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- PDB-6td3: Structure of DDB1 bound to CR8-engaged CDK12-cyclinK -

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基本情報

登録情報
データベース: PDB / ID: 6td3
タイトルStructure of DDB1 bound to CR8-engaged CDK12-cyclinK
要素
  • Cyclin-K
  • Cyclin-dependent kinase 12
  • DNA damage-binding protein 1
キーワードLIGASE / ubiquitin ligase kinase cyclin CDK
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 / regulation of cyclin-dependent protein serine/threonine kinase activity ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / host-mediated suppression of viral genome replication / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / spindle assembly involved in female meiosis / 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 / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / 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 / RNA Polymerase II Transcription Elongation / negative regulation of MAPK cascade / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / positive regulation of gluconeogenesis / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA splicing / cyclin binding / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of transcription elongation by RNA polymerase II / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Wnt signaling pathway / mRNA processing / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transcription by RNA polymerase II / chromosome, telomeric region / protein kinase activity / protein ubiquitination / 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-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal ...Cyclin-T2-like, C-terminal domain / DNA polymerase; domain 1 - #910 / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / 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-RC8 / 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: 3.46 Å
データ登録者Bunker, R.D. / Petzold, G. / Kozicka, Z. / Thoma, N.H.
資金援助 スイス, 1件
組織認可番号国
European Research Council666068 スイス
引用ジャーナル: Nature / 年: 2020
タイトル: The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K.
著者: Slabicki, M. / Kozicka, Z. / Petzold, G. / Li, Y.D. / Manojkumar, M. / Bunker, R.D. / Donovan, K.A. / Sievers, Q.L. / Koeppel, J. / Suchyta, D. / Sperling, A.S. / Fink, E.C. / Gasser, J.A. / ...著者: Slabicki, M. / Kozicka, Z. / Petzold, G. / Li, Y.D. / Manojkumar, M. / Bunker, R.D. / Donovan, K.A. / Sievers, Q.L. / Koeppel, J. / Suchyta, D. / Sperling, A.S. / Fink, E.C. / Gasser, J.A. / Wang, L.R. / Corsello, S.M. / Sellar, R.S. / Jan, M. / Gillingham, D. / Scholl, C. / Frohling, S. / Golub, T.R. / Fischer, E.S. / Thoma, N.H. / Ebert, B.L.
履歴
登録2019年11月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年6月17日Provider: repository / タイプ: Initial release
改定 1.12020年9月23日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.22023年9月13日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / software / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _software.classification / _struct_ref.pdbx_db_isoform
改定 1.32024年1月24日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model
改定 1.42024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)497,85212
ポリマ－496,5589
非ポリマー1,2953
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)165,9514
ポリマ－165,5193
非ポリマー4321
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-32 kcal/mol
Surface area60110 Å2
手法PISA
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)165,9514
ポリマ－165,5193
非ポリマー4321
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-30 kcal/mol
Surface area59930 Å2
手法PISA
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)165,9514
ポリマ－165,5193
非ポリマー4321
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-30 kcal/mol
Surface area59370 Å2
手法PISA
単位格子
Length a, b, c (Å)250.749, 250.749, 217.92
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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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 / Mutation: K965R / 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-RC8 / (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol


分子量: 431.533 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C24H29N7O / 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: 4.11 Å3/Da / 溶媒含有率: 70.04 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: 0.9 M ammonium citrate tribasic

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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: X06SA / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年7月14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: 3.46→54 Å / Num. obs: 89203 / % possible obs: 95.1 % / 冗長度: 12 % / CC1/2: 0.416 / Rpim(I) all: 0.092 / Rrim(I) all: 0.318 / Net I/σ(I): 7.2
反射 シェル解像度: 3.46→3.63 Å / 冗長度: 11.6 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4460 / CC1/2: 0.416 / % possible all: 68.3

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解析

ソフトウェア
名称バージョン分類
BUSTER2.11.7 (3-OCT-2019)精密化
DIALSデータ削減
STARANISOデータスケーリング
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6H0F, 4NST

6h0f

4nst


解像度: 3.46→54 Å / Cor.coef. Fo:Fc: 0.733 / Cor.coef. Fo:Fc free: 0.708 / 交差検証法: THROUGHOUT / SU Rfree Blow DPI: 0.473
Rfactor反射数%反射Selection details
Rfree0.22 4439 -RANDOM
Rwork0.1938 ---
obs0.1951 89183 86.5 %-
原子変位パラメータBiso mean: 80.62 Å2
Baniso -1Baniso -2Baniso -3
1-4.0043 Å20 Å20 Å2
2--4.0043 Å20 Å2
3----8.0085 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
精密化ステップサイクル: LAST / 解像度: 3.46→54 Å
タンパク質核酸リガンド溶媒全体
原子数33781 0 96 0 33877
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00968300HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.01123593HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d20468SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes10733HARMONIC5
X-RAY DIFFRACTIONt_it34489HARMONIC10
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion4434SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact48152SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion15.25
LS精密化 シェル解像度: 3.46→4 Å
Rfactor反射数%反射
Rfree0.2586 80 -
Rwork0.2428 --
obs0.2435 1784 22.52 %
精密化 TLS

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)
12.26390.6098-0.43372.84930.1972.3403-0.13740.52430.54590.52430.07750.52030.54590.52030.05980.41280.186-0.36520.23670.02470.3086-58.4305-7.09728.8304
23.44330.50350.064210.683-5.91165.547-0.05361.28970.0861.2897-0.20110.4750.0860.4750.25470.44770.0387-0.14740.293-0.2604-0.1082-75.017810.964539.3358
34.73620.1532-1.18637.3573-0.80170.3250.03540.208-0.12790.208-0.0303-0.0016-0.1279-0.0016-0.00510.2514-0.023-0.0277-0.1755-0.1724-0.2032-86.64816.994327.7317
45.9905-1.816-0.62864.9466-0.53754.70320.4626-0.3575-0.2476-0.3575-0.06920.1558-0.24760.1558-0.39340.1866-0.0968-0.0557-0.4036-0.2605-0.1779-76.165131.266112.9434
56.66071.65471.67382.394-1.33036.3240.15090.9231-1.12210.92310.06980.4812-1.12210.4812-0.22070.4009-0.1242-0.19560.1517-0.26910.4133-55.638529.437229.6503
65.9452-0.72713.34843.59592.57527.0135-0.11090.4254-0.52660.42540.03980.7531-0.52660.75310.07110.3495-0.146-0.27260.5255-0.11360.6079-44.204626.050433.406
73.9045-0.3238-1.43516.0241-0.3293.4336-0.02650.0478-0.64950.04780.17620.0098-0.64950.0098-0.14980.2126-0.0346-0.02360.0967-0.21390.0881-60.947825.9772-12.6567
86.5908-1.21722.7344.3148-1.88753.5991-0.2838-0.8840.3984-0.884-0.57941.48690.39841.48690.86320.6509-0.00460.17230.4681-0.2470.5485-47.735118.3051-19.2866
94.9351-0.4073-0.5744.5710.17716.56950.06290.5402-0.35020.54020.07430.6371-0.35020.6371-0.13720.18680.0402-0.09260.1126-0.24620.4497-45.83256.8769-4.037
105.3508-5.51544.00212.6255-0.33285.75120.2612-0.22280.0256-0.22280.399-0.38080.0256-0.3808-0.6602-0.0974-0.13010.193-0.1089-0.13820.1666-61.158840.2993-42.5053
113.4364-1.47311.59713.8488-1.85946.8211-0.0786-0.203-0.1902-0.2030.06290.6654-0.19020.66540.0156-0.0976-0.24820.1136-0.0139-0.28540.3083-47.310941.5536-35.5713
129.71443.0491-3.0276.0363-5.2249.8165-0.08811.19150.06651.1915-0.52190.98460.06650.98460.610.18560.0072-0.16410.1293-0.20250.5257-37.768441.6249-25.4774
13-1.1827-1.35531.33178.2429-2.86271.6944-0.09150.9006-0.95070.9006-0.10510.708-0.95070.7080.19660.2999-0.20410.08130.0053-0.25930.3953-47.229549.0896-26.8816
143.9006-6.1472-4.29279.59284.24294.2628-0.56390.89430.98080.89430.09180.30910.98080.30910.47210.0238-0.06470.12990.1515-0.26040.3232-48.417121.9478-38.268
150.5128-0.29610.7826-0.51287.173110.70280.2899-0.1869-0.0051-0.1869-0.19961.254-0.00511.254-0.09030.0216-0.07730.21460.2431-0.22710.5374-38.398423.4318-48.2327
164.9317-4.1946-3.229115.68711.70217.07020.2717-0.3573-0.3867-0.3573-0.3948-0.8062-0.3867-0.80620.1231-0.1036-0.0482-0.0702-0.1433-0.25950.0349-49.975626.9447-49.1587
170.2629-1.77782.13069.81197.95142.9286-0.0938-0.6470.2892-0.6470.1123-0.36020.2892-0.3602-0.01850.26520.05270.06630.0654-0.18340.5675-50.038413.4225-54.3546
185.20617.4562-6.41210.039-0.53575.9338-0.3031-0.2315-0.2269-0.23150.10311.1259-0.22691.12590.20010.52860.0429-0.17060.4428-0.1870.5386-45.308232.7204-55.3015
192.5144-0.11160.15232.51930.22252.9823-0.1211-0.8106-0.3303-0.81060.13460.525-0.33030.525-0.01340.4952-0.28910.18560.127-0.0482-0.0321-75.050667.8557-67.8448
206.718-1.8263-1.02594.7721.3764.0298-0.1752-0.11590.4035-0.1159-0.03420.29150.40350.29150.2094-0.1182-0.2329-0.1754-0.1697-0.3042-0.4024-78.234763.535-32.4471
212.55590.4245-0.20093.8532-1.57644.515-0.0008-0.274-0.8587-0.2740.0144-0.6897-0.8587-0.6897-0.01360.22420.02-0.1697-0.1449-0.2838-0.0822-98.579379.8641-44.2589
2216.07345.12280.7130.55754.7395.72560.2311-0.38-0.022-0.38-0.3562-0.5692-0.022-0.56920.12510.09950.0436-0.08120.3485-0.09130.1638-123.283353.7125-37.3604
2315.2021.61624.3164-0.1068-2.91815.0337-0.53660.5496-0.97150.54960.5234-0.4849-0.9715-0.48490.0132-0.0798-0.2525-0.1577-0.0004-0.31450.0754-123.7657.1658-39.3646
246.5188-1.4269-3.15882.63062.226.36250.06910.1249-0.14270.1249-0.1692-0.0237-0.1427-0.02370.10.12130.0237-0.2165-0.1382-0.1057-0.0134-119.831151.1884-50.9885
256.7617-5.89074.88430.12110.652900.1967-0.8925-0.3984-0.89250.5819-1.4869-0.3984-1.4869-0.77860.6075-0.1347-0.13490.4525-0.37420.4642-128.305650.695-61.5787
267.916-1.58721.71078.47270.1744.82650.1509-1.1302-0.9655-1.13020.1944-0.5046-0.9655-0.5046-0.34540.73820.0784-0.3012-0.0543-0.0862-0.0495-116.429459.7307-74.6668
278.2862.50975.22475.76852.59227.13520.10631.0312-0.121.03120.17241.1554-0.121.1554-0.27870.46060.0434-0.18640.7072-0.28510.3877-99.998747.6109-58.1819
283.3645-0.1191-0.781510.12290.60927.5965-0.15470.2126-0.22980.21260.2127-0.4395-0.2298-0.4395-0.058-0.38080.1225-0.2922-0.1779-0.0161-0.2927-151.455249.7461-43.6552
292.95532.26661.71778.7857.7139.0693-0.1567-0.1804-0.1342-0.18040.06560.015-0.13420.0150.0911-0.14820.1331-0.2115-0.23380.0837-0.2283-148.484139.306-54.8278
301.5105-4.3953-1.968910.69425.584614.439-0.36940.30940.95630.30940.31210.52070.95630.52070.05730.12950.125-0.0834-0.18760.0834-0.0465-148.125820.9055-63.3057
3117.5695-0.2332-4.90374.39613.89024.83730.2173-0.6018-0.3984-0.6018-0.1401-1.4869-0.3984-1.4869-0.07720.6968-0.0090.12560.0053-0.15340.1153-160.9731.1423-52.0148
323.12470.07790.26583.24950.55323.6944-0.0183-0.20120.0211-0.20120.1216-0.92670.0211-0.9267-0.10320.24460.2117-0.02370.19630.21230.6079-173.660817.7693-3.1434
337.04972.03023.58479.27170.400713.4098-0.3108-1.5081-0.0707-1.50810.2471-0.6484-0.0707-0.64840.06370.5830.1383-0.41520.20360.11130.5146-171.391126.054-23.6851
343.7861.30551.5193.994-0.06034.4637-0.2266-0.1533-0.6541-0.15330.1426-0.417-0.6541-0.4170.0840.59350.2663-0.1016-0.27130.0970.1558-155.813743.0913-9.6329
355.29220.5364-0.43364.4742-0.99941.8787-0.22691.0327-0.56281.03270.1135-0.0438-0.5628-0.04380.11330.66280.1995-0.0584-0.2597-0.1142-0.1798-144.342433.950312.8797
368.6472-6.1078-7.066412.23940.597710.5326-0.2440.7708-0.67640.7708-0.263-1.0055-0.6764-1.00550.5070.6608-0.03050.31260.5551-0.12340.6079-170.964136.526633.736
374.22861.923.33946.923-2.03295.0134-0.44260.7907-0.39140.79070.17350.3224-0.39140.32240.26910.17360.03890.0335-0.1944-0.08750.0784-122.41878.193415.8038
386.18761.31672.68764.61741.29885.3235-0.37870.1715-0.32610.17150.40040.2272-0.32610.2272-0.02180.0960.03930.1799-0.3243-0.0846-0.1917-132.22472.555910.6668
394.3198-0.72040.44245.9347-1.19495.4245-0.01750.2628-0.64020.2628-0.0795-0.164-0.6402-0.1640.0970.0368-0.03890.1347-0.28530.0349-0.076-150.4824-3.78288.8244
4012.68770.54890.73680.8793.05564.5294-0.36830.5079-0.11540.5079-0.24140.2365-0.11540.23650.60970.27270.09550.1514-0.5179-0.0164-0.6079-107.3422-9.326929.6323
417.73620.55642.99724.22870.77362.6943-0.38890.9532-0.4510.9532-0.2326-0.3971-0.451-0.39710.62150.5066-0.02670.22580.2646-0.1399-0.3058-117.2926-6.353242.1364
422.96940.59220.733415.72824.73323.1522-0.34810.12860.18970.12860.0069-0.33480.1897-0.33480.34120.0792-0.03260.3198-0.19340.0541-0.6079-113.605-20.064422.8991
4310.5442.92063.5315.6824-0.509116.6309-0.45470.80740.57530.8074-0.04090.61310.57530.61310.49560.38280.03180.3445-0.3558-0.1521-0.0418-110.9844-39.143410.5016
4418.5742.4552-1.09512.29646.089116.6309-0.1831-0.67810.1341-0.6781-0.65690.12090.13410.12090.840.3695-0.20280.3093-0.0982-0.1278-0.512-109.1653-28.26828.6678
454.33120.0888-1.715711.6489-1.053815.7344-0.21031.32821.1861.3282-0.48710.12281.1860.12280.69740.23640.00610.17180.3139-0.17920.2594-101.9021-29.092426.6602
461.7544-1.42997.95147.8146-2.13067.0864-0.09621.2184-0.91581.2184-0.2550.433-0.91580.4330.35120.45680.07610.1180.0197-0.22990.0879-62.573424.4044-4.5004
472.72063.5237-2.2523.1619-7.43851.83580.120.1004-0.78410.10040.06490.6283-0.78410.6283-0.18490.2868-0.0646-0.172-0.0776-0.103-0.1189-113.762156.959-46.7543
48-1.242-0.07493.56813.98535.46160-0.23530.78080.02290.78080.1782-1.09670.0229-1.09670.05710.213-0.2794-0.036-0.0583-0.12680.1434-132.734212.686410.7704
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 326}
2X-RAY DIFFRACTION2{A|327 - 385}
3X-RAY DIFFRACTION3{A|386 - 819}
4X-RAY DIFFRACTION4{A|820 - 991}
5X-RAY DIFFRACTION5{A|992 - 1061}
6X-RAY DIFFRACTION6{A|1062 - 1140}
7X-RAY DIFFRACTION7{B|715 - 872}
8X-RAY DIFFRACTION8{B|873 - 890}
9X-RAY DIFFRACTION9{B|891 - 1047}
10X-RAY DIFFRACTION10{C|20 - 42}
11X-RAY DIFFRACTION11{C|43 - 106}
12X-RAY DIFFRACTION12{C|107 - 123}
13X-RAY DIFFRACTION13{C|124 - 150}
14X-RAY DIFFRACTION14{C|151 - 174}
15X-RAY DIFFRACTION15{C|175 - 194}
16X-RAY DIFFRACTION16{C|195 - 218}
17X-RAY DIFFRACTION17{C|219 - 243}
18X-RAY DIFFRACTION18{C|244 - 267}
19X-RAY DIFFRACTION19{D|1 - 385}
20X-RAY DIFFRACTION20{D|386 - 856}
21X-RAY DIFFRACTION21{D|857 - 1140}
22X-RAY DIFFRACTION22{E|715 - 740}
23X-RAY DIFFRACTION23{E|741 - 768}
24X-RAY DIFFRACTION24{E|769 - 872}
25X-RAY DIFFRACTION25{E|873 - 890}
26X-RAY DIFFRACTION26{E|891 - 1010}
27X-RAY DIFFRACTION27{E|1011 - 1047}
28X-RAY DIFFRACTION28{F|20 - 135}
29X-RAY DIFFRACTION29{F|136 - 218}
30X-RAY DIFFRACTION30{F|219 - 243}
31X-RAY DIFFRACTION31{F|244 - 267}
32X-RAY DIFFRACTION32{G|1 - 236}
33X-RAY DIFFRACTION33{G|237 - 289}
34X-RAY DIFFRACTION34{G|290 - 819}
35X-RAY DIFFRACTION35{G|820 - 1099}
36X-RAY DIFFRACTION36{G|1100 - 1140}
37X-RAY DIFFRACTION37{H|715 - 794}
38X-RAY DIFFRACTION38{H|795 - 890}
39X-RAY DIFFRACTION39{H|891 - 1047}
40X-RAY DIFFRACTION40{I|20 - 106}
41X-RAY DIFFRACTION41{I|107 - 135}
42X-RAY DIFFRACTION42{I|136 - 218}
43X-RAY DIFFRACTION43{I|219 - 233}
44X-RAY DIFFRACTION44{I|234 - 243}
45X-RAY DIFFRACTION45{I|244 - 267}
46X-RAY DIFFRACTION46{B|1101 - 1101}
47X-RAY DIFFRACTION47{E|1101 - 1101}
48X-RAY DIFFRACTION48{H|1101 - 1101}

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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