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Yorodumi- PDB-2n13: Complex structure of MyUb (1080-1122) of human Myosin VI with K63-diUb -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n13 | ||||||
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Title | Complex structure of MyUb (1080-1122) of human Myosin VI with K63-diUb | ||||||
Components |
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Keywords | MOTOR PROTEIN/PROTEIN BINDING / MOTOR PROTEIN-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information regulation of secretion / minus-end directed microfilament motor activity / unconventional myosin complex / actin filament-based movement / inner ear auditory receptor cell differentiation / clathrin-coated vesicle membrane / Gap junction degradation / vesicle transport along actin filament / Trafficking of AMPA receptors / hypothalamus gonadotrophin-releasing hormone neuron development ...regulation of secretion / minus-end directed microfilament motor activity / unconventional myosin complex / actin filament-based movement / inner ear auditory receptor cell differentiation / clathrin-coated vesicle membrane / Gap junction degradation / vesicle transport along actin filament / Trafficking of AMPA receptors / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / RHOBTB1 GTPase cycle / mitochondrion transport along microtubule / fat pad development / inner ear morphogenesis / microfilament motor activity / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cytoskeletal motor activity / filamentous actin / microvillus / RHOU GTPase cycle / DNA damage response, signal transduction by p53 class mediator / endocytic vesicle / autophagosome / RHOBTB2 GTPase cycle / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / clathrin-coated pit / Maturation of protein E / Maturation of protein E / 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 / 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 / ruffle / 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 / filopodium / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | He, F. / Walters, K. | ||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Myosin VI Contains a Compact Structural Motif that Binds to Ubiquitin Chains. Authors: He, F. / Wollscheid, H.P. / Nowicka, U. / Biancospino, M. / Valentini, E. / Ehlinger, A. / Acconcia, F. / Magistrati, E. / Polo, S. / 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 | 2n13.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2n13.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 2n13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2n13_validation.pdf.gz | 508.6 KB | Display | wwPDB validaton report |
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Full document | 2n13_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2n13_validation.xml.gz | 112.9 KB | Display | |
Data in CIF | 2n13_validation.cif.gz | 145.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/2n13 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/2n13 | HTTPS FTP |
-Related structure data
Related structure data | 2n0zC 2n10C 2n11C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 5212.982 Da / Num. of mol.: 2 / Fragment: K63R, G76C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0389, MYO6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UM54 #2: Protein | | Mass: 8604.845 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 #3: Protein | | Mass: 8622.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-13C; U-15N] protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.5 mM / Component: entity-1 / Isotopic labeling: [U-13C; U-15N] |
Sample conditions | Ionic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 283 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz |
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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: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |