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Yorodumi- PDB-2kde: NMR structure of major S5a (196-306):K48 linked diubiquitin species -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kde | ||||||
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Title | NMR structure of major S5a (196-306):K48 linked diubiquitin species | ||||||
Components |
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Keywords | PROTEIN BINDING / protein complex / ubiquitin interacting motifs / Cytoplasm / Nucleus / Ubl conjugation / Alternative splicing / Phosphoprotein / Proteasome | ||||||
Function / homology | Function and homology information proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / polyubiquitin modification-dependent protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin ...proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / polyubiquitin modification-dependent protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / modification-dependent protein catabolic process / Regulation of PTEN stability and activity / Interleukin-1 signaling / Regulation of RAS by GAPs / protein tag activity / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / Ub-specific processing proteases / protein ubiquitination / ubiquitin protein ligase binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Zhang, N. / Wang, Q. / Ehlinger, A. / Randles, L. / Lary, J.W. / Kang, Y. / Haririnia, A. / Cole, J.L. / Fushman, D. / Walters, K.J. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13. Authors: Zhang, N. / Wang, Q. / Ehlinger, A. / Randles, L. / Lary, J.W. / Kang, Y. / Haririnia, A. / Storaska, A.J. / Cole, J.L. / Fushman, D. / Walters, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kde.cif.gz | 309.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kde.ent.gz | 265.8 KB | Display | PDB format |
PDBx/mmJSON format | 2kde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kde_validation.pdf.gz | 364.8 KB | Display | wwPDB validaton report |
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Full document | 2kde_full_validation.pdf.gz | 479.1 KB | Display | |
Data in XML | 2kde_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 2kde_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/2kde ftp://data.pdbj.org/pub/pdb/validation_reports/kd/2kde | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11826.878 Da / Num. of mol.: 1 / Fragment: UNP residues 196-306, S5a fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4, MCB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55036 |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62972 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 7 |