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- PDB-6zej: Structure of PP1-Phactr1 chimera [PP1(7-304) + linker (SGSGS) + P... -

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基本情報

登録情報
データベース: PDB / ID: 6zej
タイトルStructure of PP1-Phactr1 chimera [PP1(7-304) + linker (SGSGS) + Phactr1(526-580)]
要素Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
キーワードHYDROLASE / PP1 / Phosphatase / Phactr / RPEL
機能・相同性
機能・相同性情報


regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress ...regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / regulation of canonical Wnt signaling pathway / protein phosphatase inhibitor activity / glycogen metabolic process / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / phosphatase activity / protein serine/threonine phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / DARPP-32 events / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / lung development / adherens junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / regulation of circadian rhythm / response to lead ion / : / presynapse / actin binding / perikaryon / dendritic spine / protein stabilization / iron ion binding / cell division / synapse / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase ...RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
: / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Phosphatase and actin regulator
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 / 分子置換 / 解像度: 1.78 Å
データ登録者Mouilleron, S. / Treisman, R. / Fedoryshchak, R. / Lee, R. / Butler, A.M. / Prechova, M.
引用ジャーナル: Elife / 年: 2020
タイトル: Molecular basis for substrate specificity of the Phactr1/PP1 phosphatase holoenzyme.
著者: Fedoryshchak, R.O. / Prechova, M. / Butler, A. / Lee, R. / O'Reilly, N. / Flynn, H.R. / Snijders, A.P. / Eder, N. / Ultanir, S. / Mouilleron, S. / Treisman, R.
履歴
登録2020年6月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年9月30日Provider: repository / タイプ: Initial release
改定 1.12020年10月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22024年1月24日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
I: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
L: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
O: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)250,36226
ポリマ－248,9966
非ポリマー1,36620
水12,142674
1
D: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,6093
ポリマ－41,4991
非ポリマー1102
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,8556
ポリマ－41,4991
非ポリマー3565
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,7014
ポリマ－41,4991
非ポリマー2023
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
I: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,7014
ポリマ－41,4991
非ポリマー2023
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
L: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,6093
ポリマ－41,4991
非ポリマー1102
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
O: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,8856
ポリマ－41,4991
非ポリマー3865
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)137.370, 137.370, 238.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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要素

#1: タンパク質
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator / PP-1A


分子量: 41499.309 Da / 分子数: 6 / 変異: N-terminal Vector derived sequence GHMGS / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PPP1CA, PPP1A, PHACTR1, hCG_1818446 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P62136, UniProt: Q4VY12, protein-serine/threonine phosphatase
#2: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Mn
#3: 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: 7 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6O2
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 674 / 由来タイプ: 天然 / 式: H2O
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: 2.69 Å3/Da / 溶媒含有率: 54.23 %
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 / pH: 8.4 / 詳細: 20% PEG 3350, 0.2M Potassium Citrate

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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: Diamond / ビームライン: I04-1 / 波長: 0.911 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2019年11月29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: 0.911 Å / 相対比: 1
反射解像度: 1.78→68.68 Å / Num. obs: 241814 / % possible obs: 99.7 % / 冗長度: 20.7 % / Biso Wilson estimate: 26.42 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.04 / Rrim(I) all: 0.18 / Net I/σ(I): 12.9
反射 シェル解像度: 1.78→1.84 Å / 冗長度: 21 % / Rmerge(I) obs: 3.18 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 24087 / CC1/2: 0.54 / Rpim(I) all: 0.7 / Rrim(I) all: 3.26 / % possible all: 99.6

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18_3845精密化
PHENIX1.18_3845精密化
xia2データ削減
Aimless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: 4MOV

4mov


解像度: 1.78→68.68 Å / SU ML: 0.2931 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.8105
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2714 12173 5.04 %
Rwork0.2418 229225 -
obs0.2433 241398 99.72 %
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: 41.03 Å2
精密化ステップサイクル: LAST / 解像度: 1.78→68.68 Å
タンパク質核酸リガンド溶媒全体
原子数16660 0 58 674 17392
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.010617102
X-RAY DIFFRACTIONf_angle_d0.839623135
X-RAY DIFFRACTIONf_chiral_restr0.05232501
X-RAY DIFFRACTIONf_plane_restr0.00563025
X-RAY DIFFRACTIONf_dihedral_angle_d21.91346307
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80.38743940.36117623X-RAY DIFFRACTION99.52
1.8-1.820.4154590.3537543X-RAY DIFFRACTION99.6
1.82-1.840.38964230.34817611X-RAY DIFFRACTION99.63
1.84-1.870.37363900.34537606X-RAY DIFFRACTION99.76
1.87-1.890.36383960.33297602X-RAY DIFFRACTION99.63
1.89-1.920.34543960.32197635X-RAY DIFFRACTION99.7
1.92-1.940.33794110.31567695X-RAY DIFFRACTION99.83
1.94-1.970.32294400.3117581X-RAY DIFFRACTION99.7
1.97-20.36113680.30177652X-RAY DIFFRACTION99.45
2-2.040.33693980.31067672X-RAY DIFFRACTION99.75
2.04-2.070.31833960.30637625X-RAY DIFFRACTION99.81
2.07-2.110.32874130.28687633X-RAY DIFFRACTION99.89
2.11-2.150.29524110.28217668X-RAY DIFFRACTION99.9
2.15-2.190.30674140.27497583X-RAY DIFFRACTION99.8
2.2-2.240.30014350.27727652X-RAY DIFFRACTION99.9
2.24-2.290.3074320.27147623X-RAY DIFFRACTION99.84
2.29-2.350.32364050.27197617X-RAY DIFFRACTION99.84
2.35-2.420.31133610.27047706X-RAY DIFFRACTION99.93
2.42-2.490.32333950.26017653X-RAY DIFFRACTION99.8
2.49-2.570.27844190.25887676X-RAY DIFFRACTION99.82
2.57-2.660.29884310.25187557X-RAY DIFFRACTION99.9
2.66-2.770.28943770.25127721X-RAY DIFFRACTION99.99
2.77-2.890.28643700.24427674X-RAY DIFFRACTION99.9
2.89-3.040.28994060.24247681X-RAY DIFFRACTION99.9
3.04-3.230.25964370.23257630X-RAY DIFFRACTION99.9
3.23-3.480.24154270.21877635X-RAY DIFFRACTION99.93
3.48-3.830.21543860.20087733X-RAY DIFFRACTION99.98
3.83-4.390.20093970.17457675X-RAY DIFFRACTION99.96
4.39-5.530.20294200.18477702X-RAY DIFFRACTION99.9
5.53-68.680.25993660.23477561X-RAY DIFFRACTION97.25
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)
10.2049649688190.0059837953629-0.03135683110550.00512739266651-0.0253395246930.2182958041080.1144920181510.00559586289995-0.0380309877378-0.004411184245290.1319202008690.220753149265-0.0905762761754-0.1596148891520.4424559892350.587632445262-0.0226638730581-0.2349940150.1589847952420.0990345422590.35074702611862.2703554553-9.13583814116-15.3088990909
20.3146043905740.210052195472-0.0289912995360.52320081816-0.2873813218860.6284398352690.0152146039254-0.059639582212-0.167575325302-0.137570441245-0.1352912213030.0453617022119-0.3046231288580.120276153848-0.001591348848120.483902105181-0.103210125058-0.1474498020090.3151506111370.09578985151380.392741548869.9909923229-19.1958295783-7.79458586189
30.6951951599620.590784513906-0.1913880003680.6157086024190.1251107788971.012099176590.0148647131923-0.192371637507-0.1110370517280.0098567567455-0.208690730461-0.0362511381584-0.3809913998410.118855373605-0.01608806032170.40852224467-0.103765963735-0.1349980141910.4331450313270.1200014150310.38955752730670.8925209345-20.9841709723.0708439432
40.151649659977-0.02844058564510.04615167082250.00587054508102-0.01017743862670.01646699263810.0621984139477-0.181991356432-0.1690614395610.0745340449228-0.0749707491333-0.0206931285127-0.04913611110010.1833084891930.4359023023270.314419251788-0.208582547728-0.1945764731470.754416612680.3980370581830.59490084355687.4444897715-26.182528983810.5961773955
50.110136373889-0.03371737540770.04719632866230.4909360409040.09345399460330.052006591382-0.0187492877652-0.0685342981649-0.196003276014-0.000271446940226-0.0471678682262-0.258650252109-0.1343496629460.30777179620.02615895663730.362120275427-0.260484215974-0.1518521153760.5754196570760.2302158097530.47642501542287.6781097069-20.3229204546-2.10676345766
60.307013966125-0.08447453825350.2496430464660.3478157960530.1514018624120.3598238924730.181264386733-0.128074284692-0.310501133431-0.0149866763605-0.241471360808-0.0527891057373-0.005763762847070.396162528266-0.04359037577550.568951432747-0.189884331125-0.1194908294250.4232188916480.1219513542070.46134887232984.3437004187-17.0387853353-8.09400226692
70.2431796231550.05109526650230.1696226440120.09917872480680.03411623057910.1026760362270.0537054985806-0.2859203053730.09991399892170.337481574769-0.182524983673-0.296783626018-0.3420436327670.2975365780570.002465056526950.649876817543-0.163642058924-0.0647578403030.6112636538120.05826563757120.40420606975880.1170788486-5.33509995949-5.21367239157
80.26926632187-0.242271690887-0.0860755521670.3921310983450.06587836718810.0421448661811-0.0128775275477-0.3248803892230.01620629304830.148788941675-0.1660788672680.358717727809-0.711086308473-0.4214268100210.00222415496610.672230041313-0.0409485755449-0.0745830222340.562584782393-0.07734104692020.40770404809462.0526008-16.464466384317.00710228
90.147489211310.0633762514881-0.03832774062360.0289757262392-0.01860203611880.008468444663160.0796424267087-0.03459939158760.1234184770550.15005267748-0.090491739129-0.000203459813963-0.1169861996080.1483116786240.236415894510.395868858115-0.546558219113-0.09492428264240.3319402390330.3482985466110.36149809103623.173501342119.272472134923.3214606158
100.694291033089-0.0205263258038-0.4270647645560.355678019398-0.08451099878820.340660368336-0.2416087335520.248956268890.145757198674-0.06068335016180.05717730871560.0766734255644-0.261743678730.497265928738-0.05804367901370.208074461222-0.147209112626-0.04320511502230.438201836360.09573871108030.27447432424518.69144054097.3290040761730.4325435462
111.07741328966-0.134130336003-0.3513475342270.492659076064-0.02417572860430.927693040228-0.2198412969030.007176303654530.1035733493080.07076109324250.09507628742570.0709957236608-0.3021762844550.501992872013-0.04840358356720.203814860842-0.117356692995-0.05132363073460.2235612930690.08485620707330.25588091274616.535049557.8350008625238.7878836109
120.04956915123620.05029309955820.1436709246780.05039102499590.1432175742250.420788309892-0.170195443635-0.180953996243-0.2631984987070.0169448014314-0.0326196437160.1280018806960.3252541447740.43802438423-0.08201688026430.1848571504520.07704219029910.03988604288880.2972511051990.09082721745470.29200314934917.4130287654-1.8247397131149.1977442401
130.2289264518520.00901618146781-0.2084202907540.012791428575-0.003778655272420.192486137-0.160106040931-0.24157351109-0.08462668325630.0721682165460.0104361644492-0.009637800699920.2201787691860.323583851164-0.1589835399130.3076104105650.2229058740890.1397354147570.2965875561520.1286961839880.36046616444621.1402208082-10.847332975849.1060006829
140.426641522788-0.002967640075020.05841988665620.1206071165390.1600837517170.569689161163-0.2007902837120.0827261688-0.346770745864-0.07359195181970.148360899089-0.2192184272430.4196069333740.6552790873480.05136897227150.305092561220.1272250723150.07025454612050.4758535367140.04951780021860.33171936349726.7448849218-8.1094182406536.7752757669
150.119061661657-0.1071496646910.1482207041890.241659223473-0.08793404108040.192307610703-0.0759211279606-0.15679702423-0.0744051710373-0.117522613633-0.0710335085115-0.1761219187860.1760483889930.524496292373-0.002728826834330.296160401512-0.01520634071110.04303372061770.654442899826-0.0008999914857620.34498052267228.7317004483-3.1802309904631.0564293215
160.357935461477-0.1881796671110.4781963494550.100126504215-0.2500232319810.633919505219-0.03606939969750.2073328578660.115023561929-0.0762446888608-0.216102247715-0.05099545093380.01003834938730.716725658302-0.1258484035870.247646983419-0.1398553301750.02702261644560.6855957887390.0655391610640.38585908689335.13363521735.8083658312833.7944361208
170.01219106126720.0196280526519-0.003451563234540.04539691356520.01495863196410.03505808552590.0273527816037-0.1890314375470.3198429192490.107581134399-0.0241193028146-0.249490541456-0.3186897938330.4134505083992.15682878565E-50.410938049681-0.141613477217-0.03747007011430.3853569241690.03874648286340.36223042507720.340736040719.719441878856.1629907879
180.380339408230.00800969175189-0.3689371054840.00343499130019-0.008267868360190.358015273622-0.0889619209415-0.5773450614080.4717860807260.1553126439470.03231763314750.169606751149-0.5053652820680.09697585652010.03285844272610.274419452042-0.00250523237201-0.03637818953980.3272943300320.04248951655410.32491667519610.64945532111.957924574654.1590348564
190.09325090981130.0404010285234-0.061093226650.032253067849-0.01176300977380.06306414631480.0672600414654-0.01812852154790.03959235185650.1556439096870.04160263982330.0437995646372-0.2040290301390.08224370782710.4770386912150.623972877527-0.377904169611-0.1829366338780.8506770990190.4958994975960.53596690139392.2024685734-19.43172531223.8856987348
200.687148916226-0.676278553323-0.4106847472481.002874527720.5077504260620.295148116443-0.1547104108220.3949265076420.211350553758-0.170038371278-0.09365575377720.145424252898-0.4414750520580.22494947079-0.3194950047070.414725568575-0.146649773017-0.1016588466980.5636872034970.1907034151790.38575440521382.1995108322-29.76049387234.5090001176
210.2004147556930.0493988533459-0.02010633263960.0420893784816-0.03263804138350.025054532684-0.104466229810.196912894526-0.0581621563355-0.05724417694280.07738881466520.0147911260793-0.1130728661960.1996612418570.331524243450.275497181901-0.391715621015-0.1165899375930.908967763760.3192223070430.42033355219993.0862956221-32.101390160928.6024285244
220.710036832035-0.374374280348-0.2193565760430.516279497864-0.3310417022510.723762050676-0.1850850276370.1921859533980.1271562113960.1569861129280.05516362432790.112710169584-0.5144375393150.236011259591-0.0431976201250.43300920977-0.154913779832-0.0833749300730.5474675888060.2289648082990.4145586889985.9920315511-30.002027371540.2775026816
230.192866177845-0.04063843717820.1801236334320.1006695725830.1418384057980.434779886636-0.20823062216-0.0580509048634-0.1341715361740.1071009751190.1491497744410.3236200714820.04412330133950.297193844745-4.66846236059E-50.2277617650610.06968759597360.05550173331070.4589977646340.198058607540.43522720113388.8828038719-43.836665151250.7054064014
240.795416522230.21971137179-0.0475569872531.21990689197-0.5345511269760.249335620776-0.1844204277950.587518216793-0.23076973488-0.3135223045910.250644303977-0.1070709458150.1110061817520.46206156766-0.1265222418030.23922818919-0.0753304647366-0.02055269252720.8453874859530.1624981895140.37759772274495.9751712488-44.98306336135.7214088216
250.2748883616270.007401858184680.1712204510990.196138760741-0.2085184813980.309456475012-0.08233210912250.358817135410.1609037909870.359027918066-0.0701861596951-0.218906590072-0.3123169693140.2428526284130.0003118074622540.696429453725-0.214789783346-0.08733198493850.8534130452040.1718210062750.45705119522899.4631712948-27.576661500442.5273226976
260.04819096513180.0360189198946-0.04362758198440.06630121273970.007154100834550.0770497568018-0.0495463393436-0.1977475044590.359167957172-0.0194215896872-0.1592953306180.0130151156036-0.6389170985130.222792670761-4.00933653796E-50.614764456190.0285406249211-0.1095457083630.5167296299360.09466552608730.46566016001881.0989058037-25.327172198355.9575370747
270.5539576892660.436360624479-0.1539229718090.604993159817-0.1231432698510.777826885090.110167713636-0.1077995136230.183085303627-0.11774283234-0.132670210552-0.1040342450810.157456870416-0.470016600315-0.006016774055980.474988900108-0.1822094389990.1584705517720.45879576007-0.1113052220840.39333439447949.8861713826-51.534724136810.4717421123
280.7591816446920.1350347421890.7077951439060.6411798951640.1866178030191.38655074378-0.0396228157415-0.1818088512980.0877176993529-0.413875495941-0.0702529634878-0.1990023705730.412537311168-0.336121221488-0.04116676149080.67443412496-0.07056190278460.2521834791380.310259136783-0.02615361791380.42612723314556.8502404087-53.5642434777-3.50673126698
292.49625390310.350505851955-0.4968010629630.9620990754220.3372353724990.959937528760.22117909925-0.183848445733-0.0255336345197-0.0947733487595-0.0654877759206-0.3393007102740.5008874112640.005246474003460.1729441061490.869373686779-0.1372259693770.2451709454230.249690837836-0.01975282722350.49215786834360.7599792678-66.3480466884.18245235045
300.1219587520860.0179478061453-0.06384630517020.1849599794310.1001206712270.1166957295440.07369122676810.39755670711-0.374563649623-0.352780438070.0481856218420.02260320698780.497267721024-0.1345106224950.0004773190078650.898787779015-0.2673838512250.08372882706280.617160940705-0.04184326038240.46291997785546.2230411867-67.5472192265.79840394398
310.0567087250507-0.04393197676060.02908246828650.0326779946162-0.0212076567440.01828603107040.09374838940050.0697684196768-0.101481174101-0.1452029316480.1294549981820.3183526743460.19468335971-0.2742459509670.001318459987690.591615264658-0.0956604044739-0.02464352933050.832921000402-0.1061344900320.415001975641.1399986524-47.3006191815-17.0202604393
320.0550316449736-0.020249549724-0.01993694659410.0440127884508-0.04676174343760.08263459295520.03148839655140.1462327229840.384982067465-0.359452758855-0.1161798996110.2351181278950.014687608232-0.2364117898980.0002437387714550.629579841005-0.02148535652320.009303614767950.447327703736-0.1194921215740.42946766242753.134844154-42.4130857782-14.6720652736
330.215438823332-0.0603989779525-0.1359550543510.2409622105780.127540385640.142083595997-0.165476754776-0.3765724132360.2616574771310.05819885119250.0715274585513-0.128526284421-0.242360421851-0.221502807792-0.3485547621760.4005497437350.303282301398-0.128344966760.715571957111-0.3377272229870.48927252842851.7728184019-26.960868797649.4320940899
340.0217705241460.01535851316350.0278383377780.00973252869350.004020138597680.0630642936633-0.216860778017-0.3618284196660.03714749682330.09606374261990.079606754321-0.167535420744-0.0326621443035-0.2665057901110.1030636266760.2820900368820.299503940958-0.04775425017860.781520323616-0.3619757264690.42844491291647.9999490291-31.628145116748.9567010187
350.7042083331940.3392656454720.03702325068420.353196161977-0.3181289944280.771038315392-0.1695882401310.02271285378230.007993695544790.1678909581380.0804064862079-0.0983747947981-0.19956096529-0.1635424000024.80491859211E-60.3698535577970.0594852672953-0.007234677111450.525955324175-0.1710635854110.42450797160451.7203198425-34.957414869334.349288638
360.02137162149780.06779576759120.1020037118160.212590397810.3270436251080.512481720666-0.03988882169630.0184158723268-0.1295083927890.05527441288840.158286081959-0.2377676438620.2148096523290.07183080174440.009056184735760.286065062895-0.09079719723340.07943987802280.522676624074-0.2101288924730.44274463757847.0141935746-50.11829027129.256335275
370.3292990420260.0431090381805-0.5675670101850.328285706866-0.02218175775471.00044765359-0.146748675776-0.316472026026-0.240734857090.1678123495360.277300223275-0.08186283014240.347524426041-0.3867444024280.05675359852620.2794771030230.0622683736149-0.05555264610130.663983499566-0.172613205980.39011610797342.8465279984-47.632064876841.6859461295
380.515032203471-0.1625382661730.6264614905380.7828373365550.2274663631.03304022737-0.183543655688-0.2322949431610.04491110303730.2211269623050.277406335699-0.01508817457510.213904005566-0.239993825498-0.1123758329040.2584918959760.170649780951-0.04144609621120.769467312691-0.1576735583260.40633547106240.1142518897-42.425000802547.6472278832
390.1547781027920.06216793864150.09985346773740.143782725870.1508690020030.1571123326010.106359524481-0.179462060624-0.0420645724502-0.0156573938326-0.1091842924760.1425819728250.181287264844-0.3733574837580.009343127272290.5196708910730.215537499364-0.0109910400590.873295583783-0.1585054855980.43774442627633.3675488658-33.014949294844.5890643806
400.009242273762110.00354934745361-0.004413013640180.0482669248095-0.002188364758810.03003100967590.04676768085880.06291259251270.175927727861-0.058188983701-0.04660359713510.22556024614-0.141383248034-0.02303693376343.15932349064E-50.7035732555520.113815479577-0.03123431038250.532239841464-0.1158810807010.48101348012948.5534724285-19.978751508522.4735263398
410.0535211516701-0.00338575493246-0.06988550565850.0938425234309-0.006805314631260.0911582595135-0.07110568190310.2796937545390.487517888282-0.1860733333470.0686644045188-0.053731970832-0.38864672428-0.1674212113170.0001291639485180.45716941730.0461149293011-0.1046694347710.495752038984-0.07465305080620.55932156224458.3277620848-27.817955250824.5232201589
420.0459445282664-0.1295508666230.05717903511880.400150733823-0.1346572233470.195140838380.02727539850310.03409381030330.0310900259180.01427754828170.06878539435510.2615565634850.157497991891-0.3276682538320.1600125255760.150247006834-0.1854637800750.122045997120.628227910478-0.2164452613460.37197155988107.880451721-8.7502039479614.6766909475
430.2905086766990.25392185749-0.1734085724040.406147079687-0.0642955334150.543160910069-0.0420711760287-0.2324149506750.1048854755460.0155213358578-0.169726934024-0.001099743465680.128112657864-0.364977570094-0.003927232789570.193582653405-0.03088675176820.0406541398790.276725300642-0.09105284053630.299989527678122.023774529-6.393779366324.420383718
440.7476881980.5729040073310.4264574529440.469086662280.3428906195340.2612203823950.14074466493-0.166009172912-0.2205313121310.20196552057-0.2524418901590.03551996300780.449611900249-0.329793362077-0.07482231710790.27304035253-0.1930728751860.08205087185490.351258090088-0.08053005932830.255878580646118.338412589-16.865489919510.2842086307
450.4423816795020.3951278397360.03614483068590.7438172146160.1857608305281.74342439702-0.0694809918315-0.180372475076-0.0145216012334-0.0608633302353-0.206217585083-0.05688655145560.608133885852-0.328665180959-0.1649980448940.225276539851-0.001636724373890.09391003218390.182172785839-0.01835140667750.28716410297125.291470295-15.7137782841-3.8233728287
460.0703333672109-0.0688839040696-0.0690520797690.181459866281-0.004842788886650.114945991322-0.294029352622-0.124550349482-0.2444515123120.162651989246-0.038275502664-0.1607421452120.505154332486-0.006375523845760.0004099825098890.524341899719-0.04230505627280.06338052608730.4073077279630.07286678770840.411032655043125.439262077-25.01644233627.61431281936
470.00457501844562-0.0305690113849-0.02387743341340.3782334915730.2736799576470.198816912369-0.1924331299410.0402781596731-0.1891678525780.274780363732-0.2106335912110.06259488547550.608062386997-0.228488581271-0.01996359374410.574339834062-0.2085460568160.1469594676560.519857445132-0.02791640124270.480560972683113.933988544-27.15701654915.24258222323
480.0342656224101-0.0169071496713-0.03990599930940.0118301401425-0.02549376910120.548490365949-0.08310054455850.325571217783-0.0311710835274-0.234879377358-0.04220556476020.4645371700840.357029412769-0.438539686115-0.009215276990570.284732035259-0.0534863265882-0.03468860731930.654232625877-0.1606094077770.393015421991107.494533053-8.64494424189-18.3121919102
490.05804452762540.00318507004815-0.07514865162740.192264286636-0.06825338233130.130681837434-0.159017381630.1156469275490.574929327613-0.303442798887-0.07232437077980.412415071965-0.173396284769-0.4659630084910.0004075952457030.2693815432180.0195566508958-0.010334072460.291723252203-0.07416891798720.331380321475119.312302983-2.83564399032-16.579476241
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 6 through 30 )DA6 - 301 - 25
22chain 'D' and (resid 31 through 98 )DA31 - 9826 - 93
33chain 'D' and (resid 99 through 214 )DA99 - 21494 - 211
44chain 'D' and (resid 215 through 238 )DA215 - 238212 - 235
55chain 'D' and (resid 239 through 270 )DA239 - 270236 - 267
66chain 'D' and (resid 271 through 289 )DA271 - 289268 - 286
77chain 'D' and (resid 290 through 330 )DA290 - 330287 - 316
88chain 'D' and (resid 331 through 364 )DA331 - 364317 - 350
99chain 'A' and (resid 6 through 30 )AD6 - 301 - 25
1010chain 'A' and (resid 31 through 98 )AD31 - 9826 - 93
1111chain 'A' and (resid 99 through 186 )AD99 - 18694 - 183
1212chain 'A' and (resid 187 through 214 )AD187 - 214184 - 211
1313chain 'A' and (resid 215 through 238 )AD215 - 238212 - 235
1414chain 'A' and (resid 239 through 270 )AD239 - 270236 - 267
1515chain 'A' and (resid 271 through 289 )AD271 - 289268 - 286
1616chain 'A' and (resid 290 through 330 )AD290 - 330287 - 316
1717chain 'A' and (resid 331 through 347 )AD331 - 347317 - 333
1818chain 'A' and (resid 348 through 364 )AD348 - 364334 - 350
1919chain 'F' and (resid 6 through 30 )FJ6 - 301 - 25
2020chain 'F' and (resid 31 through 67 )FJ31 - 6726 - 62
2121chain 'F' and (resid 68 through 98 )FJ68 - 9863 - 93
2222chain 'F' and (resid 99 through 186 )FJ99 - 18694 - 183
2323chain 'F' and (resid 187 through 238 )FJ187 - 238184 - 235
2424chain 'F' and (resid 239 through 289 )FJ239 - 289236 - 286
2525chain 'F' and (resid 290 through 347 )FJ290 - 347287 - 333
2626chain 'F' and (resid 348 through 364 )FJ348 - 364334 - 350
2727chain 'I' and (resid 5 through 98 )IN5 - 981 - 94
2828chain 'I' and (resid 99 through 237 )IN99 - 23795 - 233
2929chain 'I' and (resid 238 through 289 )IN238 - 289234 - 285
3030chain 'I' and (resid 290 through 330 )IN290 - 330286 - 317
3131chain 'I' and (resid 331 through 347 )IN331 - 347318 - 334
3232chain 'I' and (resid 348 through 364 )IN348 - 364335 - 351
3333chain 'L' and (resid 6 through 67 )LR6 - 671 - 62
3434chain 'L' and (resid 68 through 126 )LR68 - 12663 - 121
3535chain 'L' and (resid 127 through 214 )LR127 - 214122 - 209
3636chain 'L' and (resid 215 through 237 )LR215 - 237210 - 232
3737chain 'L' and (resid 238 through 270 )LR238 - 270233 - 265
3838chain 'L' and (resid 271 through 289 )LR271 - 289266 - 284
3939chain 'L' and (resid 290 through 330 )LR290 - 330285 - 314
4040chain 'L' and (resid 331 through 347 )LR331 - 347315 - 331
4141chain 'L' and (resid 348 through 364 )LR348 - 364332 - 348
4242chain 'O' and (resid 5 through 30 )OU5 - 301 - 26
4343chain 'O' and (resid 31 through 67 )OU31 - 6727 - 63
4444chain 'O' and (resid 68 through 98 )OU68 - 9864 - 94
4545chain 'O' and (resid 99 through 270 )OU99 - 27095 - 268
4646chain 'O' and (resid 271 through 289 )OU271 - 289269 - 287
4747chain 'O' and (resid 290 through 330 )OU290 - 330288 - 319
4848chain 'O' and (resid 331 through 347 )OU331 - 347320 - 336
4949chain 'O' and (resid 348 through 364 )OU348 - 364337 - 353

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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

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