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- PDB-8buk: Structure of DDB1 bound to DS08-engaged CDK12-cyclin K -

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基本情報

登録情報
データベース: PDB / ID: 8buk
タイトルStructure of DDB1 bound to DS08-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-RWE / 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: 3.41 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10月23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)499,88533
ポリマ－496,5589
非ポリマー3,32724
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)166,59611
ポリマ－165,5193
非ポリマー1,0778
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)166,69211
ポリマ－165,5193
非ポリマー1,1738
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)166,59611
ポリマ－165,5193
非ポリマー1,0778
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)248.824, 248.824, 217.984
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 1140))
d_3ens_1(chain "G" and (resid 1 through 393 or resid 709 through 1140))
d_1ens_2(chain "B" and (resid 715 through 1039 or resid 1101))
d_2ens_2chain "E"
d_3ens_2(chain "H" and (resid 715 through 1039 or resid 1101))
d_1ens_3chain "C"
d_2ens_3(chain "F" and resid 20 through 267)
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_2THRTHRCYSCYSBB715 - 10397 - 331
d_12ens_2RWERWERWERWEBN1101
d_21ens_2THRTHRCYSCYSEE715 - 10397 - 331
d_22ens_2RWERWERWERWEEW1101
d_31ens_2THRTHRCYSCYSHH715 - 10397 - 331
d_32ens_2RWERWERWERWEHCA1101
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(0.262287398866, 0.932586462246, -0.247967358399), (-0.0823940763774, -0.234382340475, -0.968646547845), (-0.961465827044, 0.274494824922, 0.0153640657755)132.308458419, -70.4671903444, 108.028224638
2given(0.215692543071, -0.13117681927, -0.967610132724), (0.924218671797, -0.29235887765, 0.245654499979), (-0.315113588353, -0.947269195501, 0.0581764358668)64.6068984481, -168.898306883, -34.0215749811
3given(0.239382698435, 0.926473512819, -0.29041823933), (-0.0809161832723, -0.279037761057, -0.956864932573), (-0.967547670647, 0.252556445077, 0.00816988835301)132.85361071, -72.5573053724, 107.252576662
4given(0.219395856435, -0.114112170996, -0.968939559833), (0.926764359289, -0.286009089052, 0.24352951224), (-0.304915202198, -0.951408016263, 0.0430058839996)65.2808494573, -168.882467659, -34.2949798428
5given(0.221441606971, 0.924390189098, -0.310590394252), (-0.0707092600765, -0.302438728112, -0.950542485256), (-0.972606711493, 0.232451272394, -0.00160957167027)134.004507468, -74.0047552867, 107.049201421
6given(0.22810387998, -0.101866629605, -0.968293245722), (0.93478676907, -0.25521576864, 0.247059927568), (-0.272290867107, -0.961503042746, 0.0370078705057)65.1728367582, -168.732399987, -36.2727886561

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要素

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タンパク質 , 3種, 9分子 ADGBEHCFI

#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

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非ポリマー , 3種, 24分子

#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 20 / 由来タイプ: 合成 / 式: SO4
#5: 化合物 ChemComp-RWE / (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol


分子量: 404.508 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C23H28N6O
#6: 化合物 ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H8O7

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詳細

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: 0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7

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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7月20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: 3.406→215.488 Å / Num. obs: 92889 / % possible obs: 91.2 % / 冗長度: 20.8 % / CC1/2: 0.999 / Net I/σ(I): 15.5
反射 シェル解像度: 3.406→3.562 Å / Num. unique obs: 4644 / CC1/2: 0.514

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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: 3.41→72.66 Å / SU ML: 0.3539 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 22.0049
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2102 4659 5.02 %
Rwork0.1849 88182 -
obs0.1862 92841 87.24 %
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: 144.38 Å2
精密化ステップサイクル: LAST / 解像度: 3.41→72.66 Å
タンパク質核酸リガンド溶媒全体
原子数33652 0 203 0 33855
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004234546
X-RAY DIFFRACTIONf_angle_d0.784346722
X-RAY DIFFRACTIONf_chiral_restr0.04985167
X-RAY DIFFRACTIONf_plane_restr0.00495974
X-RAY DIFFRACTIONf_dihedral_angle_d11.980812952
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.09185404201
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.0970984377
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.899393263738
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.874662313159
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.690810250384
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.581304399594
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.41-3.410.551510.687710X-RAY DIFFRACTION11.34
3.49-3.530.32951100.31322255X-RAY DIFFRACTION75.75
3.53-3.570.30041610.29752723X-RAY DIFFRACTION82.14
3.57-3.620.31911340.28793027X-RAY DIFFRACTION89.98
3.62-3.650.32031200.30732083X-RAY DIFFRACTION90.96
3.67-3.720.28531670.27042935X-RAY DIFFRACTION99.36
3.72-3.780.29241740.27553315X-RAY DIFFRACTION99.94
3.78-3.840.28712050.27463315X-RAY DIFFRACTION100
3.84-3.860.2503740.26191230X-RAY DIFFRACTION92.75
3.91-3.970.27461640.25062929X-RAY DIFFRACTION100
3.97-4.040.24761680.23423350X-RAY DIFFRACTION100
4.04-4.120.23711730.21093372X-RAY DIFFRACTION100
4.12-4.20.20621720.19613362X-RAY DIFFRACTION100
4.2-4.290.19541660.18473346X-RAY DIFFRACTION100
4.29-4.390.18391660.18393370X-RAY DIFFRACTION100
4.39-4.50.19181980.1783311X-RAY DIFFRACTION100
4.5-4.620.18421610.17433385X-RAY DIFFRACTION100
4.62-4.760.20721980.17583345X-RAY DIFFRACTION100
4.76-4.910.2061720.17463380X-RAY DIFFRACTION100
4.91-5.090.23082010.16983356X-RAY DIFFRACTION100
5.09-5.290.20891320.17643409X-RAY DIFFRACTION100
5.29-5.530.23421560.18613399X-RAY DIFFRACTION100
5.53-5.820.1981700.18773387X-RAY DIFFRACTION100
5.82-6.190.22351950.19553376X-RAY DIFFRACTION100
6.19-6.660.24761670.19123398X-RAY DIFFRACTION100
6.67-7.330.1972070.17913400X-RAY DIFFRACTION100
7.34-8.40.20181880.16763419X-RAY DIFFRACTION100
8.4-10.570.16291910.12563423X-RAY DIFFRACTION99.86
10.57-72.660.17111680.16153572X-RAY DIFFRACTION99.18
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8393696360980.7383937926690.123897866962.109403085220.3284335585341.423028042960.0835842564770.3762748923380.117820917112-0.223909824548-0.1051189092610.193330174179-0.157988981182-0.4270882841640.02363348219581.27620202230.103316488216-0.09331819071491.700136082030.2055351234491.460425562922.0380413404-53.2721696565-27.9432613286
22.62518796691.16964216838-0.1002063871811.261933559510.1114771707421.29816189870.004017304111190.838336081160.290607329047-0.4578409556620.1215860645820.183584175716-0.13392410675-0.2098718000070.01259247227971.479794490320.04662241455240.02537051363151.628127535140.1741063643841.2788074646545.1887462728-57.8108344732-39.757077097
32.900474160710.3986803130360.7553858528892.335805319540.8170100911861.056658572110.009453144477730.0178970629921-0.254187722866-0.1379743492870.0469561309668-0.19013126410.07644168117940.1003506371210.01499408870091.22367657817-0.08231185260130.07808212738511.198412039030.08339931538231.1190039281860.4994578115-67.254972195-22.7287244894
41.30230890875-0.7061691420690.3744142241941.38128380259-0.1265323719921.687515352310.0641111130752-0.03026517255050.60649300186-0.04539419595330.0589347768281-0.192945371713-0.465547216850.024083917830.1352110574411.41905753521-0.1010150492190.1627216166361.300605569570.1897188499631.4664429649555.7869096389-36.9967099904-21.6597442095
51.306521872810.3547732628020.3509038963231.505243067040.2734037044691.853490846710.12477668565-0.09722927431250.1850383082140.15148116110.21124665352-0.219862802266-0.214746105030.4519629925540.01184308160821.44781209175-0.05880120265310.0803814527431.383457316720.07801358892551.3591021478758.0921364508-37.77810538714.8271269589
63.99569099439-0.2434503643921.660897372463.233390825010.528537422051.915398526970.02741500942630.00853307557609-0.08668011465010.0972450441428-0.07763093939210.0246786558881-0.160046630011-0.125462621929-0.002250207367161.40704997849-0.07292228230010.2382780440211.34473640070.1821445828751.2678532522645.5122796897-38.961662635812.2601627698
73.429852645280.931672629587-1.396822703612.523573441640.4222794347242.66737353675-0.01402885184850.1385469266770.346382884750.06083027159890.01057501603630.166819737727-0.262044218573-0.349690189840.0261206376461.42989358950.01393870051390.1397319596621.361266349510.1861168081161.6262533787127.9285473918-35.61706445324.84031773257
84.027776710410.7461389261960.4605865807062.25444592684-0.2442476291392.0668208445-0.509030401246-0.135447391772-0.2104471034690.1863111601480.365769198579-0.103767173201-0.382937262971-0.290610966421-0.0598186824951.44005116693-0.1630658745130.09254996199281.40678680844-0.07953362820611.2319467605965.4746278029-32.445428823442.4152658677
91.78726893949-0.4514184071961.645143648070.130396908154-0.4598567837842.872509761590.619497789896-0.9265766913570.8990846891930.665743764904-0.173357950749-0.382563872207-0.334489931673-0.3830768188360.1400827601971.70039875441-0.1247924293770.3621029264651.232069795430.05112680590931.5078013399559.4688900153-16.088695750940.8690230709
101.436753994080.6732901076780.3184914512751.595003038811.205576599272.11276128842-0.0201446843270.4814659950350.484276307332-0.038202832130.084325021320.00295522553114-0.52487043020.275515340480.02767236361291.39374541239-0.205872425730.190054688671.235405704040.1027891716191.4687436104660.2296215055-18.078825896829.6132971698
111.961489684450.453822538701-0.003377916012980.4145489872440.02850842872181.15132571437-0.07372923877840.143425241810.4284313415630.153937241286-0.03693566392990.447838283391-0.35971385896-0.0400064550587-0.01902931364761.27411120914-0.05559706830860.2314764654141.29933590656-0.02583248593731.5370853783543.6425597631-27.498557682844.5949675751
123.470743965650.536495443742-0.2312298595331.19820398038-1.083224905780.9611175849150.182235511329-0.401649963771-0.4490552886651.03567434451-0.5032669376760.4036954368610.792340753670.3386617712110.0144316352421.44597710004-0.02307747948610.2045919824711.498377558220.04550954727581.4818456505836.2112893683-36.207663600154.235008627
133.441885016010.9229886124481.008511613960.587237212290.4649520984991.3460421025-0.452620034855-0.2483954396521.698951514541.61674110557-0.341582345185-0.878701017911-0.1559742681320.7014147921690.06437328099751.68549855813-0.3001229935370.04501552163461.669867728310.08844525778091.6152927594751.0315918096-22.586721178455.0616598406
142.08662993-0.918677889114-0.08487359634311.15469663779-0.1250009889121.667935922780.00635476740353-0.3576618123240.13816671760.530679663237-0.06228247117570.081002728847-0.352250711290.01595524297490.0003081456853341.64734199493-0.27904239550.05199660032771.28862610741-0.11820386371.2151015375895.3279999155-32.756406769271.8136260265
150.353564874932-0.869728053931-0.02081817485692.089627885270.6620739245021.810776675490.2093327331080.009269192185570.4550318195840.213692842736-0.221500309819-0.21633045736-0.4068500939770.0555391290241-0.09428500698251.37793115459-0.2234203361070.1196422710821.172389625860.100796774021.3423976350997.3368746294-25.039618069743.8153382081
161.9873067605-0.7698036337560.4443916188772.523091341911.195790062752.067487981950.1484409890530.1255856511630.240377276778-0.164813258172-0.08258610314540.422954849286-0.277358117119-0.5093645039060.02709986609131.32912871945-0.08139602918310.03956974897171.020829103060.130641725821.1771113187391.133572155-40.496566345429.3433426072
171.18941967794-0.1992170072010.6108612541191.482373815350.2078307201612.23537212756-0.03765165267030.04132477618460.0879302723345-0.0419119118588-0.11971163688-0.3976251620310.1328671611420.790267207163-0.03366376598231.24312225-0.1199204912120.05974527541841.413774494320.1842446434921.35233782035117.818085608-45.403296384943.86028883
180.974238203225-0.976271902708-1.291214609123.35221423766-0.1626549221193.333060824970.130056292471-0.00468155943267-0.278378795276-0.0444289419006-0.1392869844070.00695938983945-0.2263623672-0.146526482031-0.02574475023161.15673903348-0.112406849608-0.07339713514651.247822535710.1145565041151.33695186467105.638200468-78.790664203948.2379242384
192.88126822335-0.296634609201-1.980347756832.668316344340.1020254526522.687253607930.358830818252-0.685712361440.480260860890.449312303297-0.0898232384663-0.211515408238-0.1964080322440.6083275644260.05121079784691.31899106966-0.152748714954-0.03200488336441.562038126790.1438959838091.28126240689105.121280174-69.692292706971.5071289241
202.89082038141-0.588011260899-1.448591618892.885425718671.625057210534.756236374080.01980747224640.31496698904-0.0211796223920.0955197570836-0.02281327564210.6642347437660.440185402382-0.2625573846120.1145733524731.346076033520.000791878800672-0.02035747543181.203448645260.01411450061371.38284904157105.378328006-109.17158083935.7507369621
211.467630329340.2417177293810.2360575448312.220658231990.2040858462341.30816882689-0.137509708232-0.0327430167444-0.455020718310.1164802754730.04357055691730.1275618568190.4926243077990.3903338585520.005238221903410.9629245155250.0499922222729-0.08973061836541.186999186720.1953362702721.21260756624117.586813985-105.85466506344.8243021707
221.904947564060.2460560823620.3650204860331.59059520333-0.4677135101771.776459554850.1824705444260.03480575091040.562332596425-0.0177146008201-0.283096577189-0.691350894837-0.1025325923920.9963976247840.009997005378161.10810599204-0.01617972952950.02314334550211.490211580960.08160913358161.21863986524126.239046504-99.244729951443.8965791338
231.79446800790.357853095418-0.9886615695231.69504249308-0.02782047664712.21368292564-0.198379254666-0.33130490980.0545414937070.4169383635970.124770150869-0.179674843750.192718692022-0.232779555078-0.01374020048081.167791927870.0150991974301-0.04795015776661.176571594370.0755769346961.25797967298104.325309864-111.31379681758.2500417394
241.991308326060.378244685467-1.2008696120.3289181234260.137789456333.222503925890.03814315452420.043265818827-0.0511894026075-0.1523737566260.0423693319980.7114949267610.438995720871-0.671961164977-0.1051885436471.162083577110.032846468332-0.01269702561281.47575882932-0.01190722037671.4256755138691.3653150356-116.9388472963.3119308814
252.364298041950.0944720977359-2.848377443162.485280730230.8662269143223.97509806626-0.4347530386080.340543988527-2.04462476651-0.4808516234280.375811632727-0.1991432555832.124383785831.41670946821-0.01851360938161.421519156920.2499411271480.1510829315951.563471854540.1410766375351.44653638205107.362807407-122.89576674751.9829591444
261.62881558307-0.0002945741225620.1109146416051.132957312760.009372591765563.558857800430.07592700584710.0336449878352-0.5145418830680.0386972003457-0.111783118784-0.1637659270350.4260255077310.3397207954710.03363976827631.265342954550.0598475612911-0.01488819505311.35847846325-0.04896692711541.46573329473102.948759229-140.0654990697.02209609884
270.4829842372710.08520876258760.6169444470940.990504344428-0.2739935458331.55962256421-0.1753237327360.21210572453-0.122738459890.1365839644520.0878241137169-0.365043094533-0.0285525221780.588371864960.08142046495561.1323394857-0.17238502978-0.04240372900071.624502971210.03836913325991.4315389745115.129033289-113.4156831489.59237736719
281.93075082138-1.870754973310.4552336472592.539656331990.04804007923512.271997027790.03169678883450.03383652163980.2321620167310.323922052362-0.13352211897-0.301591821146-0.6024399704380.413616158860.02538187391171.19449718129-0.368224427581-0.1390864734051.424942302480.09768147988231.4114575298107.601257911-95.28112867494.76615946489
291.00473011173-0.06287646302420.2936365958352.112009193650.7078194148071.12912642761-0.06919565479580.733952851070.178604173349-0.5345187327080.0864098628431-0.235206757823-0.1619932761760.5052782466610.04407977997911.23686793467-0.2065775560830.08329029053231.793832706410.03815679755541.27369903441102.498578275-111.800687782-17.8481253431
301.845264904240.1479389738130.6900996135311.39699694266-0.6529496837390.995194860189-0.1017904986510.434505241120.3845213429450.1315447329670.141538728583-0.0299311730323-0.1097648826510.0788070450810.01437930878391.32466352082-0.06958808700150.06585917633771.32894535786-0.02501778350531.3845715282767.9015496335-100.706126886-15.3736858698
312.412958524220.8516384952910.8079934520781.194652612120.3044359814192.313185901470.06440526211240.4618725260090.52855836328-0.192290718719-0.486683072951-0.209556179686-0.07682574219960.4048729027890.2557476133941.27187782467-0.03513287786550.06598030795711.40833779436-0.09835521273421.4322829255273.9778170662-103.054942687-14.5782063006
323.335577386890.453969945174-0.5536877705794.43193053322-0.3390326444932.0838962243-0.04214276010390.244615103479-0.121313653641-0.1011047739270.04570838315220.0984737026869-0.04291697120030.2362297341310.01302987249211.07522764454-0.1778323279760.04920399430381.11513661532-0.1083517891991.085572081467.8276818539-124.202358882-11.3966498418
333.531128161340.847471738596-0.705488761621.24490505146-0.8520853951732.920904139260.196798281282-0.21588959645-0.1733793402120.124300329144-0.4188563876750.1585244050510.2049811893270.0307090620343-0.03183572689311.14124993388-0.0350522659492-0.03556056081931.11949927939-0.02300693090061.2323988552271.5746098001-131.74244283-4.4015130114
341.81152188966-0.565286152016-0.3087987881274.50692679699-2.011471020723.27041197907-0.2153717184910.06966989847810.1605355630590.663010824059-0.0454188548480.260131635343-0.271790786939-0.1923163651550.02803144299921.26452327778-0.114797314042-0.06569819301971.339044565470.07964130096561.391458576942.3669884361-88.8307596724-21.2903303678
352.05361675634-1.599342666780.1248542499773.68470495104-0.4391160973380.239932042566-0.05897046091010.575961814739-0.542838378925-0.5748847653670.01414674153051.15866363406-0.340847476157-0.3362034267110.1500182302881.23784604511-0.2210645659730.01944482459451.69698695182-0.06035298208561.1763290031240.8310970285-98.94874895-35.5348869235
362.3855515128-1.008878082380.7999844891492.136214292850.330246936882.23661419322-0.06652654503580.4072124061350.00185833501362-0.6360127979-0.15790417549-0.187980503122-0.01279104738240.1895527663550.05224887388571.27739691983-0.1383538634260.06408763372921.30504102026-0.004760268358841.0251127428752.0366840862-100.524492525-34.1634662751
372.085678140520.538338241512-0.9740139209731.39183011819-0.3161180247011.534798758260.0517073562547-0.00411888149583-0.6170507388020.0411010122208-0.240602966112-0.2274923097030.588342742958-0.2543131148940.00148853363991.18815155127-0.1605155967830.01674897043781.2303566684-0.08545155683021.3005989658534.7756499056-109.880999671-20.0692533414
381.219821065310.2270233582-1.543392389312.95619033112-0.8974254971062.024544032060.2222116417040.1319946168360.20078741750.06877365882580.1088682745220.741030819284-0.345803494803-0.8699478919350.0345179989561.30670394946-0.06242295786140.05520467177651.4072007098-0.08003604810021.3574801647324.6825284501-112.29096124-9.34045811577
392.831808880050.532023511647-0.241259071813.07830760595-2.396199257242.08225015819-0.5247189526830.525542103411.67535067455-1.777335714350.2985829732561.11292409666-1.41986303731-1.8311563469-0.1233993540171.61658400901-0.181945415226-0.1443904485711.763455166950.0874295515411.4356149927125.7194459899-101.508139267-26.4095032463
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 716 )AA308 - 716308 - 402
33chain 'A' and (resid 717 through 856 )AA717 - 856403 - 542
44chain 'A' and (resid 857 through 1140 )AA857 - 1140543 - 826
55chain 'B' and (resid 715 through 794 )BB715 - 7941 - 80
66chain 'B' and (resid 795 through 892 )BB795 - 89281 - 178
77chain 'B' and (resid 894 through 1040 )BB894 - 1040180 - 326
88chain 'C' and (resid 20 through 42 )CD20 - 421 - 23
99chain 'C' and (resid 43 through 63 )CD43 - 6324 - 44
1010chain 'C' and (resid 64 through 150 )CD64 - 15045 - 131
1111chain 'C' and (resid 151 through 217 )CD151 - 217132 - 198
1212chain 'C' and (resid 218 through 243 )CD218 - 243199 - 224
1313chain 'C' and (resid 244 through 267 )CD244 - 267225 - 248
1414chain 'D' and (resid 1 through 307 )DE1 - 3071 - 307
1515chain 'D' and (resid 308 through 761 )DE308 - 761308 - 448
1616chain 'D' and (resid 762 through 856 )DE762 - 856449 - 543
1717chain 'D' and (resid 857 through 1140 )DE857 - 1140544 - 827
1818chain 'E' and (resid 715 through 892 )EF715 - 8921 - 178
1919chain 'E' and (resid 894 through 1039 )EF894 - 1039180 - 325
2020chain 'F' and (resid 20 through 42 )FH20 - 421 - 23
2121chain 'F' and (resid 43 through 106 )FH43 - 10624 - 87
2222chain 'F' and (resid 107 through 150 )FH107 - 15088 - 131
2323chain 'F' and (resid 151 through 218 )FH151 - 218132 - 199
2424chain 'F' and (resid 219 through 243 )FH219 - 243200 - 224
2525chain 'F' and (resid 244 through 267 )FH244 - 267225 - 248
2626chain 'G' and (resid 1 through 294 )GJ1 - 2941 - 294
2727chain 'G' and (resid 295 through 795 )GJ295 - 795295 - 481
2828chain 'G' and (resid 796 through 856 )GJ796 - 856482 - 542
2929chain 'G' and (resid 857 through 1140 )GJ857 - 1140543 - 826
3030chain 'H' and (resid 715 through 794 )HK715 - 7941 - 80
3131chain 'H' and (resid 795 through 832 )HK795 - 83281 - 118
3232chain 'H' and (resid 833 through 952 )HK833 - 952119 - 238
3333chain 'H' and (resid 953 through 1044 )HK953 - 1044239 - 330
3434chain 'I' and (resid 20 through 42 )IM20 - 421 - 23
3535chain 'I' and (resid 43 through 63 )IM43 - 6324 - 44
3636chain 'I' and (resid 64 through 150 )IM64 - 15045 - 131
3737chain 'I' and (resid 151 through 217 )IM151 - 217132 - 198
3838chain 'I' and (resid 218 through 243 )IM218 - 243199 - 224
3939chain 'I' and (resid 244 through 267 )IM244 - 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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