763990.625624394397-1.26895801542-0.5905454897620.2050947275130.5177183835330.1084991391820.02023076775410.240832209496-0.01335854937820.3349818880715.797453964867.7978444541820.3515274029
139.6979614283-2.468575104344.528103945629.16208207647-2.175763610752.304318787860.0236284415072-0.0507163699753-0.891564341852-0.255671155-0.0357224236088-0.09933227793331.19613170889-0.0670698053166-0.06123049572590.487622647334-0.03973783519380.04927988991060.225220427184-0.02403688970630.27237503912614.0794143126-25.62519584648.38664318553
145.859332896224.39383651041-5.108326606095.3254245377-4.441810996924.74214444403-0.508022609993-0.116494315542-0.7899624973110.31564212978-0.006177800065640.01139829343950.566343617548-0.184511294610.5461151030410.368493464410.03123808074890.04508152796820.245019333353-0.03320284270130.23773913990819.7762159687-24.682042553212.4751375063
154.574522194490.3390006194374.563126963827.14834962061-1.739362441648.12265365983-0.144968696660.409416939664-0.136484615181-0.3705221706540.113037183765-0.19458007844-0.2725485963060.4347267956130.007269365314140.340515411365-0.003089012511520.07773530991180.205482360377-0.07058444165960.28707559546222.6147530448-21.78931178840.872033614468
167.732199620861.29735677931-3.359368994494.360756286970.02610309413252.56484735844-0.239233505554-0.18099248456-0.0747124839723-0.1641927359450.0488921126162-0.005185377648490.2072144207320.0144385850110.1564887193570.222876770155-0.001064721898060.01236143208590.0988449345488-0.01148126605720.18575814972416.7156926786-15.13517883667.99217368015
174.814607285214.28417597891-5.054409858464.27633296704-4.798664721755.50833055893-0.404585990260.596764677124-0.7746972556020.2196341523620.1581919416390.6599298409920.660001832346-1.159506697370.3049690673570.558913979353-0.1358498576640.07120665880790.357354349716-0.05266989954870.42544826485611.0132516142-18.49834713311.3799841946
180.653013776137-1.22923922346-1.462025000592.803263325991.923873158144.71544303467-0.0598704131264-1.87266719029-1.634139587220.7994534996890.6976653238561.067125036040.369613564906-1.5254111731-0.5015594017940.342186872871-0.01447881174010.01890044605120.6148472160370.1937340724010.4728429225680.454891732617-10.841138397923.2124493478
195.35195601124-6.027935979225.136468086077.27994578663-5.27744001695.478710898290.760715263067-0.988345883158-1.54195942564-0.03603316850450.3581741745190.5937734426310.888097813793-0.908955548004-1.113240878250.357452842906-0.0808793780446-0.1192736164150.3367173902560.09712537059470.5644185988250.163247585112-14.335833490816.743086398
205.130744443530.3181976997950.3333193245799.029830383556.268314287398.47850147115-0.140374945867-0.6498951202820.502500832141-0.0867550623837-0.03541054997120.657568279557-0.453034120968-0.4718410912020.1620259457270.1790397955420.009183525708850.0073380284190.256273561203-0.03001311465730.42269066249-3.02442226515-2.8988966768314.6680176039
214.7592552939-2.8936791753.851940092846.68799723443-5.770120652138.04564623096-0.222181077571-0.01078844589280.1595102657370.1788784437860.1071087977720.151269417023-0.301794884464-0.1840730599680.16004108810.1951315514820.0106678445010.02820253901450.0999203296328-0.0180452001880.1442063832917.45307698058-5.0884795715818.361673129
225.116725200511.05794504951.5840420952.135038363550.2334804267336.58535445920.0707818990719-1.2037773613-0.2600794126910.827291102164-0.1241332304610.9747494676840.306160223383-0.77853163859-0.1220635160090.40984433164-0.0101141587870.201240798920.424551657760.006491079486670.4543301659153.10097675295-0.13647160939924.5721540372
236.67682478565-3.660866290513.303640541042.88950747959-0.1652625867867.619689051410.07188599736680.2428079663690.27150858421-0.172437133849-0.181199946471-0.671917019434-0.3114261481950.4555658232490.09186546458530.259903490518-0.03833671925890.04005558012180.2149446125880.05380922141750.29071654931433.2767896059-0.9627969392374.36458635755
243.902612059810.4913463661443.455849093688.82535591906-3.032626356544.832418927430.08566606452630.3145635214880.157235769913-0.3164399721-0.411817767403-0.9804585210130.5720643584551.029081951520.3005162054460.2343987970920.02465089662160.04524213334550.325414668140.01860930993640.38324094054336.4229174095-11.59486416588.45101448106
255.06907783581-0.807067206394-0.1308001135525.386263104650.1350184044373.47738231024-0.0351941242419-0.1128746397830.02131920769010.123758774897-0.00131992081452-0.161907681645-0.2370107376240.1349782063650.08219880388250.168805317991-0.03275708755760.02570907092210.118574329409-0.00190444092640.1008979218926.9973360557-5.0528765057412.5989309236
264.43728491234.01553942748-1.586800039994.77495889721-4.242403785357.477264541260.3958042524620.2605306273090.495045928878-0.143601931898-0.285133761374-0.507183783372-0.4942917572120.7638670201840.1401342957970.342294066674-0.03766113152510.07782797469270.2994505681660.08890723909430.38024998874634.3655568115-3.3747791584315.9326353459
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 22 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 22 )
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 29 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 6 )
6X-RAY DIFFRACTION6chain 'C' and (resid 7 through 22 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 22 )
8X-RAY DIFFRACTION8chain 'D' and (resid 23 through 29 )
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 12 )
10X-RAY DIFFRACTION10chain 'E' and (resid 13 through 22 )
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 22 )
12X-RAY DIFFRACTION12chain 'F' and (resid 23 through 29 )
13X-RAY DIFFRACTION13chain 'G' and (resid 1 through 6 )
14X-RAY DIFFRACTION14chain 'G' and (resid 7 through 12 )
15X-RAY DIFFRACTION15chain 'G' and (resid 13 through 22 )
16X-RAY DIFFRACTION16chain 'H' and (resid 1 through 22 )
17X-RAY DIFFRACTION17chain 'H' and (resid 23 through 29 )
18X-RAY DIFFRACTION18chain 'I' and (resid 1 through 7 )
19X-RAY DIFFRACTION19chain 'I' and (resid 8 through 12 )
20X-RAY DIFFRACTION20chain 'I' and (resid 13 through 22 )
21X-RAY DIFFRACTION21chain 'J' and (resid 1 through 22 )
22X-RAY DIFFRACTION22chain 'J' and (resid 23 through 29 )
23X-RAY DIFFRACTION23chain 'K' and (resid 1 through 12 )
24X-RAY DIFFRACTION24chain 'K' and (resid 13 through 22 )
25X-RAY DIFFRACTION25chain 'L' and (resid 1 through 22 )
26X-RAY DIFFRACTION26chain 'L' and (resid 23 through 29 )

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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