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- PDB-6zee: Structure of PP1(7-300) bound to Phactr1 (507-580) at pH8.4 -

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IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 6zee
タイトルStructure of PP1(7-300) bound to Phactr1 (507-580) at pH8.4
要素
  • Phosphatase and actin regulator
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
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 / dendrite arborization / RNA polymerase II promoter clearance / glycogen granule / 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 / dendrite arborization / RNA polymerase II promoter clearance / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / regulation of neuron migration / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / actomyosin structure organization / dephosphorylation / regulation of canonical Wnt signaling pathway / protein phosphatase inhibitor activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / stress fiber assembly / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / 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 / adherens junction / cell motility / positive regulation of transcription elongation by RNA polymerase II / lung development / circadian regulation of gene expression / response to lead ion / regulation of circadian rhythm / cerebral cortex development / : / presynapse / actin binding / actin cytoskeleton organization / dendritic spine / perikaryon / 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
3,6,9,12,15,18-HEXAOXAICOSANE / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Phosphatase and actin regulator / Phosphatase and actin regulator 1
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: 1.9 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
P: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Q: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
I: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
K: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
W: Phosphatase and actin regulator
X: Phosphatase and actin regulator
D: Phosphatase and actin regulator
C: Phosphatase and actin regulator
U: Phosphatase and actin regulator
V: Phosphatase and actin regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)266,45099
ポリマ－260,24712
非ポリマー6,20387
水13,331740
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)137.695, 137.695, 238.793
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

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タンパク質 , 2種, 12分子 PQBAIKWXDCUV

#1: タンパク質
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


分子量: 34162.148 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 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P62136, protein-serine/threonine phosphatase
#2: タンパク質
Phosphatase and actin regulator


分子量: 9212.388 Da / 分子数: 6 / 変異: N-terminal Vector derived sequence GPLGS / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PHACTR1, hCG_1818446 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q4VY12, UniProt: Q9C0D0*PLUS

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非ポリマー , 6種, 827分子

#3: 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
#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: 54 / 由来タイプ: 合成 / 式: C2H6O2
#5: 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: 6 / 由来タイプ: 合成 / 式: C3H8O3
#6: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 14 / 由来タイプ: 合成 / 式: SO4
#7: 化合物 ChemComp-16P / 3,6,9,12,15,18-HEXAOXAICOSANE / 3,6,9,12,15,18-ヘキサオキサイコサン


分子量: 294.384 Da / 分子数: 1 / 由来タイプ: 天然 / 式: C14H30O6 / タイプ: SUBJECT OF INVESTIGATION
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 740 / 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Y

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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: 2.6 Å3/Da / 溶媒含有率: 52.77 %
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: 7.5% PEG 3350, 0.2M MgSO4

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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: 0.97 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2014年10月23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: 0.97 Å / 相対比: 1
反射解像度: 1.9→238.79 Å / Num. obs: 2420639 / % possible obs: 100 % / 冗長度: 12.1 % / Biso Wilson estimate: 31.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.045 / Rrim(I) all: 0.156 / Net I/σ(I): 7.8
反射 シェル解像度: 1.9→1.93 Å / 冗長度: 10 % / Rmerge(I) obs: 2.14 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 200842 / CC1/2: 0.704 / Rpim(I) all: 0.75 / % possible all: 100

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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
xia2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: 1.9→119.25 Å / SU ML: 0.2762 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 31.5392
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2683 10131 5.07 %
Rwork0.2357 189711 -
obs0.2373 199842 99.55 %
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: 44.88 Å2
精密化ステップサイクル: LAST / 解像度: 1.9→119.25 Å
タンパク質核酸リガンド溶媒全体
原子数17355 0 345 740 18440
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002718076
X-RAY DIFFRACTIONf_angle_d0.609624351
X-RAY DIFFRACTIONf_chiral_restr0.04082614
X-RAY DIFFRACTIONf_plane_restr0.00263154
X-RAY DIFFRACTIONf_dihedral_angle_d21.53656690
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.37763470.35476288X-RAY DIFFRACTION99.51
1.92-1.940.39073450.3366334X-RAY DIFFRACTION99.81
1.94-1.970.36143730.33086338X-RAY DIFFRACTION99.72
1.97-1.990.32113150.31016302X-RAY DIFFRACTION99.53
1.99-2.020.33063200.30566309X-RAY DIFFRACTION99.58
2.02-2.050.32252770.30456388X-RAY DIFFRACTION99.84
2.05-2.080.34113670.30796299X-RAY DIFFRACTION99.64
2.08-2.110.33293790.29036301X-RAY DIFFRACTION99.81
2.11-2.140.33043300.2876322X-RAY DIFFRACTION99.91
2.14-2.170.31843400.27826321X-RAY DIFFRACTION99.75
2.17-2.210.28143820.26396300X-RAY DIFFRACTION99.91
2.21-2.250.29543430.27536330X-RAY DIFFRACTION99.81
2.25-2.30.30633360.2766372X-RAY DIFFRACTION99.73
2.3-2.340.30953100.2736314X-RAY DIFFRACTION99.55
2.34-2.390.3363310.26846320X-RAY DIFFRACTION99.94
2.39-2.450.3143620.26366325X-RAY DIFFRACTION99.75
2.45-2.510.31812910.2526382X-RAY DIFFRACTION99.76
2.51-2.580.28023870.25516278X-RAY DIFFRACTION99.82
2.58-2.650.26813050.25036390X-RAY DIFFRACTION99.7
2.65-2.740.30543770.24556297X-RAY DIFFRACTION99.87
2.74-2.840.30133420.24786312X-RAY DIFFRACTION99.85
2.84-2.950.28673280.24746324X-RAY DIFFRACTION99.7
2.95-3.090.28553400.2426337X-RAY DIFFRACTION99.7
3.09-3.250.27063210.23636394X-RAY DIFFRACTION99.85
3.25-3.450.26473280.22056339X-RAY DIFFRACTION99.57
3.45-3.720.22253420.2086362X-RAY DIFFRACTION99.81
3.72-4.090.20533320.18836307X-RAY DIFFRACTION99.64
4.09-4.690.18053170.17046412X-RAY DIFFRACTION99.64
4.69-5.90.24773220.20716353X-RAY DIFFRACTION99.63
5.9-119.250.27973420.24516061X-RAY DIFFRACTION94.44
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)
10.07185736316890.0846749535239-0.06050743917380.13109011114-0.09992734695270.0745532618998-0.1165186853550.03531740886490.110415000115-0.2272998953510.301546690716-0.2961485031480.3652755065110.03800178427850.00222382197320.340931349049-0.0516844761490.02239722409210.587903133826-0.1772795720190.40792363518246.4509161127-60.838416078621.4376812659
20.04508485861110.02770947913990.09781101783660.019230591290.01982182005810.5623725845320.0729945724899-0.0203259558509-0.22754306827-0.0107440773547-0.112376988505-0.3002886724660.440956599261-0.03511501666330.00953144756650.3714973637080.101212763844-0.0263919019650.495617150601-0.1321849673280.49529352062358.970870076-58.950621026932.6483220762
30.5805117815420.0563226169591-0.1128137050870.466883794043-0.2195754671011.13806231322-0.279815620757-0.2533972892020.1390201990790.1672283027130.230609040873-0.2376458003090.0927984996289-0.284463072838-0.01604147585130.2857946152960.111013940373-0.08672005428910.527214172056-0.1857602239950.44403350803850.4139522774-48.182586915233.8565260558
40.02375096671440.0350775463288-0.01967541332590.0703449719848-0.029456627690.0115224865068-0.247473474051-0.3444148392140.3235361405530.1205903734610.0320182023603-0.13065668301-0.330834365552-0.406755464524-0.2875876362840.4006630182380.43363144426-0.2591780766350.762257512279-0.3282051410040.60340666537649.3982571249-35.178132982247.6119353916
50.1567493006370.103247139094-0.04140423232420.0784427305079-0.01554364353250.0390695529691-0.0326774330638-0.1143047160350.4770127326350.05729902624650.0162852518003-0.173303185108-0.138942098884-0.1875241905960.01429389591630.3512285836360.245582051821-0.1295338403520.715990106153-0.2913617997880.59030020830942.6724631991-32.68110534834.5128328355
60.183852846105-0.0133140998234-0.1962584082730.379926722506-0.02965414625570.217459803064-0.175113321623-0.1962429623350.3904709497730.04145846417260.197908947581-0.292379698033-0.16121002252-0.403078057561-0.01623284855530.3116473370580.124054245987-0.07972224571240.715354855664-0.2209745279040.55467385242940.4980900811-36.61294373126.50837012
70.0893715925303-0.0438385765077-0.03501909801810.06236211833670.09613776464370.169346311620.0449561062-0.07675523536860.07283030703290.07715387901510.0179525847785-0.03011889311390.09787582101630.141470868769-0.0497316696141.295018674810.01923486444560.5461857708740.411841628828-0.05585290788910.60356983033675.6300965736-69.4770251218-18.5967366542
80.4850393126850.02875247123670.1334088122430.619579860585-0.6861160373190.821400276881-0.111472160165-0.03869742121510.0393097920161-0.516620378515-0.0562534661063-0.4609007261420.3164892761650.138878563291-0.3374412738690.955347964139-0.117097951740.3658009905760.350824802555-0.09990387548080.5481126119770.5687413245-56.2711999336-8.21214836559
90.00550988700917-0.00430851511372-0.0234177503530.008473077378080.02847477678010.159476758388-0.01045199593530.03619366647630.0374120013001-0.447244836293-0.00504452315197-0.09609351720980.2427074055580.02396073826440.4133515042071.37010111187-0.1184496823470.5204111234930.21482942375-0.2078392677350.50773579542166.3081435312-62.3676079392-11.8620741097
100.1755217738220.1738256979150.1982460345590.1692102744010.1970842671260.239246285424-0.07087323151850.11283734425-0.0963122236786-0.370064225199-0.0588219864432-0.3444572427670.468992529370.267139443301-0.07462662568660.896783467864-0.01583207747530.3715644768740.430901739987-0.07539143231510.58015104449271.42218948-63.2876387431-0.818761149099
110.0202786050011-0.01374566562570.01274667216780.0175038181709-0.02644438953580.04015788826960.02312557871040.05604795049420.269320354335-0.150380463467-0.0208553906365-0.1343249002450.05237793751060.0845486960751-2.35368938579E-50.672089218859-0.1725213402310.2383371524220.434201183964-0.1733999749050.57486630145558.7775638255-48.1788251655.77200208849
120.0718903884315-0.07820630619310.03659454428230.115166977483-0.09708153590810.121486028403-0.130874651199-0.07507076402660.334636853286-0.3315859001650.0359052353689-0.1807955545450.0641489866-0.0753637934963-0.0003093970201530.598707632435-0.1664701902790.215010050650.436402857361-0.1555116357020.53854842000760.1263542597-55.54723508638.0566817347
130.771651959346-0.1594397064940.04619438460950.450641242270.1891436376960.1005079081210.03520339584510.05029842491340.260671322138-0.8803058067330.182758814283-0.1067363143420.320644694214-0.3549392306330.04432149868680.729855005246-0.2605548093430.1793051914650.398800012773-0.09722209703780.41259078176949.5190234329-57.11949029630.679763317337
140.5715318571620.177717245068-0.3990107231960.0550693183092-0.1245850074160.2809066932870.210578444418.16822056614E-60.146828940738-0.1803129829830.01704083893850.0315307435866-0.0273760851163-0.1789872951640.03562396680071.32703440109-0.2541914449380.1809917741830.425621886748-0.02774442538450.36846083328751.5257348102-63.4831993711-12.7836461078
150.363260487340.165608516963-0.05119824387350.0794570269694-0.01616450875710.01766744994330.01974730307210.0101158988564-0.2535431924460.139808020327-0.112486973768-0.02015725775440.0922786382097-0.102535628065-0.2959864529090.428875851278-0.2962508606040.1113231810740.461572288184-0.1551016786390.40714134805546.0048506328-138.3532893620.3081209945
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620.01886299678640.00861065022481-0.001606189752570.0117657200286-0.003558184364240.01069503817690.0185099361663-0.0690026885108-0.2321565929350.000900727562956-0.054505767797-0.2950897090220.2206415650760.07188530650020.0001235475937130.3324728610760.0394427849704-0.0004416706013970.42672583717-0.06651998547150.40184290937963.5939160468-127.10214599850.4707413496
630.006206083611950.0002224751685020.001809819403680.01350743603390.0004671392335730.0113363747140.03057605953-0.21196929125-0.08997357118340.181990081871-0.01398165042840.2135403984190.119934312634-0.22087812903-0.0001351770900180.3293047898210.0610934305810.01772383232960.433125804070.03344055018340.34433953939650.3196239389-131.57801036555.943603975
640.008989956112790.00609459268847-0.004219451962460.00405997881938-0.003710714281460.00423577321568-0.009889560326990.03012717600180.02750379537430.06016166570240.02272740011720.1931648604030.00837365985263-0.06701963245264.04396209342E-50.3996584739040.06937737644130.02408245698290.71443025553-0.1255271896780.64539936482658.1781880566-95.4532373757-0.0724400688261
650.000680108535750.000923414347214-0.0006666167900440.00652276000629-0.01137008995910.0167202558152-0.0931204414608-0.1405497371680.09867930838040.253032912354-0.1284188417030.0669817677216-0.220031412902-0.0214085623355-4.93957369061E-50.688578465915-0.0249791888711-0.05110016556960.406817091182-0.1706790523690.38845970132677.4509242434-89.439074428612.3096331952
660.177868422349-0.1708139059960.09566897053290.164718725952-0.09248631038290.0518083362899-0.285259155466-0.061736420155-0.03723306890240.07552719393240.124933066195-0.257779280881-0.05268591134650.082322475827-0.01283466034450.618009874887-0.240675984577-0.01163110596140.6106993251240.03446651391540.427749399357100.982366559-94.2924666379-4.55303137485
670.191293239453-0.1193838773290.005383741062710.1343073848440.1122721255580.211287371076-0.001762424027530.204662022433-0.285562860439-0.2568849281490.024845664793-0.267081518198-0.08402061881670.459047382540.001253564081490.319953267574-0.0586124500977-0.02032779349360.3762211217530.05058401063040.40490686974792.5074173896-113.826796405-20.6871776742
680.03017365325570.00844400936201-0.02961712248580.0234814810269-0.002687266547560.023573900902-0.114539819304-0.003905867628740.1582951120980.1021251283390.08839123254740.0327258262891-0.3658397938580.0452410281574-5.88400865155E-50.8083994351710.399190646857-0.01881694666150.908952256670.01485816568370.51090321486227.8147995327-71.325393870549.326628774
690.0393279967003-0.0474566826508-0.0243160054990.05603325091950.0417341988530.0295557874119-0.08111426609370.0161946449702-0.130055906318-0.08336821907890.1964783782580.02699807508440.4427338659550.179739821027-7.3262511327E-50.5895795421060.0569798100998-0.02825435881950.7051335109290.09108573372840.43034619095927.2986855418-96.804091123524.2143316604
700.0185710197635-0.01733989279410.02879209792240.0768501994813-0.02268599650730.0527237260741-0.01544866881480.118356464751-0.25534942009-0.06262996735620.2134671566920.2062021800340.1443840145270.0233288945649-0.000110181944240.4669433461060.005728045262850.01399694161950.6150352018040.08200871488870.55693088006910.5942484596-91.007491263521.1898030179
710.006399206652020.00562510736798-0.004436689922540.00529922147305-0.005005984533350.00459309787506-0.15237462451-0.02199327913070.1898755438210.00750020071011-0.05703333661410.034374301406-0.0035099574854-0.00816196225877-0.0001086066620491.154037373640.03702175912220.1842581954310.578457549387-0.03949815246410.67225586306641.8983617922-41.8811525564-5.06544279534
720.5546867860960.169058738707-0.01263635126850.3101524212590.126688798390.06678699296410.02700151987110.04804442737770.0891472555923-0.0601946528667-0.02423973467020.0389238595585-0.1016282343480.07796823192440.005825565557971.46116796371-0.3530451256760.09991745227560.596651256506-0.05435726885320.40999610858646.0388428551-62.1812132584-19.0082560301
730.083754714363-0.0274908391596-0.05649714712220.0358263620278-0.01617839495370.09216041974730.05343692904760.0159379517444-0.0123022904728-0.106527346637-0.0081787197748-0.166402515856-0.00895401297441-0.00996638683306-0.0001323722006691.32499833654-0.2717538570160.2080381217510.434212841935-0.04794953059810.46897474433860.2745877678-79.4748608611-9.48795954901
740.00287684360875-0.0007385743225890.004597539185950.00323981796502-0.0023268670140.007066939112130.0397916491530.028220951651-0.0103554166455-0.007222164816880.0152634295791-0.02668852843870.0168181629624-0.004726072145839.29167947953E-60.964268426551-0.1211555561260.2080651423710.667195165351-0.1847167108460.84787202392366.8557307861-80.31046788488.0095331778
750.0135932984906-0.007684956755560.01734563048820.0207847211132-0.001888976434810.023037717649-0.04964460927570.0224623895023-0.01586117650630.1384997782980.00930984855829-0.2614365097240.275380710820.0845456794132-1.66387362297E-60.7336267944210.00291144335390.2345118414260.652733195345-0.1052996046270.66066773741377.5049534872-66.462090950112.8208714602
760.0331742035252-0.0167846973650.01656600390840.0257016250920.01772821478470.0461241421998-0.0686719849479-0.02569380932520.1455280341950.16930782561-0.0504780902017-0.08049299092270.1015399697290.13528494738-6.37267265399E-50.563821818548-0.03142401028240.2122515932790.546201934202-0.1152047295870.59417123347973.2101188129-57.875888511615.2643362999
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 'P' and (resid 6 through 31 )PA6 - 311 - 26
22chain 'P' and (resid 32 through 48 )PA32 - 4827 - 43
33chain 'P' and (resid 49 through 187 )PA49 - 18744 - 182
44chain 'P' and (resid 188 through 239 )PA188 - 239183 - 234
55chain 'P' and (resid 240 through 271 )PA240 - 271235 - 266
66chain 'P' and (resid 272 through 299 )PA272 - 299267 - 294
77chain 'Q' and (resid 6 through 31 )QD6 - 311 - 26
88chain 'Q' and (resid 32 through 68 )QD32 - 6827 - 63
99chain 'Q' and (resid 69 through 127 )QD69 - 12764 - 124
1010chain 'Q' and (resid 128 through 171 )QD128 - 171125 - 168
1111chain 'Q' and (resid 172 through 187 )QD172 - 187169 - 184
1212chain 'Q' and (resid 188 through 215 )QD188 - 215185 - 212
1313chain 'Q' and (resid 216 through 271 )QD216 - 271213 - 268
1414chain 'Q' and (resid 272 through 299 )QD272 - 299269 - 296
1515chain 'B' and (resid 6 through 31 )BG6 - 311 - 26
1616chain 'B' and (resid 32 through 48 )BG32 - 4827 - 43
1717chain 'B' and (resid 49 through 145 )BG49 - 14544 - 144
1818chain 'B' and (resid 146 through 171 )BG146 - 171145 - 170
1919chain 'B' and (resid 172 through 187 )BG172 - 187171 - 186
2020chain 'B' and (resid 188 through 238 )BG188 - 238187 - 237
2121chain 'B' and (resid 239 through 254 )BG239 - 254238 - 255
2222chain 'B' and (resid 255 through 271 )BG255 - 271256 - 272
2323chain 'B' and (resid 272 through 299 )BG272 - 299273 - 300
2424chain 'A' and (resid 6 through 31 )AJ6 - 311 - 26
2525chain 'A' and (resid 32 through 48 )AJ32 - 4827 - 43
2626chain 'A' and (resid 49 through 145 )AJ49 - 14544 - 142
2727chain 'A' and (resid 146 through 171 )AJ146 - 171143 - 168
2828chain 'A' and (resid 172 through 199 )AJ172 - 199169 - 196
2929chain 'A' and (resid 200 through 271 )AJ200 - 271197 - 272
3030chain 'A' and (resid 272 through 299 )AJ272 - 299273 - 302
3131chain 'I' and (resid 6 through 31 )IM6 - 311 - 26
3232chain 'I' and (resid 32 through 48 )IM32 - 4827 - 43
3333chain 'I' and (resid 49 through 68 )IM49 - 6844 - 63
3434chain 'I' and (resid 69 through 145 )IM69 - 14564 - 142
3535chain 'I' and (resid 146 through 199 )IM146 - 199143 - 196
3636chain 'I' and (resid 200 through 239 )IM200 - 239197 - 236
3737chain 'I' and (resid 240 through 271 )IM240 - 271237 - 270
3838chain 'I' and (resid 272 through 299 )IM272 - 299271 - 298
3939chain 'K' and (resid 6 through 31 )KP6 - 311 - 26
4040chain 'K' and (resid 32 through 48 )KP32 - 4827 - 43
4141chain 'K' and (resid 49 through 99 )KP49 - 9944 - 94
4242chain 'K' and (resid 100 through 145 )KP100 - 14595 - 142
4343chain 'K' and (resid 146 through 171 )KP146 - 171143 - 168
4444chain 'K' and (resid 172 through 199 )KP172 - 199169 - 196
4545chain 'K' and (resid 200 through 216 )KP200 - 216197 - 213
4646chain 'K' and (resid 217 through 271 )KP217 - 271214 - 270
4747chain 'K' and (resid 272 through 299 )KP272 - 299271 - 298
4848chain 'W' and (resid 513 through 527 )WS513 - 5271 - 15
4949chain 'W' and (resid 528 through 540 )WS528 - 54016 - 28
5050chain 'W' and (resid 541 through 568 )WS541 - 56829 - 56
5151chain 'W' and (resid 569 through 580 )WS569 - 58057 - 68
5252chain 'X' and (resid 513 through 522 )XT513 - 5221 - 10
5353chain 'X' and (resid 523 through 527 )XT523 - 52711 - 15
5454chain 'X' and (resid 528 through 540 )XT528 - 54016 - 28
5555chain 'X' and (resid 541 through 568 )XT541 - 56829 - 56
5656chain 'X' and (resid 569 through 580 )XT569 - 58057 - 68
5757chain 'D' and (resid 516 through 520 )DU516 - 5201 - 5
5858chain 'D' and (resid 521 through 525 )DU521 - 5256 - 10
5959chain 'D' and (resid 526 through 535 )DU526 - 53511 - 20
6060chain 'D' and (resid 536 through 546 )DU536 - 54621 - 31
6161chain 'D' and (resid 547 through 568 )DU547 - 56832 - 53
6262chain 'D' and (resid 569 through 574 )DU569 - 57454 - 59
6363chain 'D' and (resid 575 through 580 )DU575 - 58060 - 65
6464chain 'C' and (resid 512 through 521 )CV512 - 5211 - 10
6565chain 'C' and (resid 522 through 531 )CV522 - 53111 - 20
6666chain 'C' and (resid 532 through 546 )CV532 - 54621 - 35
6767chain 'C' and (resid 547 through 580 )CV547 - 58036 - 69
6868chain 'U' and (resid 516 through 535 )UW516 - 5351 - 20
6969chain 'U' and (resid 536 through 563 )UW536 - 56321 - 48
7070chain 'U' and (resid 564 through 580 )UW564 - 58049 - 65
7171chain 'V' and (resid 512 through 521 )VX512 - 5211 - 10
7272chain 'V' and (resid 522 through 531 )VX522 - 53111 - 20
7373chain 'V' and (resid 532 through 540 )VX532 - 54021 - 29
7474chain 'V' and (resid 541 through 546 )VX541 - 54630 - 35
7575chain 'V' and (resid 547 through 568 )VX547 - 56836 - 57
7676chain 'V' and (resid 569 through 580 )VX569 - 58058 - 69

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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