[English] 日本語
![](img/lk-miru.gif)
- PDB-6fq3: Crystal structure of Danio rerio Lin41 filamin-NHL domains in com... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6fq3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Danio rerio Lin41 filamin-NHL domains in complex with lin-29A 5'UTR 13mer RNA | ||||||
![]() |
| ||||||
![]() | RNA BINDING PROTEIN / post-transcriptional regulation | ||||||
Function / homology | ![]() Antigen processing: Ubiquitination & Proteasome degradation / regulation of neural precursor cell proliferation / miRNA-mediated gene silencing by inhibition of translation / neural tube development / miRNA binding / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / stem cell proliferation / P-body / RING-type E3 ubiquitin transferase ...Antigen processing: Ubiquitination & Proteasome degradation / regulation of neural precursor cell proliferation / miRNA-mediated gene silencing by inhibition of translation / neural tube development / miRNA binding / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / stem cell proliferation / P-body / RING-type E3 ubiquitin transferase / G1/S transition of mitotic cell cycle / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumari, P. / Aeschimann, F. / Gaidatzis, D. / Keusch, J.J. / Ghosh, P. / Neagu, A. / Pachulska-Wieczorek, K. / Bujnicki, J.M. / Gut, H. / Grosshans, H. / Ciosk, R. | ||||||
![]() | ![]() Title: Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition. Authors: Kumari, P. / Aeschimann, F. / Gaidatzis, D. / Keusch, J.J. / Ghosh, P. / Neagu, A. / Pachulska-Wieczorek, K. / Bujnicki, J.M. / Gut, H. / Grosshans, H. / Ciosk, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 190.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 148.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 446.1 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fptSC ![]() 6fqlC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 44624.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fragment of Lin41 encompassing filamin-NHL domains (residues 435-824) Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: E7FAM5, RING-type E3 ubiquitin transferase | ||
---|---|---|---|
#2: RNA chain | Mass: 4116.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fragment of lin-29a 5'UTR / Source: (gene. exp.) ![]() ![]() | ||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.56 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 10% PEG 8000 20% ethylene glycol 0.1M carboxylic acids 0.1 M bicine/Trizma base pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 51941 / % possible obs: 99.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 56.1 Å2 / CC1/2: 0.99 / Rsym value: 0.042 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 0.81 / Num. unique obs: 3516 / CC1/2: 0.381 / Rsym value: 2.172 / % possible all: 92.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6FPT Resolution: 1.901→46.637 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.04
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→46.637 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|