+Open data
-Basic information
Entry | Database: PDB / ID: 2c7n | ||||||
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Title | Human Rabex-5 residues 1-74 in complex with Ubiquitin | ||||||
Components |
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Keywords | PROTEIN BINDING / PROTEIN-BINDING / UBIQUITIN BINDING DOMAIN / ENDOCYTOSIS / NUCLEAR PROTEIN / POLYPROTEIN / UBIQUITIN COMPLEX | ||||||
Function / homology | Function and homology information dendritic transport / negative regulation of Kit signaling pathway / : / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / Kit signaling pathway / negative regulation of mast cell degranulation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH ...dendritic transport / negative regulation of Kit signaling pathway / : / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / Kit signaling pathway / negative regulation of mast cell degranulation / 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 / negative regulation of mast cell activation / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Penengo, L. / Mapelli, M. / Murachelli, A.G. / Confalioneri, S. / Magri, L. / Musacchio, A. / Di Fiore, P.P. / Polo, S. / Schneider, T.R. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Crystal Structure of the Ubiquitin Binding Domains of Rabex-5 Reveals Two Modes of Interaction with Ubiquitin. Authors: Penengo, L. / Mapelli, M. / Murachelli, A.G. / Confalonieri, S. / Magri, L. / Musacchio, A. / Di Fiore, P.P. / Polo, S. / Schneider, T.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c7n.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c7n.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 2c7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/2c7n ftp://data.pdbj.org/pub/pdb/validation_reports/c7/2c7n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Details | THE QUATERNARY STRUCTURE FOR THIS ENTRY IS NOT RELEVANTSINCE THE COMPLEX IS ONLY MADE UP OF FRAGMENTS OF RABEX-5IN COMPLEX WITH UBIQUITIN. HOWEVER, THESE REMARKSONLY INDICATE THE COMPLEX AS SEEN IN THE PDB FILE, ANDDO NOT HAVE RELEVANCE TO THE BIOLOGICAL STATE OF THEMOLECULE. |
-Components
#1: Protein | Mass: 8784.761 Da / Num. of mol.: 6 / Fragment: TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q53FG0, UniProt: Q9UJ41*PLUS #2: Protein | Mass: 8576.831 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: BOSTON BIOCHEM / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: P62990, UniProt: P0CH28*PLUS #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Compound details | INVOLVED IN THE ATP-DEPENDENT SELECTIVE DEGRADATION OF CELLULAR PROTEINS, THE MAINTENANCE OF ...INVOLVED IN THE ATP-DEPENDENT SELECTIVE DEGRADATIO | Sequence details | THE CONSTRUCT USED IN THE STRUCTURE DETERMINAT | |
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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: 3.08 Å3/Da / Density % sol: 59.77 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 16, 2005 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 57954 / % possible obs: 92.3 % / Observed criterion σ(I): -4 / Redundancy: 2.7 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.5 / % possible all: 66.4 |
Reflection | *PLUS Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS % possible obs: 66.4 % / Rmerge(I) obs: 0.169 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.127 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-17 ARE DISORDERED IN ALL COPIES OF RABEX-5 1-74. THE C-TERMINUS OF RABEX-5 1-74 IS ORDERED TO A VARIABLE DEGREE. RESIDUES 74-76 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-17 ARE DISORDERED IN ALL COPIES OF RABEX-5 1-74. THE C-TERMINUS OF RABEX-5 1-74 IS ORDERED TO A VARIABLE DEGREE. RESIDUES 74-76 OF UBIQUTIN ARE DISORDERED IN ALL COPIES
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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: 44.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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