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Open data
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Basic information
Entry | Database: PDB / ID: 2y5b | ||||||
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Title | Structure of USP21 in complex with linear diubiquitin-aldehyde | ||||||
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![]() | PROTEIN BINDING/HYDROLASE / PROTEIN BINDING-HYDROLASE COMPLEX / UBIQUITIN / UBIQUITIN SPECIFIC PROTEASE / USP / NEDD8 / ISG15 / CELL SIGNALING | ||||||
Function / homology | ![]() deNEDDylase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / TNFR1-induced proapoptotic signaling / fat pad development / female gonad development / seminiferous tubule development / male meiosis I ...deNEDDylase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / TNFR1-induced proapoptotic signaling / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / cysteine-type peptidase activity / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / transcription initiation-coupled chromatin remodeling / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / neuron projection morphogenesis / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ye, Y. / Akutsu, M. / Reyes-Turcu, F. / Enchev, R.I. / Wilkinson, K.D. / Komander, D. | ||||||
![]() | ![]() Title: Polyubiquitin Binding and Cross-Reactivity in the Usp Domain Deubiquitinase Usp21. Authors: Ye, Y. / Akutsu, M. / Reyes-Turcu, F. / Enchev, R.I. / Wilkinson, K.D. / Komander, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.8 KB | Display | ![]() |
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PDB format | ![]() | 148 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.8 KB | Display | ![]() |
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Full document | ![]() | 488.5 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 45.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41744.570 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 196-565 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UK80, EC: 3.1.2.15, ubiquitinyl hydrolase 1 #2: Protein | Mass: 17200.750 Da / Num. of mol.: 2 / Fragment: LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152 / Mutation: YES Source method: isolated from a genetically manipulated source Details: NON-CLEAVABLE LINEAR DIUBIQUITIN ALDEHYDE WITH G76H MUTATION Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | AMINO-ACETALDEHY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: 15% PEG8000, 0.2 M NH4SO4, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.8 Å / Num. obs: 24840 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.4 / % possible all: 86.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2HD5 AND 1UBQ Resolution: 2.7→45 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.829 / SU B: 14.82 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. COVALENT LINK BETWEEN C221 IN CHAIN A,E AND GLZ152 IN CHAIN B,F.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.315 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→45 Å
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