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- PDB-8buh: Structure of DDB1 bound to WX3-engaged CDK12-cyclin K -

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基本情報

登録情報
データベース: PDB / ID: 8buh
タイトルStructure of DDB1 bound to WX3-engaged CDK12-cyclin K
要素
  • Cyclin-K
  • Cyclin-dependent kinase 12
  • DNA damage-binding protein 1
キーワードLIGASE / kinase / cyclin / ubiquitin / degrader
機能・相同性
機能・相同性情報


cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / host-mediated suppression of viral genome replication / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation by virus of viral protein levels in host cell / negative regulation of stem cell differentiation / spindle assembly involved in female meiosis ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / host-mediated suppression of viral genome replication / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation by virus of viral protein levels in host cell / negative regulation of stem cell differentiation / spindle assembly involved in female meiosis / regulation of cyclin-dependent protein serine/threonine kinase activity / epigenetic programming in the zygotic pronuclei / cyclin-dependent protein serine/threonine kinase activator activity / UV-damage excision repair / 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 / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-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 / cellular response to estrogen stimulus / regulation of signal transduction / ectopic germ cell programmed cell death / 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 / negative regulation of MAPK cascade / 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 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / positive regulation of transcription elongation by RNA polymerase II / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / regulation of circadian rhythm / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Wnt signaling pathway / mRNA processing / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / chromosome, telomeric region / protein ubiquitination / protein kinase activity / nuclear speck / cell division / protein serine kinase activity / DNA repair / apoptotic process / DNA damage response / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / 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
Chem-RR9 / 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: 3.79 Å
データ登録者Kozicka, Z. / Kempf, G. / Focht, V. / Thoma, N.H.
資金援助European Union, スイス, 7件
組織認可番号国
European Research Council (ERC)666068European Union
Swiss National Science Foundation31003A_179541 スイス
Swiss National Science Foundation310030_301206 スイス
Swiss Cancer League4980-02-2020 スイス
Swiss National Science FoundationCRSII5_186230 スイス
Marie Sklodowska-Curie Actions, FragNET ITN765445European Union
Other private スイス
引用ジャーナル: Nat.Chem.Biol. / 年: 2024
タイトル: Design principles for cyclin K molecular glue degraders.
著者: Kozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. / Cigler, M. / Mayor-Ruiz, C. / Schmid-Burgk, J.L. / ...著者: Kozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. / Cigler, M. / Mayor-Ruiz, C. / Schmid-Burgk, J.L. / Haussinger, D. / Winter, G.E. / Fischer, E.S. / Slabicki, M. / Gillingham, D. / Ebert, B.L. / Thoma, N.H.
履歴
登録2022年11月30日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年9月13日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年11月20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)499,05624
ポリマ－496,5589
非ポリマー2,49815
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)166,4489
ポリマ－165,5193
非ポリマー9296
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)166,2567
ポリマ－165,5193
非ポリマー7374
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)166,3528
ポリマ－165,5193
非ポリマー8335
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)249.143, 249.143, 217.390
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 1033 or resid 1101))
d_2ens_2(chain "E" and (resid 715 through 1033 or resid 1101))
d_3ens_2chain "H"
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_2THRTHRLEULEUBB715 - 10337 - 325
d_12ens_2RR9RR9RR9RR9BN1101
d_21ens_2THRTHRLEULEUEE715 - 10337 - 325
d_22ens_2RR9RR9RR9RR9ER1101
d_31ens_2THRTHRLEULEUHH715 - 10337 - 325
d_32ens_2RR9RR9RR9RR9HW1101
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(-0.48366824703, -0.513017284033, 0.709139121117), (0.501089552813, 0.501987301857, 0.704924115658), (-0.717617089315, 0.696291616392, 0.0142722831208)-127.588164537, 78.9875612039, -107.772801308
2given(-0.512408454196, 0.504878516935, -0.694647579141), (-0.54931880102, 0.429055844236, 0.717049466476), (0.660065474718, 0.749005184004, 0.0574874196744)-178.774984889, -28.5914866495, 33.9733134736
3given(-0.514035909827, -0.515027810448, 0.685939820883), (0.497551094521, 0.472373647082, 0.72753422317), (-0.698720252854, 0.715268824994, 0.013435633341)-129.310021775, 79.1811779211, -106.880503559
4given(-0.51199897248, 0.505030524906, -0.694838989329), (-0.539286203881, 0.440632949486, 0.717644058103), (0.668601108646, 0.742150101219, 0.0467523772429)-178.951178864, -28.1433329217, 34.2693365403
5given(-0.547253040518, -0.515749835879, 0.659178440511), (0.486211673302, 0.445157884068, 0.751952569646), (-0.681257894185, 0.732008582629, 0.0071495851413)-131.714901194, 79.9676164894, -106.505101141
6given(-0.494667223113, 0.523962260027, -0.693374277318), (-0.516680911912, 0.46421654006, 0.719405198202), (0.698816981508, 0.714119425588, 0.0410885915233)-178.775848033, -27.6498314356, 36.7517832461

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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: 12 / 由来タイプ: 合成 / 式: SO4
#5: 化合物 ChemComp-RR9 / 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one


分子量: 448.521 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C23H28N8O2 / タイプ: SUBJECT OF INVESTIGATION
研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.93 Å3/Da / 溶媒含有率: 68.68 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.7 M ammonium sulfate, 0.45 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: 2021年6月27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: 3.789→215.765 Å / Num. obs: 63976 / % possible obs: 95.5 % / 冗長度: 21.2 % / CC1/2: 0.994 / Net I/σ(I): 7
反射 シェル解像度: 3.789→4.019 Å / Num. unique obs: 3199 / CC1/2: 0.294

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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: 3.79→37.21 Å / SU ML: 0.4027 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 23.7152
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.232 3167 4.96 %
Rwork0.1866 60694 -
obs0.1888 63861 82.46 %
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: 152.66 Å2
精密化ステップサイクル: LAST / 解像度: 3.79→37.21 Å
タンパク質核酸リガンド溶媒全体
原子数33494 0 159 0 33653
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005934342
X-RAY DIFFRACTIONf_angle_d0.874946435
X-RAY DIFFRACTIONf_chiral_restr0.05355149
X-RAY DIFFRACTIONf_plane_restr0.00615944
X-RAY DIFFRACTIONf_dihedral_angle_d11.804112901
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.03757511916
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.05513393394
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.86164854069
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.83218138698
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.639731275005
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.575642816569
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.79-3.850.535150.340994X-RAY DIFFRACTION2.97
3.85-3.910.3199270.3304605X-RAY DIFFRACTION19.12
3.91-3.970.2894730.31741182X-RAY DIFFRACTION37.61
3.97-4.040.2958730.28791645X-RAY DIFFRACTION51.3
4.04-4.110.29931110.27712010X-RAY DIFFRACTION64.31
4.11-4.190.30881260.26392377X-RAY DIFFRACTION74.99
4.19-4.280.29311190.2542633X-RAY DIFFRACTION82.03
4.28-4.370.26371100.23962867X-RAY DIFFRACTION89.24
4.37-4.470.29571880.23842909X-RAY DIFFRACTION92.23
4.47-4.580.26221560.21612967X-RAY DIFFRACTION93.73
4.58-4.710.26061710.19663005X-RAY DIFFRACTION95.06
4.71-4.840.24781630.19353066X-RAY DIFFRACTION96.22
4.84-50.24411710.18913097X-RAY DIFFRACTION97.35
5-5.180.23021790.19663137X-RAY DIFFRACTION98.63
5.18-5.380.22751280.20293206X-RAY DIFFRACTION99.67
5.38-5.630.23811500.19553214X-RAY DIFFRACTION99.88
5.63-5.920.22841580.19523204X-RAY DIFFRACTION100
5.93-6.290.26471960.19713165X-RAY DIFFRACTION100
6.29-6.780.24511550.18533239X-RAY DIFFRACTION100
6.78-7.450.23941920.18693214X-RAY DIFFRACTION100
7.45-8.520.1951820.15813221X-RAY DIFFRACTION100
8.52-10.690.16961770.11933270X-RAY DIFFRACTION99.94
10.69-37.210.19831570.1543367X-RAY DIFFRACTION99.24
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)
10.697696693310.529413611852-0.4398479790340.442607141855-0.2141840905540.611251566508-0.0587737076091-0.258593919501-0.1336461743480.18441392351-0.0486575043885-0.07194248872250.2472833863660.2500880813553.67888943046E-61.492097153310.169802863901-0.2750073997461.44818972094-0.02983047732691.40533091271-57.1941189357-7.6964764109127.8871848769
21.06605658667-0.708466914569-0.691720823180.9544635030630.5797592342470.394752590578-0.182965556696-0.3863903695620.3117673310860.1439705415130.21339381448-0.1126214851640.1064890501450.187914523807-3.50514796653E-51.40169505073-0.00338244640005-0.1379996030921.3237028188-0.07915746339651.19038205572-77.256907313111.558399246136.337385334
30.562005733453-0.57225842690.08505656600491.30380201104-1.602372582561.5897426373-0.05267271891740.0673472955291-0.128595336984-0.2078703301480.242104644921-0.0646478711385-0.272041251878-0.0366334723844.05385571102E-51.24117157463-0.02778671790210.08049967399661.17099731451-0.1186043157421.22413292599-89.311815168220.263819005120.0014511973
41.11266930922-0.124720364228-0.660009781394-0.327642001825-0.1963434421230.6057107280670.2034982935120.039786975980.338982881592-0.0040388220397-0.062678701689-0.261498425579-0.2555919160330.2057528970961.84055919893E-51.38224044813-0.0888814461897-0.1464424124861.16416082521-0.2324346161321.45380145288-60.014773989229.696549640721.7442001419
50.5043488821490.8782831298470.27874489710.3824621370410.1911911563410.2487103028460.488391245205-0.2565190914150.109003168046-0.316186821427-0.1267225331150.382386685635-0.4182164668870.16006844850.00012366451551.46141043473-0.0785646918204-0.007515908811541.44676406533-0.08592697150321.35485851417-61.592033490831.4225208138-14.8616010496
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71.98815190392-1.82370663761-0.6588722032322.513864767930.3518317927461.434308929350.007413658018840.01938170876620.07735472388790.134169350622-0.112569801998-0.2569648863980.1547820619140.252265028672-1.74176056271E-51.30626349924-0.0323390425481-0.109258643081.45772246175-0.2637837358081.54082090236-44.64246367236.18382654682-5.03287508302
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202.14252926692-0.194508736531-1.733231237791.604714571211.762156379233.289671566210.1603337763080.1324069886490.330369300576-0.9413436373010.125123008696-0.0811691524351-0.540213214458-0.370770540391-1.50975634045E-51.566878748170.042802265904-0.2081260844541.20135993309-0.06819995562741.21638013006-113.9110681856.2243907796-72.4739601867
210.008046810371710.1585216027020.1165681930260.4051388677570.6347884381360.64768704451-0.0769142469148-0.340795844848-0.3204811108620.4520525050570.2887322910590.0531122964690.219796143386-0.598908351594-0.0001798296606021.288213436960.006579400862750.1781877895151.461282570450.1619770943191.47709853996-147.32570839736.6657840758-35.7073279831
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230.811131043706-0.3035128469211.212060167851.61117026871-0.5699453664841.45569537942-0.505710141777-0.06791778830610.889549352374-0.2485587273290.0201040755688-0.307462587697-0.602010530004-0.312378720585-8.59010483863E-51.382724056770.0752471597373-0.07171816996521.1913767411-0.04841057860751.18702438086-149.54680404859.7209925541-43.6111393438
241.343019866920.299658550521-1.618336236860.701934912851-0.2920105035091.556145750980.00859302737480.6027471274320.2470985285810.0420891914710.0146139532668-0.3285072224350.5233546388690.105236657815-2.57639280915E-51.094698576940.0404017013018-0.1024550716791.127615125140.01614970683711.17771457069-148.83212450434.7997280121-58.1322317541
250.1860333267320.299418448271-0.1390177925340.340519764091-0.1588502782160.0216803929732-0.2743833921490.62929869435-0.354428296983-0.134452517620.0600794693991-0.343880825694-0.169900394750.414600449120.0003061419975621.261001169450.274373690482-0.04288585909711.17662353146-0.1488339374631.38856941437-147.08320391320.7074083092-63.2599477724
260.0764452490479-0.0558731110677-0.004213228293670.0395908533774-0.1348060790360.202451269610.897440739462-0.70044896034-1.457775431091.54120603353-0.1657291575161.09033946178-0.519441943738-0.8659641577370.0004095002318331.290001506340.06743884827040.06283405859611.37257427710.02468262050781.29552518346-160.34159833331.2880967166-51.726205302
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280.4591242681910.9121022756890.3771377169671.231910670070.011770436571.20652080418-0.2588730502390.2896457799970.4668465433940.2566236961380.09660147581670.342870174205-0.2713269409380.0207881427687-4.05566102966E-51.478303396730.163984123219-0.05522581878091.07643668428-0.02325457544981.40226285743-155.0877196643.5361273255-8.99234717858
292.017588828120.518914971320.4019983323610.256997533795-0.2250798218132.09172061182-0.4753998927190.1844613119690.207548969225-0.07402652699710.33337141653-0.230753858179-0.4969446506390.174214532794-2.61024992966E-51.58051279855-0.0203447289852-0.1528957767170.8884263877570.05912751699961.28974469166-136.30438000545.4483229609-4.72656707198
302.776879035330.707258200073-0.5909371277430.839314669776-0.5626635761940.458040660744-0.0672941592882-0.385833288108-0.02118690383710.5357807200430.0145901987528-0.188199952647-0.433583641503-0.03366311190622.80608815348E-61.679376688650.109043661695-0.006385659747771.10863313872-0.05908709878721.14210569283-148.13616301332.771552688917.898273912
310.62963116716-0.316934288563-0.3321566813180.852320343357-0.3483800174160.438476417159-0.04747896406790.283722321152-0.001383053061190.314888781126-0.0540404815627-0.382670137704-0.329674545392-0.0348600834741.81407251846E-51.326653359180.02769624814890.03895991314981.14466848478-0.05176645220251.29529421134-121.2274761688.174016320115.7176434667
321.976668488210.7840931271561.692311495372.76708659715-0.196858858511.48447333012-0.06060352135380.09683565966640.0293082539606-0.4779104829170.136300885253-0.1275592426460.218346763315-0.0641972206482-4.15067912883E-51.19563052058-0.01357953702010.08775319641331.033999786780.03857436705251.07523365919-131.4284535572.251138146510.8580140601
330.8716985414940.4428898042740.6452516760372.50307926591-0.2182485197720.652179591107-0.133328063549-0.150966519859-0.1213686016630.123531766151-0.08528647561370.116190401120.0162411499772-0.065965244682-1.02311605877E-51.241854260340.00789776757450.06192876291461.127388019220.02508027265311.13674357121-149.872374389-6.417093448179.45171687383
340.548369916720.312557541856-0.3852283162940.293798126206-0.5265944045530.533169946997-0.1692079898560.262640460940.3695394335430.170908614282-0.2389288646220.09906659207530.277189308687-0.1453403281274.85410098931E-51.29132296889-0.106275605717-0.03167879390751.34237793795-0.05938125421021.33885766176-98.1320063938-7.8281717098221.4252555876
350.1720555276540.2885749490460.2451818985760.329737383310.4233123727730.416579617149-1.11917517868-0.0204828009484-2.565932461080.4359696447180.4918181341320.1328500837151.114920743220.889791063894-0.0005718834263351.722512218610.1462484872710.03055158272631.195154110050.1171833268931.17986949745-105.916146393-14.282046378535.7826958342
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372.739040294830.4896051007610.6639788691340.2678235121510.5463112426470.8488085393180.0950105857867-0.04107316435750.0765554304718-0.657969252964-0.07131719983010.4355746003690.468510308159-0.271572449045-7.46298196781E-51.35228010287-0.091174776560.06764652659910.953093447679-0.004594980817491.07604656806-112.409450164-25.199512914820.3828153211
380.297991334618-0.180583407784-0.1041490529830.112379323680.1678272781610.1918467758850.123926681856-0.3763856631120.1372051477991.25087761279-0.4246974577620.4535552260060.151725801461.255785898630.0004638780672381.66451071867-0.07488641388570.2101414197051.36946983045-0.09047096644731.12925946071-109.578328754-34.74310320689.1277838749
390.06961950356680.159347618005-0.03263808028560.0178771485204-0.04233149147960.1312707149920.366941351388-0.3878239073350.3196477843380.468422689191-1.2046985554-1.323946036681.292517057822.17583152251-0.002575926939271.56824759727-0.0283041075433-0.08919945388161.305082578330.0968067068121.31433902978-100.607788658-28.596674971226.5563264809
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 761 )AA308 - 761308 - 447
33chain 'A' and (resid 762 through 856 )AA762 - 856448 - 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 1039 )BB894 - 1039180 - 325
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 218 )CD151 - 218132 - 199
1212chain 'C' and (resid 219 through 243 )CD219 - 243200 - 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 814 )EF715 - 8141 - 100
1919chain 'E' and (resid 815 through 892 )EF815 - 892101 - 178
2020chain 'E' and (resid 894 through 1034 )EF894 - 1034180 - 320
2121chain 'F' and (resid 20 through 42 )FH20 - 421 - 23
2222chain 'F' and (resid 43 through 106 )FH43 - 10624 - 87
2323chain 'F' and (resid 107 through 150 )FH107 - 15088 - 131
2424chain 'F' and (resid 151 through 218 )FH151 - 218132 - 199
2525chain 'F' and (resid 219 through 243 )FH219 - 243200 - 224
2626chain 'F' and (resid 244 through 267 )FH244 - 267225 - 248
2727chain 'G' and (resid 1 through 299 )GI1 - 2991 - 299
2828chain 'G' and (resid 300 through 795 )GI300 - 795300 - 481
2929chain 'G' and (resid 796 through 856 )GI796 - 856482 - 542
3030chain 'G' and (resid 857 through 1140 )GI857 - 1140543 - 826
3131chain 'H' and (resid 715 through 794 )HJ715 - 7941 - 80
3232chain 'H' and (resid 795 through 892 )HJ795 - 89281 - 178
3333chain 'H' and (resid 894 through 1033 )HJ894 - 1033180 - 319
3434chain 'I' and (resid 20 through 42 )IL20 - 421 - 23
3535chain 'I' and (resid 43 through 63 )IL43 - 6324 - 44
3636chain 'I' and (resid 64 through 150 )IL64 - 15045 - 131
3737chain 'I' and (resid 151 through 218 )IL151 - 218132 - 199
3838chain 'I' and (resid 219 through 243 )IL219 - 243200 - 224
3939chain '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://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る