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- PDB-8buq: Structure of DDB1 bound to DS43-engaged CDK12-cyclin K -

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基本情報

登録情報
データベース: PDB / ID: 8buq
タイトルStructure of DDB1 bound to DS43-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 / host-mediated suppression of viral genome replication / 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 ...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 / host-mediated suppression of viral genome replication / 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 / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / negative regulation of stem cell differentiation / 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 / positive regulation of transcription elongation by RNA polymerase II / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Recognition of DNA damage by PCNA-containing replication complex / 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 / protein autophosphorylation / ubiquitin-dependent protein catabolic process / 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-RQ9 / 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: 3.2 Å
データ登録者Kozicka, Z. / Kempf, G. / Focht, V. / 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3月27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10月16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
E: Cyclin-dependent kinase 12
F: Cyclin-K
G: DNA damage-binding protein 1
H: Cyclin-dependent kinase 12
I: Cyclin-K
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)499,07518
ポリマ－496,5589
非ポリマー2,5189
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)166,3586
ポリマ－165,5193
非ポリマー8393
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: DNA damage-binding protein 1
E: Cyclin-dependent kinase 12
F: Cyclin-K
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,3586
ポリマ－165,5193
非ポリマー8393
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: DNA damage-binding protein 1
H: Cyclin-dependent kinase 12
I: Cyclin-K
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,3586
ポリマ－165,5193
非ポリマー8393
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)250.162, 250.162, 218.849
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
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 1 through 393 or resid 709 through 1140))
d_2ens_1(chain "D" and (resid 1 through 393 or resid 709 through 1015 or resid 1020 through 1140))
d_3ens_1(chain "G" and (resid 1 through 393 or resid 709 through 1015 or resid 1020 through 1140))
d_1ens_2(chain "B" and resid 715 through 1027)
d_2ens_2(chain "E" and (resid 715 through 796 or resid 801 through 1027))
d_3ens_2(chain "H" and (resid 715 through 796 or resid 801 through 1027))
d_1ens_3chain "C"
d_2ens_3chain "F"
d_3ens_3chain "I"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETGLYGLYAA1 - 3935 - 397
d_12ens_1LYSLYSHISHISAA709 - 1140409 - 840
d_21ens_1METMETGLYGLYDD1 - 3935 - 397
d_22ens_1LYSLYSHISHISDD709 - 1140409 - 840
d_31ens_1METMETGLYGLYGG1 - 3935 - 397
d_32ens_1LYSLYSHISHISGG709 - 1140409 - 840
d_11ens_2THRTHRLYSLYSBB715 - 10277 - 319
d_12ens_2RQ9RQ9RQ9RQ9BK1101
d_21ens_2THRTHRLYSLYSEE715 - 10277 - 319
d_22ens_2RQ9RQ9RQ9RQ9EN1101
d_31ens_2THRTHRLYSLYSHH715 - 10277 - 319
d_32ens_2RQ9RQ9RQ9RQ9HP1101
d_11ens_3THRTHRHISHISCC20 - 26724 - 271
d_21ens_3THRTHRHISHISFF20 - 26724 - 271
d_31ens_3THRTHRHISHISII20 - 26724 - 271

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.474369687863, -0.515733781056, 0.713436799103), (0.508527911192, 0.500995977612, 0.700287365269), (-0.718590817347, 0.694997624093, 0.0246077168915)-127.418077367, 80.0574492374, -108.519782716
2given(-0.518764067027, 0.501635800118, -0.692275499206), (-0.546693024757, 0.427905465113, 0.71973859811), (0.657275117013, 0.751836708978, 0.0522588135078)-180.0101681, -28.619248572, 33.9866325653
3given(-0.504266933748, -0.517330383134, 0.691436283554), (0.501598945885, 0.476293641536, 0.722179246807), (-0.702931971826, 0.710994825381, 0.0193132406736)-129.153930935, 79.8104322734, -107.597463197
4given(-0.513439519537, 0.503468763224, -0.694909392824), (-0.54276681097, 0.436702144323, 0.717422766612), (0.664668374972, 0.74552695565, 0.0490459958766)-179.800646124, -28.5010206035, 34.2404492635
5given(-0.557665041078, -0.512701324379, 0.652799397931), (0.47935919449, 0.443129369586, 0.757529619532), (-0.677661024862, 0.73537317995, -0.00134966422462)-133.199414018, 80.2920541761, -107.318022725
6given(-0.489042538698, 0.525207046971, -0.696415790428), (-0.520373902622, 0.465089948872, 0.716172005127), (0.7000345683, 0.712635178244, 0.0458552713971)-179.395973784, -28.2662843311, 37.2558253166

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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: 6 / 由来タイプ: 合成 / 式: C6H8O7
#5: 化合物 ChemComp-RQ9 / (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol


分子量: 454.956 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C22H27ClN8O / 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, Jeff600 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: 2021年3月19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: 3.199→216.647 Å / Num. obs: 105078 / % possible obs: 96.4 % / 冗長度: 21 % / CC1/2: 0.999 / Net I/σ(I): 14.6
反射 シェル解像度: 3.199→3.393 Å / Num. unique obs: 5252 / CC1/2: 0.463

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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: 3.2→54.3 Å / SU ML: 0.3245 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.045
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2156 5174 4.93 %
Rwork0.195 99837 -
obs0.196 105011 80.71 %
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: 132.21 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→54.3 Å
タンパク質核酸リガンド溶媒全体
原子数33402 0 174 0 33576
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002834268
X-RAY DIFFRACTIONf_angle_d0.626246328
X-RAY DIFFRACTIONf_chiral_restr0.04545134
X-RAY DIFFRACTIONf_plane_restr0.00375941
X-RAY DIFFRACTIONf_dihedral_angle_d11.740112888
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.986166870798
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.05820581133
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.875007947354
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.785732480904
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.681554737783
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.546090769237
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.230.521950.3699115X-RAY DIFFRACTION2.82
3.23-3.270.424220.3583537X-RAY DIFFRACTION13.09
3.27-3.310.3059560.35721114X-RAY DIFFRACTION27.24
3.31-3.350.3271750.33491653X-RAY DIFFRACTION39.89
3.35-3.40.321840.32091881X-RAY DIFFRACTION46.05
3.4-3.450.30551110.30562189X-RAY DIFFRACTION53.65
3.45-3.490.2991360.30022473X-RAY DIFFRACTION60.14
3.49-3.550.30251290.28562656X-RAY DIFFRACTION65.18
3.55-3.60.3071660.28242885X-RAY DIFFRACTION70.84
3.6-3.660.28241380.27023199X-RAY DIFFRACTION77.33
3.66-3.720.27241690.27263333X-RAY DIFFRACTION81.57
3.72-3.790.28571900.25963609X-RAY DIFFRACTION86.97
3.79-3.860.26842170.25933784X-RAY DIFFRACTION93.79
3.87-3.940.26292040.25514062X-RAY DIFFRACTION98.57
3.94-4.030.24552380.23814091X-RAY DIFFRACTION99.95
4.03-4.120.222050.22614102X-RAY DIFFRACTION100
4.12-4.230.24262010.20784120X-RAY DIFFRACTION100
4.23-4.340.21031970.19524137X-RAY DIFFRACTION100
4.34-4.470.20962260.18634111X-RAY DIFFRACTION100
4.47-4.610.19942220.18044103X-RAY DIFFRACTION100
4.61-4.780.2122280.17674081X-RAY DIFFRACTION100
4.78-4.970.19732220.17764139X-RAY DIFFRACTION100
4.97-5.190.2152270.18254128X-RAY DIFFRACTION99.98
5.19-5.470.23041570.19084178X-RAY DIFFRACTION100
5.47-5.810.2222110.19714165X-RAY DIFFRACTION100
5.81-6.260.22892320.19644129X-RAY DIFFRACTION100
6.26-6.890.25442240.19584149X-RAY DIFFRACTION100
6.89-7.880.19852370.18014170X-RAY DIFFRACTION100
7.88-9.920.1542390.14264200X-RAY DIFFRACTION100
9.92-54.30.17412060.15754344X-RAY DIFFRACTION99.37
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)
11.576192975280.669093800716-0.2558078509581.25001493998-0.1155080481171.37519190238-0.0840457585594-0.320651050677-0.2158838596160.4380182666510.0365891804613-0.3424983018090.2189345225780.4253459198790.02449647676321.236320211010.164599770404-0.3328122379231.110497676050.01713890180921.26328499564-57.5767335652-7.7173851312327.8454991961
20.6438609169840.330789066202-0.6998951460322.80172277519-0.2451211330080.3249154691760.0529336352036-0.6111772878470.219905408640.740118555082-0.103101647753-0.370292121756-0.0821419314380.1810798770440.02309939062881.38475002119-0.0768792716454-0.218236949391.26626178342-0.1389948480581.06355832194-73.423586214810.055082001239.6896149253
31.84621099957-0.424894660527-0.2370011986973.15844773982-1.111813268760.9917824413430.0778888315059-0.0426559603462-0.005546221437030.144238042171-0.06109294887070.291033784679-0.0878796144134-0.140235243730.03363558824381.10764854566-0.0585370256463-0.07695199185760.877780368924-0.1157019230120.959349026233-89.081226888718.839156824722.6602511741
41.98752086124-0.3781663986760.1500253622590.702236635396-0.2592838534641.791676819960.152294524031-0.04283915935630.3911188055940.1409834906940.00322169326957-0.440768663054-0.3403220332240.4337272375690.1021137066451.16325076955-0.157561364232-0.1471633763840.917403431733-0.2308611891341.22341135955-60.291656031729.569313656521.5181808972
50.8827940107310.0753043029367-1.52816724671.98007216028-1.169537503253.85501435453-0.03347847549920.0159615455091.302022513250.05285275323830.0930301864146-0.310748579797-0.9400426823690.1990558008610.0351933721471.2190966465-0.00807401241283-0.06616195936111.138815623670.02403801278951.39016622919-65.652012064634.3944999209-13.5265109633
61.48008006095-0.369595284103-1.195643096021.81593343476-0.5136799723462.065394647570.1361660393070.2137492863980.3696439403570.128974464490.0381535307615-0.15514872692-0.7828132296870.04249088202830.02234098859581.22902737963-0.106833582032-0.07488700536560.941552740626-0.1776775509711.13233085533-60.471174868730.10060627-15.5199657919
72.276513409350.3052178273240.008285939136642.2524355929-0.6949468438171.30840922436-0.156988217054-0.5728340005560.3474277618120.5086716347310.3490724689830.456500875102-0.7086646034150.018267519323-0.03601801697631.52654112770.007454822499320.04285501741531.25505942233-0.1693040938561.17801864974-61.997474131227.7397866702-7.37203656376
81.188282578130.16091419761-0.03937766277812.69868816877-0.5787922663332.444824490290.0796514470538-0.0580079024848-0.311764736987-0.361620095092-0.169871567190.15241622053-0.246044058577-0.1452776963340.001244792226341.12625254568-0.0726351127810.09148206627240.934821626386-0.2315945097511.29230069096-57.223570711112.6118564223-12.2506520522
90.1814885697910.336346916391-0.09390807379540.56310233259-0.1556693448970.0259099481121.011884031610.2050306478570.0684216128856-0.922204492257-0.340341597936-1.615490040511.18899391152.532919453060.001129729607811.79053414267-0.0650549329260.306129518552.133418478480.002521452536992.24942073501-41.05286857818.3045055527-15.7898776939
102.95509354036-1.336284878-1.011028754852.71300464551-0.1154164773792.09281963472-0.131360790689-0.0374257711380.1698140002450.1434253188940.0742649041653-0.6328574272560.001610040694860.7719850041250.03315089857381.1334208686-0.0336575536671-0.0946969035631.26195445412-0.2573275495081.49635639313-41.26392066955.38116721266-5.5309100202
110.103730458335-0.174717561815-0.09365797731830.09674599369470.1799864054650.08746420949230.2325178669210.2562376640810.109594014267-0.640917519296-0.566914429814-0.11208174532-0.922192006908-0.3352625342750.1976862827251.78806710687-0.126007279314-0.1221642377271.85881150282-0.5748747982112.33947521022-69.8014170896.3015571511-2.51970914643
122.24547420613-0.1574575621510.9109612708214.91465963144-0.2564762977292.346547363270.2375026744520.1923457514450.2005210191530.423808545923-0.1912112577770.3499755760190.003045741124240.251173113594-0.08856049936731.14805658029-0.09307007038210.1987526826751.05456155935-0.1093182387420.996330777824-61.225489814240.6475993465-42.389493916
131.27479362043-1.243814503931.657015691661.56162329046-1.359195790472.824881082910.2729995007850.2191959967020.597909198345-0.928051954790.174405979546-1.131526847290.1716330514640.9416770504920.06997578926651.12982853712-0.3493732592570.1924516301171.28204596877-0.3419615008931.46589111441-44.03762847343.6824977686-40.9629035849
141.839120164981.08107514714-1.024121482262.13442159336-0.9700676494652.140824705650.0882298913449-0.2548102828940.4651533024140.5788610051690.0105024893467-0.470013549594-0.4316644850060.4294968431670.02208970100531.08660814692-0.13915966514-0.0324051669080.948445345628-0.2209689010291.3112623628-46.106188833943.2507031083-29.622629559
150.542791390451-1.07752608578-0.3429900201152.527366614290.562860768371.27951331655-0.198184843155-0.292886081362-0.5599904703220.1678466551750.0275752935659-0.6532141280810.1517124184770.3639484212390.02393344510421.00530113234-0.05032572293180.1567386105340.962503500311-0.1782833897851.35894164564-45.922640082724.2239393493-44.9568731862
161.35130149321-1.134976955270.599958337313.647081674770.7321210564241.44482026673-0.3711461302170.53021157055-0.0848416792975-0.5118197082660.452564662731-0.0224066664954-0.357764181137-0.1947366641780.05489289968771.278243702790.0219537027789-0.008781457994491.13121486848-0.2789936056191.60741958564-50.293478103413.2372926976-54.3701237103
170.765307877070.144091416948-1.092856119254.2939679259-0.8825334055272.20021801437-0.5592314688361.510637744851.49165452714-0.5692322489960.0136796885686-1.57943992253-0.8334729076310.288618886098-0.004414724964151.45945586428-0.0974770105259-0.0011654379861.102888737180.1151504332641.62355057259-45.573259444133.1250274334-55.2790828477
182.43086880669-0.3831842676030.202118579690.749218635076-0.0522611605491.19497511171-0.1027869840080.4471139127240.114499174269-0.5456724125410.125778499796-0.0925887710887-0.2434740742340.248960851089-0.01488771323931.60134091924-0.2576406568990.1011045497761.042201773630.01156154980960.904818701651-76.273996757566.3944258459-71.8433219847
191.42394268184-0.432127695205-0.5986151497350.699375835435-0.1904187444281.82538692087-0.175442885882-0.1426864806590.256401422812-0.2644063950350.131982806923-0.487395136563-0.4793499222220.359966899469-0.0718818969191.08213735909-0.246591984955-0.06355708616130.803639508157-0.1501970729091.01167484064-70.632231596972.0391543302-43.8404081701
202.409354306780.6971994448430.405386773421.4767266276-0.2237547114392.537564178420.00246428037508-0.445577423517-0.12957412445-0.0308305914895-0.0379455774506-0.07973237975890.0564202224515-0.07509175710220.006975628162320.793002918413-0.133926683842-0.08412413269940.734946486943-0.1210621924330.627176891792-86.81657539360.3529886427-28.2818064553
211.104551421550.307534143452-0.2148463721791.09179362668-0.9466568598722.29123133967-0.07950537739380.1737167587060.470329544343-0.3164411211220.03994727653480.226714595316-0.795978280441-0.572117423088-0.09863177026541.472824500440.0710099993068-0.1806556371510.87649152393-0.1146307977221.17357830697-99.400495383984.3323816752-48.8184013851
224.582058371131.180048077311.365856205340.2512668375350.07085890051131.900102107680.0802720008273-0.672981818555-0.3793087491230.2183642984510.1414744771310.1752735807110.3359580273790.133864031972-0.01500542960190.9963252760990.0507116256667-0.1418903270580.969267969177-0.1392345551861.19636893525-123.77936886355.3384387059-38.4038077517
232.753103897510.972795110523-0.9490934682231.642423384810.4284966536671.25834212221-0.220411654819-0.578631983643-0.135200952969-0.284792877127-0.0996104422511-0.0023766215885-0.2671895334020.181844914707-0.02215087219661.0771565281-0.0114331203365-0.1256789193431.22340016923-0.1096789589190.98524667348-126.59939683452.3214587058-42.6431259608
241.294533816780.726256714093-1.30379048233.912661264060.5985339765125.049830951350.09514296023730.3488736001560.300904173471-0.361041163937-0.04404202663770.317590555652-0.683895657864-0.263141422696-0.01518746871131.191676638750.0982058548966-0.3399131416580.885871039172-0.1400804590791.01773856346-117.51409612153.1629688478-62.6456568903
253.84827582274-0.00031828232534-1.065800763783.258565627291.582564842423.264115362470.08618127278220.399467233612-0.00978747501886-1.060487164710.04303051541190.0201402990308-0.806476290393-0.37670905358-0.003461188436291.669527403780.0760653836616-0.3767001079850.907330790121-0.09123993938340.844604790083-113.0985048956.3217861433-75.7452229125
262.538018353520.776365206921-0.5068256072292.465768867380.1498807993933.0006738748-0.198074696052-0.0645425481992-0.2169355685950.07664757183930.0513379275130.2354451046610.0778311350816-0.338127363168-0.05215454704820.7596026734390.0792085042505-0.2021939969880.658702106418-0.01000421476940.856852830927-150.31924667445.8199523467-42.4205231344
272.82821690433-0.1769016200870.7233933401833.20725026662-0.1653820395242.00439228578-0.2499843291090.05006997664060.8747006689730.006790558123110.135764242024-0.533644848771-0.887575763209-0.207072236725-0.04933719406791.180333956920.112760839136-0.06168696482940.871434172549-0.06861095719130.947856789629-150.02844697259.9143250136-43.8555800268
281.07986237412-0.121426671019-0.1633662318062.402034829141.287954434013.02606008751-0.03379004184690.296542410928-0.0700788074716-0.04783421934750.0437303388355-0.2520843966430.3538318520140.122134963993-0.04946857308050.8234625068770.0613056248605-0.08327632542940.777396386544-0.0281562582660.917887275716-149.11969340935.0331265055-58.2564239226
290.425978575935-0.850776043485-0.5035512080221.72551968521.258271782861.868976722320.03097661776210.319751763655-0.2770253404610.175470852536-0.2223477179560.1168641816540.6372696189650.166393373065-0.1133325414751.195587757090.168618882178-0.05610311593670.881927984603-0.04094592204321.1283484496-147.90417093221.0474996706-63.5358434107
303.68111737503-0.461905010501-2.265812048652.763175527312.327686447023.926310557880.349928060673-0.448187631159-0.6662521242731.19653342593-0.06974720803731.13179694142-0.0952846176887-1.71572513422-0.09968747599861.08881102207-0.008087286053970.04139904405291.33532757231-0.008977132796381.11826258799-160.73870731231.383870569-51.9022518291
310.953974481751-0.1076748439790.1091098312821.98193358784-0.2895382695182.23660684765-0.170512901769-0.0127429126139-0.150031851464-0.1946735805810.1034554305530.95020622964-0.0473121849404-0.442453685246-0.01800986290881.101113380370.10710521874-0.08045369379771.088615077480.03530348362741.47960139584-173.27664234619.0932270262-7.36133337312
322.053395789510.7639491860090.2807283476742.00171154666-0.09020777779181.94250842058-0.08332526069610.08810047265870.3641139179120.1839643780110.1068055204340.278989351573-0.470100834988-0.1410485765440.003419915142721.340028106640.240341251211-0.07760945488490.6785025831810.04056898118971.04592610881-156.34249458743.0172849875-9.71682750881
331.849933124070.0133074487357-0.1123478892152.02238537492-0.3224711381060.926912807564-0.222516298693-0.4750636746720.1736024360320.7690837927680.08852699653850.0347602620566-0.433578500908-0.0971707146057-0.06759529234411.55795370590.1547021711310.01128722277940.833527946259-0.09816327706650.94264124259-146.78031694335.089393522813.8528137108
341.52916070787-0.751292999571.502813194924.19968525571-2.453612248132.28311523107-0.211285896084-0.2769762479670.2582183234120.3842449604620.397599828278-0.5371107900760.04789160268550.489219132998-0.01407780281451.290698944790.0965963652265-0.1005684106170.872094184936-0.04112579924441.06776505303-120.85495327512.163225605617.0935268238
352.939670716170.3114129119291.575339638722.751378262230.5027895451742.3803891866-0.201701260348-0.02479588731060.304697610942-0.08979851937790.101091574553-0.324178488853-0.1651842681410.1252668812520.04313026503660.864505422839-0.04769678512140.09889182362540.618052753307-0.01975643847240.742970598046-129.6251998044.075047886910.0099936337
362.548684880840.571064646857-0.1553617011880.8808381933731.654139654673.670115891370.182466445284-0.620774110455-0.8575914285190.731885807892-0.1650195881490.05011693509940.4653391764690.0310974977760.08265815969881.29528057504-0.0902505550861-0.06618452327410.994105585970.1367654359681.23055184506-133.180557405-9.5456190192516.8108575987
372.093006951210.5416976031420.7304277931225.07713719049-0.7696633724762.35576997127-0.0288328053805-0.144384056414-0.1423800007980.160831675756-0.03672259354450.5555210641-0.213210924365-0.172687790144-0.0369808213740.8470920482490.01833730658760.1007533616680.6345894048940.03045629516570.770695652332-150.22317915-6.019566742529.15437117734
383.944780415721.002352982411.127290131071.910817734070.5748388058673.29925288841-0.3815984137280.439961064302-0.293633327736-0.1850864166840.0471382169437-0.139609333890.09492537246410.06949394256450.0404986930181.25185924728-0.00120855919896-0.08322960522670.927043986280.01330600400991.05853641369-98.6066150587-7.8668933900821.3787657963
396.009429769540.335240962101-0.1439938110471.411070576950.2859459670140.622223347423-0.424739757-0.740683598304-1.602178444580.5799892124760.1918226670470.1402613455250.6911040467890.5012806924590.06735514743631.420000499460.1700240427960.01764044132890.7476965232910.08767526635620.926099667484-106.443905769-14.344785583335.7460872917
402.92209760714-0.4377370787550.523526705942.16397047946-0.8615864521542.12284538866-0.0658321211724-0.6505066457410.1608484568190.510375305971-0.1930854863610.135833671268-0.343221814032-0.2134862129480.003772931823411.25384326292-0.003354057077160.08534514511520.90282619266-0.1030640570920.690979169256-113.49756749-5.4279050075734.4327314565
411.639229123680.06056871817360.05694098573232.531793228161.353120711851.3999856915-0.2626216749090.0973536200485-0.183771675393-0.09953473790180.1013801461670.4854377918710.241305308452-0.4065342736120.01036981161981.08081992529-0.06550770431980.1262461379140.6909556204920.01508325541670.836873307855-112.903604473-25.280050142120.3047369367
422.215584235941.019676408190.323834168262.060023822821.214632177172.17301336884-0.1478362698850.330663404417-0.443052704104-0.2503658488560.337949908075-0.09386787214820.6347378290510.4212795726120.04190826702361.36211926233-0.005150722338480.2662401747110.906780031298-0.0628974644830.983480565559-110.051177291-34.80687129869.02177286511
432.91006071480.3365536034642.535920674084.15267709250.8058843935854.577646184830.654303820491-1.42267629807-0.7383594653211.38321149491-0.246510696793-1.844973056451.069949622510.919886924930.1539385128311.491041020060.0471947534898-0.1175542214281.073134142450.2108465986361.25407843477-101.107892039-28.676074539926.4395860886
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 856 )AA720 - 856406 - 542
44chain 'A' and (resid 857 through 1140 )AA857 - 1140543 - 822
55chain 'B' and (resid 715 through 740 )BC715 - 7401 - 26
66chain 'B' and (resid 741 through 794 )BC741 - 79427 - 80
77chain 'B' and (resid 795 through 832 )BC795 - 83281 - 114
88chain 'B' and (resid 833 through 880 )BC833 - 880115 - 162
99chain 'B' and (resid 881 through 901 )BC881 - 901163 - 183
1010chain 'B' and (resid 902 through 1020 )BC902 - 1020184 - 302
1111chain 'B' and (resid 1021 through 1039 )BC1021 - 1039303 - 321
1212chain 'C' and (resid 20 through 42 )CE20 - 421 - 23
1313chain 'C' and (resid 43 through 63 )CE43 - 6324 - 44
1414chain 'C' and (resid 64 through 150 )CE64 - 15045 - 131
1515chain 'C' and (resid 151 through 218 )CE151 - 218132 - 199
1616chain 'C' and (resid 219 through 243 )CE219 - 243200 - 224
1717chain 'C' and (resid 244 through 267 )CE244 - 267225 - 248
1818chain 'D' and (resid 1 through 307 )DG1 - 3071 - 307
1919chain 'D' and (resid 308 through 761 )DG308 - 761308 - 448
2020chain 'D' and (resid 762 through 917 )DG762 - 917449 - 604
2121chain 'D' and (resid 918 through 1140 )DG918 - 1140605 - 827
2222chain 'E' and (resid 715 through 768 )EI715 - 7681 - 54
2323chain 'E' and (resid 769 through 819 )EI769 - 81955 - 105
2424chain 'E' and (resid 820 through 931 )EI820 - 931106 - 217
2525chain 'E' and (resid 932 through 1027 )EI932 - 1027218 - 313
2626chain 'F' and (resid 20 through 106 )FK20 - 1061 - 87
2727chain 'F' and (resid 107 through 150 )FK107 - 15088 - 131
2828chain 'F' and (resid 151 through 217 )FK151 - 217132 - 198
2929chain 'F' and (resid 218 through 243 )FK218 - 243199 - 224
3030chain 'F' and (resid 244 through 267 )FK244 - 267225 - 248
3131chain 'G' and (resid 1 through 294 )GM1 - 2941 - 294
3232chain 'G' and (resid 295 through 795 )GM295 - 795295 - 481
3333chain 'G' and (resid 796 through 1140 )GM796 - 1140482 - 826
3434chain 'H' and (resid 715 through 768 )HN715 - 7681 - 54
3535chain 'H' and (resid 769 through 872 )HN769 - 87255 - 158
3636chain 'H' and (resid 873 through 892 )HN873 - 892159 - 178
3737chain 'H' and (resid 894 through 1035 )HN894 - 1035180 - 321
3838chain 'I' and (resid 20 through 42 )IQ20 - 421 - 23
3939chain 'I' and (resid 43 through 63 )IQ43 - 6324 - 44
4040chain 'I' and (resid 64 through 150 )IQ64 - 15045 - 131
4141chain 'I' and (resid 151 through 218 )IQ151 - 218132 - 199
4242chain 'I' and (resid 219 through 243 )IQ219 - 243200 - 224
4343chain 'I' and (resid 244 through 267 )IQ244 - 267225 - 248

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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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