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- PDB-6wea: YTH domain of human YTHDC1 with a 10mer Oligo Containing N6mA -

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データを開く


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: 6wea
タイトルYTH domain of human YTHDC1 with a 10mer Oligo Containing N6mA
要素
  • DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')
  • YTH domain-containing protein 1
キーワードDNA BINDING PROTEIN/DNA / N6-methyladenine binding protein domain / ssDNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
機能・相同性
機能・相同性情報


primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome / spermatogenesis / in utero embryonic development / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane
類似検索 - 分子機能
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
類似検索 - ドメイン・相同性
DNA / YTH domain-containing protein 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: 1.8 Å
データ登録者Horton, J.R. / Cheng, X.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134744 米国
引用ジャーナル: Nucleic Acids Res. / 年: 2020
タイトル: Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA.
著者: Woodcock, C.B. / Horton, J.R. / Zhou, J. / Bedford, M.T. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
履歴
登録2020年4月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月15日Provider: repository / タイプ: Initial release
改定 1.12020年7月29日Group: Database references / Derived calculations
カテゴリ: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.id
改定 1.22020年10月21日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年10月18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
A: YTH domain-containing protein 1
B: YTH domain-containing protein 1
C: YTH domain-containing protein 1
D: YTH domain-containing protein 1
E: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')
F: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')
G: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')
H: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)89,45234
ポリマ－87,4358
非ポリマー2,01726
水8,953497
1
A: YTH domain-containing protein 1
E: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,83115
ポリマ－21,8592
非ポリマー97213
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-59 kcal/mol
Surface area9650 Å2
手法PISA
2
B: YTH domain-containing protein 1
G: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,49110
ポリマ－21,8592
非ポリマー6338
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-44 kcal/mol
Surface area9800 Å2
手法PISA
3
C: YTH domain-containing protein 1
F: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,0174
ポリマ－21,8592
非ポリマー1582
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: YTH domain-containing protein 1
H: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,1135
ポリマ－21,8592
非ポリマー2543
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)82.936, 42.641, 119.869
Angle α, β, γ (deg.)90.000, 101.791, 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 / DNA鎖 , 2種, 8分子 ABCDEFGH

#1: タンパク質
YTH domain-containing protein 1 / Splicing factor YT521 / YT521-B


分子量: 18823.826 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: YTHDC1, KIAA1966, YT521 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q96MU7
#2: DNA鎖
DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3')


分子量: 3035.006 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)

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非ポリマー , 4種, 523分子

#3: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


分子量: 62.068 Da / 分子数: 12 / 由来タイプ: 天然 / 式: C2H6O2
#4: 化合物
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 13 / 由来タイプ: 合成 / 式: SO4
#5: 化合物 ChemComp-NA / SODIUM ION


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Na
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 497 / 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: 2.37 Å3/Da / 溶媒含有率: 48.17 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 0.1 M Bis-Tris pH 7.0, 0.24 M ammonium sulfate, 23% PEG 3350, 15% glycerol

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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: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年2月6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: 1 Å / 相対比: 1
反射解像度: 1.79→40.59 Å / Num. obs: 73744 / % possible obs: 96.9 % / 冗長度: 3.4 % / Biso Wilson estimate: 16.45 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.083 / Net I/σ(I): 8.7
反射 シェル解像度: 1.79→1.85 Å / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6380 / CC1/2: 0.645 / CC star: 0.886 / Rpim(I) all: 0.678

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解析

ソフトウェア
名称バージョン分類
SERGUIデータ収集
PHENIX1.17.1_3660精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4r3h

4r3h


解像度: 1.8→40.59 Å / SU ML: 0.2272 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 28.9836
Rfactor反射数%反射
Rfree0.2375 1997 2.71 %
Rwork0.2104 --
obs0.2112 73624 95.12 %
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: 26.86 Å2
精密化ステップサイクル: LAST / 解像度: 1.8→40.59 Å
タンパク質核酸リガンド溶媒全体
原子数5110 804 114 497 6525
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00416299
X-RAY DIFFRACTIONf_angle_d0.68248680
X-RAY DIFFRACTIONf_chiral_restr0.0453930
X-RAY DIFFRACTIONf_plane_restr0.0038959
X-RAY DIFFRACTIONf_dihedral_angle_d18.13412409
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.3474900.39343248X-RAY DIFFRACTION60.93
1.84-1.890.40091330.3394838X-RAY DIFFRACTION91.6
1.89-1.950.30891480.29195262X-RAY DIFFRACTION97.78
1.95-2.010.28241450.25695220X-RAY DIFFRACTION98.46
2.01-2.080.25921470.24215264X-RAY DIFFRACTION98.61
2.08-2.160.26991480.23935297X-RAY DIFFRACTION98.95
2.16-2.260.27921460.2365260X-RAY DIFFRACTION98.01
2.26-2.380.2341450.20295212X-RAY DIFFRACTION96.84
2.38-2.530.27391480.2095284X-RAY DIFFRACTION98.96
2.53-2.730.24021470.20435288X-RAY DIFFRACTION98.76
2.73-30.24271490.20195319X-RAY DIFFRACTION98.31
3-3.430.21091470.18265253X-RAY DIFFRACTION97.23
3.43-4.330.18721500.15975407X-RAY DIFFRACTION99.37
4.33-40.590.18351540.1815475X-RAY DIFFRACTION97.47
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)
16.695615097530.2468750205123.397413804314.65360195552-0.9163515561635.790394156170.08005421090560.3488361081990.5757090936260.00324958262583-0.2007215922250.3791100368370.0530562868636-0.6645933614720.147686741630.1776733120820.0353740697394-0.04865585268350.321693905392-0.006377701853460.2432616364913.3295277855-2.3358641919434.8664476613
21.597338198920.350521071063-0.9466797757511.164769715220.1515159633421.653386017310.00842618046602-0.02494500034730.0235581118298-0.03063669951490.0173758215816-0.01796971301590.0656810830953-0.0123460479521-0.03434730763610.127851416418-0.00836197231414-0.008387440946760.03504922851590.005505397241340.069321465537329.526527292-12.488539709840.0271074834
39.26109818801-4.859734641956.088786944583.74981979014-1.596306154846.383914991930.110824198469-0.290876750927-0.1848514491370.13766462679-0.05081258345680.1974125144970.23395101707-0.101805041067-0.06566556928360.209424079249-0.02350416524340.03703206020340.08176398406030.01872866874020.096525416804821.8891134034-19.04552649548.8704776063
42.013816409465.92789932533-4.141990934574.36068065698-0.9641000460272.76359917794-0.05636999151410.347113065580.275084066058-0.08470147289080.10774239630.218907225916-0.164876408883-0.460414853508-0.06780785827590.141182773006-0.0480721472067-0.05034783210470.033685976270.01869883961520.09431818028423.0034797121-9.3615943753841.6178368425
53.955293052041.323391358870.1636943605384.65121360872-0.6521664705292.16565375758-0.104485395481-0.0520360960723-0.114837328636-0.1991822345910.10224505220.03029038082460.0168552325266-0.117938454221-0.02267882199040.08002563344110.004140109259890.02207118207610.0542487703959-0.004478030241-0.0045097549523128.3044852299-10.89303862539.970443729
68.415413053937.165351333811.667589412439.190843334160.7301274797321.490186371020.03314506693460.16759717393-0.801177588625-0.05841204954130.271305864337-0.6626520472780.138173539952-0.100270358482-0.3113689340860.1501473692540.0357191033136-0.0262401113730.0965501870976-0.01849434723010.15728277467834.1640344916-25.260021899437.2771932861
78.95458047047-4.023884616092.204933911072.29119293457-1.851354874482.06809928820.348459378489-0.450557442749-0.237524757794-0.0576890120548-0.0835430328015-0.1730214260740.248661550429-0.0165284013787-0.2514961844460.1842535148294.16780269972E-60.03597548544870.08129468793270.004687394397920.13003253790334.3795822362-22.460475894743.4048247288
80.6972746168820.0586428221552-0.1896303784141.19682768394-0.09599534369041.799334472560.026895174626-0.01672805395470.06422560917270.02729047566210.03901132369750.0213212930952-0.2197654623070.0213088858619-0.07000049946770.136640153059-0.00113003871072-8.58410124937E-50.04147269333690.001027458895660.099719822833127.9250432336-1.9961921856944.770875306
92.370646939020.6373363853690.4511105738410.3533473484241.04373179124.295855516820.08792389191280.234365197151-0.086570948152-0.1636389365150.02419859475970.09403755826930.0601676896861-0.209357261066-0.08004848900110.2077653266190.0292095741277-0.05304074342180.1146439881280.02989563506430.14100276957918.7395501416-4.4018473505934.5001195222
102.51829867936-1.31504092877-1.146302061292.27724414825-0.3343715128193.122801355050.0888844954156-0.1404523340510.1418280133660.203154143463-0.0832608006221-0.25362481612-0.06394976280810.3896099458850.01049197387680.15404059767-0.035668414909-0.01585803604390.0907537934191-0.01018394983730.091701059746244.4013160675-10.426135117819.8451350457
116.430878694523.664343945323.978225166993.455824070280.7965347529744.220606732330.03707385848660.491981689791-0.366468583261-0.2051827782410.0155725746546-0.3559159004020.2447772572580.268656825558-0.04281335037650.2234446010710.06068454014390.0590481991890.153145921859-0.01281623901970.15399279797148.7126136035-18.89628955499.82631423453
127.63929092705-6.33822923458-3.276514603536.483150052980.6934900192634.41228626629-0.101575045723-0.1127889193290.6854415633340.01764529664730.182916417759-0.5355513778060.1511292860660.373768547123.5777519626E-50.129802630816-0.01814979886370.007616041522790.0854172152862-0.002144737302440.10740144298947.4702704116-9.2879804644417.1567994701
134.19796862003-1.660301274630.1460803129022.81789988150.2344481261841.60370112299-0.0323015470246-0.135211220016-0.05122397273540.09467835507240.0452221544276-0.03772546795780.01116121875870.06552574540130.0004974298707670.158919632104-0.04270956556740.01853975140450.09322252144780.02815990613450.025000529756342.1768944437-10.801705583118.7356498949
149.22648785658-8.985666298030.8135253008022.07028076875-0.09980389719750.831282032561-0.0492894474001-0.105131618681-0.7215539322580.09209574413770.04574049691590.5430557221190.355049235899-0.0260827790029-0.07953574160880.29407579466-0.02858780099150.02702348477860.1148112945720.03870926974520.24385169980336.377721565-25.314018557321.4400279683
151.254510923220.0560203319939-0.3649986226421.86399354234-0.05343870188982.49236260790.04234017441450.0986309168936-0.00520373202664-0.06275597601860.001093666905320.00253106019353-0.0664479574971-0.00548854279527-0.03439911666690.1458262795660.0001766236704980.02343699793570.08177158753670.003996716930020.093759629681841.2081331333-6.5335166614.3628227811
162.62099828884-0.92685159602-2.025979287573.394494643111.358627395937.788660977490.0684772772529-0.02275477141490.148642539648-0.08194038734980.052389907998-0.418094989981-0.7715040240130.532235924409-0.1628013342440.212230326099-0.08694315995980.02483087137660.1425054048120.009842071295940.16068656076849.96184598361.7690357443215.8563654205
178.85634750993-3.57274787155-3.639722730524.603283801150.03679955573279.34367997348-0.630701232704-1.25290523178-0.579221266870.8257621982630.429471386215-0.4118788277310.9365521791171.65651361880.1507334292940.542465478784-0.0651655044701-0.1084138485460.356977116384-0.02604872414570.2200852422152.0653616903-7.5369321126429.3537698773
182.000642187361.355728932264.090935602136.839553938531.009941940332.008362508990.4475483942481.61813709036-1.3786342324-0.6300868344230.25736255798-1.028936791020.7097388035460.56656437631-0.6823574493980.4717960433660.04427933059690.02899250003640.641017096301-0.1847214605840.61176947333472.8096070279-63.51372118836.5656724971
191.94294617390.07286453209420.05618057168520.795708008321-0.6212660538720.491494592760.0427349482320.311359865810.06969816159290.1213848745210.01529769460280.113349523744-0.0318100427389-0.25497645728-0.07269214577910.1958743871390.001943310443540.02868935817890.6351924207360.02971648317090.2174322211465.3786086438-48.116210864544.5503422297
202.300089326051.378576944-0.3895816477823.287637371450.3300105236821.16594288250.164175045281-0.463942341475-0.01139101895190.454256855615-0.191046396425-0.00519077436688-0.006574372245720.06818563496060.00546012871090.221673822109-0.0159226644958-0.01131732264360.7255478673990.03348983769310.19992592163267.778555785-49.765118134455.7102376226
212.92785748754-1.36074744675-0.06718174148132.01290705537-0.06402120833480.503506922670.04031857465040.606510392232-0.21971120403-0.1783284201550.03800059635740.3149013122240.263441968438-0.2153750611030.00882788583629-0.265085454083-0.0342323387444-0.08970642947261.58611577857-0.02711563806690.26797143705555.0574752083-53.938290145544.8162714177
223.244048272643.239583247490.4444575452842.013729512272.904125568193.087442756830.0550688503190.254221124799-0.16882453781-0.244534869914-0.3379084881020.05160770648230.0456638492997-0.4415618312960.2554428921870.233577395458-0.00385105392363-0.03556953375140.4775167471310.01805837921460.24066847232266.8333131551-54.196797864943.2982329706
232.302420889652.244889124780.01461882395525.92331632250.1723916602361.518281344290.34194565143-0.0669832967906-0.02666305775090.265547783385-0.4574004048010.33366178781-0.0121272706507-0.3706864643410.1023523032450.1782190409580.004275058933890.003661691888250.5297147953520.01501477412050.22331764870767.6953066463-50.845594572548.0152906193
242.195196162971.265308214-0.1992162385982.264193395841.997772411492.836402225050.325087200134-0.40913419605-0.03383251893580.3346529671-0.4027252575360.236138142339-0.209165497605-0.773426875032-0.002752367354770.266585700304-0.01140761853440.04625010626640.9664814874740.05675357446530.32133715201959.0484178917-49.02145804259.0419847533
251.790666943710.8417504296080.2603777969813.345700469310.6206563132430.8358337655890.06012843257790.625879528310.00480715455364-0.1953871785680.131069671364-0.353614468088-0.274165528399-0.371262139652-0.160919705520.2012868769770.004131089502650.03468877809690.7964159798180.08120532384140.31173684510274.1307521782-48.920059170141.1889861966
261.09878735570.3489591358260.5145090123263.522929490610.7323749854670.8610887900740.07398014918180.5612213535470.0350774816579-0.662524469992-0.0634887347781-0.0855866383413-0.260060415706-0.183279429021-0.06325036257290.3305580616990.02743771621870.04657615977990.8026464111810.08601952154010.2674663025868.7420002729-46.843899751235.8268478972
270.008936391253590.169999578105-0.183031712443.41512432529-3.517500554433.6277535819-0.0137034719657-0.06331790294090.0690919722090.0753673223936-0.0932492526577-0.7905482840960.1290522426690.4178970032010.1003914143730.2862267273930.1202029921890.06409344411820.7446675306640.1072133096450.61777316457781.2904758733-58.202675027546.5377033373
284.82919141352-1.557548023172.282864531396.854516264920.4647535506543.942041300370.0793182309896-0.05025709039590.4727460857850.2957342222670.1547846413940.5182693815130.644915050551-0.237543342631-0.1912264317860.555743822119-0.003556947204030.1342410700480.5307410996150.07928232568410.39931461648371.1480420163-68.437911053446.8858168586
296.79546721848-1.09963617049-1.264162233745.629446082760.5452730985427.772151407390.159307982269-0.567241942843-1.815154892370.6005932041470.07403216049410.4127237023011.38156457414-0.77580256335-0.2280201282350.461968461771-0.090825398646-0.01184349977820.2888079994830.0538154478810.463258455371-2.36419230847-61.117246595721.9488022853
302.00210742160.28337581919-0.3407637675113.271883926340.4174529151273.14633691660.09092065925260.384945977315-0.0058899977656-0.234666496915-0.06011623121440.0784668063037-0.134407144008-0.0154972493128-0.005843013035270.1064928192240.0280403961344-0.0006088382657860.2031107532790.009518350135810.1445967612973.73018504216-46.49421868887.37875154556
312.061589613172.39320647121-0.8413977796935.97409499067-1.970130984293.098233344050.0663043264583-0.06537366768950.09968567670130.0445067596307-0.143376992382-0.4615837536510.04919550823960.4623840005650.1083869701670.09703143140350.0272994255687-0.01449466317550.253895822087-0.0071379219650.21484201361715.6790702588-51.435198995413.9479745947
329.57926663922-8.284670775073.893748625217.09945622008-3.031273395794.951361235520.137840973115-0.0500867383209-0.4648782440110.0712735844058-0.01691727580460.4941409854130.19284541299-0.0386016764764-0.1733462068080.0929628116521-0.0180173226623-0.02953773943450.108733403416-0.01263096710040.151089424583.57511273312-51.513787407915.3637127149
332.85402348701-1.96596969992-0.8502071030945.612948008980.1718783595931.564504946770.2087562345580.128364295445-0.111119418558-0.356297293413-0.1730173159080.0296867961655-0.0008308517138830.0931090997033-0.02549418938420.123908742965-0.00146487929037-0.05215927170410.2045697225470.007368494649150.1272031962662.87352262017-48.173696498910.6355057413
343.61453315222-2.307051846320.5464216597712.44273933953-2.677614068045.63823607970.3860880506910.6462867494580.31955165835-0.347692648549-0.412813034421-0.40075133861-0.3168550447770.920545240539-0.04276390589750.271733255153-0.003642134894950.05476201668030.5372779606350.02586844227180.22440293912311.4353827581-46.6005693485-0.365680970968
352.3583810418-0.4378643695620.1373057900124.537537012881.654267267743.532843247020.0236767910772-0.09573448803040.04840106600970.0475038247834-0.1666781107150.5109569656620.00224601987983-0.4145733813040.1404482463930.1071360341490.003813704329960.005047794752020.1939594949290.02205165073440.190978472429-3.51012575493-45.780087347717.5342629359
364.36933990343-1.30106124721-0.361662688245.90166117811-0.1023823391726.18049368298-0.122096212516-0.4752010849890.2919108968750.429027907102-0.036771018477-0.455530777553-0.6312104542480.4284212757360.02709546839660.169525077529-0.0234951584908-0.002878939206230.22706595-0.01235580693980.1774044105515.25233692358-40.00650374122.1238544707
372.05071481976-0.872095440161-0.2804030056235.362265310953.425398815345.130964455080.0393763019165-0.0746475260917-0.2732259481550.102620333046-0.3203079512940.6596683489790.472525027637-0.5758738702020.2002709512910.178799716051-0.05210452163320.007558312443760.1935141636570.03046150026930.277918670369-6.7125066856-52.502357613718.1811580894
386.313913914071.835360005230.3920431196227.39832497317-4.529430735993.865798889810.1407896607460.2132661994720.004022936281950.0196995768619-0.212024341958-0.5009606836970.1843641222040.3244124343530.09488947278810.370161727243-0.01004144007910.008417677351270.183047208148-0.05696702403090.309192474466-0.307801226363-65.591938824411.5841928074
390.364695297499-0.7146053580440.2966800271131.76875601044-0.770408907141.59386047044-0.1008812035560.0103304704584-0.0076460873151-0.06448585300710.164642152016-0.145135752395-0.00685582064248-0.00161691815946-0.007249232359740.1133893864690.007445683287040.002824698480190.0841266153276-0.02218398897570.11609027724839.7460537675-16.126144658952.7457781918
402.89352938411-0.465280971641-2.257997806620.07052075582870.1587725367671.777308223620.1145917962550.2790094188260.264999080157-0.197315526964-0.120888347216-0.2168117939-0.1697438511070.594019401952-0.002233616238620.1654012008930.004301021069790.04310352774240.5219552204310.03155475101920.26981333295459.7292038386-33.895778923251.4939871839
410.6538028576841.25513956899-0.1917392979143.069714501420.7396809854141.56996574758-0.1305549228960.1099323062280.0121350014479-0.4452759242580.244150437041-0.0544803921407-0.125322993536-0.0352774453484-0.04764245890290.143006736168-0.0108991733397-0.002061342798730.1488433913610.005361711028010.087150347292530.9215559688-15.90653800235.85257509228
422.580174671370.913387249445-2.099287988280.431983477121-0.07827360851782.595171663140.167553765110.08264210507370.161414953376-0.0111620987619-0.0968819159950.112818517185-0.198484429297-0.0575250571523-0.08817923100210.1879265166510.003530433928920.03166627218160.2350665640490.02431081337590.23070119836411.05084636-32.06834222597.06551678303
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 345 through 352 )
2X-RAY DIFFRACTION2chain 'A' and (resid 353 through 380 )
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 403 )
5X-RAY DIFFRACTION5chain 'A' and (resid 404 through 420 )
6X-RAY DIFFRACTION6chain 'A' and (resid 421 through 430 )
7X-RAY DIFFRACTION7chain 'A' and (resid 431 through 444 )
8X-RAY DIFFRACTION8chain 'A' and (resid 445 through 481 )
9X-RAY DIFFRACTION9chain 'A' and (resid 482 through 507 )
10X-RAY DIFFRACTION10chain 'B' and (resid 345 through 380 )
11X-RAY DIFFRACTION11chain 'B' and (resid 381 through 393 )
12X-RAY DIFFRACTION12chain 'B' and (resid 394 through 403 )
13X-RAY DIFFRACTION13chain 'B' and (resid 404 through 420 )
14X-RAY DIFFRACTION14chain 'B' and (resid 421 through 430 )
15X-RAY DIFFRACTION15chain 'B' and (resid 431 through 481 )
16X-RAY DIFFRACTION16chain 'B' and (resid 482 through 491 )
17X-RAY DIFFRACTION17chain 'B' and (resid 492 through 507 )
18X-RAY DIFFRACTION18chain 'C' and (resid 345 through 354 )
19X-RAY DIFFRACTION19chain 'C' and (resid 355 through 364 )
20X-RAY DIFFRACTION20chain 'C' and (resid 365 through 380 )
21X-RAY DIFFRACTION21chain 'C' and (resid 381 through 393 )
22X-RAY DIFFRACTION22chain 'C' and (resid 394 through 403 )
23X-RAY DIFFRACTION23chain 'C' and (resid 404 through 420 )
24X-RAY DIFFRACTION24chain 'C' and (resid 421 through 444 )
25X-RAY DIFFRACTION25chain 'C' and (resid 445 through 466 )
26X-RAY DIFFRACTION26chain 'C' and (resid 467 through 491 )
27X-RAY DIFFRACTION27chain 'C' and (resid 492 through 499 )
28X-RAY DIFFRACTION28chain 'C' and (resid 500 through 507 )
29X-RAY DIFFRACTION29chain 'D' and (resid 346 through 354 )
30X-RAY DIFFRACTION30chain 'D' and (resid 355 through 380 )
31X-RAY DIFFRACTION31chain 'D' and (resid 381 through 393 )
32X-RAY DIFFRACTION32chain 'D' and (resid 394 through 403 )
33X-RAY DIFFRACTION33chain 'D' and (resid 404 through 420 )
34X-RAY DIFFRACTION34chain 'D' and (resid 421 through 444 )
35X-RAY DIFFRACTION35chain 'D' and (resid 445 through 466 )
36X-RAY DIFFRACTION36chain 'D' and (resid 467 through 481 )
37X-RAY DIFFRACTION37chain 'D' and (resid 482 through 499 )
38X-RAY DIFFRACTION38chain 'D' and (resid 500 through 507 )
39X-RAY DIFFRACTION39chain 'E' and (resid 1 through 10 )
40X-RAY DIFFRACTION40chain 'F' and (resid 1 through 10 )
41X-RAY DIFFRACTION41chain 'G' and (resid 1 through 10 )
42X-RAY DIFFRACTION42chain 'H' and (resid 1 through 10 )

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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