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- PDB-8bub: Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K -

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基本情報

登録情報
データベース: PDB / ID: 8bub
タイトルStructure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K
要素
  • Cyclin-K
  • Cyclin-dependent kinase 12
  • DNA damage-binding protein 1
キーワードLIGASE / kinase / cyclin / ubiquitin / degrader
機能・相同性
機能・相同性情報


cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / positive regulation by virus of viral protein levels in host cell / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / positive regulation by virus of viral protein levels in host cell / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / RNA polymerase II CTD heptapeptide repeat S7 kinase activity / negative regulation of stem cell differentiation / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / cyclin-dependent protein serine/threonine kinase activator activity / UV-damage excision repair / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / regulation of cyclin-dependent protein serine/threonine kinase activity / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ectopic germ cell programmed cell death / regulation of signal transduction / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / positive regulation of viral genome replication / Formation of HIV elongation complex in the absence of HIV Tat / proteasomal protein catabolic process / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / positive regulation of gluconeogenesis / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA splicing / cyclin binding / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / Recognition of DNA damage by PCNA-containing replication complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / mRNA processing / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein autophosphorylation / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / damaged DNA binding / chromosome, telomeric region / protein kinase activity / nuclear speck / protein ubiquitination / cell division / protein serine kinase activity / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm
類似検索 - 分子機能
Cyclin-T2-like, C-terminal domain / DNA polymerase; domain 1 - #910 / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region ...Cyclin-T2-like, C-terminal domain / DNA polymerase; domain 1 - #910 / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
CITRIC ACID / Chem-RNU / Cyclin-K / DNA damage-binding protein 1 / Cyclin-dependent kinase 12
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: 3.42 Å
データ登録者Kozicka, Z. / Kempf, G. / Petzold, G. / Thoma, N.H.
資金援助European Union, スイス, 7件
組織認可番号国
European Research Council (ERC)666068European Union
Swiss National Science Foundation31003A_179541 スイス
Swiss National Science Foundation310030_301206 スイス
Swiss Cancer League4980-02-2020 スイス
Swiss National Science FoundationCRSII5_186230 スイス
Marie Sklodowska-Curie Actions, FragNET ITN765445European Union
Other private スイス
引用ジャーナル: Nat.Chem.Biol. / 年: 2024
タイトル: Design principles for cyclin K molecular glue degraders.
著者: Kozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. / Cigler, M. / Mayor-Ruiz, C. / Schmid-Burgk, J.L. / ...著者: Kozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. / Cigler, M. / Mayor-Ruiz, C. / Schmid-Burgk, J.L. / Haussinger, D. / Winter, G.E. / Fischer, E.S. / Slabicki, M. / Gillingham, D. / Ebert, B.L. / Thoma, N.H.
履歴
登録2022年11月30日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年9月13日Provider: repository / タイプ: Initial release
改定 1.12024年1月3日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
D: DNA damage-binding protein 1
F: Cyclin-K
G: DNA damage-binding protein 1
I: Cyclin-K
E: Cyclin-dependent kinase 12
H: Cyclin-dependent kinase 12
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)498,92119
ポリマ－496,5589
非ポリマー2,36310
水00
1
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,2436
ポリマ－165,5193
非ポリマー7243
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: DNA damage-binding protein 1
F: Cyclin-K
E: Cyclin-dependent kinase 12
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,4357
ポリマ－165,5193
非ポリマー9164
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: DNA damage-binding protein 1
I: Cyclin-K
H: Cyclin-dependent kinase 12
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,2436
ポリマ－165,5193
非ポリマー7243
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)247.861, 247.861, 220.715
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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要素

#1: タンパク質 DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


分子量: 93675.438 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DDB1, XAP1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q16531
#2: タンパク質 Cyclin-dependent kinase 12 / Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 ...Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 / CDC2-related protein kinase 7 / Cell division protein kinase 12 / hCDK12


分子量: 40143.328 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CDK12, CRK7, CRKRS, KIAA0904 / 発現宿主: Trichoplusia ni (イラクサキンウワバ)
参照: UniProt: Q9NYV4, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#3: タンパク質 Cyclin-K


分子量: 31700.471 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CCNK, CPR4 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: O75909
#4: 化合物
ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C6H8O7
#5: 化合物 ChemComp-RNU / ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide


分子量: 339.433 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C14H17N3O3S2 / タイプ: SUBJECT OF INVESTIGATION
研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.93 Å3/Da / 溶媒含有率: 68.68 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive

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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: SLS / ビームライン: X10SA / 波長: 1 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2020年9月21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: 3.417→214.654 Å / Num. obs: 89624 / % possible obs: 96.2 % / 冗長度: 21 % / CC1/2: 0.999 / Net I/σ(I): 15.2
反射 シェル解像度: 3.417→3.611 Å / Num. unique obs: 4481 / CC1/2: 0.39

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
Cootモデル構築
STARANISOデータスケーリング
autoPROCdata processing
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.42→60.04 Å / SU ML: 0.4 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 26.1814
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.237 4460 4.98 %
Rwork0.2118 85099 -
obs0.2131 89559 84.61 %
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: 157.55 Å2
精密化ステップサイクル: LAST / 解像度: 3.42→60.04 Å
タンパク質核酸リガンド溶媒全体
原子数33702 0 157 0 33859
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003534564
X-RAY DIFFRACTIONf_angle_d0.581446741
X-RAY DIFFRACTIONf_chiral_restr0.04335170
X-RAY DIFFRACTIONf_plane_restr0.0046013
X-RAY DIFFRACTIONf_dihedral_angle_d12.820712966
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.460.552170.579980X-RAY DIFFRACTION2.49
3.46-3.50.5284170.5016495X-RAY DIFFRACTION14.55
3.5-3.540.4727690.4551090X-RAY DIFFRACTION33.44
3.54-3.580.4371840.41031577X-RAY DIFFRACTION47.51
3.58-3.630.4164690.3791890X-RAY DIFFRACTION56.67
3.63-3.680.33911220.34842183X-RAY DIFFRACTION65.3
3.68-3.730.37371370.32282375X-RAY DIFFRACTION72.37
3.73-3.790.2861400.29662632X-RAY DIFFRACTION79.11
3.79-3.850.32671790.29252806X-RAY DIFFRACTION85.29
3.85-3.910.2971440.28223019X-RAY DIFFRACTION90.45
3.91-3.980.29321610.27163096X-RAY DIFFRACTION93.38
3.98-4.050.29181720.26783277X-RAY DIFFRACTION96.75
4.05-4.130.26491720.26073247X-RAY DIFFRACTION98.28
4.13-4.210.28151760.25993331X-RAY DIFFRACTION100
4.21-4.310.29071550.26463367X-RAY DIFFRACTION100
4.31-4.410.21551600.24123348X-RAY DIFFRACTION100
4.41-4.520.24042160.21593298X-RAY DIFFRACTION100
4.52-4.640.21651520.20263356X-RAY DIFFRACTION100
4.64-4.770.22871980.19823339X-RAY DIFFRACTION100
4.77-4.930.22231570.19613367X-RAY DIFFRACTION99.97
4.93-5.10.23042090.20323301X-RAY DIFFRACTION100
5.1-5.310.23791270.22133414X-RAY DIFFRACTION100
5.31-5.550.23121560.22933367X-RAY DIFFRACTION100
5.55-5.840.22591690.22143367X-RAY DIFFRACTION100
5.84-6.210.26691890.22283364X-RAY DIFFRACTION100
6.21-6.690.29131710.21463397X-RAY DIFFRACTION100
6.69-7.360.27172090.22183352X-RAY DIFFRACTION100
7.36-8.420.19051820.17953395X-RAY DIFFRACTION100
8.42-10.60.16991970.14113419X-RAY DIFFRACTION99.86
10.6-60.040.20311640.1733550X-RAY DIFFRACTION99.12
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.300909108550.9582570419120.1311594956371.29206038707-0.1026938698711.3919352343-0.186977618179-0.472090295343-0.5535813308820.5565526522110.124192911882-0.364048951870.3457233553960.27717468185-0.01055587485041.676475430220.323515910098-0.4348289116481.29303999239-0.1352719471771.56396076524-57.012347703-8.2131404917726.5291388949
21.372529347580.9281576991960.179894194472.18893326918-0.2643354492641.07013369425-0.145123546936-0.8025466220170.4860458088890.7563481772770.166678786132-0.210799756499-0.0005400356133920.391183132143-0.01927619874671.839746618870.16207908343-0.3268883876141.53783188248-0.2566295386821.31811172738-72.87657680419.0014840434438.997499592
32.61199447070.686402083089-1.063507065814.18453704897-1.294208464140.6355795561540.002890701553530.10900146140.08730891526140.1757358541420.01015192932710.2702820714230.0772458408686-0.17132601314-0.01795538825421.450341273590.00394124356771-0.1273643510461.01187542905-0.1232511956371.19069353118-88.733221827315.4652696124.072366926
41.89119916276-1.14443343555-2.236971574122.95629773253-0.1245921995533.881202779020.3531539316520.1297009622140.628416657583-0.112165723266-0.0357016369223-0.202869351705-0.272066459540.181803556083-0.0546808567871.419288569920.0471993669978-0.2557027079341.00667013076-0.231767408161.19563800354-78.639749856330.72832984613.1419374541
52.153721906720.2940076052190.4062128674512.179257374970.1824244993952.588246075030.1980490035480.002722242806450.3879405831180.6091008584080.144213268578-0.401069627419-0.1883877102530.580757490016-0.04466673228041.61441969151-0.0322810787389-0.3852262769331.37321651332-0.3627002356391.6756634328-55.531858468629.628556483824.3046555772
61.118625487740.0800473422617-1.943308488410.4538448576870.128639773752.63557078895-0.301828939265-0.5764907778650.4596614510670.360272757274-0.211519088511-0.476547071192-1.215675543720.247811243577-0.02433790207741.91084739728-0.0190955247602-0.6801026915391.79862439259-0.3930364509521.99670030826-43.645408318725.189143406932.6114509469
70.6903933209570.0308929583216-0.8355810666910.690838283317-0.09282527448081.344731903040.08834001661030.2092453369010.1074605997570.3229254434490.217090103797-0.0287001349761-0.464693743788-0.0402108711534-0.04521274690111.68381083896-0.209469430869-0.2389901527081.41714059061-0.1373755023911.50821597477-61.784100218231.4137117381-12.6224336259
82.44827895669-0.24524462558-0.250474516752.48906220025-0.8379164723041.94468246135-0.1523483806350.09690660693170.128685006904-0.660439884758-0.121453688576-0.58261698763-0.0886624292827-0.219389334057-0.04410966526861.601431239410.00237252913771-0.1888734248721.36467342237-0.4679809513921.67856294091-57.288608080813.3424630769-12.3753724752
90.2995701841690.5911553941280.07616776554981.007314193830.1341444411580.002236880356371.24924262096-1.035126756621.688391732920.634958248146-0.00342791487359-0.48500826819-0.7118392317670.9521264756580.6517724617691.6089445766-0.381177688260.1801946817271.71614356675-0.4971390700462.68587042726-43.539369428722.0225788424-3.51833011892
101.88290862648-0.440193754723-1.29940352452.47523902565-0.3702554576042.40031033284-0.2443576644250.610755865432-0.47701560545-0.05346155816410.205747479616-0.63126936934-0.1524524526680.629253403958-0.08165441327461.299734865340.0852403310001-0.1202310537341.41649383939-0.5387999728411.84182690332-42.73838067014.41286727925-6.24829642509
110.896704997289-0.3890845180150.2875626526180.147562745163-0.07601511295330.100397997628-1.46153852814-0.6292254969520.4868795103660.411131571680.5093218726640.8369312878250.06923225218560.320732376198-0.3479271753271.818077343630.248154342426-0.2820747409412.08532710691-0.2411869294232.13303570783-71.621984932410.16976010495.63849006866
121.36782354223-0.1947138357790.7821003239343.82208379376-0.4749804395731.130458503210.1793543650520.362819395679-0.080005808189-0.378830810955-0.3491414563990.9034195453970.5290685437770.657332379421-0.1354320455591.49942170305-0.0734440824740.02887199906011.29937200442-0.3111668451771.37896208491-60.800029821640.0351084473-42.4713379091
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160.4911965806-1.22192603319-0.5466173162692.226263988591.29694562392.20496706360.362947746611-0.502739696730.1116203415980.5318130496680.15378906024-1.77494061146-0.256815217150.02452745522540.05727465345071.26665029629-0.1427319520620.2118905951421.32479890101-0.2963986710641.82698544535-47.888271016521.1103384524-37.9062853509
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180.902828388939-0.7437455642640.68856443923.01482075784-0.03432235896820.5297209900580.118814718890.52564420749-0.117537129852-1.13499228028-0.00156624720916-0.4121446354450.289101341154-0.1069991168270.02064089086441.46941744088-0.1090613153750.05795829580841.47543099099-0.4676927786711.86197008178-50.150614543512.1030889265-53.4147066653
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221.482413946420.05926164034780.1147799892271.7272377841-0.8824148328082.971435105470.0350234468901-0.1417679989440.395884936585-0.136974948920.03453788242960.322781777077-0.632069780821-0.341368999823-0.1335480904261.34879359071-0.0172520175168-0.1147673710130.989932781147-0.2232826065731.24425194775-96.259893996777.2395117496-41.5786269943
232.77532725784-0.404112629384-2.162327922312.520510936940.3759613284063.45757303804-0.9094196196520.379188023809-0.5416865482890.6769162196290.5940689301690.04650432195930.661577911269-0.318454299946-0.07818638072231.324694986320.0399310159788-0.02606755289151.165526507930.2461874101231.32760283772-146.43586994236.6722417435-36.041299424
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252.062088275880.7907129594460.338874857143.42735141902-0.2824735662650.872688326859-0.5783086143780.104230490448-0.3960275785260.0463557239945-0.1200456076480.2032063052530.442772974657-0.533119222071-0.1294413109480.9670829094730.18024396318-0.08800928970670.8913555988490.1240547572071.0900742828-146.88637918149.6987718186-44.6111190841
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272.86843839818-2.90235012951-0.6293916987035.93294445350.003471725314320.884813330836-0.137989051197-0.2737790188830.7475693254790.352549057427-0.952934201839-1.36347960106-2.199010682320.162898529577-0.08984312327291.308052461420.11517380796-0.2616543869770.945947942476-0.1833918016331.32315093216-141.91309437357.7072005476-38.9081529046
281.052299896460.7876352437580.4409341650892.095008032042.208882930942.839170959930.002540750191790.720211809962-0.0752392244071-1.19564066042-0.0132327179528-0.680423530714-0.7740111413750.17470571497-0.3384466378930.954319239740.0849745087822-0.1607148123521.057682347280.08641600400721.24582328658-141.15329033537.6468808151-58.8705094579
291.209995442620.1427640687180.2228945941072.582883516380.7931376623673.209374497390.1277917837310.2863738151760.03542382464950.2226302280240.09108489279360.5062064588420.328412824161-0.365112918878-0.1110511485131.13507100399-0.0878097643959-0.01144174346631.048843687680.09985439836861.15727772428-151.53031617433.4897292426-58.174665462
300.31543447217-0.7737449356760.1424695025061.71726727520.81037916171.76656693126-0.1950290335420.281972445944-0.7737721407780.281426514186-0.2678314801360.02293707410831.243498947980.123500109803-0.1738454545361.193016116240.1333951345610.02890114974360.870901866504-0.08040726231721.17202092419-146.3311804621.1464262966-63.8679555021
312.70312750869-0.32660979414-1.879084326432.212391233172.27023064953.371706622240.257373102728-0.999467757563-1.667774768651.812324771020.2855784518872.91466933934-0.838152952048-2.24730855871-0.1866613164951.33734719080.1856161579480.04165683946441.565549604130.09493432236661.53685457926-159.37273237131.2684430711-52.2304142305
320.2628635894950.592453286852-0.1840092180280.5796065149510.5497017868152.115051872220.0219682270855-0.08177952873980.3199753212910.3841994336530.08490877919671.10383677469-0.452076463349-0.587753022476-0.1307853799091.635506214340.333271872080.2794274993941.547049187070.2955047028492.18354857479-174.47535430524.70167351723.53669169746
331.905734046080.825519755637-0.01635591699921.368083009890.380425512464.001028859350.007600408763230.407522107332-0.599524315182-0.6747589076650.227778448351.100589486480.134226463833-0.904351160584-0.1785277953361.485918109340.161264246913-0.3196661206771.454518756410.2997663165832.07750988721-170.54078916515.3495152429-17.4695972278
342.221844911690.7586313100540.2201805319642.73899292663-0.9726466204091.47264785441-0.265904775842-0.1854008120350.8926055826480.6538740658070.2299665028621.2962424355-0.776679179869-0.428005136118-0.04607819214791.863442072760.3609013001040.1064228126941.090432501290.07569497800921.65547146774-159.47861634344.7099399654-5.01251504576
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361.582159824740.233617181434-0.1303307011651.32287747698-0.3085394085471.35431611069-0.163407817716-0.7523184379090.2279844711510.9631426562380.16665662330.223888101158-0.3500623176230.0403519187509-0.1586916761212.106659248840.209836706620.1023910703581.170083840250.01979171680531.27530641811-146.04700462635.039428207613.6623155148
373.25345110270.3794597878510.9286993724141.845743709720.6294247985053.05079900580.1863826585630.150200198329-1.09891112922-0.4213210718730.385817885603-0.3489888851740.478439559420.174333328079-0.04845252872261.809087238610.11747817824-0.08320444018341.002894822320.03176049481581.17902707507-98.2249386938-8.1809700976720.4623827705
383.212547334030.5861659080190.4827509756222.885864379950.5411913969092.05535326968-0.361278914563-0.582494974642-0.5438714693730.8115044725060.0151365468516-0.04343289361040.423491951441-0.180494339257-0.06444874615571.932662861530.2007985619310.2049513181181.08574917660.04594020995470.857362912788-111.531647065-9.9611824211132.8458943773
391.79700952517-0.1389501335030.4813901337360.5338781133670.6103671661962.688973010970.254681764932-0.9287023620350.9389061944850.450195460506-0.381209122316-0.08479287940290.130384935390.744672779965-0.07477065024321.993579161720.105759088513-0.2435829690791.18185449761-0.2822342238490.922921679724-111.035959738-0.83862609493538.0873366523
401.006701404690.7371937110860.2517219061543.651117582091.333250657460.218609139202-0.4060841977040.344588152966-0.257516671477-0.754580963134-0.2985813601511.74003033747-0.0563863736555-1.012438641-0.04772585121451.80387826766-0.1431263602130.175260775051.05028055499-0.1588677120231.3241495043-117.505452744-20.63253074716.5430625811
411.705138281.0372052730.5301708421782.238908726750.5368085291111.81508401705-0.826163490075-0.113211379829-0.429883254259-0.706221101220.555056853854-0.3807187393560.587297419609-0.499244157935-0.04540377191471.88311586822-0.05346715522350.307190580920.825377529125-0.1058566639131.24020664181-110.048177187-28.034775932420.8845660232
421.29754196272-0.5470777203680.6272365614111.8670849468-0.09631852301193.207405341270.332285734012-0.172156697454-0.3233591820510.8143189718920.6326035031890.07539426750480.8930936918221.66498181065-0.01180365699262.14493602007-0.08124835084280.3400474374131.4933976701-0.2763328979161.58169374081-111.053815172-39.04148235548.38998048932
434.744632052340.919982172655-0.3607187155330.6322961232240.6223018106371.0437773424-0.4263119884830.501051817298-0.317079278999-1.297209896330.06990100712820.09374942929230.7043966667-0.730307081359-0.07568644228761.96861965053-0.1669596349640.3515057335061.24473325117-0.2002926870691.12339617629-109.057971315-27.896070426.70042221164
441.723429842440.4353096355391.785109172042.571200647950.7164779684422.60043660455-0.394143337007-1.35160857326-0.2902255622820.140934121608-0.863630312515-2.019166203230.5024593962051.638657892150.03641877920732.048500037940.1722491942880.1465637413931.313394023480.1555144879621.52250371659-100.865341433-29.033688010125.0826807492
454.215289894911.307873141391.944057230480.556085031085-0.2103083334912.60525630514-5.51142199914E-5-0.386786564318-0.4504298655820.4299097411890.4656538709350.1940380203980.1762692899070.263420406122-0.09443286693981.305984343340.0341122352489-0.09149617841691.28633912289-0.04787257069921.52755082435-122.93378806155.6297695409-37.6583563597
461.42866590714-0.615188038059-0.9848950535880.1795048618170.3109656723760.9783391650680.416461919818-0.245967064054-0.1343607826030.157774159255-0.203973030309-0.7807914177390.543456829267-0.089403699998-0.06546033500781.20475062192-0.0291023673752-0.1468906062770.985048831158-0.0915547543221.42510948201-124.72998532948.4537665898-48.1982271811
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480.0734951418432-0.336096331134-0.4874687891680.6006392229650.8764740285771.882790890680.828191642426-0.07916821057972.002621658120.04868053802241.122342894610.327905773596-1.064093123790.5023402638880.221527893081.913808468470.1908704776510.1886149563871.57475654108-0.01858868055282.53690658078-116.551378665.3769110626-55.2858818176
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502.99285144561-0.0708008659336-0.5978840412743.422550855610.9752122647742.939593421230.2942060253270.519257378384-0.404661981603-0.855808879443-0.1779992414970.124496763676-0.5166071579890.039529135259-0.06425581405431.939963554250.0624356694402-0.4445698355060.956099256425-0.08707829819561.2069570727-109.52792677356.0608466012-71.0846821565
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523.800786967370.979252490246-0.7581645986254.51058004921-1.355738538333.72610547917-0.0301453690761-0.452677140949-0.1858605312110.556392990857-0.1310380250460.717844348189-0.1075894675850.0872625520045-0.02695249479521.354631200750.04630576217970.22533666640.9809121767170.1625532461091.17361677951-147.754819032-4.420126239978.90120189537
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 'A' and (resid 1 through 307 )AA1 - 3071 - 307
22chain 'A' and (resid 308 through 719 )AA308 - 719308 - 405
33chain 'A' and (resid 720 through 819 )AA720 - 819406 - 505
44chain 'A' and (resid 820 through 963 )AA820 - 963506 - 649
55chain 'A' and (resid 964 through 1061 )AA964 - 1061650 - 747
66chain 'A' and (resid 1062 through 1140 )AA1062 - 1140748 - 826
77chain 'B' and (resid 715 through 832 )BC715 - 8321 - 118
88chain 'B' and (resid 833 through 880 )BC833 - 880119 - 166
99chain 'B' and (resid 881 through 914 )BC881 - 914167 - 200
1010chain 'B' and (resid 915 through 1026 )BC915 - 1026201 - 312
1111chain 'B' and (resid 1027 through 1041 )BC1027 - 1041313 - 327
1212chain 'C' and (resid 20 through 42 )CE20 - 421 - 23
1313chain 'C' and (resid 43 through 64 )CE43 - 6424 - 45
1414chain 'C' and (resid 65 through 123 )CE65 - 12346 - 104
1515chain 'C' and (resid 124 through 150 )CE124 - 150105 - 131
1616chain 'C' and (resid 151 through 174 )CE151 - 174132 - 155
1717chain 'C' and (resid 175 through 218 )CE175 - 218156 - 199
1818chain 'C' and (resid 219 through 243 )CE219 - 243200 - 224
1919chain 'C' and (resid 244 through 267 )CE244 - 267225 - 248
2020chain 'D' and (resid 1 through 353 )DH1 - 3531 - 353
2121chain 'D' and (resid 354 through 819 )DH354 - 819354 - 506
2222chain 'D' and (resid 820 through 1140 )DH820 - 1140507 - 827
2323chain 'F' and (resid 20 through 42 )FJ20 - 421 - 23
2424chain 'F' and (resid 43 through 63 )FJ43 - 6324 - 44
2525chain 'F' and (resid 64 through 106 )FJ64 - 10645 - 87
2626chain 'F' and (resid 107 through 135 )FJ107 - 13588 - 116
2727chain 'F' and (resid 136 through 150 )FJ136 - 150117 - 131
2828chain 'F' and (resid 151 through 174 )FJ151 - 174132 - 155
2929chain 'F' and (resid 175 through 217 )FJ175 - 217156 - 198
3030chain 'F' and (resid 218 through 243 )FJ218 - 243199 - 224
3131chain 'F' and (resid 244 through 267 )FJ244 - 267225 - 248
3232chain 'G' and (resid 1 through 129 )GM1 - 1291 - 129
3333chain 'G' and (resid 130 through 307 )GM130 - 307130 - 307
3434chain 'G' and (resid 308 through 743 )GM308 - 743308 - 429
3535chain 'G' and (resid 744 through 795 )GM744 - 795430 - 481
3636chain 'G' and (resid 796 through 1140 )GM796 - 1140482 - 826
3737chain 'I' and (resid 20 through 42 )IO20 - 421 - 23
3838chain 'I' and (resid 43 through 123 )IO43 - 12324 - 104
3939chain 'I' and (resid 124 through 150 )IO124 - 150105 - 131
4040chain 'I' and (resid 151 through 174 )IO151 - 174132 - 155
4141chain 'I' and (resid 175 through 218 )IO175 - 218156 - 199
4242chain 'I' and (resid 219 through 233 )IO219 - 233200 - 214
4343chain 'I' and (resid 234 through 243 )IO234 - 243215 - 224
4444chain 'I' and (resid 244 through 267 )IO244 - 267225 - 248
4545chain 'E' and (resid 715 through 768 )EP715 - 7681 - 54
4646chain 'E' and (resid 769 through 794 )EP769 - 79455 - 80
4747chain 'E' and (resid 795 through 872 )EP795 - 87281 - 158
4848chain 'E' and (resid 873 through 901 )EP873 - 901159 - 187
4949chain 'E' and (resid 902 through 931 )EP902 - 931188 - 217
5050chain 'E' and (resid 932 through 1043 )EP932 - 1043218 - 329
5151chain 'H' and (resid 715 through 880 )HR715 - 8801 - 166
5252chain 'H' and (resid 881 through 1044 )HR881 - 1044167 - 330

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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