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Yorodumi- PDB-4xkh: CRYSTAL STRUCTURE OF THE AIRAPL TANDEM UIMS IN COMPLEX WITH A LYS... -
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-Basic information
Entry | Database: PDB / ID: 4xkh | ||||||
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Title | CRYSTAL STRUCTURE OF THE AIRAPL TANDEM UIMS IN COMPLEX WITH A LYS48-LINKED TRI-UBIQUITIN | ||||||
Components |
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Keywords | UBIQUITIN-BINDING PROTEIN / TANDEM UBIQUITIN-INTERACTING MOTIFS / UBIQUITIN-BINDING | ||||||
Function / homology | Function and homology information regulation of insulin-like growth factor receptor signaling pathway / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 ...regulation of insulin-like growth factor receptor signaling pathway / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / : / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Activation of NF-kappaB in B cells / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Rahighi, S. / Kawasaki, M. / Stanhill, A. / Wakatsuki, S. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Selective Binding of AIRAPL Tandem UIMs to Lys48-Linked Tri-Ubiquitin Chains. Authors: Rahighi, S. / Braunstein, I. / Ternette, N. / Kessler, B. / Kawasaki, M. / Kato, R. / Matsui, T. / Weiss, T.M. / Stanhill, A. / Wakatsuki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xkh.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xkh.ent.gz | 92.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/4xkh ftp://data.pdbj.org/pub/pdb/validation_reports/xk/4xkh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 8576.831 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 77-152 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: UBC / Cell (production host): ERYTHROCYTE / Production host: Bos taurus (cattle) / References: UniProt: P0CH28 #2: Protein | Mass: 5800.263 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 187-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zfand2b, Airapl / Plasmid: PGEX-4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q91X58 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% (W/V) POLYETHYLENE GLYCOL 3350, 0.02 M CALCIUM CHLORIDE, 0.02 M CADMIUM CHLORIDE, AND 0.02 M COBALT CHLORIDE PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 1, 2010 | |||||||||||||||
Radiation | Monochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL MONOCHROMATOR, LIQUID NITROGEN COOLING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3→78.687 Å / Num. obs: 11212 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.163 / Rsym value: 0.231 / Net I/σ(I): 6.8 | |||||||||||||||
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.5 / Rsym value: 1.075 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.22 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.804 / SU B: 16.68 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.53 Å2
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Refinement step | Cycle: LAST / Resolution: 3→48.22 Å
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Refine LS restraints |
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