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- PDB-8buj: Structure of DDB1 bound to DS06-engaged CDK12-cyclin K -

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基本情報

登録情報
データベース: PDB / ID: 8buj
タイトルStructure of DDB1 bound to DS06-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 / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / negative regulation of stem cell differentiation ...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 / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / negative regulation of stem cell differentiation / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / cyclin-dependent protein serine/threonine kinase activator activity / cyclin-dependent kinase / positive regulation of DNA-templated transcription, elongation / cyclin-dependent protein serine/threonine kinase activity / [RNA-polymerase]-subunit kinase / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of reproductive process / negative regulation of developmental process / RNA polymerase II CTD heptapeptide repeat kinase activity / cullin family protein binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / cyclin binding / viral release from host cell / regulation of signal transduction / ectopic germ cell programmed cell death / proteasomal protein catabolic process / Formation of HIV elongation complex in the absence of HIV Tat / positive regulation of viral genome replication / positive regulation of transcription elongation by RNA polymerase II / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of gluconeogenesis / RNA Polymerase II Pre-transcription Events / RNA splicing / regulation of circadian rhythm / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / Recognition of DNA damage by PCNA-containing replication complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / DNA Damage Recognition in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA processing / positive regulation of protein catabolic process / rhythmic process / cellular response to UV / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / chromosome, telomeric region / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein autophosphorylation / transcription by RNA polymerase II / damaged DNA binding / protein kinase activity / protein ubiquitination / nuclear speck / cell division / DNA repair / protein serine kinase activity / DNA damage response / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / protein kinase binding / apoptotic process / 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 / Haspin like kinase domain / Cyclin, C-terminal domain / Cyclin_C / Cyclin/Cyclin-like subunit Ssn8 / : / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / : / Cleavage/polyadenylation specificity factor, A subunit, C-terminal ...Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin, C-terminal domain / Cyclin_C / Cyclin/Cyclin-like subunit Ssn8 / : / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / : / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / Protein kinase 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
類似検索 - ドメイン・相同性
Chem-RUW / 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: 3.62 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

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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)499,03226
ポリマ－496,5589
非ポリマー2,47417
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)166,3769
ポリマ－165,5193
非ポリマー8576
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)166,2808
ポリマ－165,5193
非ポリマー7615
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)166,3769
ポリマ－165,5193
非ポリマー8576
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)249.353, 249.353, 218.417
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_2chain "B"
d_2ens_2(chain "E" and (resid 715 through 1041 or resid 1101))
d_3ens_2(chain "H" and (resid 715 through 1041 or resid 1101))
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_2THRTHRASPASPBB715 - 10327 - 324
d_12ens_2RUWRUWRUWRUWBM1101
d_21ens_2THRTHRASPASPEE715 - 10327 - 324
d_22ens_2RUWRUWRUWRUWES1101
d_31ens_2THRTHRASPASPHH715 - 10327 - 324
d_32ens_2RUWRUWRUWRUWHW1101
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(-0.475509504409, -0.511067619121, 0.716031144506), (0.506307831203, 0.506627720123, 0.697840048483), (-0.719404678383, 0.694361751459, 0.0178512417196)-127.3751185, 79.7985126517, -108.159966986
2given(-0.508659446524, 0.502535122402, -0.699087990324), (-0.554746806985, 0.429659817149, 0.712494506412), (0.658423532084, 0.750233891716, 0.0602292297655)-178.726096771, -28.9330307557, 33.8669459493
3given(-0.510838806481, -0.519933627185, 0.684625983377), (0.494427990501, 0.473793031721, 0.728739408363), (-0.703267144122, 0.71076661881, 0.0150378716398)-129.320432221, 79.3433048373, -107.289621609
4given(-0.513036266849, 0.506141058663, -0.693264031688), (-0.536276125052, 0.441628087341, 0.719286139287), (0.670225116357, 0.740800824248, 0.0448601404041)-179.307116849, -28.0780595029, 34.3295147446
5given(-0.546994078541, -0.512028720522, 0.66228699776), (0.483529647192, 0.452573914798, 0.749250246534), (-0.683371464379, 0.730070846566, 2.58150893107E-5)-131.927604295, 79.6972443074, -107.072110459
6given(-0.494346936173, 0.518028364232, -0.698045643598), (-0.520868883058, 0.466375121651, 0.714975420952), (0.695928669734, 0.717036163492, 0.0392737429745)-179.045097273, -28.2761610422, 36.3683335513

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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-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 14 / 由来タイプ: 合成 / 式: SO4
#5: 化合物 ChemComp-RUW / (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol


分子量: 376.539 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C20H36N6O / タイプ: SUBJECT OF INVESTIGATION
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 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: 1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0

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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: 0.99995 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: 0.99995 Å / 相対比: 1
反射解像度: 3.618→215.946 Å / Num. obs: 81004 / % possible obs: 95.8 % / 冗長度: 21.1 % / CC1/2: 0.99 / Net I/σ(I): 11.6
反射 シェル解像度: 3.618→3.784 Å / Num. unique obs: 4053 / CC1/2: 0.41

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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: 3.62→76.78 Å / SU ML: 0.4013 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 21.2903
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2059 4039 4.99 %
Rwork0.164 76916 -
obs-80955 90.47 %
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: 158.71 Å2
精密化ステップサイクル: LAST / 解像度: 3.62→76.78 Å
タンパク質核酸リガンド溶媒全体
原子数33696 0 151 0 33847
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00534542
X-RAY DIFFRACTIONf_angle_d0.850246704
X-RAY DIFFRACTIONf_chiral_restr0.05085169
X-RAY DIFFRACTIONf_plane_restr0.00565976
X-RAY DIFFRACTIONf_dihedral_angle_d11.739312899
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.02482687802
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.08580747802
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.958772135804
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.897705491673
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.703613257438
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.571117681238
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.62-3.660.3891120.3258215X-RAY DIFFRACTION7.4
3.66-3.710.3322480.3081812X-RAY DIFFRACTION28.45
3.71-3.750.3579860.30081527X-RAY DIFFRACTION52.47
3.75-3.80.32521030.2912049X-RAY DIFFRACTION71.14
3.8-3.850.35091420.27932387X-RAY DIFFRACTION81.92
3.85-3.910.33381360.26542581X-RAY DIFFRACTION89.4
3.91-3.970.31561540.252762X-RAY DIFFRACTION94.52
3.97-4.030.26681490.23142834X-RAY DIFFRACTION97.9
4.03-4.10.2471430.22792914X-RAY DIFFRACTION99.45
4.1-4.170.24991580.20392889X-RAY DIFFRACTION99.93
4.17-4.240.23511350.20352915X-RAY DIFFRACTION100
4.24-4.320.21911340.17712960X-RAY DIFFRACTION100
4.32-4.410.2171570.17442880X-RAY DIFFRACTION100
4.41-4.510.20651730.16572880X-RAY DIFFRACTION100
4.51-4.610.20151400.15792967X-RAY DIFFRACTION100
4.61-4.730.20741730.15372885X-RAY DIFFRACTION100
4.73-4.860.19921490.14862928X-RAY DIFFRACTION100
4.86-50.20441550.14242931X-RAY DIFFRACTION100
5-5.160.19831770.14022896X-RAY DIFFRACTION100
5.16-5.340.18631070.15422990X-RAY DIFFRACTION100
5.34-5.560.21861340.16152930X-RAY DIFFRACTION100
5.56-5.810.20171520.16192931X-RAY DIFFRACTION100
5.81-6.120.20411530.17282955X-RAY DIFFRACTION100
6.12-6.50.26851680.16482920X-RAY DIFFRACTION100
6.5-70.20571550.16192958X-RAY DIFFRACTION100
7-7.70.20451760.16532954X-RAY DIFFRACTION100
7.71-8.820.17691670.13372964X-RAY DIFFRACTION100
8.82-11.10.13841660.10672986X-RAY DIFFRACTION99.84
11.11-76.780.17861370.14893116X-RAY DIFFRACTION99
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)
12.411084420941.655624998290.002808615939331.52996588827-0.1393303384161.55732930618-0.10521394314-0.383419793137-0.3010831219240.2579527462950.00241861648465-0.2541060506110.2336840444310.2792369990490.008299522717711.553653527720.221265282645-0.2723888922521.3574190230.02130232957411.56595738199-57.3730690186-7.8104008884427.953982616
20.926958201069-0.384139983141-0.6399118244162.31571476055-0.2218503919370.859031059754-0.0201667569112-0.4045640273810.04930591043850.2861013974930.131336397745-0.0619791348324-0.09025547119410.0121104327346-0.006143802839241.536119856320.00796522128117-0.03999595587071.32584327254-0.1319786698021.19919173812-81.23667984813.02169737231.8615312648
31.96379066678-0.298464810071-0.1019556567750.143608623564-0.2191643346021.635445722640.0927338623443-0.04905697050730.4578271119490.2150220181440.0287237592211-0.398471352182-0.3065798973450.368083793840.06875177029951.65266918286-0.078095837844-0.1185719601121.27300255035-0.2406293479661.58170971326-63.311138302429.204046064521.2802578663
41.88905054246-0.147568583204-1.234507048510.914865727282-0.2769532861191.606721160280.418252676996-0.201366981302-0.0643355314596-0.107296341230.0132606818831-0.106364713641-0.648674622084-0.003702474448070.005142289689921.50315075235-0.056902808091-0.06014744165851.34660024551-0.06916109247551.54558071542-61.851343797231.3975492015-14.7936295646
52.452547978740.6222494001890.8933485685412.62539919991-1.456628266620.14748257336-0.1210954176360.269476174835-0.210792652954-0.02788040314290.3924348141710.315584001809-0.2495119746790.0378706166172-0.0109469599421.58732629785-0.004934309538890.04827776586711.36344694704-0.274194422981.40677926236-59.043909177120.1583646743-10.5967514523
60.6868541334150.06861468690090.2154599770661.20501335828-0.4696896554640.2002561452940.732515085078-0.2241173730420.4168108008030.184642524593-0.162912146137-1.140460393341.369193537562.11211759572-0.04456024195421.75072527859-0.08011934226060.1004479819991.98141970915-0.07469964349192.103322096-40.953708897218.3146346347-15.8435730756
72.04924851547-1.24649460178-0.7900049242112.75329182490.5686746159572.90770325763-0.0148161960859-0.05908520771740.06760027056010.125900034428-0.0669516976797-0.2226533774480.2628499996970.375972646432-0.01213896988231.37672167295-0.0181456906898-0.09941607311631.32934301938-0.2492978649471.79850370225-45.26993771315.58272420867-4.74284407503
81.84374101925-0.7648996458320.3960740526261.15939771721-0.4617950203542.0508539294-0.163654919580.5759364668490.198819733387-0.6476327265880.0910214570475-0.7578367038310.06156618765830.349108990360.03704059836431.53690944764-0.1312476867040.1556192992541.26191623558-0.2130105844361.4417495328-51.010296200539.9403444872-39.3388334218
91.297369141130.530892147895-0.6132166716581.67648852851-0.775935393141.76670225140.0570888490913-0.3235520686480.4830428029980.9253368867180.217697813433-0.325329085448-0.8374625514690.4925202047690.03408301331791.58200060944-0.184650509797-0.1020656578811.2637471724-0.1804612224871.63806835798-45.443116087345.590369744-28.1291586673
100.705126852472-1.09109976482-0.590073494512.276358803041.349582283051.86138699554-0.2671725478490.301319465167-0.405089931785-0.01845963231420.0498444061284-0.6893102231990.1712361743690.1866970696650.03656910835481.5144295307-0.0443757651380.2435005788351.42917691276-0.1137864349981.7848493494-43.487722473722.2618043937-42.5921459862
111.48274800858-0.7697643016520.3796319004924.271665829170.3723246509181.58424155521-0.0200748123520.313229426166-0.41725640253-0.2180801138710.10664709133-0.202977167735-0.2604395455050.1239824420180.04053806330451.56977888333-0.008905321212920.156638798281.22704994206-0.2150964276161.73902595119-48.238304037420.6585019909-52.0501501199
121.6641373358-1.349368876712.285324809912.93746542859-2.108679354623.14563926041-0.8340603690350.288243777293-2.10065266198-0.2757303222650.1823908704890.2331714818860.897961691723-0.193943451778-0.01077805957981.45173971125-0.000677078833042-0.2226988698711.64926195573-0.1240880370271.69340848123-54.683664763116.0510093795-50.3700620748
131.523507659020.776648065578-0.7577509838683.12412770083-0.7131987781831.28868333942-0.3653115637351.096367308991.91637018937-0.648114994360.0253963207661-1.61630323556-0.7685349138430.2038848221460.00752334644751.96116314178-0.0913250094157-0.09769632277561.50578719097-0.04484743300352.19780306224-45.162157343432.9868877721-55.1764144047
142.26005860168-1.02601043268-0.005551478732951.390413902970.1268518068581.39545447034-0.1444685164660.4331064651410.0503776528604-0.4194017898940.100505645229-0.253509919362-0.2582341803010.350555882351-0.01341524065391.67544006375-0.269635227020.1261596607251.38252104251-0.003416990577991.28127925435-74.450638578567.1680960179-69.1246604523
152.66650685103-1.06852907884-0.07872403607552.2841244355-0.1484125304562.47489478263-0.0607115700281-0.3670818468740.0830524330432-0.3528467892030.0659082037549-0.135083802483-0.09874159195690.1357095282210.001026808813861.30035481885-0.152205891034-0.02088233511851.27804860956-0.1642631954311.25265017659-75.507137016165.8429261159-34.5148703189
161.37335348930.1545952213860.1161277927860.998649424956-1.001377487112.34049981967-0.0530045042504-0.05713940784220.419008244663-0.0367667721113-0.0712670022140.0926118919071-0.557327831289-0.458408252495-0.06429885168331.58412297236-0.0209399845214-0.1337060058091.27779105756-0.177624538331.42131048291-96.946930587977.4126235799-41.9284102228
174.377895734330.8421890059811.590487657010.3846553421280.2815074146482.46535581928-0.273346669108-0.179319320016-0.1151213262060.1450489651930.02994369137480.386823234997-0.01002985066970.22850458582-0.02181998094811.38731654193-0.0322751599074-0.07664680816121.313902265410.008626556806851.42487155031-123.52634909655.2971190697-38.2346614554
182.466706763290.336474395002-0.2630361926281.242225428210.3342242842141.51496040427-0.104506747596-0.545274379108-0.0369073910838-0.05951521375890.130678609087-0.1214186624040.03671449136570.20757601877-0.08018583174181.4117861708-0.0819624542695-0.1399470368111.35058741141-0.03140485968351.29033678697-121.70991849253.2514817713-45.0108741413
192.841081039710.433551572867-0.672625061712.232413736130.2284003852891.88035469766-0.6138415044010.363915338147-0.3629057435590.2282503069440.3938288235820.2428647353270.1082317645510.384331913909-0.04488751472951.466675405960.0973368142149-0.2740786686211.21673028505-0.1057171889731.40161811908-115.03091474148.2657249258-58.6437062542
200.481768122272-0.293525222921-0.1677422182620.525007404492-0.2561467199510.28391764668-0.3379707694050.2849638569750.320845889232-0.1146973040020.6562195376270.4676361515660.107922534823-1.40110987830.0232200895212.018660684830.10639990862-0.2230400979361.968325566070.1724437819822.21590411716-129.1635856456.344471497-65.7951326766
211.661357382270.01258089460350.1132542595112.05331561325-0.505524963821.975663792730.3844484299380.8455242642840.391363898113-1.081143556810.187983483072-0.0748777262384-0.832519610768-0.239677543843-0.01372047264762.183723037620.133046670364-0.2765804363581.486125218260.1116093222771.34720678579-117.69035292861.7724471821-74.8501900924
223.319611838150.428764348975-0.01279178573472.605774336331.11048739651.603042273520.2636500793170.258729626801-0.279988453112-1.302712321380.1135465034870.2489269051490.2687458790660.33131022602-0.02676961017191.66018077419-0.0707196081971-0.1852697446281.22319332372-0.1259511980721.22919197504-109.23544616547.5970051139-73.4158317258
232.023725199190.00174537112883-0.4932179868780.275870927278-0.9107972558972.78297202602-0.2218212551120.2533186844660.9591038043910.7955016034550.2138557149380.36951100299-0.6215169504110.776471932346-0.04002692780491.916154645790.146931841111-0.04350500679862.33499475258-0.05746127825252.42867672211-92.42766670453.9588250598-49.4162326112
242.90355237397-0.422643270434-2.07706978222.804892178480.8314804945974.07245844811-0.163287540363-0.507931515692-0.9065104897740.5421392354280.341034437634-0.1805540345750.251419151852-0.03874417240850.02573897873431.2915719857-0.09534633433730.09490159807051.36955384270.04297583045551.45770924265-147.48641893636.7884599336-35.807941954
250.862061174810.978998625614-1.242640902162.93073630291-2.870071037663.7327077029-0.4561937532150.555036645869-0.213664050415-0.9383373773710.2724671326730.1958866618210.554646122737-1.37524496205-0.1659266056121.370766995960.2131932613630.01435030886391.35959161449-0.05885578533071.70076757048-157.30826604647.6027529411-45.4545703431
262.570325787910.2912539403390.05140403863572.573687769860.1776750592472.33866920495-0.05208075097890.2428893409810.13526774826-0.1686218506960.03741102207460.0289530732429-0.545873113996-0.327849483689-0.06997532088961.199233100490.0875200445557-0.1466376695061.192192927060.07950329996581.34270525099-148.21282125252.8264096682-46.407896914
272.40839117955-0.534414330221-0.2691371488711.926828877460.5602368227390.827928903401-0.204500954567-0.2479561682951.068744467420.327912998683-0.1161831284620.188385303378-1.08491138966-0.785185035146-0.04807118970071.542361851250.207182773343-0.07106721622681.47405248227-0.1413312024461.37970432015-149.46036734259.3492785664-39.1693181861
281.325887018111.211749983780.4305911609082.091435726692.594766955154.122752769040.2569696394180.6008443862070.351252969505-0.876574516776-0.147331084314-0.700221950198-0.665387654016-0.326704613692-0.2591731012771.080882399340.0590456331308-0.1325039652731.354138846590.06278845936361.42737931115-142.20044806937.5166880269-58.7121034997
291.756299200370.220223934701-0.3930250026052.107560870020.8728836595463.31199188813-0.1069156742880.4044601184690.09153138185380.04574486797140.2807928249290.06937916764620.116174566822-0.23774357559-0.05457718264791.34115931212-0.0796399253499-0.0338021288951.27252830380.0121179011091.35625853925-152.70069254533.5797974443-57.9915034978
300.554069637561-0.99209360013-0.4511003899231.881976215180.8368064464392.49809809453-0.0480636141095-0.0560482009487-1.06531425224-0.2386127360990.49217201444-0.06356405071610.35174492954-0.0255463697529-0.1637712539791.481503425450.0923210936916-0.01506387610031.39115596569-0.01889872360521.50629730924-147.68678759721.0967393769-63.5360866979
312.636042340730.246566580242-1.484503583751.533782491461.740719291753.518049616390.77919356005-0.2709906361550.5405807867950.887884939336-0.7934760708531.85017848634-1.32356611129-1.68577437808-0.123931930961.60613221427-0.00328242844055-0.03905014105061.76520812088-0.170090894341.67134293034-160.58589857331.5822886014-51.9815130775
320.640571833351-0.19487044430.2415171638091.23037634570.02837750094124.13511858391-0.0472291483229-0.111582315112-0.057862858272-0.03871044973560.1340503288130.6827476756050.0885767024285-0.606285973779-0.0696219650411.382352580240.05936118512440.05407897905061.385596444770.1628173898741.6928850485-173.00829561518.9511438698-7.24208217556
330.81511116960.196781461572-0.380691738570.899423081344-0.06876336840090.917125611753-0.1471663031480.1604418011520.6630306184010.2345894503670.1151312186290.55098048347-0.635924317499-0.2008841186210.03295363387661.764920147090.2137014450650.01639286149651.149072684280.09849061206611.53865467764-161.4781773543.1943607156-6.8326729359
341.588684833111.664220155571.186189348831.507191915780.7552379100452.884786968040.1144211457180.5084362919270.1881059765870.0176261625367-0.261517760842-0.372345010666-0.169316901911-0.184767570653-0.08885741344181.465913384750.0158228063998-0.02621922059181.148075955880.1402524354761.39091818868-140.9580434842.0905625956-17.6149575786
351.78272307514-0.1102013540140.2111176737152.06742764365-0.8407627684261.9598984539-0.0392146737837-0.03095662667410.27190634190.223947642364-0.117661924261-0.533921425736-0.3680599987190.15036082037-0.007578541997231.61723077983-0.0467502603861-0.1916502061370.996730479048-0.0393165689421.41424661449-132.68855611839.98387071662.81441981453
361.672392343211.21795362855-0.2090818073650.3619216185390.1331959704682.141311639830.128456790292-0.674622795850.1113416197540.7518736552870.0205373084460.119347820284-0.478452357587-0.204748751117-0.0907788289252.09843411840.2575332981340.2244509242881.494769843250.0326495650261.41605664982-157.32378740430.947494040322.6890861474
371.71425534286-0.4072724831331.238995809153.18235219135-1.872745568311.529276762170.1966576751620.2983056784980.1715657069260.2344191577110.368039981583-0.010925449328-0.1590580074920.334582977633-0.04971664953351.577040274120.01962960383250.006078517860121.249268043770.04054949078661.55027295587-120.53563654112.119856597616.8342123275
383.862553260410.5232366653671.5278632632.873972730850.6217841257372.66207250391-0.124843353938-0.1153806060110.05204066438360.131727342810.0698982930021-0.289475228641-0.06451523603520.211734503706-0.01766111677261.36519296986-0.009686432871050.09700090548981.077191446040.01381812116321.2104188349-130.9997504661.6342615432111.6556645086
392.191518162520.568763889453-0.1042797793533.30889436148-0.4614324185262.45400613001-0.061889834967-0.159457785183-0.158072648618-0.0271934002771-0.01788157076160.6759247058570.100079958494-0.216789690743-0.08639814584191.25125755118-0.0334367985380.06678307669971.019724154220.05666178687241.25227995241-149.993506129-4.079453107337.66705079368
404.623418892990.7787842118960.7533521116651.701369295090.06615916975741.90546757829-0.167906071397-0.520564878205-0.137989978540.3911546561780.0133537505053-0.204847115030.1991815060120.0060699069565-0.03152531616691.540092465310.0452043645992-0.04291155368611.19371755926-0.02773106803681.10250655316-109.529507922-7.3640178525832.1346359657
411.625069794860.7640263150870.2195521354432.572348619830.7948588636911.04069963158-0.252961749117-0.113715458477-0.109418733782-0.1696673889150.08565425228730.6072273683050.290294519177-0.266434815179-0.03438694818571.55045820226-0.04950521319270.06597496118491.106848877340.023804768641.38031068315-112.723192075-25.31409138120.1821170916
423.492082464310.8330196999760.4649525337471.543316332361.917967010732.67187274485-0.2234638827360.0687752096078-0.25519116709-0.1033422824490.5588345632220.4541742801230.7441961392760.08318608076810.002721028155811.60964107635-0.01004041911090.1472308909151.48141794677-0.09471133508931.25042695504-109.830576602-34.89955127118.90987210887
433.093418260920.5534158322841.699181109673.701996723450.2040256379073.502018158620.0724727843581-1.07731124799-0.3961607627881.39811012821-0.883242868132-2.119960951910.4584492885311.143315309610.08573241288651.831500299510.0927365238996-0.03108475102871.396037215180.1057346095821.59930597211-100.966992359-28.754350655426.445147717
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 819 )AA308 - 819308 - 505
33chain 'A' and (resid 820 through 1140 )AA820 - 1140506 - 826
44chain 'B' and (resid 715 through 794 )BB715 - 7941 - 80
55chain 'B' and (resid 795 through 880 )BB795 - 88081 - 166
66chain 'B' and (resid 881 through 901 )BB881 - 901167 - 187
77chain 'B' and (resid 902 through 1041 )BB902 - 1041188 - 327
88chain 'C' and (resid 20 through 83 )CD20 - 831 - 64
99chain 'C' and (resid 84 through 150 )CD84 - 15065 - 131
1010chain 'C' and (resid 151 through 192 )CD151 - 192132 - 173
1111chain 'C' and (resid 193 through 233 )CD193 - 233174 - 214
1212chain 'C' and (resid 234 through 243 )CD234 - 243215 - 224
1313chain 'C' and (resid 244 through 267 )CD244 - 267225 - 248
1414chain 'D' and (resid 1 through 365 )DE1 - 3651 - 365
1515chain 'D' and (resid 366 through 819 )DE366 - 819366 - 506
1616chain 'D' and (resid 820 through 1140 )DE820 - 1140507 - 827
1717chain 'E' and (resid 715 through 768 )EF715 - 7681 - 54
1818chain 'E' and (resid 769 through 832 )EF769 - 83255 - 118
1919chain 'E' and (resid 833 through 880 )EF833 - 880119 - 166
2020chain 'E' and (resid 881 through 901 )EF881 - 901167 - 187
2121chain 'E' and (resid 902 through 980 )EF902 - 980188 - 266
2222chain 'E' and (resid 981 through 1026 )EF981 - 1026267 - 312
2323chain 'E' and (resid 1027 through 1043 )EF1027 - 1043313 - 329
2424chain 'F' and (resid 20 through 42 )FH20 - 421 - 23
2525chain 'F' and (resid 43 through 63 )FH43 - 6324 - 44
2626chain 'F' and (resid 64 through 123 )FH64 - 12345 - 104
2727chain 'F' and (resid 124 through 150 )FH124 - 150105 - 131
2828chain 'F' and (resid 151 through 174 )FH151 - 174132 - 155
2929chain 'F' and (resid 175 through 217 )FH175 - 217156 - 198
3030chain 'F' and (resid 218 through 243 )FH218 - 243199 - 224
3131chain 'F' and (resid 244 through 267 )FH244 - 267225 - 248
3232chain 'G' and (resid 1 through 294 )GI1 - 2941 - 294
3333chain 'G' and (resid 295 through 743 )GI295 - 743295 - 429
3434chain 'G' and (resid 744 through 795 )GI744 - 795430 - 481
3535chain 'G' and (resid 796 through 947 )GI796 - 947482 - 633
3636chain 'G' and (resid 948 through 1140 )GI948 - 1140634 - 826
3737chain 'H' and (resid 715 through 768 )HJ715 - 7681 - 54
3838chain 'H' and (resid 769 through 901 )HJ769 - 90155 - 187
3939chain 'H' and (resid 902 through 1043 )HJ902 - 1043188 - 329
4040chain 'I' and (resid 20 through 150 )IL20 - 1501 - 131
4141chain 'I' and (resid 151 through 218 )IL151 - 218132 - 199
4242chain 'I' and (resid 219 through 243 )IL219 - 243200 - 224
4343chain 'I' and (resid 244 through 267 )IL244 - 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://pdbjlc1.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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