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- PDB-8buf: Structure of DDB1 bound to Z12-engaged CDK12-cyclin K -

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基本情報

登録情報
データベース: PDB / ID: 8buf
タイトルStructure of DDB1 bound to Z12-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 / positive regulation of DNA-templated transcription, elongation / [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 / cullin family protein binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / viral release from host cell / regulation of signal transduction / ectopic germ cell programmed cell death / proteasomal protein catabolic process / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / positive regulation of viral genome replication / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of gluconeogenesis / RNA Polymerase II Pre-transcription Events / cyclin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA splicing / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / Recognition of DNA damage by PCNA-containing replication complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / 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 / cellular response to UV / rhythmic process / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / protein autophosphorylation / damaged DNA binding / chromosome, telomeric region / protein kinase activity / protein ubiquitination / nuclear speck / cell division / DNA repair / protein serine kinase activity / DNA damage response / protein-containing complex binding / apoptotic process / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of apoptotic process / protein kinase binding / 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 / CPSF A subunit region ...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 / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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-RW6 / 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: 3.3 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
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)502,04958
ポリマ－496,5589
非ポリマー5,49149
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)167,02916
ポリマ－165,5193
非ポリマー1,51013
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)167,51021
ポリマ－165,5193
非ポリマー1,99018
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)167,51021
ポリマ－165,5193
非ポリマー1,99018
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)249.618, 249.618, 220.667
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 1032 or resid 1101))
d_2ens_2(chain "E" and (resid 715 through 1032 or resid 1101))
d_3ens_2chain "H"
d_1ens_3chain "C"
d_2ens_3(chain "F" and resid 20 through 266)
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_2RW6RW6RW6RW6BR1101
d_21ens_2THRTHRASPASPEE715 - 10327 - 324
d_22ens_2RW6RW6RW6RW6EFA1101
d_31ens_2THRTHRASPASPHH715 - 10327 - 324
d_32ens_2RW6RW6RW6RW6HXA1101
d_11ens_3THRTHRPROPROCC20 - 26624 - 270
d_21ens_3THRTHRPROPROFF20 - 26624 - 270
d_31ens_3THRTHRPROPROII20 - 26624 - 270

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.473863211253, -0.515785840588, 0.713735681937), (0.506057287631, 0.503806631479, 0.700060640026), (-0.720666135362, 0.692924126241, 0.022281755243)-127.346978506, 79.973239641, -108.517630331
2given(-0.513005722182, 0.507639497391, -0.692190197632), (-0.542083098612, 0.433650037109, 0.71978716265), (0.665560698365, 0.744479540353, 0.0527178412623)-179.733413865, -28.2772408632, 34.4462232335
3given(-0.509044333239, -0.522848419857, 0.683742200431), (0.499888935168, 0.467088102309, 0.729342002889), (-0.700703160614, 0.713062574067, 0.0235975882525)-129.24314741, 80.0395725249, -107.576332462
4given(-0.507860759901, 0.512863961936, -0.692132938893), (-0.538352595267, 0.438279074315, 0.719783256395), (0.672498276371, 0.738161235479, 0.053516901197)-179.75023209, -28.0930986069, 34.6826076077
5given(-0.544111173023, -0.515745022395, 0.661777986387), (0.489099035024, 0.445897991329, 0.749637989477), (-0.681707536507, 0.731561380339, 0.00963231366157)-131.943563841, 80.4206502413, -107.292837069
6given(-0.49705057912, 0.520580570164, -0.694216530893), (-0.521443839001, 0.460275906539, 0.718500113172), (0.693568341669, 0.719125830316, 0.0426731251152)-179.686985713, -27.9831297861, 36.2606911446

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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: 46 / 由来タイプ: 合成 / 式: SO4
#5: 化合物 ChemComp-RW6 / 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one


分子量: 357.427 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C18H19N3O3S / 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: 1.47 M amonium 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: 1 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2020年9月21日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.298→216.176 Å / Num. obs: 100908 / % possible obs: 96.1 % / 冗長度: 21 % / CC1/2: 0.999 / Net I/σ(I): 11.9
反射 シェル解像度: 3.298→3.484 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5044 / CC1/2: 0.388

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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
STARANISOデータスケーリング
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換 / 解像度: 3.3→60.33 Å / SU ML: 0.3488 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 22.8979
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2204 5043 5 %
Rwork0.1837 95792 -
obs0.1855 100835 84.53 %
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: 143.44 Å2
精密化ステップサイクル: LAST / 解像度: 3.3→60.33 Å
タンパク質核酸リガンド溶媒全体
原子数33500 0 305 0 33805
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005534460
X-RAY DIFFRACTIONf_angle_d0.870746617
X-RAY DIFFRACTIONf_chiral_restr0.05415146
X-RAY DIFFRACTIONf_plane_restr0.00585941
X-RAY DIFFRACTIONf_dihedral_angle_d11.881512877
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.0493183599
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.25208706513
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.00000785632
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.849692774118
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.655178284717
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.648381953688
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.340.2797100.3808219X-RAY DIFFRACTION5.81
3.34-3.370.4112270.3426578X-RAY DIFFRACTION15.41
3.37-3.420.3735600.31631152X-RAY DIFFRACTION31
3.42-3.460.3288910.32231733X-RAY DIFFRACTION46.42
3.46-3.50.34121080.2992090X-RAY DIFFRACTION55.74
3.5-3.550.31191390.29742380X-RAY DIFFRACTION63.97
3.55-3.60.32091550.28352631X-RAY DIFFRACTION70.55
3.6-3.660.28911370.27732899X-RAY DIFFRACTION77.13
3.66-3.710.29291730.27043025X-RAY DIFFRACTION81.19
3.71-3.770.30361830.25363339X-RAY DIFFRACTION88.98
3.78-3.840.29491930.25773670X-RAY DIFFRACTION97.18
3.84-3.910.2791960.24413728X-RAY DIFFRACTION99.57
3.91-3.990.25912090.22933725X-RAY DIFFRACTION100
3.99-4.070.23611960.22053778X-RAY DIFFRACTION100
4.07-4.150.24661930.20463774X-RAY DIFFRACTION100
4.15-4.250.19651890.18523768X-RAY DIFFRACTION100
4.25-4.360.19091710.17033752X-RAY DIFFRACTION100
4.36-4.480.17612200.16683771X-RAY DIFFRACTION100
4.48-4.610.19861990.16473782X-RAY DIFFRACTION100
4.61-4.760.19792010.15983780X-RAY DIFFRACTION100
4.76-4.930.18971940.15733762X-RAY DIFFRACTION100
4.93-5.120.19692290.17093766X-RAY DIFFRACTION100
5.12-5.360.20051550.17063808X-RAY DIFFRACTION100
5.36-5.640.22041740.1823830X-RAY DIFFRACTION100
5.64-5.990.20481970.18473800X-RAY DIFFRACTION100
5.99-6.450.25882180.19423787X-RAY DIFFRACTION100
6.45-7.10.27292060.19373823X-RAY DIFFRACTION100
7.1-8.130.22552140.1753823X-RAY DIFFRACTION100
8.13-10.230.18092120.13963833X-RAY DIFFRACTION99.85
10.23-60.330.19391940.16143986X-RAY DIFFRACTION99.12
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.145388606740.387465202971-0.3544407748170.4176290532030.03200838051670.39347937808-0.0181094402951-0.311645101791-0.1607921733850.2415753915530.0212369508293-0.1819001822520.1361044859920.231457804943-0.01386905284361.523575636580.153585783718-0.2719764538521.39509558286-0.01518333517851.42575326113-61.0993955756-3.7034115060630.4157492215
21.946861270820.311287817191-0.2932549936283.70642496697-0.9083645750780.7145592211630.03368862364720.03222501014360.05887374403150.2030982302180.03511815305930.01629276095770.06266024394890.005670251242330.01230908914121.293435417040.000279887061809-0.02105484458131.12060398365-0.08385931722741.14221931756-89.065135521815.898034407124.7004826754
31.2223972199-0.2286377073250.3233131838780.649900437555-0.1285122857791.503501771940.1190201074990.002964410070090.2746225089930.1375784339540.0256698147129-0.457316155257-0.1809233373140.3766198162820.02576050769441.39423316159-0.059700298771-0.1301762784051.25833518969-0.2457410541031.39217577983-63.534931939229.329230214521.1405554001
41.64931556429-0.652932061075-0.9213997849511.20521397304-0.543540491911.835504755920.1784794425530.2166963865850.2877525707-0.1903764717380.1352084381530.285746431705-0.382477695772-0.0716009103611-0.01833940387991.42790477232-0.0439492733138-0.03554635979991.30700745266-0.1119195313261.3765133669-62.271563313431.5416154739-14.9385030576
51.94502817811-0.1047690222750.5892606358873.76955956375-0.9030512847091.700074064730.04279668493750.242607996664-0.25528094959-0.302443786965-0.110797963218-0.0114652808266-0.1270313931180.136355034786-0.01127288917981.52093101810.01414003431940.04404645079211.38694719159-0.2345768806311.32223034182-57.500180631620.0033922645-12.3296043857
62.47658455238-0.382012113553-0.5663862419992.17980733932-0.03647095238372.755335944130.00842908445170.02921141645820.3832052176840.1424138800260.0371595159445-0.4180551268210.06867244629890.590387984779-0.01847868283761.389972550190.0112480933612-0.1094890529991.47967202794-0.26361884131.59436440137-43.6863032066.33422722537-6.52887581205
72.17398831373-0.4960234165440.9412747922384.36842118474-0.1711074623732.182257097930.320957344827-0.0321764379470.1047709495650.343194020311-0.1170696345480.5743101372350.1381067820250.30716145367-0.09731166347471.31528996618-0.01711586282250.08192022085651.34523509905-0.07866481448121.23140209082-61.416763497740.5796083316-42.5561418972
81.04063280225-1.052554540941.242464792371.48328384963-1.162483831482.69861189497-0.1822688602720.6216240108260.493394293631-0.772413182360.110269351172-0.558284647149-0.04024848253170.994614272670.04549893224621.4384671999-0.2026130731380.2153817918811.51747639398-0.2999128253231.58038724079-43.761694506143.252991485-40.5890529638
91.411634863290.437493954982-0.9158050801191.5529244992-0.7554147801091.79097186515-0.115551678318-0.1160407700180.6279742615230.5619493877110.161339917767-0.366141621476-0.368033088530.263594688015-0.004313882808211.39601997798-0.0865349275814-0.05600206763961.22425967525-0.2637950362741.51554208523-46.377050095543.2791823433-29.8594746432
100.793327254991-1.017586810540.03483440651151.638656993110.4793683214261.01735320834-0.0955039742096-0.315859660372-0.3492275012660.104824342523-0.000747503386705-0.3056326478310.06871163739120.304746964068-0.01358281389691.37433081243-0.05242472822230.156266548951.28883322094-0.1822510339491.47374641251-46.188324633124.0352150451-45.0227780604
111.66551903699-1.088400978960.8556657979643.434461326430.6634138876080.919655015793-0.471578056335-0.0557536875146-0.697084400759-1.136203810570.04576380135680.3807642162160.197665706343-0.3522685298470.01229766326781.41917344253-0.05808532698970.05461628626091.27403593197-0.2014201705671.38664788887-50.621763228113.0310270474-54.2789838652
120.219022033676-0.458260908802-0.04104325335284.6342790835-1.688021914010.9552972359550.1504044952650.9512780537681.78210617382-0.76510460939-0.448924885273-2.72531363228-1.168106473210.3373954044840.188509208281.51802077319-0.0731709732240.1677550149211.37598304814-0.02478999883912.02741063373-46.539318678333.2102611256-55.4379863052
131.99819465153-0.615837203560.2868978191010.585309010246-0.1849952698691.04128605776-0.03966255363180.3374444101260.114752331512-0.4571648505080.114216041814-0.122906146596-0.190024920450.255970308735-0.02136411037731.58938052902-0.294277127150.1245398374081.23760695557-0.0003165511474751.12639794505-74.531703857166.9124728932-69.9625692476
141.159234151580.2333528662480.2123074291081.096966198020.1208058178792.189163105990.00321487684337-0.1660889829170.0834919666564-0.2258657665580.0238956172718-0.105919760028-0.06093148083220.11128310242-0.01386743805081.15225250639-0.144051117787-0.08265145345661.11208134771-0.1915144641191.15958558372-78.082646889365.5984506581-33.2902691754
150.6262691421810.00725761338860.5496996442910.778460360868-0.9692873731852.00113913331-0.113810997907-0.1885539197510.383651247972-0.06776985314260.06670127139680.156843417767-0.378070914318-0.383052626362-0.0693070377041.43087006803-0.0231894715566-0.1051403833181.24487547617-0.1620053514111.34254367969-98.659806473179.509359259-43.9481157394
161.861705181720.3822663641750.04883857304051.141079189450.5575482938732.71984268868-0.169200459192-0.219848758167-0.243095150330.05034454030230.274366246404-0.194547440980.2276150615230.232185605620.02379090465351.32331632378-0.044729000213-0.1459831943941.34712724825-0.0523245711681.28487292819-124.3582047352.8543535583-41.7908416791
172.67709731408-0.872061803807-1.93259855382.4566193150.8889686881992.467869574090.0759744383229-0.0951858695513-0.286009623219-0.3293044242470.02766023593560.2778900662320.161776412357-0.0836285932781-0.007329583445041.356458251510.0157693614861-0.2077629345291.28275773199-0.1363405951191.2730381794-118.85908396351.6503785678-53.3002472188
183.051393310010.239951185351-0.2285821094732.826315244450.0004739696334873.51930630389-0.05148742794680.1468919810310.14474395526-0.3499330203270.1876213803360.00389666622708-0.487176101349-0.03707597063170.02729714286351.582815361780.033829677297-0.2109975666091.12183997993-0.04827614165681.21181187633-112.72754323556.5693342981-70.6592172683
193.46180671267-0.547016305804-1.929623757312.56451669980.1475959609274.24461844218-0.465129930148-0.0593436534932-0.133334071066-0.1231594531770.44970932146-0.2983757534120.4585442692560.2675778554590.05564938602511.13048090623-0.0100220080663-0.1003980912321.256850902760.1216599603691.1201098346-147.63654642636.6467764306-36.1723919495
201.876824778590.37578245782-0.5061604667852.01400750538-0.3624493858721.51158454051-0.2366597246060.312453867897-0.201454616410.01965550869650.07483515101730.284061274776-0.00381059784699-0.588285561867-0.02709900272651.042531872850.0894847841252-0.2061788676660.952160748025-0.005001116060061.17002641301-151.05808985248.9088107107-45.094087162
211.826369824030.0794373156350.4298023338841.87814450293-0.239023385141.34864387551-0.147837911804-0.1659050321230.905408719077-0.08880606868260.179447589149-0.233632103662-0.560635320705-0.303435313063-0.03002815443911.336126569450.0710679268847-0.07734148579181.19646035542-0.02200822739061.24940206072-149.70393941859.7221470072-44.0643383573
221.093014447460.6233927039350.5067949953381.811411320811.069308795091.76636823639-0.08307209617540.401465252149-0.0305168907498-0.1179088316850.196689070145-0.344872738653-0.158768501890.241143826327-0.0349151051931.121401844650.0505889197605-0.05719574825971.089196196010.01103814632021.11862548526-148.78100880334.9545935574-58.5479723071
233.35779572016-2.440192005350.4040017309152.318088321050.4155141818390.775656592208-0.270182019287-0.588377010648-0.4259964001130.003021720257860.01915026607140.6873930825530.500382712825-0.144350985017-0.07355201549041.473584697870.1341864969750.04579794260511.18226092863-0.08611236724571.18866543029-150.14896897219.953173715-67.3427897205
242.917673055791.25700086469-1.209895935674.20512447877-1.593018319654.939510293030.8246884166410.7056673752980.2055905845510.4428592092290.31711483859-0.8338761517511.586581407170.867811224590.04026490212171.446573470290.173293715767-0.1800002667511.213143264520.04919086867171.42885611234-143.45923370422.6219262288-58.4227098517
252.306143644050.503180017062-2.221948241371.969427371641.468259463924.180305773890.28984773412-0.0222484199799-0.3580431147740.642079739948-0.4659837718012.04698885388-0.399572575762-2.26973890756-0.1249575042751.267599465470.165908506803-0.01183620718141.59576253053-0.1007519613471.53682228576-160.79948343230.6654047179-52.4974506065
261.14728671345-0.1896330608070.5074486567641.53915781704-0.1818695822312.8424270402-0.0348795967354-0.101429856033-0.07543028892250.04715308392220.04601483654180.606344545986-0.068454618582-0.378758870854-0.01335306285281.177843402550.05816742121410.05661350499121.258701392010.04829905390161.5014740438-173.26300795118.9766858844-7.31264504133
270.9847919609370.8698970018530.454735891481.419156233520.3037971782551.85929984695-0.1430269723560.01836885262660.2932335203630.2603765974470.08158858076750.277463206584-0.340987352493-0.1727903213540.01811116561791.495192226310.156942992775-0.05840988348561.017947450850.05247478552771.32590019534-156.33543772842.9102511878-9.99193199756
282.91082778196-0.543640920328-0.1729526653381.18016439236-0.7748891589961.92018144521-0.197599505365-0.03125295038640.2842354891280.06250931296630.0875295415436-0.285483763257-0.5364370077540.345911551516-0.003861517621171.53973456223-0.0746406442797-0.125192808150.9121338133170.08425445356091.26794256997-136.8554642545.5161210676-5.14639875658
292.112160157490.160265487761-0.4407442878421.10377032523-0.3158358541571.036869867920.00464001436563-0.6022759829250.1467284727370.836535190875-0.02343414849440.0662530559881-0.32818306341-0.118365358409-0.04509355989441.77211128760.09348126814010.007198998570891.23224664914-0.06410909100811.19076216634-148.66546504532.874362401917.5708971362
301.80129549416-0.5826055909641.283234507143.03822161633-1.363315394381.19275256699-0.0625863106563-0.1682971418890.123810080666-0.2635293139890.2887444400040.2320039770080.252002192530.370093848947-0.03150830011751.51889328756-0.00702304713517-0.1782469280651.22560257344-0.02791069499631.4360260994-120.75174258112.350042147116.6550945155
311.217214544-0.008757313800110.4271341358110.8454837599610.4857433371861.44697334843-0.3431410273450.1540139365870.4822467539550.2690450148430.128556852663-0.296324600285-0.748224461042-0.56228319317-0.009734942443151.32131856141-0.0544747201197-0.07465606827651.06972889382-0.07811926776791.20392439257-123.4015540350.62541284954412.4405088222
320.570694086895-0.3279101324080.5513348034961.11617323489-0.6683665373442.229867976-0.628547867222-0.3386199588320.040129556354-0.03427688343230.244944696328-0.383090743636-0.258499302270.06862076233020.1905049573441.541511732840.1881645535660.01869834892571.267614691580.05421933248681.39621314797-126.67169463312.33390314.4785255108
331.822500239130.04946285576890.09552373352781.79349478218-0.2931333246732.316043888870.1395568542430.164179546712-0.05340634709-0.2189318642270.03583460733630.211485751571-0.161241955240.0543049452212-0.01360112982541.28232283917-0.09658715269060.1224881715890.934556853581-0.01204598487281.035628197-136.124792318-0.9775339587973.65140997503
342.709977820940.7003260699890.2895910712361.968318757851.651110974222.754812708220.279868009034-0.655974566889-0.3461418438490.8510537245570.1619637378820.6058077201680.115165812279-0.6330141747760.06397790850921.67110930503-0.139068645278-0.1288993382151.29221027608-0.003017986056721.50538909769-132.402575005-8.9615096725515.5777775685
352.729271524960.111179456369-0.4502083764664.39336407467-0.4122755967721.83267138357-0.147833685111-0.175598052568-0.2326156172840.2882923399080.003926045408430.564089116433-0.0257735272238-0.0698972790028-0.02911512633151.15928874896-0.005972577931010.04924611629230.9890688284740.008685589565571.11595932446-149.8610811-6.691875152169.74118042165
364.33374313571.367474648080.962238213582.168270709890.9399908043713.95019977438-0.04869562279260.447465394763-0.4665122921510.007893131943070.0781466322178-0.160046896160.1269042775620.229912561435-0.01327491301881.475863375790.0458155577194-0.0595351657221.119867381230.06805040180351.291334614-98.5763590548-7.861228366320.9619935207
374.442768584-0.06302753056870.3237974076110.9858187656030.3503084568240.268453198848-0.153058923711-1.41531956216-1.464761247140.561864527093-0.1362871784080.08974797836930.552008680740.503976667450.02398999091811.870363188260.0914680437609-0.06500436885971.133978800860.09757674975121.31330331119-106.494007533-14.450202839235.1847320464
382.44294032826-0.4905664179650.535611248471.88590441661-0.4146835660852.0039706674-0.013405550448-0.5261822223160.3087203025530.158379273865-0.1780517576660.105708923873-0.3935783474510.0614318047453-0.02001071195251.438013316320.03959319984550.05750956294531.16071852745-0.05750302208350.933509347693-113.485511232-5.4660245606633.9498197026
391.227317754350.0255752015422-0.1953482309762.489960718571.033092957350.953976261179-0.172046158892-0.11387296327-0.09570371280910.059653018814-0.08101105307740.4378089574760.453577350669-0.232980062614-0.0212506700171.36802498413-0.01502452193950.06583220987410.9854457083780.03802869023381.16035307521-112.979135886-24.928156385219.5735823618
402.193703740261.026175456570.3450438577251.592319473851.541684260632.116851352770.0832642615134-0.0396818983802-0.4103853792320.04340325043040.287245169704-0.2301883638450.2806649878870.07468352988790.007407220710571.6366715308-0.05102985480960.1599293055441.26469477513-0.0661949462821.16118024295-110.055247212-34.71978104118.73654668877
415.064445509160.2754951714993.426911556832.861228451640.9234500822662.683356737310.0574121077521-1.90685395713-0.4170228901311.79120443657-0.815148558479-1.659876123270.8090299733980.709688617004-0.03261077548841.803013560080.0998372943302-0.07127989863581.585187887370.1631876375971.35979291498-100.781022648-28.295313046425.4905891944
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 716 )AA1 - 7161 - 402
22chain 'A' and (resid 717 through 819 )AA717 - 819403 - 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 890 )BB795 - 89081 - 176
66chain 'B' and (resid 891 through 1033 )BB891 - 1033177 - 319
77chain 'C' and (resid 20 through 42 )CD20 - 421 - 23
88chain 'C' and (resid 43 through 64 )CD43 - 6424 - 45
99chain 'C' and (resid 65 through 150 )CD65 - 15046 - 131
1010chain 'C' and (resid 151 through 218 )CD151 - 218132 - 199
1111chain 'C' and (resid 219 through 243 )CD219 - 243200 - 224
1212chain 'C' and (resid 244 through 266 )CD244 - 266225 - 247
1313chain 'D' and (resid 1 through 353 )DE1 - 3531 - 353
1414chain 'D' and (resid 354 through 856 )DE354 - 856354 - 543
1515chain 'D' and (resid 857 through 1140 )DE857 - 1140544 - 827
1616chain 'E' and (resid 715 through 794 )EF715 - 7941 - 80
1717chain 'E' and (resid 795 through 890 )EF795 - 89081 - 176
1818chain 'E' and (resid 891 through 1043 )EF891 - 1043177 - 329
1919chain 'F' and (resid 20 through 42 )FH20 - 421 - 23
2020chain 'F' and (resid 43 through 106 )FH43 - 10624 - 87
2121chain 'F' and (resid 107 through 150 )FH107 - 15088 - 131
2222chain 'F' and (resid 151 through 217 )FH151 - 217132 - 198
2323chain 'F' and (resid 218 through 233 )FH218 - 233199 - 214
2424chain 'F' and (resid 234 through 243 )FH234 - 243215 - 224
2525chain 'F' and (resid 244 through 267 )FH244 - 267225 - 248
2626chain 'G' and (resid 1 through 294 )GI1 - 2941 - 294
2727chain 'G' and (resid 295 through 795 )GI295 - 795295 - 481
2828chain 'G' and (resid 796 through 856 )GI796 - 856482 - 542
2929chain 'G' and (resid 857 through 1140 )GI857 - 1140543 - 826
3030chain 'H' and (resid 715 through 768 )HJ715 - 7681 - 54
3131chain 'H' and (resid 769 through 794 )HJ769 - 79455 - 80
3232chain 'H' and (resid 795 through 832 )HJ795 - 83281 - 118
3333chain 'H' and (resid 833 through 872 )HJ833 - 872119 - 158
3434chain 'H' and (resid 873 through 890 )HJ873 - 890159 - 176
3535chain 'H' and (resid 891 through 1032 )HJ891 - 1032177 - 318
3636chain 'I' and (resid 20 through 42 )IL20 - 421 - 23
3737chain 'I' and (resid 43 through 63 )IL43 - 6324 - 44
3838chain 'I' and (resid 64 through 150 )IL64 - 15045 - 131
3939chain 'I' and (resid 151 through 217 )IL151 - 217132 - 198
4040chain 'I' and (resid 218 through 243 )IL218 - 243199 - 224
4141chain 'I' and (resid 244 through 266 )IL244 - 266225 - 247

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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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