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- PDB-1ec6: CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN BOU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ec6 | ||||||
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Title | CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN BOUND TO 20-MER RNA HAIRPIN | ||||||
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![]() | RNA BINDING PROTEIN/RNA / KH domain / alpha-beta fold / RNA-binding motif / protein/RNA structure / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | ![]() regulation of axon guidance / regulation of RNA metabolic process / sequence-specific mRNA binding / negative regulation of cold-induced thermogenesis / central nervous system neuron development / regulation of alternative mRNA splicing, via spliceosome / neuron differentiation / mRNA splicing, via spliceosome / mRNA binding / RNA binding ...regulation of axon guidance / regulation of RNA metabolic process / sequence-specific mRNA binding / negative regulation of cold-induced thermogenesis / central nervous system neuron development / regulation of alternative mRNA splicing, via spliceosome / neuron differentiation / mRNA splicing, via spliceosome / mRNA binding / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lewis, H.A. / Musunuru, K. / Jensen, K.B. / Edo, C. / Chen, H. | ||||||
![]() | ![]() Title: Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Authors: Lewis, H.A. / Musunuru, K. / Jensen, K.B. / Edo, C. / Chen, H. / Darnell, R.B. / Burley, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.4 KB | Display | ![]() |
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PDB format | ![]() | 50.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.2 KB | Display | ![]() |
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Full document | ![]() | 419.9 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 10.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 6341.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Product of SELEX protein binding study #2: Protein | Mass: 9437.835 Da / Num. of mol.: 2 / Fragment: KH3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.71 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 25% PEG 5000, 150 mM ammonium sulfate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, temperature 293.0K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / Details: protein:RNA 1:1.25 ratio | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: OTHER / Detector: CCD / Date: Sep 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 12459 / Num. obs: 12004 / % possible obs: 96.5 % / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.9 |
Reflection shell | Highest resolution: 2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.215 / % possible all: 93.7 |
Reflection | *PLUS Num. obs: 67678 / % possible obs: 98 % / Num. measured all: 143241 |
Reflection shell | *PLUS % possible obs: 93.7 % / Rmerge(I) obs: 0.211 |
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Processing
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Refinement | Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(I): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.208 / Num. reflection obs: 67678 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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