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Yorodumi- PDB-3vht: Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in comp... -
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-Basic information
Entry | Database: PDB / ID: 3vht | ||||||
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Title | Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin | ||||||
Components |
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Keywords | FLUORESCENT PROTEIN/PROTEIN BINDING / GREEN FLUORESCENT PROTEIN / FUSION PROTEIN / ZINC FINGER / UBIQUITIN-BINDING DOMAIN / FLUORESCENT PROTEIN-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 ...translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of BACH1 activity / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Regulation of innate immune responses to cytosolic DNA / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / PINK1-PRKN Mediated Mitophagy / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Termination of translesion DNA synthesis / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Inactivation of CSF3 (G-CSF) signaling / Senescence-Associated Secretory Phenotype (SASP) / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR1-induced NF-kappa-B signaling pathway / Josephin domain DUBs / Dual Incision in GG-NER / Regulation of FZD by ubiquitination / Downregulation of ERBB2 signaling / Dual incision in TC-NER / IKK complex recruitment mediated by RIP1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Oncogene Induced Senescence / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Metalloprotease DUBs / Gap-filling DNA repair synthesis and ligation in TC-NER / Degradation of AXIN / Regulation of TNFR1 signaling / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Deactivation of the beta-catenin transactivating complex / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / Ovarian tumor domain proteases / RAS processing / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Suzuki, N. / Wakatsuki, S. / Kawasaki, M. | ||||||
Citation | Journal: Febs J. / Year: 2016 Title: A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1. Authors: Suzuki, N. / Rohaim, A. / Kato, R. / Dikic, I. / Wakatsuki, S. / Kawasaki, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vht.cif.gz | 237.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vht.ent.gz | 192.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/3vht ftp://data.pdbj.org/pub/pdb/validation_reports/vh/3vht | HTTPS FTP |
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-Related structure data
Related structure data | 3vhsC 3wupC 4z4kC 4z4mC 3ai5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26306.564 Da / Num. of mol.: 1 / Fragment: GFP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212*PLUS |
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#2: Protein | Mass: 30543.525 Da / Num. of mol.: 1 / Fragment: GFP,Wrnip1 UBZ domain (UNP RESIDUES 9-46) Source method: isolated from a genetically manipulated source Details: THE FUSION PROTEIN OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN, LINKER (GLY-SER) AND HUMAN WRNIP1 UBZ Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human) Gene: GFP, WRNIP1, WHIP / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96S55, UniProt: P42212*PLUS, EC: 3.6.1.3 |
#3: Protein | Mass: 8576.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62983 |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Sequence details | (1) THE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN NOT CURRENTLY EXIST IN UNIPROT. THIS ...(1) THE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCEN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M DL-Malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 17, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→75.63 Å / Num. obs: 26943 / % possible obs: 99.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1328 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AI5 Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 16.892 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.581 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -14.8285 Å / Origin y: -56.4302 Å / Origin z: -10.6721 Å
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Refinement TLS group |
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