+Open data
-Basic information
Entry | Database: PDB / ID: 2oii | ||||||
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Title | Structure of EMILIN-1 C1q-like domain | ||||||
Components | EMILIN-1 | ||||||
Keywords | STRUCTURAL PROTEIN / Emilin-1 / C1q-like domain / homotrimeric protein complex / beta-sandwich | ||||||
Function / homology | Function and homology information EMILIN complex / negative regulation of collagen fibril organization / negative regulation of macrophage migration / extracellular matrix constituent conferring elasticity / negative regulation of cell activation / integrin alpha4-beta1 complex / integrin binding involved in cell-matrix adhesion / elastic fiber assembly / positive regulation of defense response to bacterium / negative regulation of vascular endothelial growth factor signaling pathway ...EMILIN complex / negative regulation of collagen fibril organization / negative regulation of macrophage migration / extracellular matrix constituent conferring elasticity / negative regulation of cell activation / integrin alpha4-beta1 complex / integrin binding involved in cell-matrix adhesion / elastic fiber assembly / positive regulation of defense response to bacterium / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of collagen biosynthetic process / positive regulation of extracellular matrix assembly / collagen trimer / positive regulation of platelet aggregation / aortic valve morphogenesis / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / cell adhesion mediated by integrin / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of SMAD protein signal transduction / positive regulation of blood coagulation / negative regulation of angiogenesis / cell-matrix adhesion / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / regulation of blood pressure / positive regulation of angiogenesis / cell migration / regulation of cell population proliferation / collagen-containing extracellular matrix / molecular adaptor activity / cell adhesion / positive regulation of apoptotic process / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Verdone, G. / Colebrooke, S.A. / Corazza, A. / Cicero, D.O. / Eliseo, T. / Viglino, P. / Campbell, I.D. / Colombatti, A. / Esposito, G. | ||||||
Citation | Journal: To be Published Title: The solution structure of the C-terminal domain of EMILIN-1 Authors: Verdone, G. / Colebrooke, S.A. / Corazza, A. / Cicero, D.O. / Eliseo, T. / Viglino, P. / Campbell, I.D. / Colombatti, A. / Esposito, G. #1: Journal: J.Biomol.NMR / Year: 2004 Title: Sequence-specific backbone NMR assignments for the C-terminal globular domain of EMILIN-1 Authors: Verdone, G. / Colebrooke, S.A. / Boyd, J. / Viglino, P. / Corazza, A. / Doliana, R. / Mungiguerra, G. / Colombatti, A. / Esposito, G. / Campbell, I.D. #2: Journal: J.Biol.Chem. / Year: 2000 Title: Self-assembly and supramolecular organization of Emillin Authors: Mongiat, M. / Mungiguerra, G. / Bot, S. / Mucignat, M.T. / Giacomello, E. / Doliana, R. / Colombatti, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oii.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2oii.ent.gz | 995.3 KB | Display | PDB format |
PDBx/mmJSON format | 2oii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/2oii ftp://data.pdbj.org/pub/pdb/validation_reports/oi/2oii | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 17227.217 Da / Num. of mol.: 3 / Fragment: C-Terminal domain, C1q domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EMILIN1, EMI / Cell line (production host): M15 cells / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6C2 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 20 mM Phosphate buffer, 100 mM NaCl / pH: 7.5 / Pressure: 1 atm / Temperature: 310 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structure was obtained as the refinement of the homology model of emilin trimer C1q-domain based on the chain A of ACRP-30 crystal structure. The quaternary structure of C1q-domain ...Details: The structure was obtained as the refinement of the homology model of emilin trimer C1q-domain based on the chain A of ACRP-30 crystal structure. The quaternary structure of C1q-domain homology model was built with a three-fold simmetry axis. The region between Tyr927 and Gly945 was not modelled and was not included in the refinement. Dihedral angles (obtained with TALOS), RDC values, NOE constraints were used in the refinement procedure. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |