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- PDB-5vey: Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H... -

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基本情報

登録情報
データベース: PDB / ID: 5vey
タイトルSolution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708)
要素
  • E3 ubiquitin-protein ligase RNF169
  • Histone H2B type 1-J,Histone H2A type 1-B/E
  • Polyubiquitin-B
キーワードTRANSFERASE / STRUCTURAL PROTEIN / SIGNALING PROTEIN / Nucleosome / Ubiquitin / Ubiquitin ligase / Complex
機能・相同性
機能・相同性情報


negative regulation of double-strand break repair / ubiquitin-modified histone reader activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development ...negative regulation of double-strand break repair / ubiquitin-modified histone reader activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / nucleosome binding / negative regulation of tumor necrosis factor-mediated signaling pathway / protein localization to CENP-A containing chromatin / regulation of neuron apoptotic process / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / regulation of proteasomal protein catabolic process / Packaging Of Telomere Ends / energy homeostasis / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Maturation of protein E / Maturation of protein E / Deposition of new CENPA-containing nucleosomes at the centromere / ER Quality Control Compartment (ERQC) / nucleosomal DNA binding / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Inhibition of DNA recombination at telomere / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Meiotic synapsis / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / RNA Polymerase I Promoter Opening / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Assembly of the ORC complex at the origin of replication / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / DNA methylation / neuron projection morphogenesis / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Condensation of Prophase Chromosomes / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PINK1-PRKN Mediated Mitophagy / HCMV Late Events / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / innate immune response in mucosa / positive regulation of protein ubiquitination / PRC2 methylates histones and DNA / N-glycan trimming in the ER and Calnexin/Calreticulin cycle
類似検索 - 分子機能
: / Histone, subunit A / Histone, subunit A / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Histone H2B signature. / Histone H2B / Histone H2B ...: / Histone, subunit A / Histone, subunit A / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Histone H2A type 1-B/E / Histone H2B type 1-J / Polyubiquitin-B / E3 ubiquitin-protein ligase RNF169
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法溶液NMR / simulated annealing
データ登録者Hu, Q. / Botuyan, M.V. / Cui, G. / Mer, G.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM116829 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 米国
引用ジャーナル: Mol. Cell / 年: 2017
タイトル: Mechanisms of Ubiquitin-Nucleosome Recognition and Regulation of 53BP1 Chromatin Recruitment by RNF168/169 and RAD18.
著者: Hu, Q. / Botuyan, M.V. / Cui, G. / Zhao, D. / Mer, G.
履歴
登録2017年4月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年5月17日Provider: repository / タイプ: Initial release
改定 1.12017年5月31日Group: Database references
改定 1.22019年12月4日Group: Author supporting evidence / Data collection / カテゴリ: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
改定 1.32022年2月23日Group: Database references / Derived calculations
カテゴリ: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年10月9日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Histone H2B type 1-J,Histone H2A type 1-B/E
B: Polyubiquitin-B
C: E3 ubiquitin-protein ligase RNF169


分子量 (理論値)分子数
合計 (水以外)37,2533
ポリマ－37,2533
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration, isothermal titration calorimetry, SAXS
タイプ名称対称操作数
identity operation1_5551
NMR アンサンブル
データ基準
コンフォーマー数 (登録 / 計算)20 / 200structures with the lowest energy
代表モデルモデル #1

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要素

#1: タンパク質 Histone H2B type 1-J,Histone H2A type 1-B/E / Histone H2B.1 / Histone H2B.r / H2B/r / Histone H2A.2 / Histone H2A/a / Histone H2A/m


分子量: 21658.943 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
遺伝子: HIST1H2BJ, H2BFR, HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
プラスミド: pT7.7 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P06899, UniProt: P04908
#2: タンパク質 Polyubiquitin-B


分子量: 8576.831 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / プラスミド: pET / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P0CG47
#3: タンパク質 E3 ubiquitin-protein ligase RNF169 / RING finger protein 169 / RING-type E3 ubiquitin transferase RNF169


分子量: 7016.938 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RNF169, KIAA1991 / プラスミド: pTEV / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q8NCN4, RING-type E3 ubiquitin transferase
Has protein modificationY

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実験情報

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実験

実験手法: 溶液NMR
NMR実験
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDタイプ
111isotropic12D TROSY 1H-15N HSQC
122isotropic12D TROSY 1H-15N HSQC
133isotropic12D TROSY 1H-15N HSQC
144isotropic122D TROSY 1H-15N HSQC
155isotropic12D TROSY 1H-15N HSQC
166isotropic12D TROSY 1H-15N HSQC
177isotropic12D TROSY 1H-15N HSQC
188isotropic12D TROSY 1H-15N HSQC
199isotropic12D TROSY 1H-15N HSQC
11010isotropic12D TROSY 1H-15N HSQC
11111isotropic12D TROSY 1H-15N HSQC
11212isotropic12D TROSY 1H-15N HSQC
11313isotropic12D TROSY 1H-15N HSQC
11414isotropic12D TROSY 1H-15N HSQC
11515isotropic12D TROSY 1H-15N HSQC
11616isotropic12D TROSY 1H-15N HSQC
11717isotropic12D TROSY 1H-15N HSQC
11818isotropic12D TROSY 1H-15N HSQC
11919isotropic12D TROSY 1H-15N HSQC
12020isotropic12D TROSY 1H-15N HSQC
12121isotropic12D TROSY 1H-15N HSQC
12222isotropic12D TROSY 1H-15N HSQC
22323isotropic12D 1H-15N HSQC
22424isotropic12D 1H-15N HSQC
22525isotropic12D 1H-15N HSQC
22626isotropic12D 1H-15N HSQC
22727isotropic12D 1H-15N HSQC
22828isotropic12D 1H-15N HSQC
22929isotropic12D 1H-15N HSQC
23030isotropic12D 1H-15N HSQC
13131isotropic12D TROSY 1H-15N HSQC
13232isotropic12D TROSY 1H-15N HSQC
13333isotropic12D TROSY 1H-15N HSQC
13434isotropic12D TROSY 1H-15N HSQC
13535isotropic12D TROSY 1H-15N HSQC
13636isotropic12D TROSY 1H-15N HSQC
13737isotropic12D TROSY 1H-15N HSQC
13838isotropic12D TROSY 1H-15N HSQC
13939isotropic12D TROSY 1H-15N HSQC
14040isotropic12D TROSY 1H-15N HSQC
14141isotropic12D TROSY 1H-15N HSQC
1421isotropic12D 1H-13C HMQC
1431isotropic12D 1H-13C HSQC
1441isotropic13D TROSY HNCO
1451isotropic13D TROSY HNCA
1461isotropic13D TROSY HN(CO)CA
1471isotropic13D TROSY HN(CA)CB
1481isotropic13D TROSY HN(COCA)CB
1493isotropic13D HBHA(CO)NH
1503isotropic13D (H)CC(CO)NH
1513isotropic13D CCCH-TOCSY
1523isotropic13D 1H-15N NOESY
1533isotropic13D 1H-13C NOESY-HSQC
1544isotropic13D HBHA(CO)NH
1554isotropic13D (H)CC(CO)NH
1564isotropic13D CCCH-TOCSY
1574isotropic13D 1H-15N NOESY
1584isotropic13D 1H-13C NOESY-HSQC
1595isotropic13D 1H-15N NOESY
1605isotropic13D 1H-13C NOESY-HSQC
1617isotropic13D TROSY HNCO
1627isotropic13D TROSY HNCA
1637isotropic13D TROSY HN(CO)CA
1647isotropic13D TROSY HN(CA)CB
1657isotropic13D TROSY HN(COCA)CB
1668isotropic13D HBHA(CO)NH
1678isotropic13D (H)CC(CO)NH
1688isotropic13D CCCH-TOCSY
1699isotropic13D HBHA(CO)NH
1709isotropic13D (H)CC(CO)NH
1719isotropic13D CCCH-TOCSY
1729isotropic13D 1H-15N NOESY
1739isotropic13D 1H-13C NOESY-HSQC
17410isotropic13D 1H-15N NOESY
1758isotropic13D 1H-13C NOESY-HSQC
1768isotropic113C-edited/filtered NOESY
1779isotropic113C-edited/filtered NOESY
1788isotropic115N-edited/filtered NOESY
1799isotropic115N-edited/filtered NOESY
1808isotropic13D 1H-13C NOESY aromatic
1819isotropic13D 1H-13C NOESY aromatic
18220isotropic12D 1H-13C HMQC
18321isotropic12D 1H-13C HMQC
18420isotropic13D 1H-13C NOESY-HMQC
18521isotropic13D 1H-13C NOESY-HMQC
18620isotropic13D 1H-13C NOESY-HSQC
18721isotropic13D 1H-13C NOESY-HSQC
18812isotropic13D 1H-13C NOESY
18913isotropic13D 1H-15N NOESY
19014isotropic13D 1H-15N NOESY
19115isotropic13D 1H-13C NOESY
116216isotropic13D 1H-15N NOESY
19216isotropic13D 1H-13C NOESY
19317isotropic13D 1H-15N NOESY
19418isotropic13D 1H-15N NOESY
116118isotropic13D 1H-13C NOESY-HSQC
19519isotropic13D 1H-13C NOESY
19622isotropic13D 1H-13C NOESY-HMQC
29723isotropic13D CBCA(CO)NH
29823isotropic13D HN(CA)CB
29923isotropic13D HNCO
210023isotropic13D HN(CA)CO
210123isotropic13D HBHA(CO)NH
211523isotropic13D (H)CC(CO)NH
210223isotropic13D CCCH-TOCSY
210323isotropic13D 1H-15N NOESY
210423isotropic13D 1H-13C NOESY-HSQC
210523isotropic113C-edited/filtered NOESY
210624isotropic13D CBCA(CO)NH
210724isotropic13D HN(CA)CB
210824isotropic13D HNCO
210924isotropic13D HN(CA)CO
211024isotropic13D HBHA(CO)NH
211624isotropic13D (H)CC(CO)NH
211124isotropic13D CCCH-TOCSY
211224isotropic13D 1H-15N NOESY
211324isotropic13D 1H-13C NOESY-HSQC
211424isotropic113C-edited/filtered NOESY
211729isotropic13D CBCA(CO)NH
211829isotropic13D HN(CA)CB
211929isotropic13D HNCO
212029isotropic13D HN(CA)CO
212129isotropic13D HBHA(CO)NH
212229isotropic13D (H)CC(CO)NH
212329isotropic13D CCCH-TOCSY
212429isotropic13D 1H-15N NOESY
212529isotropic13D 1H-13C NOESY-HSQC
212629isotropic113C-edited/filtered NOESY
212730isotropic13D CBCA(CO)NH
212830isotropic13D HN(CA)CB
212930isotropic13D HNCO
213030isotropic13D HN(CA)CO
213130isotropic13D HBHA(CO)NH
213230isotropic13D (H)CC(CO)NH
213330isotropic13D CCCH-TOCSY
213430isotropic13D 1H-15N NOESY
213530isotropic13D 1H-13C NOESY-HSQC
213630isotropic113C-edited/filtered NOESY
213725isotropic13D CBCA(CO)NH
213825isotropic13D HN(CA)CB
213925isotropic13D HNCO
214025isotropic13D HN(CA)CO
214125isotropic13D HBHA(CO)NH
214225isotropic13D (H)CC(CO)NH
214325isotropic13D CCCH-TOCSY
214425isotropic13D 1H-15N NOESY
214525isotropic13D 1H-13C NOESY-HSQC
214627isotropic13D CBCA(CO)NH
214727isotropic13D HN(CA)CB
214827isotropic13D HNCO
214927isotropic13D HN(CA)CO
215027isotropic13D HBHA(CO)NH
215127isotropic13D (H)CC(CO)NH
215227isotropic13D CCCH-TOCSY
215328isotropic13D CBCA(CO)NH
215428isotropic13D HN(CA)CB
215528isotropic13D HNCO
215628isotropic13D HN(CA)CO
215728isotropic13D HBHA(CO)NH
215828isotropic13D (H)CC(CO)NH
215928isotropic13D CCCH-TOCSY
216028isotropic13D 1H-15N NOESY

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試料調製

詳細
タイプSolution-IDLabel溶媒系
solution1Sample_190% H2O/10% D2O
solution2Sample_290% H2O/10% D2O
solution3Sample_390% H2O/10% D2O
solution4Sample_490% H2O/10% D2O
solution5Sample_590% H2O/10% D2O
solution6Sample_690% H2O/10% D2O
solution7Sample_790% H2O/10% D2O
solution8Sample_890% H2O/10% D2O
solution9Sample_990% H2O/10% D2O
solution10Sample_1090% H2O/10% D2O
solution11Sample_1190% H2O/10% D2O
solution12Sample_1290% H2O/10% D2O
solution13Sample_1390% H2O/10% D2O
solution14Sample_1490% H2O/10% D2O
solution15Sample_1590% H2O/10% D2O
solution16Sample_1690% H2O/10% D2O
solution17Sample_1790% H2O/10% D2O
solution18Sample_1890% H2O/10% D2O
solution19Sample_1990% H2O/10% D2O
solution20Sample_2090% H2O/10% D2O
solution21Sample_2190% H2O/10% D2O
solution22Sample_2290% H2O/10% D2O
solution23Sample_2390% H2O/10% D2O
solution24Sample_2490% H2O/10% D2O
solution25Sample_2590% H2O/10% D2O
solution26Sample_2690% H2O/10% D2O
solution27Sample_2790% H2O/10% D2O
solution28Sample_2890% H2O/10% D2O
solution29Sample_2990% H2O/10% D2O
solution30Sample_3090% H2O/10% D2O
solution31Sample_3190% H2O/10% D2O
solution32Sample_3290% H2O/10% D2O
solution33Sample_3390% H2O/10% D2O
solution34Sample_3490% H2O/10% D2O
solution35Sample_3590% H2O/10% D2O
solution36Sample_3690% H2O/10% D2O
solution37Sample_3790% H2O/10% D2O
solution38Sample_3890% H2O/10% D2O
solution39Sample_3990% H2O/10% D2O
solution40Sample_4090% H2O/10% D2O
solution41Sample_4190% H2O/10% D2O
試料
濃度 (mg/ml)構成要素Isotopic labelingSolution-ID
1 mMH2A-H2B100% 2H; 13C; 15N1
25 mMMES-Bis-TRISnatural abundance1
50 mMKClnatural abundance1
4 mMEDTAnatural abundance1
1 mMH2A-H2B100% 2H, 15N2
25 mMMES-Bis-TRISnatural abundance2
50 mMKClnatural abundance2
4 mMEDTAnatural abundance2
1 mMH2A-H2B70% 2H, 13C, 15N3
25 mMMES-Bis-TRISnatural abundance3
50 mMKClnatural abundance3
4 mMEDTAnatural abundance3
1 mMH2A-H2B30% 2H; 13C; 15N4
25 mMMES-Bis-TRISnatural abundance4
50 mMKClnatural abundance4
4 mMEDTAnatural abundance4
1 mMH2A-H2B13C; 15N5
25 mMMES-Bis-TRISnatural abundance5
50 mMKClnatural abundance5
4 mMEDTAnatural abundance5
1 mMH2A-H2B15N6
25 mMMES-Bis-TRISnatural abundance6
50 mMKClnatural abundance6
4 mMEDTAnatural abundance6
0.8 mMH2A-H2B100% 2H; 13C; 15N7
8 mMRNF169 (688-704)natural abundance7
25 mMMES-Bis-TRISnatural abundance7
50 mMKClnatural abundance7
4 mMEDTAnatural abundance7
0.8 mMH2A-H2B70% 2H; 13C; 15N8
8 mMRNF169 (688-704)natural abundance8
25 mMMES-Bis-TRISnatural abundance8
50 mMKClnatural abundance8
4 mMEDTAnatural abundance8
0.8 mMH2A-H2B30% 2H; 13C; 15N9
8 mMRNF169 (688-704)natural abundance9
25 mMMES-Bis-TRISnatural abundance9
50 mMKClnatural abundance9
4 mMEDTAnatural abundance9
0.8 mMH2A-H2B13C; 15N10
8 mMRNF169 (688-704)natural abundance10
25 mMMES-Bis-TRISnatural abundance10
50 mMKClnatural abundance10
4 mMEDTAnatural abundance10
0.8 mMH2A-H2B100% 2H; 13C; 15N11
0.8 mMH2A K15-linked ubiquitinnatural abundance11
2.4 mMRNF169 (653-708)natural abundance11
25 mMMES-Bis-TRISnatural abundance11
50 mMKClnatural abundance11
4 mMEDTAnatural abundance11
0.8 mMH2A-H2B30% 2H; 13C; 15N12
0.8 mMH2A K15-linked ubiquitinnatural abundance12
2.4 mMRNF169 (653-708)natural abundance12
25 mMMES-Bis-TRISnatural abundance12
50 mMKClnatural abundance12
4 mMEDTAnatural abundance12
0.8 mMH2A-H2B30% 2H; 15N13
0.8 mMH2A K15-linked ubiquitinnatural abundance13
2.4 mMRNF169 (653-708)natural abundance13
25 mMMES-Bis-TRISnatural abundance13
50 mMKClnatural abundance13
4 mMEDTAnatural abundance13
0.8 mMH2A-H2B30% 2H; 15N14
0.8 mMH2A K15-linked ubiquitin100% 2H14
2.4 mMRNF169 (653-708)natural abundance14
25 mMMES-Bis-TRISnatural abundance14
50 mMKClnatural abundance14
4 mMEDTAnatural abundance14
0.8 mMH2A-H2B30% 2H; 13C; 15N15
0.8 mMH2A K15-linked ubiquitin100% 2H15
2.4 mMRNF169 (653-708)natural abundance15
25 mMMES-Bis-TRISnatural abundance15
50 mMKClnatural abundance15
4 mMEDTAnatural abundance15
0.8 mMH2B-H2B100% 2H16
0.8 mMH2A K15-linked ubiquitin13C; 15N16
2.4 mMRNF169 (653-708)natural abundance16
25 mMMES-Bis-TRISnatural abundance16
50 mMKClnatural abundance16
4 mMEDTAnatural abundance16
0.8 mMH2A-H2B100% 2H17
0.8 mMH2A K15-linked ubiquitin15N17
2.4 mMRNF169 (653-708)natural abundance17
25 mMMES-Bis-TRISnatural abundance17
50 mMKClnatural abundance17
4 mMEDTAnatural abundance17
1 mMH2A-H2B100% 2H18
1 mMH2A K15-linked ubiquitinnatural abundance18
0.3 mMRNF169 (653-708)13C; 15N18
25 mMMES-Bis-TRISnatural abundance18
50 mMKClnatural abundance18
4 mMEDTAnatural abundance18
1 mMH2A-H2B30% 2H19
1 mMH2A K15-linked ubiquitin100% 2H19
0.3 mMRNF169 (653-708)13C; 15N19
25 mMMES-Bis-TRISnatural abundance19
50 mMKClnatural abundance19
4 mMEDTAnatural abundance19
0.8 mMH2A-H2B100% 2H (13CH3/12CD3-Leu, Val, Ile); 15N20
0.8 mMH2A K15-linked ubiquitinnatural abundance20
2.4 mMRNF169 (653-708)natural abundance20
25 mMMES-Bis-TRISnatural abundance20
50 mMKClnatural abundance20
4 mMEDTAnatural abundance20
0.8 mMH2A-H2B100% 2H (13CH3/13CH3-Leu, Val); 15N21
0.8 mMH2A K15-linked ubiquitinnatural abundance21
2.4 mMRNF169 (653-708)natural abundance21
25 mMMES-Bis-TRISnatural abundance21
50 mMKClnatural abundance21
4 mMEDTAnatural abundance21
0.8 mMH2A-H2B100% 2H22
0.8 mMH2A K15-linked ubiquitin100% 2H (13CH3/12CD3-Leu, Val, Ile); 15N22
2.4 mMRNF169 (653-708)natural abundance22
25 mMMES-Bis-TRISnatural abundance22
50 mMKClnatural abundance22
4 mMEDTAnatural abundance22
1 mMUbiquitin13C; 15N23
6 mMRNF169 (653-708)natural abundance23
25 mMMES-Bis-TRISnatural abundance23
50 mMKClnatural abundance23
4 mMEDTAnatural abundance23
6 mMUbiquitinnatural abundance24
1 mMRNF169 (653-708)13C; 15N24
25 mMMES-Bis-TRISnatural abundance24
50 mMKClnatural abundance24
4 mMEDTAnatural abundance24
1 mMRNF169 (653-687)13C; 15N25
25 mMMES-Bis-TRISnatural abundance25
50 mMKClnatural abundance25
4 mMEDTAnatural abundance25
1 mMRNF169 (653-708)13C; 15N26
25 mMMES-Bis-TRISnatural abundance26
50 mMKClnatural abundance26
4 mMEDTAnatural abundance26
1 mMRNF169 (688-708)13C; 15N27
25 mMMES-Bis-TRISnatural abundance27
50 mMKClnatural abundance27
4 mMEDTAnatural abundance27
1 mMUbiquitin13C; 15N28
25 mMMES-Bis-TRISnatural abundance28
50 mMKClnatural abundance28
4 mMEDTAnatural abundance28
1 mMUbiquitin13C; 15N29
6 mMRNF169 (653-687)natural abundance29
25 mMMES-Bis-TRISnatural abundance29
50 mMKClnatural abundance29
4 mMEDTAnatural abundance29
6 mMUbiquitinnatural abundance30
1 mMRNF169 (653-687)13C; 15N30
25 mMMES-Bis-TRISnatural abundance30
50 mMKClnatural abundance30
4 mMEDTAnatural abundance30
0.5 mMH2A-H2B_MTSL_H2A_G37100% 2H31
0.5 mMH2A K15-linked ubiquitin15N31
1.5 mMRNF169 (653-708)natural abundance31
25 mMMES-Bis-TRISnatural abundance31
50 mMKClnatural abundance31
4 mMEDTAnatural abundance31
0.5 mMH2A-H2B_MTSL_H2A_K74100% 2H32
0.5 mMH2A K15-linked ubiquitin15N32
1.5 mMRNF169 (653-708)natural abundance32
25 mMMES-Bis-TRISnatural abundance32
50 mMKClnatural abundance32
4 mMEDTAnatural abundance32
0.5 mMH2A-H2B_MTSL_H2B_S56100% 2H33
0.5 mMH2A K15-linked ubiquitin15N33
1.5 mMRNF169 (653-708)natural abundance33
25 mMMES-Bis-TRISnatural abundance33
50 mMKClnatural abundance33
4 mMEDTAnatural abundance33
0.5 mMH2A-H2B_MTSL_H2B_S87100% 2H34
0.5 mMH2A K15-linked ubiquitin15N34
1.5 mMRNF169 (653-708)natural abundance34
25 mMMES-Bis-TRISnatural abundance34
50 mMKClnatural abundance34
4 mMEDTAnatural abundance34
0.5 mMH2A-H2B_MTSL_H2B_S112100% 2H35
0.5 mMH2A K15-linked ubiquitin15N35
1.5 mMRNF169 (653-708)natural abundance35
25 mMMES-Bis-TRISnatural abundance35
50 mMKClnatural abundance35
4 mMEDTAnatural abundance35
0.5 mMH2A-H2B_MTSL_H2B_S123100% 2H36
0.5 mMH2A K15-linked ubiquitin15N36
1.5 mMRNF169 (653-708)natural abundance36
25 mMMES-Bis-TRISnatural abundance36
50 mMKClnatural abundance36
4 mMEDTAnatural abundance36
0.5 mMH2A-H2B100% 2H; 15N37
0.5 mMH2A K15-linked ubiquitin_MTSL_T9natural abundance37
1.5 mMRNF169 (653-708)natural abundance37
25 mMMES-Bis-TRISnatural abundance37
50 mMKClnatural abundance37
4 mMEDTAnatural abundance37
0.5 mMH2A-H2B100% 2H; 15N38
0.5 mMH2A K15-linked ubiquitin_MTSL_T14natural abundance38
1.5 mMRNF169 (653-708)natural abundance38
25 mMMES-Bis-TRISnatural abundance38
50 mMKClnatural abundance38
4 mMEDTAnatural abundance38
0.5 mMH2A-H2B100% 2H; 15N39
0.5 mMH2A K15-linked ubiquitin_MTSL_E34natural abundance39
1.5 mMRNF169 (653-708)natural abundance39
25 mMMES-Bis-TRISnatural abundance39
50 mMKClnatural abundance39
4 mMEDTAnatural abundance39
0.5 mMH2A-H2B100% 2H; 15N40
0.5 mMH2A K15-linked ubiquitin_MTSL_D39natural abundance40
1.5 mMRNF169 (653-708)natural abundance40
25 mMMES-Bis-TRISnatural abundance40
50 mMKClnatural abundance40
4 mMEDTAnatural abundance40
0.5 mMH2A-H2B100% 2H; 15N41
0.5 mMH2A K15-linked ubiquitin_MTSL_S57natural abundance41
1.5 mMRNF169 (653-708)natural abundance41
25 mMMES-Bis-TRISnatural abundance41
50 mMKClnatural abundance41
4 mMEDTAnatural abundance41
試料状態
Conditions-IDイオン強度LabelpH圧 (kPa)温度 (K)
150 mM KCl mMConditions_161 atm303 K
250 mM KCl mMConditions_261 atm298 K

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NMR測定

NMRスペクトロメータータイプ: Bruker AVANCE III / 製造業者: Bruker / モデル: AVANCE III / 磁場強度: 700 MHz

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解析

NMR software
名称開発者分類
X-PLOR NIHSCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE精密化
TopSpin構造決定
NMRDraw構造決定
NMRView構造決定
NMRPipe構造決定
Sparky構造決定
TALOS構造決定
X-PLOR NIH構造決定
精密化手法: simulated annealing / ソフトェア番号: 1
NMRアンサンブルコンフォーマー選択の基準: structures with the lowest energy
計算したコンフォーマーの数: 200 / 登録したコンフォーマーの数: 20

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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